From 99247aead82b69da89012fd772f15330ce527b27 Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Fri, 15 Sep 2023 20:25:12 +0530
Subject: [PATCH 01/35] Allow Simulation Tests to Run Independently  (#2407)

* Modify test_packet_source.py so that sim and tardis/tests can run

* remove BasePacketSource

* format

* Add docstrings
---
 tardis/montecarlo/tests/test_packet_source.py | 87 ++++++++++++++-----
 1 file changed, 64 insertions(+), 23 deletions(-)

diff --git a/tardis/montecarlo/tests/test_packet_source.py b/tardis/montecarlo/tests/test_packet_source.py
index 259db6c54b5..43338903967 100644
--- a/tardis/montecarlo/tests/test_packet_source.py
+++ b/tardis/montecarlo/tests/test_packet_source.py
@@ -10,27 +10,68 @@
 )
 
 
-@pytest.fixture
-def packet_unit_test_fpath(tardis_ref_path):
-    return os.path.abspath(os.path.join(tardis_ref_path, "packet_unittest.h5"))
-
-
-def test_bb_packet_sampling(request, tardis_ref_data, packet_unit_test_fpath):
-    montecarlo_configuration.LEGACY_MODE_ENABLED = True
-    bb = BlackBodySimpleSource(base_seed=1963, legacy_second_seed=2508)
-    # ref_df = pd.read_hdf('test_bb_sampling.h5')
-    if request.config.getoption("--generate-reference"):
-        ref_bb = pd.read_hdf(packet_unit_test_fpath, key="/blackbody")
-        ref_bb.to_hdf(
-            tardis_ref_data, key="/packet_unittest/blackbody", mode="a"
+class TestPacketSource:
+    @pytest.fixture(scope="class")
+    def packet_unit_test_fpath(self, tardis_ref_path):
+        """
+        Path to `packet_unittest.h5`.
+
+        Parameters
+        ----------
+        tardis_ref_path : pd.HDFStore
+
+        Returns
+        -------
+        os.path
+        """
+        return os.path.abspath(
+            os.path.join(tardis_ref_path, "packet_unittest.h5")
         )
-        pytest.skip("Reference data was generated during this run.")
-
-    ref_df = tardis_ref_data["/packet_unittest/blackbody"]
-    bb.temperature = 10000
-    nus = bb.create_packet_nus(100)
-    mus = bb.create_packet_mus(100)
-    unif_energies = bb.create_packet_energies(100)
-    assert np.all(np.isclose(nus, ref_df["nus"]))
-    assert np.all(np.isclose(mus, ref_df["mus"]))
-    assert np.all(np.isclose(unif_energies, ref_df["energies"]))
+
+    @pytest.fixture(scope="class")
+    def blackbodysimplesource(self, request):
+        """
+        Create BlackBodySimpleSource instance.
+
+        Yields
+        -------
+        tardis.montecarlo.packet_source.BlackBodySimpleSource
+        """
+        cls = type(self)
+        montecarlo_configuration.LEGACY_MODE_ENABLED = True
+        cls.bb = BlackBodySimpleSource(base_seed=1963, legacy_second_seed=2508)
+        yield cls.bb
+        montecarlo_configuration.LEGACY_MODE_ENABLED = False
+
+    def test_bb_packet_sampling(
+        self,
+        request,
+        tardis_ref_data,
+        packet_unit_test_fpath,
+        blackbodysimplesource,
+    ):
+        """
+        Test generate_plot_mpl method.
+
+        Parameters
+        ----------
+        request : _pytest.fixtures.SubRequest
+        tardis_ref_data: pd.HDFStore
+        packet_unit_test_fpath: os.path
+        blackbodysimplesource: tardis.montecarlo.packet_source.BlackBodySimpleSource
+        """
+        if request.config.getoption("--generate-reference"):
+            ref_bb = pd.read_hdf(packet_unit_test_fpath, key="/blackbody")
+            ref_bb.to_hdf(
+                tardis_ref_data, key="/packet_unittest/blackbody", mode="a"
+            )
+            pytest.skip("Reference data was generated during this run.")
+
+        ref_df = tardis_ref_data["/packet_unittest/blackbody"]
+        self.bb.temperature = 10000
+        nus = self.bb.create_packet_nus(100)
+        mus = self.bb.create_packet_mus(100)
+        unif_energies = self.bb.create_packet_energies(100)
+        assert np.all(np.isclose(nus, ref_df["nus"]))
+        assert np.all(np.isclose(mus, ref_df["mus"]))
+        assert np.all(np.isclose(unif_energies, ref_df["energies"]))

From 7312e0b50da5e2543bbf98db2a7bbddad14231d8 Mon Sep 17 00:00:00 2001
From: tardis-bot <60989672+tardis-bot@users.noreply.github.com>
Date: Sat, 16 Sep 2023 20:51:19 -0400
Subject: [PATCH 02/35] Pre-release 2023.09.17 (#2411)

Automated changes for pre-release 2023.09.17
---
 .zenodo.json        |   18 +-
 conda-linux-64.lock |   90 ++--
 conda-lock.yml      | 1017 ++++++++++++++++++++++---------------------
 conda-osx-64.lock   |   50 +--
 4 files changed, 589 insertions(+), 586 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index 5f165b276a1..ee0b1896bbe 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -103,10 +103,10 @@
       "name": "Smith, Isaac"
     },
     {
-      "name": "Cawley, Kevin"
+      "name": "Arya, Atharva"
     },
     {
-      "name": "Arya, Atharva"
+      "name": "Cawley, Kevin"
     },
     {
       "name": "Singhal, Jaladh",
@@ -128,10 +128,10 @@
       "name": "Patel, Maryam"
     },
     {
-      "name": "Varanasi, Kaushik"
+      "name": "Rathi, Shikha"
     },
     {
-      "name": "Rathi, Shikha"
+      "name": "Varanasi, Kaushik"
     },
     {
       "name": "Chitchyan, Sona"
@@ -141,19 +141,19 @@
       "orcid": "0000-0002-8094-6108"
     },
     {
-      "name": "Savel, Arjun"
+      "name": "Shields, Joshua"
     },
     {
-      "name": "Reinecke, Martin"
+      "name": "Singh, Shreyas"
     },
     {
-      "name": "Eweis, Youssef"
+      "name": "Savel, Arjun"
     },
     {
-      "name": "Shields, Joshua"
+      "name": "Reinecke, Martin"
     },
     {
-      "name": "Singh, Shreyas"
+      "name": "Eweis, Youssef"
     },
     {
       "name": "Bylund, Tomas"
diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index fef1f451c49..1e60a3f3300 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -10,16 +10,14 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77
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 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.1.0-h15d22d2_0.conda#afb656a334c409dd9805508af1c89c7a
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.1.0-hfd8a6a1_0.conda#067bcc23164642f4c226da631f2a2e1d
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_1.conda#acfb4817400db5804030a3a7ef7909a1
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-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.1.0-h69a702a_0.conda#506dc07710dd5b0ba63cbf134897fc10
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.1.0-he5830b7_0.conda#56ca14d57ac29a75d23a39eb3ee0ddeb
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_1.conda#8bb001683321dcbde117a7337b5aace7
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.1.0-he5830b7_0.conda#cd93f779ff018dd85c7544c015c9db3c
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_1.conda#ff8999574b465089ba0aa25a5e865bd0
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
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@@ -37,14 +35,14 @@ https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda
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+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_1.conda#a0d27fd5c6f05aa45e9602b1db49581c
 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2#b62b52da46c39ee2bc3c162ac7f1804d
-https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-h0b41bf4_0.conda#1edd9e67bdb90d78cea97733ff6b54e6
+https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-hd590300_1.conda#323e90742f0f48fc22bea908735f55e6
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
-https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.24-pthreads_h413a1c8_0.conda#6e4ef6ca28655124dcde9bd500e44c32
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-https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.1-hd590300_0.conda#82bf6f63eb15ef719b556b63feec3a77
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_0.conda#30de3fd9b3b602f7473f30e684eeea8c
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
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 https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h516909a_1000.tar.bz2#bb14fcb13341b81d5eb386423b9d2bac
@@ -64,10 +62,10 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
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-https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-18_linux64_openblas.conda#bcddbb497582ece559465b9cd11042e7
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+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_1.conda#394218a92951499aed2ab1bafb30b570
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.52.0-h61bc06f_0.conda#613955a50485812985c059e7b269f42e
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@@ -84,13 +82,12 @@ https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c
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-https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-hca18f0e_1.conda#e1232042de76d24539a436d37597eb06
+https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-18_linux64_openblas.conda#93dd9ab275ad888ed8113953769af78c
-https://conda.anaconda.org/conda-forge/linux-64/libglib-2.76.4-hebfc3b9_0.conda#c6f951789c888f7bbd2dd6858eab69de
-https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-18_linux64_openblas.conda#a1244707531e5b143c420c70573c8ec5
+https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.0-hebfc3b9_0.conda#e618003da3547216310088478e475945
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-https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.5.1-h8b53f26_1.conda#5b09e13d732dda1a2bc9adc711164f4d
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.24-pthreads_h413a1c8_0.conda#6e4ef6ca28655124dcde9bd500e44c32
+https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h8b53f26_0.conda#097c175e54beba8b42dcc5dd49299ca1
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@@ -112,7 +109,7 @@ https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.cond
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-https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.7.0-py38h17151c0_0.conda#e3237ea8d0e1a353d413f91745046e09
+https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.0-py38h17151c0_0.conda#bdd3e5d573420e5c7f254659d96aa830
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@@ -122,7 +119,7 @@ https://conda.anaconda.org/conda-forge/noarch/executing-1.2.0-pyhd8ed1ab_0.tar.b
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-https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.42.10-h6b639ba_2.conda#ee8220db21db8094998005990418fe5b
+https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.42.10-h6c15284_3.conda#06f97c8b69157d91993af0c4f2e16bdc
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@@ -130,12 +127,13 @@ https://conda.anaconda.org/conda-forge/noarch/imagesize-1.4.1-pyhd8ed1ab_0.tar.b
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-https://conda.anaconda.org/conda-forge/noarch/jsonpointer-2.0-py_0.tar.bz2#07d85c22a3beb102a48cd123df84c2a6
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 https://conda.anaconda.org/conda-forge/noarch/pytest-html-3.2.0-pyhd8ed1ab_1.tar.bz2#d5c7a941dfbceaab4b172a56d7918eb0
-https://conda.anaconda.org/conda-forge/noarch/radioactivedecay-0.4.21-pyhd8ed1ab_0.conda#673319f48d9b160c8056783d301e090c
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.5.3-py38hb2138dd_0.tar.bz2#e0ab8ace182b8d88a43c7e25a3ed092f
 https://conda.anaconda.org/conda-forge/noarch/sphinx-7.0.1-pyhd8ed1ab_0.conda#51a8d037b28276b4f68263e890e0f35b
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-apidoc-0.3.0-py_1.tar.bz2#855b087883443abb10f5faf6eef40860
+https://conda.anaconda.org/conda-forge/linux-64/astropy-5.0.4-py38h71d37f0_0.tar.bz2#4156d702236001f841bc3404a007ea74
 https://conda.anaconda.org/conda-forge/linux-64/gtk2-2.24.33-h90689f9_2.tar.bz2#957a0255ab58aaf394a91725d73ab422
 https://conda.anaconda.org/conda-forge/noarch/jsonschema-with-format-nongpl-4.19.0-pyhd8ed1ab_1.conda#d273b30bcf4db0ef6b1195b3b61b3d68
 https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.3.1-pyhd8ed1ab_0.conda#b7cc0981484fcb6390e6d341e55618b3
@@ -293,6 +291,8 @@ https://conda.anaconda.org/conda-forge/linux-64/librsvg-2.56.3-h98fae49_0.conda#
 https://conda.anaconda.org/conda-forge/noarch/nbformat-5.9.2-pyhd8ed1ab_0.conda#61ba076de6530d9301a0053b02f093d2
 https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.5.0-pyhd8ed1ab_0.tar.bz2#3c275d7168a6a135329f4acb364c229a
 https://conda.anaconda.org/conda-forge/noarch/prompt_toolkit-3.0.39-hd8ed1ab_0.conda#4bbbe67d5df19db30f04b8e344dc9976
+https://conda.anaconda.org/conda-forge/linux-64/pytables-3.7.0-py38hf632491_2.tar.bz2#a53a269544f1c3e27204dc35d0b6cdc7
+https://conda.anaconda.org/conda-forge/noarch/radioactivedecay-0.4.21-pyhd8ed1ab_0.conda#673319f48d9b160c8056783d301e090c
 https://conda.anaconda.org/conda-forge/noarch/recommonmark-0.7.1-pyhd8ed1ab_0.tar.bz2#b3becf9905b8c7ba839072f65e693253
 https://conda.anaconda.org/conda-forge/noarch/sphinx-automodapi-0.16.0-pyh6ff6d48_0.conda#c2dfb5d38d19546cf818d75801c21ed0
 https://conda.anaconda.org/conda-forge/noarch/sphinx-gallery-0.14.0-pyhd8ed1ab_0.conda#b3788794f88c9512393032e448428261
@@ -311,13 +311,13 @@ https://conda.anaconda.org/conda-forge/linux-64/pygraphviz-1.11-py38h83a7919_0.c
 https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_0.conda#969249eb7c2f7a9b820520a355dc7d04
 https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.8.0-pyhd8ed1ab_0.conda#1dba1a577df2625a24667612a069e91c
 https://conda.anaconda.org/conda-forge/noarch/jupyter-lsp-2.2.0-pyhd8ed1ab_0.conda#38589f4104d11f2a59ff01a9f4e3bfb3
-https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.24.0-pyhd8ed1ab_0.conda#327bfe1c99154f02259d29810bd70afc
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.25.0-pyhd8ed1ab_0.conda#a52834fa7e3d12abc5efdf06b2097a05
 https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.8.0-pyhd8ed1ab_0.conda#43bce95e8c474dd21d7ed5de8b4806f7
 https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.3-pyhd8ed1ab_0.conda#67e0fe74c156267d9159e9133df7fd37
-https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.5-pyhd8ed1ab_0.conda#fce8108e7dfb3622873a85e495a72dda
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.6-pyhd8ed1ab_0.conda#80bb1cc3b540790cb5afecd73c2d4d1f
 https://conda.anaconda.org/conda-forge/noarch/nbclassic-1.0.0-pyhb4ecaf3_1.conda#a0be31e9bd84d6eae87cdbf74c56b90b
 https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.3-pyhd8ed1ab_0.conda#0dbaa7d08d3d79b2a1a4dd6a02cc4581
 https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.3-pyhd8ed1ab_0.conda#1f2d368cde97926b5e351d1a0286bb1e
-https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.5-pyhd8ed1ab_0.conda#27e94943c68cc04f54125faa76c52fba
+https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda#fe79dfe7d51794d665ec3c2fdd4e47c3
 https://conda.anaconda.org/conda-forge/noarch/ipywidgets-7.8.0-pyhd8ed1ab_0.conda#518b05adab6cfe6ea249319932d9d4a3
 https://conda.anaconda.org/conda-forge/noarch/qgrid-1.3.1-pyhd8ed1ab_4.tar.bz2#fff68c7404813a1eb2678425f00e9917
diff --git a/conda-lock.yml b/conda-lock.yml
index b110da86252..b5369385d75 100644
--- a/conda-lock.yml
+++ b/conda-lock.yml
@@ -114,25 +114,14 @@ package:
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-  platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.1.0-h15d22d2_0.conda
-  version: 13.1.0
-- category: main
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+    md5: acfb4817400db5804030a3a7ef7909a1
+    sha256: b4ee92e483b24dbcdbaab0928e14bf338342268e3c413111413ee36284006d56
   manager: conda
   name: libstdcxx-ng
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.1.0-hfd8a6a1_0.conda
-  version: 13.1.0
+  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_1.conda
+  version: 13.2.0
 - category: main
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   url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
   version: '1'
-- category: main
-  dependencies:
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-  manager: conda
-  name: libgfortran-ng
-  optional: false
-  platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.1.0-h69a702a_0.conda
-  version: 13.1.0
 - category: main
   dependencies:
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-    sha256: 5d441d80b57f857ad305a65169a6b915d4fd6735cdc9e9bded35d493c91ef16d
+    md5: 8bb001683321dcbde117a7337b5aace7
+    sha256: cc9b25e3a0329326936164ca666861738e2833460cd1e0bb2086acb5781a7795
   manager: conda
   name: libgomp
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.1.0-he5830b7_0.conda
-  version: 13.1.0
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_1.conda
+  version: 13.2.0
 - category: main
   dependencies:
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@@ -224,14 +201,14 @@ package:
     _libgcc_mutex: 0.1 conda_forge
     _openmp_mutex: '>=4.5'
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-    sha256: fba897a02f35b2b5e6edc43a746d1fa6970a77b422f258246316110af8966911
+    md5: ff8999574b465089ba0aa25a5e865bd0
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   manager: conda
   name: libgcc-ng
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.1.0-he5830b7_0.conda
-  version: 13.1.0
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_1.conda
+  version: 13.2.0
 - category: main
   dependencies:
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@@ -441,6 +418,18 @@ package:
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   url: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
   version: 3.4.2
+- category: main
+  dependencies:
+    libgcc-ng: '>=13.2.0'
+  hash:
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+    sha256: 30b4194151c1d6cdede3da8c33aabb848cde4db2fc68e7f5607f2e4a38d881d7
+  manager: conda
+  name: libgfortran5
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_1.conda
+  version: 13.2.0
 - category: main
   dependencies:
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@@ -457,13 +446,13 @@ package:
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-    sha256: b19de7bda34eac4fa931be11fa8d7640cdf1441dfd51c91786586a4a4c64c92f
+    md5: 323e90742f0f48fc22bea908735f55e6
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   manager: conda
   name: libjpeg-turbo
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-h0b41bf4_0.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-hd590300_1.conda
   version: 2.1.5.1
 - category: main
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   url: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2
   version: 2.0.0
-- category: main
-  dependencies:
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-    libgfortran-ng: ''
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-  manager: conda
-  name: libopenblas
-  optional: false
-  platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.24-pthreads_h413a1c8_0.conda
-  version: 0.3.24
 - category: main
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@@ -531,14 +506,14 @@ package:
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   name: libwebp-base
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.1-hd590300_0.conda
-  version: 1.3.1
+  url: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_0.conda
+  version: 1.3.2
 - category: main
   dependencies:
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@@ -772,18 +747,6 @@ package:
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   url: https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda
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-- category: main
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-18_linux64_openblas.conda
-  version: 3.9.0
 - category: main
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@@ -823,6 +786,18 @@ package:
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   url: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2
   version: 3.1.20191231
+- category: main
+  dependencies:
+    libgfortran5: 13.2.0 ha4646dd_1
+  hash:
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+    sha256: 08f9cd5830b5f498cbea2f32cdf755c1cdee8d3c48dd2c48d6dda142cdb5d473
+  manager: conda
+  name: libgfortran-ng
+  optional: false
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+  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_1.conda
+  version: 13.2.0
 - category: main
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   name: freetype
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-hca18f0e_1.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda
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-  url: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-18_linux64_openblas.conda
-  version: 3.9.0
+  url: https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.0-hebfc3b9_0.conda
+  version: 2.78.0
 - category: main
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@@ -1136,6 +1087,20 @@ package:
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   url: https://conda.anaconda.org/conda-forge/linux-64/libllvm10-10.0.1-he513fc3_3.tar.bz2
   version: 10.0.1
+- category: main
+  dependencies:
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+    libgfortran-ng: ''
+    libgfortran5: '>=12.3.0'
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+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.24-pthreads_h413a1c8_0.conda
+  version: 0.3.24
 - category: main
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@@ -1146,16 +1111,16 @@ package:
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     xz: '>=5.2.6,<6.0a0'
-    zstd: '>=1.5.2,<1.6.0a0'
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.5.1-h8b53f26_1.conda
-  version: 4.5.1
+  url: https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h8b53f26_0.conda
+  version: 4.6.0
 - category: main
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@@ -1449,14 +1414,14 @@ package:
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-  version: 5.16.1
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-  version: 2.24.0
+  url: https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.25.0-pyhd8ed1ab_0.conda
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-  url: https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.5-pyhd8ed1ab_0.conda
-  version: 4.0.5
+  url: https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.6-pyhd8ed1ab_0.conda
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-  url: https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.5-pyhd8ed1ab_0.conda
-  version: 3.6.5
+  url: https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda
+  version: 3.6.6
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diff --git a/conda-osx-64.lock b/conda-osx-64.lock
index 9ff4aef01ee..59889512fc9 100644
--- a/conda-osx-64.lock
+++ b/conda-osx-64.lock
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-https://conda.anaconda.org/conda-forge/osx-64/libtiff-4.5.1-hf955e92_1.conda#3436c5763732687918ce258b0184c7c9
+https://conda.anaconda.org/conda-forge/osx-64/libtiff-4.6.0-hf955e92_0.conda#6764dde526b39dc4e3532aac18d8a839
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+https://conda.anaconda.org/conda-forge/osx-64/debugpy-1.8.0-py38h940360d_0.conda#b1797f2519f9259202548d71acfbc350
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+https://conda.anaconda.org/conda-forge/osx-64/gdk-pixbuf-2.42.10-h5968b1e_3.conda#5e8f0d38ce2eb825059ea2293d439f01
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-https://conda.anaconda.org/conda-forge/osx-64/rpds-py-0.10.2-py38h7510fb3_0.conda#907c6f091d1cecf91a344aa45edb986c
+https://conda.anaconda.org/conda-forge/osx-64/rpds-py-0.10.3-py38h7510fb3_0.conda#206a93128f3f42b05fa100d6f5a93084
 https://conda.anaconda.org/conda-forge/osx-64/setuptools-59.8.0-py38h50d1736_1.tar.bz2#c25b5974862472ee3e681a920ceaceb4
 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2
 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303
@@ -169,15 +169,15 @@ https://conda.anaconda.org/conda-forge/noarch/tenacity-8.2.3-pyhd8ed1ab_0.conda#
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-https://conda.anaconda.org/conda-forge/noarch/traitlets-5.9.0-pyhd8ed1ab_0.conda#d0b4f5c87cd35ac3fb3d47b223263a64
+https://conda.anaconda.org/conda-forge/noarch/traitlets-5.10.0-pyhd8ed1ab_0.conda#efd3f63a93621367d4fa6e274c511696
 https://conda.anaconda.org/conda-forge/osx-64/typed-ast-1.5.4-py38hef030d1_1.tar.bz2#3f931219be427788019ab080416376df
 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.7.1-pyha770c72_0.conda#c39d6a09fe819de4951c2642629d9115
 https://conda.anaconda.org/conda-forge/noarch/typing_utils-0.1.0-pyhd8ed1ab_0.tar.bz2#eb67e3cace64c66233e2d35949e20f92
 https://conda.anaconda.org/conda-forge/osx-64/unicodedata2-15.0.0-py38hef030d1_0.tar.bz2#51020c740c53f14657f6307b9eb23f85
 https://conda.anaconda.org/conda-forge/noarch/uri-template-1.3.0-pyhd8ed1ab_0.conda#0944dc65cb4a9b5b68522c3bb585d41c
 https://conda.anaconda.org/conda-forge/noarch/webcolors-1.13-pyhd8ed1ab_0.conda#166212fe82dad8735550030488a01d03
-https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-py_1.tar.bz2#3563be4c5611a44210d9ba0c16113136
-https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.6.2-pyhd8ed1ab_0.conda#23f16ffe9711ac76b391c60ce4ea4656
+https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_2.conda#daf5160ff9cde3a468556965329085b9
+https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.6.3-pyhd8ed1ab_0.conda#38563b419c06ed97458d081df36beec0
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.2-pyhd8ed1ab_0.conda#1ccd092478b3e0ee10d7a891adbf8a4f
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 https://conda.anaconda.org/conda-forge/noarch/anyio-4.0.0-pyhd8ed1ab_0.conda#3c4e99d3ae4ec033d4dd99fb5220e540
@@ -205,13 +205,13 @@ https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.2-pyhd8ed1ab_1.tar.bz2#
 https://conda.anaconda.org/conda-forge/noarch/jupyterlab_pygments-0.2.2-pyhd8ed1ab_0.tar.bz2#243f63592c8e449f40cd42eb5cf32f40
 https://conda.anaconda.org/conda-forge/noarch/latexcodec-2.0.1-pyh9f0ad1d_0.tar.bz2#8d67904973263afd2985ba56aa2d6bb4
 https://conda.anaconda.org/conda-forge/osx-64/libblas-3.9.0-18_osx64_openblas.conda#6461cded280f7a46ebef0f1b687d4883
-https://conda.anaconda.org/conda-forge/osx-64/libgd-2.3.3-heb3472c_7.conda#b132292086c2c3d99cb6e5770b99fdc0
+https://conda.anaconda.org/conda-forge/osx-64/libgd-2.3.3-h91ac1b9_8.conda#d95f54aee29df07a51fd3c99e61d04b7
 https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.1.6-pyhd8ed1ab_0.tar.bz2#b21613793fcc81d944c76c9f2864a7de
 https://conda.anaconda.org/conda-forge/noarch/overrides-7.4.0-pyhd8ed1ab_0.conda#4625b7b01d7f4ac9c96300a5515acfaa
 https://conda.anaconda.org/conda-forge/noarch/pexpect-4.8.0-pyh1a96a4e_2.tar.bz2#330448ce4403cc74990ac07c555942a1
-https://conda.anaconda.org/conda-forge/osx-64/pillow-10.0.0-py38h16710f9_0.conda#8f73f0573ab381d56588e001754c53d3
+https://conda.anaconda.org/conda-forge/osx-64/pillow-10.0.1-py38ha0d9280_0.conda#c60c3924808f9d88c3962553d7ee39eb
 https://conda.anaconda.org/conda-forge/noarch/pip-23.2.1-pyhd8ed1ab_0.conda#e2783aa3f9235225eec92f9081c5b801
-https://conda.anaconda.org/conda-forge/noarch/plotly-5.16.1-pyhd8ed1ab_0.conda#80a84dd5ca82e99f7a4092639aa14f8a
+https://conda.anaconda.org/conda-forge/noarch/plotly-5.17.0-pyhd8ed1ab_0.conda#76a0b213abcd3ffc1e8fa78804b69dc0
 https://conda.anaconda.org/conda-forge/osx-64/pyobjc-core-9.2-py38h095c2e5_0.conda#8dbb4798b2066b678d8da47734d1c763
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@@ -229,7 +229,7 @@ https://conda.anaconda.org/conda-forge/noarch/arrow-1.2.3-pyhd8ed1ab_0.tar.bz2#f
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 https://conda.anaconda.org/conda-forge/osx-64/cryptography-40.0.2-py38h4257468_0.conda#e60e91caecdb7719724e6e2124e4cffc
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-https://conda.anaconda.org/conda-forge/osx-64/harfbuzz-8.1.1-h7666e2a_1.conda#788f8c541b0ee6d1ab25f0cc8944149a
+https://conda.anaconda.org/conda-forge/osx-64/harfbuzz-8.2.0-h7666e2a_0.conda#7b263a6bd9fbebd829f10f529209ff50
 https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-6.8.0-hd8ed1ab_0.conda#b279b07ce18058034e5b3606ba103a8b
 https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2023.7.1-pyhd8ed1ab_0.conda#7c27ea1bdbe520bb830dcadd59f55cbf
 https://conda.anaconda.org/conda-forge/noarch/jupyter_server_terminals-0.4.4-pyhd8ed1ab_1.conda#7c0965e1d4a0ee1529e8eaa03a78a5b3
@@ -296,13 +296,13 @@ https://conda.anaconda.org/conda-forge/noarch/sphinx-astropy-1.9.1-pyhd8ed1ab_0.
 https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_0.conda#969249eb7c2f7a9b820520a355dc7d04
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-https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.24.0-pyhd8ed1ab_0.conda#327bfe1c99154f02259d29810bd70afc
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.25.0-pyhd8ed1ab_0.conda#a52834fa7e3d12abc5efdf06b2097a05
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 https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.3-pyhd8ed1ab_0.conda#67e0fe74c156267d9159e9133df7fd37
-https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.5-pyhd8ed1ab_0.conda#fce8108e7dfb3622873a85e495a72dda
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.6-pyhd8ed1ab_0.conda#80bb1cc3b540790cb5afecd73c2d4d1f
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 https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.3-pyhd8ed1ab_0.conda#0dbaa7d08d3d79b2a1a4dd6a02cc4581
 https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.3-pyhd8ed1ab_0.conda#1f2d368cde97926b5e351d1a0286bb1e
-https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.5-pyhd8ed1ab_0.conda#27e94943c68cc04f54125faa76c52fba
+https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda#fe79dfe7d51794d665ec3c2fdd4e47c3
 https://conda.anaconda.org/conda-forge/noarch/ipywidgets-7.8.0-pyhd8ed1ab_0.conda#518b05adab6cfe6ea249319932d9d4a3
 https://conda.anaconda.org/conda-forge/noarch/qgrid-1.3.1-pyhd8ed1ab_4.tar.bz2#fff68c7404813a1eb2678425f00e9917

From a9be74fd560407b3ee61159b59de6a52c12ebe54 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Wed, 20 Sep 2023 16:55:18 -0400
Subject: [PATCH 03/35] upgrading env in 2022 (#2410)

* fix several bugs related to upgrade

* fix the get function in pandas

* fixed several incompatibilities for new libraries

* fixed up the changes in pandas testing and other reindexing issues

* fix other bugs with new environment

* blackify tardis

* updated the conda-lock file

* add lock files

* update cache number

* fix simulation tests

* remove units for testing

* blackify

* Update tardis/visualization/tools/tests/test_sdec_plot.py

good catch

Co-authored-by: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>

* add assert

* reset caches

---------

Co-authored-by: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
---
 conda-linux-64.lock                           |  129 +-
 conda-lock.yml                                | 2526 +++++++++--------
 conda-osx-64.lock                             |  133 +-
 tardis/io/atom_data/base.py                   |   24 +-
 tardis/io/model/readers/artis.py              |   14 +-
 tardis/io/tests/test_HDFWriter.py             |    9 +-
 tardis/io/tests/test_atomic.py                |    2 +-
 tardis/model/base.py                          |    2 +-
 tardis/montecarlo/montecarlo_numba/base.py    |    5 +-
 .../montecarlo_numba/formal_integral.py       |    2 +-
 tardis/montecarlo/tests/test_spectrum.py      |    6 +-
 tardis/plasma/properties/ion_population.py    |    5 +-
 tardis/plasma/standard_plasmas.py             |    2 +-
 tardis/plasma/tests/test_complete_plasmas.py  |   18 +-
 tardis/plasma/tests/test_hdf_plasma.py        |    5 +-
 tardis/simulation/tests/test_simulation.py    |   16 +-
 .../tests/test_tardis_full_formal_integral.py |    5 -
 tardis/visualization/tools/sdec_plot.py       |    6 +-
 .../tools/tests/test_sdec_plot.py             |   10 +-
 tardis/visualization/widgets/line_info.py     |    6 +-
 .../widgets/tests/test_shell_info.py          |   11 +-
 tardis_env3.yml                               |   20 +-
 22 files changed, 1599 insertions(+), 1357 deletions(-)

diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index 1e60a3f3300..1aaa04b654c 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: bbdba7762d98ab5e33b2739d850c8034fb4a270a611f78498151cbf856de1886
+# input_hash: 31d323d670a8deec16e2186403aa54ab8464102ac712829e12e62d80bc50f272
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
@@ -12,7 +12,8 @@ https://conda.anaconda.org/conda-forge/linux-64/git-lfs-3.4.0-ha770c72_0.conda#8
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_1.conda#acfb4817400db5804030a3a7ef7909a1
 https://conda.anaconda.org/conda-forge/noarch/nomkl-1.0-h5ca1d4c_0.tar.bz2#9a66894dfd07c4510beb6b3f9672ccc0
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-3_cp38.conda#2f3f7af062b42d664117662612022204
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-3_cp311.conda#c2e2630ddb68cf52eec74dc7dfab20b5
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
 https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_1.conda#8bb001683321dcbde117a7337b5aace7
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
@@ -31,7 +32,7 @@ https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz
 https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f
 https://conda.anaconda.org/conda-forge/linux-64/libaec-1.0.6-hcb278e6_1.conda#0f683578378cddb223e7fd24f785ab2a
 https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hd590300_0.conda#e805cbec4c29feb22e019245f7e47b6c
-https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.19-hd590300_0.conda#1635570038840ee3f9c71d22aa5b8b6d
 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#6305a3dd2752c76335295da4e581f2fd
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
@@ -61,11 +62,13 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_10
 https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2#b4a4381d54784606820704f7b5f05a15
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae
+https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.0.7-h0b41bf4_0.conda#49e8329110001f04923fe7e864990b0c
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda#8b9b5aca60558d02ddaa09d599e55920
 https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.1.0-hd590300_0.conda#43017394a280a42b48d11d2a6e169901
 https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hd590300_0.conda#8e3e1cb77c4b355a3776bdfb74095bed
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_1.conda#394218a92951499aed2ab1bafb30b570
+https://conda.anaconda.org/conda-forge/linux-64/libllvm14-14.0.6-hcd5def8_4.conda#73301c133ded2bf71906aa2104edae8b
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 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.43.0-h2797004_0.conda#903fa782a9067d5934210df6d79220f6
@@ -82,16 +85,17 @@ https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c
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+https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.10.2-hb4ffafa_0.conda#1a88c95afde6f13403492cac91352568
 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
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+https://conda.anaconda.org/conda-forge/noarch/recommonmark-0.7.1-pyhd8ed1ab_0.tar.bz2#b3becf9905b8c7ba839072f65e693253
+https://conda.anaconda.org/conda-forge/noarch/sphinx-automodapi-0.16.0-pyh6ff6d48_0.conda#c2dfb5d38d19546cf818d75801c21ed0
+https://conda.anaconda.org/conda-forge/noarch/sphinx-gallery-0.14.0-pyhd8ed1ab_0.conda#b3788794f88c9512393032e448428261
+https://conda.anaconda.org/conda-forge/noarch/sphinx-jsonschema-1.19.1-pyhd8ed1ab_0.tar.bz2#d340bddca07283d3362b0e46b1791568
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.7-pyhd8ed1ab_0.conda#aebfabcb60c33a89c1f9290cab49bc93
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-bibtex-2.6.1-pyhd8ed1ab_1.conda#109cf3a7c844834267057e80b4f4eae3
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.5-pyhd8ed1ab_0.conda#ebf08f5184d8eaa486697bc060031953
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.4-pyhd8ed1ab_0.conda#a9a89000dfd19656ad004b937eeb6828
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda#914897066d5873acfb13e75705276ad1
+https://conda.anaconda.org/conda-forge/noarch/sphinx-astropy-1.9.1-pyhd8ed1ab_0.conda#b6a0939e7b6b3a854b8c8f04606da1a7
+https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-1.3.0-pyha770c72_0.conda#a615c369167e508293d8409973b34863
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.6-pyhd8ed1ab_0.conda#cf5c9649272c677a964a7313279e3a9b
+https://conda.anaconda.org/conda-forge/noarch/sphinx-5.3.0-pyhd8ed1ab_0.tar.bz2#f9e1fcfe235d655900bfeb6aee426472
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.9-pyhd8ed1ab_0.conda#0612e497d7860728f2cda421ea2aec09
diff --git a/conda-lock.yml b/conda-lock.yml
index b5369385d75..7b25a11453c 100644
--- a/conda-lock.yml
+++ b/conda-lock.yml
@@ -7,21 +7,22 @@
 # Install this environment as "YOURENV" with:
 #     conda-lock install -n YOURENV --file conda-lock.yml
 # To update a single package to the latest version compatible with the version constraints in the source:
-#     conda-lock lock --lockfile conda-lock.yml --update PACKAGE
+#     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
 # To re-solve the entire environment, e.g. after changing a version constraint in the source file:
-#     conda-lock -f tardis_env3.yml --lockfile conda-lock.yml
+#     conda-lock -f tardis_env3.yml -f /Users/wkerzend/python/tardis/tardis_env3.yml --lockfile conda-lock.yml
 metadata:
   channels:
   - url: conda-forge
     used_env_vars: []
   content_hash:
-    linux-64: bbdba7762d98ab5e33b2739d850c8034fb4a270a611f78498151cbf856de1886
-    osx-64: a3efbf053cb36c0788d9799a0000a04f4bd9b9f10bbea1fdfdfb79cb6095a5d4
+    linux-64: 31d323d670a8deec16e2186403aa54ab8464102ac712829e12e62d80bc50f272
+    osx-64: a32c45fe2a9272de47a9c858b1b632bb1de0c3a0cd55bffe7df61cc7ef21eecd
   platforms:
   - linux-64
   - osx-64
   sources:
   - tardis_env3.yml
+  - /Users/wkerzend/python/tardis/tardis_env3.yml
 package:
 - category: main
   dependencies: {}
@@ -136,14 +137,25 @@ package:
 - category: main
   dependencies: {}
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-    sha256: 3e55f11e96fd737e2a338464ec99a51178fc8fae9d46550a4255be39b25efa99
+    md5: c2e2630ddb68cf52eec74dc7dfab20b5
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   name: python_abi
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-3_cp38.conda
-  version: '3.8'
+  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-3_cp311.conda
+  version: '3.11'
+- category: main
+  dependencies: {}
+  hash:
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+    sha256: 0449138224adfa125b220154408419ec37c06b0b49f63c5954724325903ecf55
+  manager: conda
+  name: tzdata
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda
+  version: 2023c
 - category: main
   dependencies:
     font-ttf-dejavu-sans-mono: ''
@@ -374,14 +386,14 @@ package:
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-    sha256: 949d84ceea543802c1e085b2aa58f1d6cb5dd8cec5a9abaaf4e8ac65d6094b3a
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   optional: false
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda
-  version: '1.18'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.19-hd590300_0.conda
+  version: '1.19'
 - category: main
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     libgcc-ng: '>=7.5.0'
@@ -734,6 +746,18 @@ package:
   platform: linux-64
   url: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
   version: 0.2.5
+- category: main
+  dependencies:
+    libgcc-ng: '>=12'
+  hash:
+    md5: 49e8329110001f04923fe7e864990b0c
+    sha256: 6b3a22b7cc219e8d83f16c1ceba67aa51e0b7e3bcc4a647b97a0a510559b0477
+  manager: conda
+  name: zlib-ng
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.0.7-h0b41bf4_0.conda
+  version: 2.0.7
 - category: main
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     libexpat: 2.5.0 hcb278e6_1
@@ -798,6 +822,20 @@ package:
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   url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_1.conda
   version: 13.2.0
+- category: main
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    libzlib: '>=1.2.13,<1.3.0a0'
+  hash:
+    md5: 73301c133ded2bf71906aa2104edae8b
+    sha256: 225cc7c3b20ac1db1bdb37fa18c95bf8aecef4388e984ab2f7540a9f4382106a
+  manager: conda
+  name: libllvm14
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libllvm14-14.0.6-hcd5def8_4.conda
+  version: 14.0.6
 - category: main
   dependencies:
     c-ares: '>=1.18.1,<2.0a0'
@@ -1025,6 +1063,22 @@ package:
   platform: linux-64
   url: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hd590300_0.conda
   version: 1.1.0
+- category: main
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    lz4-c: '>=1.9.3,<1.10.0a0'
+    zlib-ng: '>=2.0.7,<2.1.0a0'
+    zstd: '>=1.5.2,<1.6.0a0'
+  hash:
+    md5: 1a88c95afde6f13403492cac91352568
+    sha256: cd2157e19514bbe00f1025f9c31b081b748ba43dae0e53b104550248a03af1c6
+  manager: conda
+  name: c-blosc2
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.10.2-hb4ffafa_0.conda
+  version: 2.10.2
 - category: main
   dependencies:
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@@ -1104,22 +1158,22 @@ package:
 - category: main
   dependencies:
     lerc: '>=4.0.0,<5.0a0'
-    libdeflate: '>=1.18,<1.19.0a0'
+    libdeflate: '>=1.19,<1.20.0a0'
     libgcc-ng: '>=12'
     libjpeg-turbo: '>=2.1.5.1,<3.0a0'
     libstdcxx-ng: '>=12'
-    libwebp-base: '>=1.3.1,<2.0a0'
+    libwebp-base: '>=1.3.2,<2.0a0'
     libzlib: '>=1.2.13,<1.3.0a0'
     xz: '>=5.2.6,<6.0a0'
     zstd: '>=1.5.5,<1.6.0a0'
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-    sha256: a14a86478fb3c284b5552e33a179a3912cacc3f469d318557d20f4a72b624235
+    md5: 4e9afd30f4ccb2f98645e51005f82236
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   manager: conda
   name: libtiff
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h8b53f26_0.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h29866fb_1.conda
   version: 4.6.0
 - category: main
   dependencies:
@@ -1166,26 +1220,28 @@ package:
   dependencies:
     bzip2: '>=1.0.8,<2.0a0'
     ld_impl_linux-64: '>=2.36.1'
+    libexpat: '>=2.5.0,<3.0a0'
     libffi: '>=3.4,<4.0a0'
     libgcc-ng: '>=12'
     libnsl: '>=2.0.0,<2.1.0a0'
-    libsqlite: '>=3.42.0,<4.0a0'
+    libsqlite: '>=3.43.0,<4.0a0'
     libuuid: '>=2.38.1,<3.0a0'
     libzlib: '>=1.2.13,<1.3.0a0'
     ncurses: '>=6.4,<7.0a0'
-    openssl: '>=3.1.1,<4.0a0'
+    openssl: '>=3.1.2,<4.0a0'
     readline: '>=8.2,<9.0a0'
     tk: '>=8.6.12,<8.7.0a0'
+    tzdata: ''
     xz: '>=5.2.6,<6.0a0'
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-    sha256: 0e2a0ad88b2310582251ec06ef16b160ff9d8efd8d063778f373b255438a9e63
+    md5: f0288cb82594b1cbc71111d1cd3c5422
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   manager: conda
   name: python
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.8.17-he550d4f_0_cpython.conda
-  version: 3.8.17
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.11.5-hab00c5b_0_cpython.conda
+  version: 3.11.5
 - category: main
   dependencies:
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@@ -1311,16 +1367,16 @@ package:
   dependencies:
     libgcc-ng: '>=12'
     libstdcxx-ng: '>=12'
-    python: '>=3.8,<3.9.0a0'
-    python_abi: 3.8.* *_cp38
+    python: '>=3.11,<3.12.0a0'
+    python_abi: 3.11.* *_cp311
   hash:
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-    sha256: 6091cd4ead9b14120063e1d719b7ea43d614603e739344f29dc850458a60d33e
+    md5: b8128d083dbf6abd472b1a3e98b0b83d
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   manager: conda
   name: brotli-python
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py38h17151c0_0.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py311hb755f60_0.conda
   version: 1.1.0
 - category: main
   dependencies:
@@ -1411,16 +1467,16 @@ package:
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     libgcc-ng: '>=12'
     libstdcxx-ng: '>=12'
-    python: '>=3.8,<3.9.0a0'
-    python_abi: 3.8.* *_cp38
+    python: '>=3.11,<3.12.0a0'
+    python_abi: 3.11.* *_cp311
   hash:
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-    sha256: 6eb6ce121d49a9c9f6f41eb793149ad94b626c0b370f47c1508b7a8c64cdcdef
+    md5: 18855bb6c744389b662f6e2ba20acbb7
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   manager: conda
   name: debugpy
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.0-py38h17151c0_0.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.0-py311hb755f60_0.conda
   version: 1.8.0
 - category: main
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@@ -1448,17 +1504,17 @@ package:
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 - category: main
   dependencies:
-    python: '>=3.8,<3.9.0a0'
-    python_abi: 3.8.* *_cp38
+    python: '>=3.11,<3.12.0a0'
+    python_abi: 3.11.* *_cp311
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-    sha256: e491096d51ba762013a98d04ccf4fb9beb46e714af3fa514c7db214c79e55d22
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   manager: conda
   name: docutils
   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/docutils-0.18.1-py38h578d9bd_1.tar.bz2
-  version: 0.18.1
+  url: https://conda.anaconda.org/conda-forge/linux-64/docutils-0.17.1-py311h38be061_3.tar.bz2
+  version: 0.17.1
 - category: main
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@@ -1558,16 +1614,16 @@ package:
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     mpfr: '>=4.1.0,<5.0a0'
-    python: '>=3.8,<3.9.0a0'
-    python_abi: 3.8.* *_cp38
+    python: '>=3.11,<3.12.0a0'
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-    sha256: f77bd4176ad7cc57954d28bdfe829f79c3320a23d23e98ed2906fffc6153e138
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   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/gmpy2-2.1.2-py38h793c122_1.tar.bz2
+  url: https://conda.anaconda.org/conda-forge/linux-64/gmpy2-2.1.2-py311h6a5fa03_1.tar.bz2
   version: 2.1.2
 - category: main
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@@ -1645,16 +1701,16 @@ package:
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 - category: main
   dependencies:
-    python: '>=3.8,<3.9.0a0'
-    python_abi: 3.8.* *_cp38
+    python: '>=3.11,<3.12.0a0'
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+    md5: 46786941fbb695d0c1fa25af64526e7c
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   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/jsonpointer-2.4-py38h578d9bd_2.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/jsonpointer-2.4-py311h38be061_2.conda
   version: '2.4'
 - category: main
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     libgcc-ng: '>=12'
     libstdcxx-ng: '>=12'
-    python: '>=3.8,<3.9.0a0'
-    python_abi: 3.8.* *_cp38
+    python: '>=3.11,<3.12.0a0'
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-    sha256: d227634d38982a975ebac73b90649a6bc4637ac41ea355b1e70d5ebe57004e6a
+    md5: f53903649188b99e6b44c560c69f5b23
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   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.5-py38h7f3f72f_0.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.5-py311h9547e67_0.conda
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-    python_abi: 3.8.* *_cp38
-    zlib: '>=1.2.11,<1.3.0a0'
+    libgcc-ng: '>=12'
+    libllvm14: '>=14.0.6,<14.1.0a0'
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+    libzlib: '>=1.2.13,<1.3.0a0'
+    python: '>=3.11,<3.12.0a0'
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-  version: 0.36.0
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+  url: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.4-pyhd8ed1ab_0.conda
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+  optional: false
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+  url: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda
+  version: '4.1'
+- category: main
+  dependencies:
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+    numpydoc: ''
+    packaging: ''
+    pillow: ''
+    pytest-doctestplus: '>=0.11'
+    python: '>=3.7'
+    sphinx: '>=3'
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+    sphinx-gallery: ''
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+  optional: false
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+  url: https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-1.3.0-pyha770c72_0.conda
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+  optional: false
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+  url: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.6-pyhd8ed1ab_0.conda
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+    colorama: '>=0.4.5'
+    docutils: '>=0.14,<0.20'
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+    snowballstemmer: '>=2.0'
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+    sphinxcontrib-jsmath: ''
+    sphinxcontrib-qthelp: ''
+    sphinxcontrib-serializinghtml: '>=1.1.5'
+  hash:
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+  url: https://conda.anaconda.org/conda-forge/noarch/sphinx-5.3.0-pyhd8ed1ab_0.tar.bz2
+  version: 5.3.0
+- category: main
+  dependencies:
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+    sphinx: '>=5'
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+  manager: conda
+  name: sphinxcontrib-serializinghtml
+  optional: false
+  platform: osx-64
+  url: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.9-pyhd8ed1ab_0.conda
+  version: 1.1.9
 version: 1
diff --git a/conda-osx-64.lock b/conda-osx-64.lock
index 59889512fc9..00013efcb38 100644
--- a/conda-osx-64.lock
+++ b/conda-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
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+# input_hash: a32c45fe2a9272de47a9c858b1b632bb1de0c3a0cd55bffe7df61cc7ef21eecd
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+https://conda.anaconda.org/conda-forge/osx-64/zlib-ng-2.0.7-hb7f2c08_0.conda#813b5ad3ba92b75b84f40602b6d34ffb
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+https://conda.anaconda.org/conda-forge/osx-64/libllvm14-14.0.6-hc8e404f_4.conda#ed06753e2ba7c66ed0ca7f19578fcb68
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+https://conda.anaconda.org/conda-forge/osx-64/libtiff-4.6.0-haeeb97c_1.conda#bf4e56cd02413fc3a92835251e2a8c4f
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+https://conda.anaconda.org/conda-forge/osx-64/python-3.11.5-h30d4d87_0_cpython.conda#ef2b263b5b02d2acf00908bb07c14b12
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 https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.6-pyhd8ed1ab_0.conda#078979d33523cb477bd1916ce41aacc9
@@ -251,48 +251,40 @@ https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-23.1.0-pyhd8ed1ab_0.co
 https://conda.anaconda.org/conda-forge/noarch/black-22.3.0-pyhd8ed1ab_0.tar.bz2#7ecbfaae9a30b73c1a6e36e4a0debc03
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 https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.19.0-pyhd8ed1ab_1.conda#d442886dffcee45604595fea2ad3a181
-https://conda.anaconda.org/conda-forge/osx-64/jupyter_core-5.3.1-py38h50d1736_0.conda#03a3619e222793567b29b5966c2a821d
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+https://conda.anaconda.org/conda-forge/osx-64/jupyter_core-5.3.1-py311h6eed73b_0.conda#2d45628b123595054093ff65996b98ae
+https://conda.anaconda.org/conda-forge/osx-64/numpy-1.24.4-py311hc44ba51_0.conda#31c12f08652b27a8f9cceb39ea4a1d4e
 https://conda.anaconda.org/conda-forge/osx-64/pango-1.50.14-h19c1c8a_2.conda#bf0d46d9e97cb3ae5ad7ee4b688929a9
 https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.39-pyha770c72_0.conda#a4986c6bb5b0d05a38855b0880a5f425
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+https://conda.anaconda.org/conda-forge/osx-64/pybtex-docutils-1.0.3-py311h6eed73b_0.conda#218f01e087a8a12f3474ff43c9879628
 https://conda.anaconda.org/conda-forge/noarch/pyopenssl-23.1.1-pyhd8ed1ab_0.conda#0b34aa3ab7e7ccb1765a03dd9ed29938
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 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.2-pyhd1c38e8_0.conda#2657c3de5371c571aef6678afb4aaadd
-https://conda.anaconda.org/conda-forge/noarch/sphinx-7.0.1-pyhd8ed1ab_0.conda#51a8d037b28276b4f68263e890e0f35b
+https://conda.anaconda.org/conda-forge/noarch/setuptools_scm-7.1.0-hd8ed1ab_0.conda#75abb977a0ae63a8039b12fa0925eeb8
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-apidoc-0.3.0-py_1.tar.bz2#855b087883443abb10f5faf6eef40860
+https://conda.anaconda.org/conda-forge/osx-64/contourpy-1.1.1-py311h5fe6e05_0.conda#4ee477aeedcb82edff2b3d9ab2ad98ae
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+https://conda.anaconda.org/conda-forge/osx-64/h5py-3.9.0-nompi_py311hf255e76_102.conda#8261fdb0f3ef9287449d3731ef927ed7
 https://conda.anaconda.org/conda-forge/noarch/jsonschema-with-format-nongpl-4.19.0-pyhd8ed1ab_1.conda#d273b30bcf4db0ef6b1195b3b61b3d68
 https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.3.1-pyhd8ed1ab_0.conda#b7cc0981484fcb6390e6d341e55618b3
 https://conda.anaconda.org/conda-forge/osx-64/librsvg-2.56.3-hec3db73_0.conda#c6ab56c808493cbd88267fad5297c3c1
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 https://conda.anaconda.org/conda-forge/noarch/nbformat-5.9.2-pyhd8ed1ab_0.conda#61ba076de6530d9301a0053b02f093d2
-https://conda.anaconda.org/conda-forge/osx-64/numba-0.53.1-py38h5b9a75a_1.tar.bz2#b547323b20986d1d2fc3307b9b663345
-https://conda.anaconda.org/conda-forge/osx-64/numexpr-2.8.3-py38h2b30649_0.tar.bz2#957d7b3ef70a5955530c82d4adbdca3a
-https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.5.0-pyhd8ed1ab_0.tar.bz2#3c275d7168a6a135329f4acb364c229a
-https://conda.anaconda.org/conda-forge/osx-64/pandas-1.0.5-py38h5fc983b_0.tar.bz2#0563558e72be6fa5468c42816c3a17f9
+https://conda.anaconda.org/conda-forge/osx-64/numba-0.57.1-py311h5a8220d_0.conda#8049bf49848013a9b6565c14e6621798
+https://conda.anaconda.org/conda-forge/osx-64/numexpr-2.8.4-py311hab14417_1.conda#f54b3f060b554070e12e815e97c02a1c
+https://conda.anaconda.org/conda-forge/osx-64/pandas-2.1.0-py311hab14417_0.conda#e081bf78c37d2671a7d442a56c3a8728
 https://conda.anaconda.org/conda-forge/noarch/prompt_toolkit-3.0.39-hd8ed1ab_0.conda#4bbbe67d5df19db30f04b8e344dc9976
-https://conda.anaconda.org/conda-forge/osx-64/pyerfa-2.0.0.1-py38h4277f33_2.tar.bz2#c471813135c81ba827b0d80f09cc9e9c
-https://conda.anaconda.org/conda-forge/noarch/recommonmark-0.7.1-pyhd8ed1ab_0.tar.bz2#b3becf9905b8c7ba839072f65e693253
-https://conda.anaconda.org/conda-forge/osx-64/scipy-1.5.3-py38hb6cd474_0.tar.bz2#b0574c75ef08dffa661a55c28abda13c
-https://conda.anaconda.org/conda-forge/noarch/sphinx-automodapi-0.16.0-pyh6ff6d48_0.conda#c2dfb5d38d19546cf818d75801c21ed0
-https://conda.anaconda.org/conda-forge/noarch/sphinx-jsonschema-1.19.1-pyhd8ed1ab_0.tar.bz2#d340bddca07283d3362b0e46b1791568
-https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-bibtex-2.5.0-pyhd8ed1ab_0.tar.bz2#b2e5c9aece936ebf9f26abdf71ddd74b
-https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda#914897066d5873acfb13e75705276ad1
-https://conda.anaconda.org/conda-forge/osx-64/astropy-5.0.4-py38h4277f33_0.tar.bz2#58445a843bda46aef14f89ba058ea301
+https://conda.anaconda.org/conda-forge/osx-64/pyerfa-2.0.0.3-py311h4a70a88_0.conda#261df2feb11abd22de42e0c9dc276a2e
+https://conda.anaconda.org/conda-forge/osx-64/scipy-1.11.2-py311h16c3c4d_1.conda#1a79189c98a28c9fef03ba8315bcd6b8
+https://conda.anaconda.org/conda-forge/osx-64/astropy-5.3.3-py311h4a70a88_0.conda#067a1e7c5fc33393399dc5c1969469a0
 https://conda.anaconda.org/conda-forge/osx-64/graphviz-8.1.0-hc7f41f9_0.conda#a840f2eb891fdc5c39c762e16ee09600
-https://conda.anaconda.org/conda-forge/noarch/ipython-8.12.2-pyhd1c38e8_0.conda#acc618532cbc899f5721cc96407b16cc
+https://conda.anaconda.org/conda-forge/noarch/ipython-8.15.0-pyh31c8845_0.conda#24e68bbee62de3c9c6d051d59e9ea87b
 https://conda.anaconda.org/conda-forge/noarch/jupyter_events-0.7.0-pyhd8ed1ab_2.conda#088f0493279a7f7eebd514df47d65851
+https://conda.anaconda.org/conda-forge/osx-64/matplotlib-base-3.7.2-py311haff9b01_0.conda#bd9520e9015e70f3de839ce48c9061ea
 https://conda.anaconda.org/conda-forge/noarch/nbclient-0.8.0-pyhd8ed1ab_0.conda#e78da91cf428faaf05701ce8cc8f2f9b
-https://conda.anaconda.org/conda-forge/osx-64/pytables-3.7.0-py38h83bf2f2_2.tar.bz2#e73c5cffa63e86d5d09a76d669b130e8
-https://conda.anaconda.org/conda-forge/noarch/radioactivedecay-0.4.21-pyhd8ed1ab_0.conda#673319f48d9b160c8056783d301e090c
-https://conda.anaconda.org/conda-forge/noarch/sphinx-gallery-0.14.0-pyhd8ed1ab_0.conda#b3788794f88c9512393032e448428261
-https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-1.3.0-pyha770c72_0.conda#a615c369167e508293d8409973b34863
+https://conda.anaconda.org/conda-forge/osx-64/pytables-3.8.0-py311h21e7aa0_3.conda#fe8ff91c89febadc989bc9e88c53e5a2
 https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.25.2-pyh1050b4e_0.conda#a643e6f6c33ed821664f2a69f6e4e89f
 https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.8.0-pyhd8ed1ab_0.conda#62345c9e24f898bf492979be84a6eb0a
-https://conda.anaconda.org/conda-forge/osx-64/pygraphviz-1.11-py38h92dd6f0_0.conda#986fbee52d338eec520117351d918755
-https://conda.anaconda.org/conda-forge/noarch/sphinx-astropy-1.9.1-pyhd8ed1ab_0.conda#b6a0939e7b6b3a854b8c8f04606da1a7
+https://conda.anaconda.org/conda-forge/osx-64/pygraphviz-1.11-py311hc6eba27_0.conda#fed0a15be9e09c83aba369a5049655c1
+https://conda.anaconda.org/conda-forge/noarch/radioactivedecay-0.4.21-pyhd8ed1ab_0.conda#673319f48d9b160c8056783d301e090c
 https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_0.conda#969249eb7c2f7a9b820520a355dc7d04
 https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.8.0-pyhd8ed1ab_0.conda#1dba1a577df2625a24667612a069e91c
 https://conda.anaconda.org/conda-forge/noarch/jupyter-lsp-2.2.0-pyhd8ed1ab_0.conda#38589f4104d11f2a59ff01a9f4e3bfb3
@@ -301,8 +293,23 @@ https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.8.0-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.3-pyhd8ed1ab_0.conda#67e0fe74c156267d9159e9133df7fd37
 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.6-pyhd8ed1ab_0.conda#80bb1cc3b540790cb5afecd73c2d4d1f
 https://conda.anaconda.org/conda-forge/noarch/nbclassic-1.0.0-pyhb4ecaf3_1.conda#a0be31e9bd84d6eae87cdbf74c56b90b
-https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.3-pyhd8ed1ab_0.conda#0dbaa7d08d3d79b2a1a4dd6a02cc4581
 https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.3-pyhd8ed1ab_0.conda#1f2d368cde97926b5e351d1a0286bb1e
 https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda#fe79dfe7d51794d665ec3c2fdd4e47c3
 https://conda.anaconda.org/conda-forge/noarch/ipywidgets-7.8.0-pyhd8ed1ab_0.conda#518b05adab6cfe6ea249319932d9d4a3
 https://conda.anaconda.org/conda-forge/noarch/qgrid-1.3.1-pyhd8ed1ab_4.tar.bz2#fff68c7404813a1eb2678425f00e9917
+https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.3-pyhd8ed1ab_0.conda#0dbaa7d08d3d79b2a1a4dd6a02cc4581
+https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.5.0-pyhd8ed1ab_0.tar.bz2#3c275d7168a6a135329f4acb364c229a
+https://conda.anaconda.org/conda-forge/noarch/recommonmark-0.7.1-pyhd8ed1ab_0.tar.bz2#b3becf9905b8c7ba839072f65e693253
+https://conda.anaconda.org/conda-forge/noarch/sphinx-automodapi-0.16.0-pyh6ff6d48_0.conda#c2dfb5d38d19546cf818d75801c21ed0
+https://conda.anaconda.org/conda-forge/noarch/sphinx-gallery-0.14.0-pyhd8ed1ab_0.conda#b3788794f88c9512393032e448428261
+https://conda.anaconda.org/conda-forge/noarch/sphinx-jsonschema-1.19.1-pyhd8ed1ab_0.tar.bz2#d340bddca07283d3362b0e46b1791568
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.7-pyhd8ed1ab_0.conda#aebfabcb60c33a89c1f9290cab49bc93
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-bibtex-2.6.1-pyhd8ed1ab_1.conda#109cf3a7c844834267057e80b4f4eae3
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.5-pyhd8ed1ab_0.conda#ebf08f5184d8eaa486697bc060031953
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.4-pyhd8ed1ab_0.conda#a9a89000dfd19656ad004b937eeb6828
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda#914897066d5873acfb13e75705276ad1
+https://conda.anaconda.org/conda-forge/noarch/sphinx-astropy-1.9.1-pyhd8ed1ab_0.conda#b6a0939e7b6b3a854b8c8f04606da1a7
+https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-1.3.0-pyha770c72_0.conda#a615c369167e508293d8409973b34863
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.6-pyhd8ed1ab_0.conda#cf5c9649272c677a964a7313279e3a9b
+https://conda.anaconda.org/conda-forge/noarch/sphinx-5.3.0-pyhd8ed1ab_0.tar.bz2#f9e1fcfe235d655900bfeb6aee426472
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.9-pyhd8ed1ab_0.conda#0612e497d7860728f2cda421ea2aec09
diff --git a/tardis/io/atom_data/base.py b/tardis/io/atom_data/base.py
index 32548134df0..1db66d58e09 100644
--- a/tardis/io/atom_data/base.py
+++ b/tardis/io/atom_data/base.py
@@ -168,7 +168,7 @@ def from_hdf(cls, fname=None):
 
             for name in cls.hdf_names:
                 try:
-                    dataframes[name] = store[name]
+                    dataframes[name] = store.select(name)
                 except KeyError:
                     logger.debug(f"Dataframe does not contain {name} column")
                     nonavailable.append(name)
@@ -287,25 +287,33 @@ def __init__(
         if u.u.cgs == const.u.cgs:
             atom_data.loc[:, "mass"] = Quantity(
                 atom_data["mass"].values, "u"
-            ).cgs
+            ).cgs.value
         else:
-            atom_data.loc[:, "mass"] = atom_data["mass"].values * const.u.cgs
+            atom_data.loc[:, "mass"] = (
+                atom_data["mass"].values * const.u.cgs.value
+            )
 
         # Convert ionization energies to CGS
         ionization_data = ionization_data.squeeze()
-        ionization_data[:] = Quantity(ionization_data[:], "eV").cgs
+        ionization_data[:] = Quantity(ionization_data[:], "eV").cgs.value
 
         # Convert energy to CGS
-        levels.loc[:, "energy"] = Quantity(levels["energy"].values, "eV").cgs
+        levels.loc[:, "energy"] = Quantity(
+            levels["energy"].values, "eV"
+        ).cgs.value
 
         # Create a new columns with wavelengths in the CGS units
-        lines["wavelength_cm"] = Quantity(lines["wavelength"], "angstrom").cgs
+        lines["wavelength_cm"] = Quantity(
+            lines["wavelength"], "angstrom"
+        ).cgs.value
 
         # SET ATTRIBUTES
 
         self.atom_data = atom_data
         self.ionization_data = ionization_data
         self.levels = levels
+        # Not sure why this is need - WEK 17 Sep 2023
+        self.levels.energy = self.levels.energy.astype(np.float64)
         self.lines = lines
 
         # Rename these (drop "_all") when `prepare_atom_data` is removed!
@@ -522,7 +530,9 @@ def prepare_atom_data(
                 self.macro_atom_data.loc[:, "destination_level_idx"] = -1
 
             if self.yg_data is not None:
-                self.yg_data = self.yg_data.loc[self.selected_atomic_numbers]
+                self.yg_data = self.yg_data.reindex(
+                    self.selected_atomic_numbers, level=0
+                )
 
         self.nlte_data = NLTEData(self, nlte_species)
 
diff --git a/tardis/io/model/readers/artis.py b/tardis/io/model/readers/artis.py
index d05c917a825..d013867cfde 100644
--- a/tardis/io/model/readers/artis.py
+++ b/tardis/io/model/readers/artis.py
@@ -1,6 +1,6 @@
 import numpy as np
 from astropy import units as u
-from numpy import recfromtxt
+import pandas as pd
 
 
 def read_artis_density(fname):
@@ -43,13 +43,15 @@ def read_artis_density(fname):
         "fe52_fraction",
         "cr48_fraction",
     ]
-    artis_model = recfromtxt(
+
+    artis_model = pd.read_csv(
         fname,
-        skip_header=2,
+        skiprows=2,
         usecols=(0, 1, 2, 4, 5, 6, 7),
-        unpack=True,
-        dtype=[(item, np.float64) for item in artis_model_columns],
-    )
+        dtype={item: np.float64 for item in artis_model_columns},
+        names=artis_model_columns,
+        delim_whitespace=True,
+    ).to_records(index=False)
 
     velocity = u.Quantity(artis_model["velocities"], "km/s").to("cm/s")
     mean_density = u.Quantity(10 ** artis_model["mean_densities_0"], "g/cm^3")[
diff --git a/tardis/io/tests/test_HDFWriter.py b/tardis/io/tests/test_HDFWriter.py
index 6aa3758a489..bc7be113880 100644
--- a/tardis/io/tests/test_HDFWriter.py
+++ b/tardis/io/tests/test_HDFWriter.py
@@ -1,11 +1,8 @@
-import os
-
 import numpy as np
 import pandas as pd
-import pandas.util.testing as pdt
 import pytest
 from astropy import units as u
-from astropy.tests.helper import assert_quantity_allclose
+
 from numpy.testing import assert_almost_equal, assert_array_almost_equal
 
 from tardis.io.util import HDFWriterMixin
@@ -61,6 +58,7 @@ def test_complex_obj_write(tmpdir, attr):
     actual = MockHDF(attr)
     actual.to_hdf(fname, path="test", overwrite=True)
     expected = pd.read_hdf(fname, key="/test/mock_hdf/property").values
+
     assert_array_almost_equal(actual.property, expected)
 
 
@@ -79,7 +77,8 @@ def test_multi_index_write(tmpdir):
     actual.to_hdf(fname, path="test", overwrite=True)
     expected = pd.read_hdf(fname, key="/test/mock_hdf/property")
     expected = pd.MultiIndex.from_tuples(expected.unstack().values)
-    pdt.assert_almost_equal(actual.property, expected)
+    # These are multiindex objects, so we need to compare the values
+    assert np.all(expected.values == actual.property.values)
 
 
 # Test Quantity Objects
diff --git a/tardis/io/tests/test_atomic.py b/tardis/io/tests/test_atomic.py
index 70de086d9b0..537f3a033ef 100644
--- a/tardis/io/tests/test_atomic.py
+++ b/tardis/io/tests/test_atomic.py
@@ -49,7 +49,7 @@ def test_atom_data_levels(levels):
 
 def test_atom_data_lines(lines):
     assert_quantity_allclose(
-        lines.at[(2, 0, 0, 6), "wavelength_cm"] * u.Unit("cm"),
+        lines.loc[(2, 0, 0, 6), "wavelength_cm"].values[0] * u.Unit("cm"),
         584.335 * u.Unit("Angstrom"),
     )
 
diff --git a/tardis/model/base.py b/tardis/model/base.py
index fba93a7efbd..5d0d0dd152a 100644
--- a/tardis/model/base.py
+++ b/tardis/model/base.py
@@ -593,7 +593,7 @@ def from_config(cls, config, atom_data=None):
         #       v boundaries.
         no_of_shells = len(velocity) - 1
 
-        if temperature:
+        if temperature is not None:
             t_radiative = temperature
         elif config.plasma.initial_t_rad > 0 * u.K:
             t_radiative = (
diff --git a/tardis/montecarlo/montecarlo_numba/base.py b/tardis/montecarlo/montecarlo_numba/base.py
index ada2389f1b5..028a91ff775 100644
--- a/tardis/montecarlo/montecarlo_numba/base.py
+++ b/tardis/montecarlo/montecarlo_numba/base.py
@@ -1,8 +1,5 @@
 from numba import prange, njit, objmode
-from numba.np.ufunc.parallel import (
-    _get_thread_id as get_thread_id,
-    get_num_threads,
-)
+from numba.np.ufunc.parallel import get_thread_id, get_num_threads
 
 import numpy as np
 
diff --git a/tardis/montecarlo/montecarlo_numba/formal_integral.py b/tardis/montecarlo/montecarlo_numba/formal_integral.py
index 6e2db7bbdde..fbb443e79a1 100644
--- a/tardis/montecarlo/montecarlo_numba/formal_integral.py
+++ b/tardis/montecarlo/montecarlo_numba/formal_integral.py
@@ -454,7 +454,7 @@ def make_source_function(self):
         upper_level_index = self.atomic_data.lines.index.droplevel(
             "level_number_lower"
         )
-        e_dot_lu = pd.DataFrame(Edotlu, index=upper_level_index)
+        e_dot_lu = pd.DataFrame(Edotlu.values, index=upper_level_index)
         e_dot_u = e_dot_lu.groupby(level=[0, 1, 2]).sum()
         e_dot_u_src_idx = macro_ref.loc[e_dot_u.index].references_idx.values
 
diff --git a/tardis/montecarlo/tests/test_spectrum.py b/tardis/montecarlo/tests/test_spectrum.py
index 418317f822c..7f31fbcfa2e 100644
--- a/tardis/montecarlo/tests/test_spectrum.py
+++ b/tardis/montecarlo/tests/test_spectrum.py
@@ -38,7 +38,7 @@ def spectrum(request):
         request.param["lum"],
     )
     distance = request.param["distance"]
-    if distance:
+    if distance is not None:
         data.distance = distance
     return data
 
@@ -67,7 +67,7 @@ def test_luminosity_density_lambda(spectrum):
 
 
 def test_flux_nu(spectrum):
-    if getattr(spectrum, "distance", None):
+    if getattr(spectrum, "distance", None) is not None:
 
         with pytest.warns(DeprecationWarning):
             test_helper.assert_quantity_allclose(
@@ -82,7 +82,7 @@ def test_flux_nu(spectrum):
 
 
 def test_flux_lambda(spectrum):
-    if getattr(spectrum, "distance", None):
+    if getattr(spectrum, "distance", None) is not None:
 
         with pytest.warns(DeprecationWarning):
             test_helper.assert_quantity_allclose(
diff --git a/tardis/plasma/properties/ion_population.py b/tardis/plasma/properties/ion_population.py
index caf4eb81ee4..c70bd06965a 100644
--- a/tardis/plasma/properties/ion_population.py
+++ b/tardis/plasma/properties/ion_population.py
@@ -53,7 +53,6 @@ class PhiSahaLTE(ProcessingPlasmaProperty):
 
     @staticmethod
     def calculate(g_electron, beta_rad, partition_function, ionization_data):
-
         phis = np.empty(
             (
                 partition_function.shape[0]
@@ -70,9 +69,9 @@ def calculate(g_electron, beta_rad, partition_function, ionization_data):
             current_phis = current_block[1:] / current_block[:-1]
             phis[start_id - i : end_id - i - 1] = current_phis
 
-        broadcast_ionization_energy = ionization_data[
+        broadcast_ionization_energy = ionization_data.reindex(
             partition_function.index
-        ].dropna()
+        ).dropna()
         phi_index = broadcast_ionization_energy.index
         broadcast_ionization_energy = broadcast_ionization_energy.values
 
diff --git a/tardis/plasma/standard_plasmas.py b/tardis/plasma/standard_plasmas.py
index 4961d0c6dd6..01e40fde22e 100644
--- a/tardis/plasma/standard_plasmas.py
+++ b/tardis/plasma/standard_plasmas.py
@@ -278,7 +278,7 @@ def assemble_plasma(config, model, atom_data=None):
     else:
         plasma_modules += helium_lte_properties
 
-    if model._electron_densities:
+    if model._electron_densities is not None:
         electron_densities = pd.Series(model._electron_densities.cgs.value)
         if config.plasma.helium_treatment == "numerical-nlte":
             property_kwargs[IonNumberDensityHeNLTE] = dict(
diff --git a/tardis/plasma/tests/test_complete_plasmas.py b/tardis/plasma/tests/test_complete_plasmas.py
index 5e1e9dbfa24..4320f0d8284 100644
--- a/tardis/plasma/tests/test_complete_plasmas.py
+++ b/tardis/plasma/tests/test_complete_plasmas.py
@@ -2,8 +2,10 @@
 import warnings
 
 import pandas as pd
+import pandas.testing as pdt
 import pytest
-from pandas.util import testing as pdt
+
+import numpy as np
 from numpy.testing import assert_almost_equal
 from tardis.io.configuration.config_reader import Configuration
 from tardis.simulation import Simulation
@@ -169,13 +171,21 @@ def plasma(self, request, chianti_he_db_fpath, config, tardis_ref_data):
     def test_plasma_properties(self, plasma, tardis_ref_data, config, attr):
         if hasattr(plasma, attr):
             actual = getattr(plasma, attr)
+            if hasattr(actual, "unit"):
+                actual = actual.value
             if actual.ndim == 1:
                 actual = pd.Series(actual)
             else:
                 actual = pd.DataFrame(actual)
             key = os.path.join(config.plasma.save_path, "plasma", attr)
             expected = tardis_ref_data[key]
-            pdt.assert_almost_equal(actual, expected)
+            if type(actual) == pd.DataFrame:
+                pdt.assert_frame_equal(actual, expected)
+            elif type(actual) == pd.Series:
+                pdt.assert_series_equal(actual, expected)
+            else:
+                raise TypeError(f"Unexpected type {type(actual)}")
+            # we used this before - assert_almost_equal(actual.values, expected.values)
         else:
             warnings.warn(f'Property "{attr}" not found')
 
@@ -183,7 +193,7 @@ def test_levels(self, plasma, tardis_ref_data, config):
         actual = pd.DataFrame(plasma.levels)
         key = os.path.join(config.plasma.save_path, "plasma", "levels")
         expected = tardis_ref_data[key]
-        pdt.assert_almost_equal(actual, expected)
+        pdt.assert_frame_equal(actual, expected)
 
     @pytest.mark.parametrize("attr", scalars_properties)
     def test_scalars_properties(self, plasma, tardis_ref_data, config, attr):
@@ -192,7 +202,7 @@ def test_scalars_properties(self, plasma, tardis_ref_data, config, attr):
             actual = actual.cgs.value
         key = os.path.join(config.plasma.save_path, "plasma", "scalars")
         expected = tardis_ref_data[key][attr]
-        pdt.assert_almost_equal(actual, expected)
+        assert_almost_equal(actual, expected)
 
     def test_helium_treatment(self, plasma, tardis_ref_data, config):
         actual = plasma.helium_treatment
diff --git a/tardis/plasma/tests/test_hdf_plasma.py b/tardis/plasma/tests/test_hdf_plasma.py
index 028ab4f40d1..00edec980d2 100644
--- a/tardis/plasma/tests/test_hdf_plasma.py
+++ b/tardis/plasma/tests/test_hdf_plasma.py
@@ -1,8 +1,9 @@
 import os
 import pandas as pd
 import pytest
-import pandas.util.testing as pdt
+
 from numpy.testing import assert_almost_equal
+import pandas.testing as pdt
 from tardis.plasma.properties import property_collections
 
 ###
@@ -68,7 +69,7 @@ def test_hdf_levels(hdf_file_path, simulation_verysimple):
         actual = actual.cgs.value
     path = os.path.join("plasma", "levels")
     expected = pd.read_hdf(hdf_file_path, path)
-    pdt.assert_almost_equal(pd.DataFrame(actual), expected)
+    pdt.assert_frame_equal(pd.DataFrame(actual), expected)
 
 
 scalars_list = ["time_explosion", "link_t_rad_t_electron"]
diff --git a/tardis/simulation/tests/test_simulation.py b/tardis/simulation/tests/test_simulation.py
index 3c0039f31ec..e44519281f8 100644
--- a/tardis/simulation/tests/test_simulation.py
+++ b/tardis/simulation/tests/test_simulation.py
@@ -8,10 +8,11 @@
 from tardis.io.configuration.config_reader import Configuration
 from tardis.simulation import Simulation
 from tardis import run_tardis
+import pandas.testing as pdt
 
 import numpy as np
 import pandas as pd
-import pandas.util.testing as pdt
+
 import astropy.units as u
 import tardis
 
@@ -88,10 +89,12 @@ def test_plasma_estimates(simulation_one_loop, refdata, name):
         actual = getattr(simulation_one_loop.transport, name)
     except AttributeError:
         actual = getattr(simulation_one_loop.model, name)
-
+    if name in ["t_radiative", "output_nu", "output_energy"]:
+        # removing the quantitiness of the data
+        actual = actual.value
     actual = pd.Series(actual)
 
-    pdt.assert_almost_equal(actual, refdata(name))
+    pdt.assert_series_equal(actual, refdata(name), rtol=1e-5, atol=1e-8)
 
 
 @pytest.mark.parametrize(
@@ -111,7 +114,12 @@ def test_plasma_state_iterations(simulation_one_loop, refdata, name):
     except Exception:
         actual = pd.DataFrame(actual)
 
-    pdt.assert_almost_equal(actual, refdata(name))
+    if type(actual) == pd.DataFrame:
+        pdt.assert_frame_equal(actual, refdata(name), rtol=1e-5, atol=1e-8)
+    elif type(actual) == pd.Series:
+        pdt.assert_series_equal(actual, refdata(name))
+    else:
+        raise ValueError(f"Unknown type of actual {type(actual)}")
 
 
 @pytest.fixture(scope="module")
diff --git a/tardis/tests/test_tardis_full_formal_integral.py b/tardis/tests/test_tardis_full_formal_integral.py
index e8fb5d07132..62a4abb0a21 100644
--- a/tardis/tests/test_tardis_full_formal_integral.py
+++ b/tardis/tests/test_tardis_full_formal_integral.py
@@ -90,11 +90,6 @@ def test_spectrum_integrated(self, transport, refdata):
             refdata("spectrum_integrated/luminosity"), "erg /s"
         )
 
-        print(
-            "actual, desired: ",
-            luminosity,
-            transport.spectrum_integrated.luminosity,
-        )
         assert_quantity_allclose(
             transport.spectrum_integrated.luminosity, luminosity
         )
diff --git a/tardis/visualization/tools/sdec_plot.py b/tardis/visualization/tools/sdec_plot.py
index a9ba221609b..bcd3195c11b 100644
--- a/tardis/visualization/tools/sdec_plot.py
+++ b/tardis/visualization/tools/sdec_plot.py
@@ -596,7 +596,7 @@ def _calculate_plotting_data(
         self.plot_frequency = self.data[packets_mode].spectrum_frequency
 
         # Filter their plottable range based on packet_wvl_range specified
-        if packet_wvl_range:
+        if packet_wvl_range is not None:
             packet_nu_range = packet_wvl_range.to("Hz", u.spectral())
 
             # Index of value just before the 1st value that is > packet_nu_range[1]
@@ -1224,7 +1224,7 @@ def generate_plot_mpl(
         # Set legends and labels
         self.ax.legend(fontsize=12)
         self.ax.set_xlabel(r"Wavelength $[\mathrm{\AA}]$", fontsize=12)
-        if distance:  # Set y-axis label for flux
+        if distance is not None:  # Set y-axis label for flux
             self.ax.set_ylabel(
                 r"$F_{\lambda}$ [erg $\mathrm{s^{-1}}$ $\mathrm{cm^{-2}}$ $\mathrm{\AA^{-1}}$]",
                 fontsize=12,
@@ -1632,7 +1632,7 @@ def generate_plot_ply(
 
         # Set label and other layout options
         xlabel = pu.axis_label_in_latex("Wavelength", u.AA)
-        if distance:  # Set y-axis label for flux
+        if distance is not None:  # Set y-axis label for flux
             ylabel = pu.axis_label_in_latex(
                 "F_{\\lambda}", u.Unit("erg/(s cm**2 AA)"), only_text=False
             )
diff --git a/tardis/visualization/tools/tests/test_sdec_plot.py b/tardis/visualization/tools/tests/test_sdec_plot.py
index 5e62044d7c0..975d5aa03fb 100644
--- a/tardis/visualization/tools/tests/test_sdec_plot.py
+++ b/tardis/visualization/tools/tests/test_sdec_plot.py
@@ -408,12 +408,14 @@ def test_generate_plot_mpl(
         species_list : list of str
         """
         subgroup_name = make_valid_name("mpl" + request.node.callspec.id)
+        if distance is None:
+            observed_spectrum = None
         fig = plotter.generate_plot_mpl(
             packets_mode=packets_mode,
             packet_wvl_range=packet_wvl_range,
             distance=distance,
             show_modeled_spectrum=show_modeled_spectrum,
-            observed_spectrum=observed_spectrum if distance else None,
+            observed_spectrum=observed_spectrum,
             nelements=nelements,
             species_list=species_list,
         )
@@ -549,12 +551,16 @@ def test_generate_plot_ply(
         species_list : list of str
         """
         subgroup_name = make_valid_name("ply" + request.node.callspec.id)
+        if distance is not None:
+            observed_spectrum = observed_spectrum
+        else:
+            observed_spectrum = None
         fig = plotter.generate_plot_ply(
             packets_mode=packets_mode,
             packet_wvl_range=packet_wvl_range,
             distance=distance,
             show_modeled_spectrum=show_modeled_spectrum,
-            observed_spectrum=observed_spectrum if distance else None,
+            observed_spectrum=observed_spectrum,
             nelements=nelements,
             species_list=species_list,
         )
diff --git a/tardis/visualization/widgets/line_info.py b/tardis/visualization/widgets/line_info.py
index 8b0c209e11d..c21993a5fec 100644
--- a/tardis/visualization/widgets/line_info.py
+++ b/tardis/visualization/widgets/line_info.py
@@ -328,7 +328,7 @@ class variable :code:`GROUP_MODES` (default value is
                 for (
                     line_id,
                     count,
-                ) in grouped_line_interactions.size().iteritems():
+                ) in grouped_line_interactions.size().items():
                     current_line_in = self.lines_data.loc[line_id[0]]
                     current_line_out = self.lines_data.loc[line_id[1]]
                     last_line_interaction_string.append(
@@ -350,7 +350,7 @@ class variable :code:`GROUP_MODES` (default value is
                 for (
                     line_id,
                     count,
-                ) in grouped_line_interactions.size().iteritems():
+                ) in grouped_line_interactions.size().items():
                     current_line_in = self.lines_data.loc[line_id]
                     last_line_interaction_string.append(
                         f"exc. {int(current_line_in.level_number_lower):02d}-"
@@ -368,7 +368,7 @@ class variable :code:`GROUP_MODES` (default value is
                 for (
                     line_id,
                     count,
-                ) in grouped_line_interactions.size().iteritems():
+                ) in grouped_line_interactions.size().items():
                     current_line_out = self.lines_data.loc[line_id]
                     last_line_interaction_string.append(
                         f"de-exc. {int(current_line_out.level_number_upper):02d}-"
diff --git a/tardis/visualization/widgets/tests/test_shell_info.py b/tardis/visualization/widgets/tests/test_shell_info.py
index 91b9b41cfe7..8d6af014617 100644
--- a/tardis/visualization/widgets/tests/test_shell_info.py
+++ b/tardis/visualization/widgets/tests/test_shell_info.py
@@ -43,11 +43,12 @@ def test_shells_data(self, base_shell_info, simulation_verysimple):
             2,
         )
         assert np.allclose(
-            shells_data.iloc[:, 0].map(np.float),
+            shells_data.iloc[:, 0].map(np.float64),
             simulation_verysimple.model.t_radiative.value,
         )
         assert np.allclose(
-            shells_data.iloc[:, 1].map(np.float), simulation_verysimple.model.w
+            shells_data.iloc[:, 1].map(np.float64),
+            simulation_verysimple.model.w,
         )
 
     @pytest.mark.parametrize("shell_num", [1, 20])
@@ -60,7 +61,7 @@ def test_element_count_data(
             2,
         )
         assert np.allclose(
-            element_count_data.iloc[:, -1].map(np.float),
+            element_count_data.iloc[:, -1].map(np.float64),
             simulation_verysimple.plasma.abundance[shell_num - 1],
         )
 
@@ -81,7 +82,7 @@ def test_ion_count_data(
         )
         assert ion_count_data.shape == (len(sim_ion_number_density), 2)
         assert np.allclose(
-            ion_count_data.iloc[:, -1].map(np.float),
+            ion_count_data.iloc[:, -1].map(np.float64),
             sim_ion_number_density / sim_element_number_density,
         )
 
@@ -111,7 +112,7 @@ def test_level_count_data(
         )
         assert level_count_data.shape == (len(sim_level_number_density), 1)
         assert np.allclose(
-            level_count_data.iloc[:, 0].map(np.float),
+            level_count_data.iloc[:, 0].map(np.float64),
             sim_level_number_density / sim_ion_number_density,
         )
 
diff --git a/tardis_env3.yml b/tardis_env3.yml
index 24c7e8d1432..efa0e7b399e 100644
--- a/tardis_env3.yml
+++ b/tardis_env3.yml
@@ -8,17 +8,17 @@ dependencies:
   # WARNING: any change to this section must be applied to the conda-forge
   # package recipe at https://github.com/conda-forge/tardis-sn-feedstock
 
-  - python =3.8
+  - python
   - setuptools
-  - setuptools_scm <7
+  - setuptools_scm
   - pip
-  - numpy =1.19
-  - scipy =1.5
-  - pandas =1.0
-  - astropy =5.0
-  - numba =0.53
+  - numpy
+  - scipy
+  - pandas
+  - astropy
+  - numba
   - numexpr
-  - radioactivedecay >=0.4.12
+  - radioactivedecay
 
   # Plasma
   - networkx
@@ -27,7 +27,7 @@ dependencies:
   # I/O
   - pyyaml
   - jsonschema
-  - hdf5 =1.12
+  - hdf5
   - h5py
   - pytables
   - requests
@@ -47,7 +47,7 @@ dependencies:
   - lxml
 
   # Documentation
-  - sphinx <=7.1
+  - sphinx
   - sphinx-astropy
   - sphinx_bootstrap_theme
   - sphinx-jsonschema

From ff5a120e0c980a61e0f2d2052486555d5cc5ee4a Mon Sep 17 00:00:00 2001
From: Anirban <anirban29_dutta@rediffmail.com>
Date: Thu, 21 Sep 2023 16:42:20 -0400
Subject: [PATCH 04/35] In gamma ray code : Changed times to np.geomspace
 (#2415)

* Changed times to np.geomspace

* Added myself to mailmap
---
 .mailmap                                   |  2 ++
 tardis/energy_input/gamma_ray_transport.py | 10 +---------
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/.mailmap b/.mailmap
index c005d9048fe..0baa7c0c71b 100644
--- a/.mailmap
+++ b/.mailmap
@@ -41,6 +41,8 @@ Atharwa Kharkar <atharwa.kharkar19@vit.edu> atharwa_24 <atharwa.kharkar19@vit.ed
 
 Atul Kumar <kr.atul.atk@gmail.com>
 
+Anirban Dutta <anirbaniamdutta@gmail.com>
+
 Barnabás Barna <bbarna@titan.physx.u-szeged.hu>
 
 Caroline Sofiatti <c.sofiatti@gmail.com>
diff --git a/tardis/energy_input/gamma_ray_transport.py b/tardis/energy_input/gamma_ray_transport.py
index 713a5bd209e..e89098e8ca6 100644
--- a/tardis/energy_input/gamma_ray_transport.py
+++ b/tardis/energy_input/gamma_ray_transport.py
@@ -356,15 +356,7 @@ def main_gamma_ray_loop(
     ), "Error, simulation start time greater than end time!"
 
     if time_space == "log":
-        times = np.zeros(time_steps + 1)
-
-        # log time steps
-        for i in range(time_steps + 1):
-            times[i] = (
-                np.log(time_start)
-                + (np.log(time_end) - np.log(time_start)) / time_steps * i
-            )
-            times[i] = np.exp(times[i])
+        times = np.geomspace(time_start, time_end, time_steps + 1)
     else:
         times = np.linspace(time_start, time_end, time_steps + 1)
 

From aea441c7378ae72cdd1bbd5848199c3dc755b115 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Tue, 26 Sep 2023 08:44:39 -0400
Subject: [PATCH 05/35] rename RadialModel1D to SimulationState (#2417)

* rename RadialModel1D to SimulationState

* black files
---
 tardis/grid/base.py                           |   4 +-
 tardis/io/model/model_reader.py               |   4 +-
 tardis/io/model_reader.py                     |   4 +-
 tardis/io/tests/test_model_reader.py          |   4 +-
 tardis/model/base.py                          |   2 +-
 tardis/model/tests/test_base.py               | 172 ++++++++++--------
 tardis/model/tests/test_csvy_model.py         |   8 +-
 tardis/model/tests/test_density.py            |   6 +-
 .../montecarlo_numba/tests/conftest.py        |   6 +-
 tardis/plasma/tests/test_nlte_solver.py       |   2 +-
 .../tests/test_tardis_model_density_config.py |   4 +-
 tardis/simulation/base.py                     |  86 +++++----
 tardis/simulation/tests/test_simulation.py    |   9 +-
 tardis/tests/fixtures/atom_data.py            |   4 +-
 .../integration_tests/test_integration.py     |   4 +-
 tardis/visualization/tools/sdec_plot.py       |   4 +-
 .../visualization/widgets/custom_abundance.py |   6 +-
 tardis/visualization/widgets/shell_info.py    |   8 +-
 .../widgets/tests/test_shell_info.py          |  10 +-
 19 files changed, 189 insertions(+), 158 deletions(-)

diff --git a/tardis/grid/base.py b/tardis/grid/base.py
index 30fbe740f30..91599f5833d 100644
--- a/tardis/grid/base.py
+++ b/tardis/grid/base.py
@@ -4,7 +4,7 @@
 import tardis
 
 from tardis.io.configuration.config_reader import Configuration
-from tardis.model import Radial1DModel
+from tardis.model import SimulationState
 
 
 def _set_tardis_config_property(tardis_config, key, value):
@@ -108,7 +108,7 @@ def grid_row_to_model(self, row_index):
         model : tardis.model.base.Radial1DModel
         """
         rowconfig = self.grid_row_to_config(row_index)
-        model = Radial1DModel.from_config(rowconfig)
+        model = SimulationState.from_config(rowconfig)
         return model
 
     def run_sim_from_grid(self, row_index, **tardiskwargs):
diff --git a/tardis/io/model/model_reader.py b/tardis/io/model/model_reader.py
index e388d65f1de..989157b620a 100644
--- a/tardis/io/model/model_reader.py
+++ b/tardis/io/model/model_reader.py
@@ -332,7 +332,7 @@ def model_from_hdf(fname):
     new_model : tardis.model.Radial1DModel
     """
 
-    from tardis.model import Radial1DModel
+    from tardis.model import SimulationState
 
     d = {}
 
@@ -371,7 +371,7 @@ def model_from_hdf(fname):
         d["time_explosion_cgs"],
     )
 
-    new_model = Radial1DModel(
+    new_model = SimulationState(
         velocity=d["velocity_cgs"],
         density=homologous_density,
         abundance=d["abundance"],
diff --git a/tardis/io/model_reader.py b/tardis/io/model_reader.py
index b6080301a2c..2d512a65aa2 100644
--- a/tardis/io/model_reader.py
+++ b/tardis/io/model_reader.py
@@ -881,7 +881,7 @@ def model_from_hdf(fname):
     new_model : tardis.model.Radial1DModel
     """
 
-    from tardis.model import Radial1DModel
+    from tardis.model import SimulationState
 
     d = {}
 
@@ -918,7 +918,7 @@ def model_from_hdf(fname):
         d["homologous_density"]["density_0"], d["homologous_density"]["time_0"]
     )
 
-    new_model = Radial1DModel(
+    new_model = SimulationState(
         velocity=d["velocity_cgs"],
         homologous_density=homologous_density,
         abundance=d["abundance"],
diff --git a/tardis/io/tests/test_model_reader.py b/tardis/io/tests/test_model_reader.py
index d2b7e839e53..1d3196fe19e 100644
--- a/tardis/io/tests/test_model_reader.py
+++ b/tardis/io/tests/test_model_reader.py
@@ -133,7 +133,7 @@ def test_simple_read_cmfgen_density(cmfgen_fname):
 
 
 def test_model_to_dict(simulation_verysimple):
-    model = simulation_verysimple.model
+    model = simulation_verysimple.simulation_state
 
     model_dict, isotope_abundance = model_to_dict(model)
 
@@ -181,7 +181,7 @@ def test_model_to_dict(simulation_verysimple):
 
 
 def test_store_model_to_hdf(simulation_verysimple, tmp_path):
-    model = simulation_verysimple.model
+    model = simulation_verysimple.simulation_state
 
     fname = tmp_path / "model.h5"
 
diff --git a/tardis/model/base.py b/tardis/model/base.py
index 5d0d0dd152a..4d5e94abeda 100644
--- a/tardis/model/base.py
+++ b/tardis/model/base.py
@@ -136,7 +136,7 @@ def number(self):
         return (self.mass).divide(self.composition.atomic_mass, axis=0)
 
 
-class Radial1DModel(HDFWriterMixin):
+class SimulationState(HDFWriterMixin):
     """
     An object that hold information about the individual shells.
 
diff --git a/tardis/model/tests/test_base.py b/tardis/model/tests/test_base.py
index 676717ba8a7..f86fd982204 100644
--- a/tardis/model/tests/test_base.py
+++ b/tardis/model/tests/test_base.py
@@ -6,7 +6,7 @@
 from numpy.testing import assert_almost_equal, assert_array_almost_equal
 
 from tardis.io.configuration.config_reader import Configuration
-from tardis.model import Radial1DModel
+from tardis.model import SimulationState
 from tardis.io.decay import IsotopeAbundances
 
 
@@ -16,36 +16,38 @@ def setup(self, example_configuration_dir):
         self.config = Configuration.from_yaml(
             example_configuration_dir / "paper1_tardis_configv1.yml"
         )
-        self.model = Radial1DModel.from_config(self.config)
+        self.simulation_state = SimulationState.from_config(self.config)
 
     def test_abundances(self):
         oxygen_abundance = self.config.model.abundances.O
         assert_array_almost_equal(
-            oxygen_abundance, self.model.abundance.loc[8].values
+            oxygen_abundance, self.simulation_state.abundance.loc[8].values
         )
 
     def test_velocities(self):
         velocity = self.config.model.structure.velocity
         assert_almost_equal(
-            velocity.start.cgs.value, self.model.v_inner[0].cgs.value
+            velocity.start.cgs.value, self.simulation_state.v_inner[0].cgs.value
         )
         assert_almost_equal(
-            velocity.stop.cgs.value, self.model.v_outer[-1].cgs.value
+            velocity.stop.cgs.value, self.simulation_state.v_outer[-1].cgs.value
         )
-        assert len(self.model.v_outer) == velocity.num
+        assert len(self.simulation_state.v_outer) == velocity.num
 
     def test_densities(self):
         assert_almost_equal(
-            self.model.density[0].cgs.value,
+            self.simulation_state.density[0].cgs.value,
             (7.542803599143591e-14 * u.Unit("g/cm^3")).value,
         )
         assert_almost_equal(
-            self.model.density[-1].cgs.value,
+            self.simulation_state.density[-1].cgs.value,
             (1.432259798833509e-15 * u.Unit("g/cm^3")).value,
         )
 
     def test_time_explosion(self):
-        assert_almost_equal(self.model.time_explosion.to(u.day).value, 13.0)
+        assert_almost_equal(
+            self.simulation_state.time_explosion.to(u.day).value, 13.0
+        )
 
 
 class TestModelFromASCIIDensity:
@@ -54,16 +56,16 @@ def setup(self, example_model_file_dir):
         self.config = Configuration.from_yaml(
             example_model_file_dir / "tardis_configv1_ascii_density.yml"
         )
-        self.model = Radial1DModel.from_config(self.config)
+        self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.model.v_inner.unit == u.Unit("cm/s")
-        assert_almost_equal(self.model.v_inner[0].value, 1e4 * 1e5)
+        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
+        assert_almost_equal(self.simulation_state.v_inner[0].value, 1e4 * 1e5)
 
     def test_abundances(self):
         oxygen_abundance = self.config.model.abundances.O
         assert_array_almost_equal(
-            oxygen_abundance, self.model.abundance.loc[8].values
+            oxygen_abundance, self.simulation_state.abundance.loc[8].values
         )
 
 
@@ -73,16 +75,18 @@ def setup(self, example_model_file_dir):
         self.config = Configuration.from_yaml(
             example_model_file_dir / "tardis_configv1_artis_density.yml"
         )
-        self.model = Radial1DModel.from_config(self.config)
+        self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.model.v_inner.unit == u.Unit("cm/s")
-        assert_almost_equal(self.model.v_inner[0].value, 1.259375e03 * 1e5)
+        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
+        assert_almost_equal(
+            self.simulation_state.v_inner[0].value, 1.259375e03 * 1e5
+        )
 
     def test_abundances(self):
         oxygen_abundance = self.config.model.abundances.O
         assert_array_almost_equal(
-            oxygen_abundance, self.model.abundance.loc[8].values
+            oxygen_abundance, self.simulation_state.abundance.loc[8].values
         )
 
 
@@ -95,15 +99,17 @@ def setup(self, example_model_file_dir):
         self.config.model.abundances.type = "file"
         self.config.model.abundances.filename = "artis_abundances.dat"
         self.config.model.abundances.filetype = "artis"
-        self.model = Radial1DModel.from_config(self.config)
+        self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.model.v_inner.unit == u.Unit("cm/s")
-        assert_almost_equal(self.model.v_inner[0].value, 1.259375e03 * 1e5)
+        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
+        assert_almost_equal(
+            self.simulation_state.v_inner[0].value, 1.259375e03 * 1e5
+        )
 
     def test_abundances(self):
         assert_almost_equal(
-            self.model.abundance.loc[14, 54], 0.21864420000000001
+            self.simulation_state.abundance.loc[14, 54], 0.21864420000000001
         )
 
 
@@ -117,14 +123,18 @@ def setup(self, example_model_file_dir):
         self.config.model.abundances.type = "file"
         self.config.model.abundances.filename = "artis_abundances.dat"
         self.config.model.abundances.filetype = "artis"
-        self.model = Radial1DModel.from_config(self.config)
+        self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.model.v_inner.unit == u.Unit("cm/s")
-        assert_almost_equal(self.model.v_inner[0].to(u.km / u.s).value, 9000)
+        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
+        assert_almost_equal(
+            self.simulation_state.v_inner[0].to(u.km / u.s).value, 9000
+        )
 
     def test_abundances(self):
-        assert_almost_equal(self.model.abundance.loc[14, 31], 2.156751e-01)
+        assert_almost_equal(
+            self.simulation_state.abundance.loc[14, 31], 2.156751e-01
+        )
 
 
 class TestModelFromUniformDensity:
@@ -133,11 +143,11 @@ def setup(self, example_configuration_dir):
         self.config = Configuration.from_yaml(
             example_configuration_dir / "tardis_configv1_uniform_density.yml"
         )
-        self.model = Radial1DModel.from_config(self.config)
+        self.simulation_state = SimulationState.from_config(self.config)
 
     def test_density(self):
         assert_array_almost_equal(
-            self.model.density.to(u.Unit("g / cm3")).value, 1.0e-14
+            self.simulation_state.density.to(u.Unit("g / cm3")).value, 1.0e-14
         )
 
 
@@ -148,10 +158,10 @@ def setup(self, example_configuration_dir):
             example_configuration_dir / "tardis_configv1_uniform_density.yml"
         )
         self.config.plasma.initial_t_inner = 2508 * u.K
-        self.model = Radial1DModel.from_config(self.config)
+        self.simulation_state = SimulationState.from_config(self.config)
 
     def test_initial_temperature(self):
-        assert_almost_equal(self.model.t_inner.value, 2508)
+        assert_almost_equal(self.simulation_state.t_inner.value, 2508)
 
 
 class TestModelFromArtisDensityAbundancesAllAscii:
@@ -162,55 +172,57 @@ def setup(self, example_model_file_dir):
         )
         self.config.model.structure.filename = "density.dat"
         self.config.model.abundances.filename = "abund.dat"
-        self.model = Radial1DModel.from_config(self.config)
+        self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.model.v_inner.unit == u.Unit("cm/s")
-        assert_almost_equal(self.model.v_inner[0].to(u.km / u.s).value, 11000)
+        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
+        assert_almost_equal(
+            self.simulation_state.v_inner[0].to(u.km / u.s).value, 11000
+        )
 
     def test_abundances(self):
-        assert_almost_equal(self.model.abundance.loc[14, 0], 0.1)
-        assert_almost_equal(self.model.abundance.loc[14, 1], 0.2)
-        assert_almost_equal(self.model.abundance.loc[14, 2], 0.2)
-        assert_almost_equal(self.model.abundance.loc[14, 3], 0.2)
-        assert_almost_equal(self.model.abundance.loc[14, 4], 0.2)
-        assert_almost_equal(self.model.abundance.loc[14, 5], 0.2)
-        assert_almost_equal(self.model.abundance.loc[14, 6], 0.0)
-        assert_almost_equal(self.model.abundance.loc[6, 0], 0.0)
-        assert_almost_equal(self.model.abundance.loc[6, 1], 0.0)
-        assert_almost_equal(self.model.abundance.loc[6, 2], 0.0)
-        assert_almost_equal(self.model.abundance.loc[6, 3], 0.0)
-        assert_almost_equal(self.model.abundance.loc[6, 4], 0.0)
-        assert_almost_equal(self.model.abundance.loc[6, 5], 0.0)
-        assert_almost_equal(self.model.abundance.loc[6, 6], 0.5)
+        assert_almost_equal(self.simulation_state.abundance.loc[14, 0], 0.1)
+        assert_almost_equal(self.simulation_state.abundance.loc[14, 1], 0.2)
+        assert_almost_equal(self.simulation_state.abundance.loc[14, 2], 0.2)
+        assert_almost_equal(self.simulation_state.abundance.loc[14, 3], 0.2)
+        assert_almost_equal(self.simulation_state.abundance.loc[14, 4], 0.2)
+        assert_almost_equal(self.simulation_state.abundance.loc[14, 5], 0.2)
+        assert_almost_equal(self.simulation_state.abundance.loc[14, 6], 0.0)
+        assert_almost_equal(self.simulation_state.abundance.loc[6, 0], 0.0)
+        assert_almost_equal(self.simulation_state.abundance.loc[6, 1], 0.0)
+        assert_almost_equal(self.simulation_state.abundance.loc[6, 2], 0.0)
+        assert_almost_equal(self.simulation_state.abundance.loc[6, 3], 0.0)
+        assert_almost_equal(self.simulation_state.abundance.loc[6, 4], 0.0)
+        assert_almost_equal(self.simulation_state.abundance.loc[6, 5], 0.0)
+        assert_almost_equal(self.simulation_state.abundance.loc[6, 6], 0.5)
 
     def test_densities(self):
         assert_almost_equal(
-            self.model.density[0].to(u.Unit("g/cm3")).value,
+            self.simulation_state.density[0].to(u.Unit("g/cm3")).value,
             9.7656229e-11 / 13.0**3,
         )
         assert_almost_equal(
-            self.model.density[1].to(u.Unit("g/cm3")).value,
+            self.simulation_state.density[1].to(u.Unit("g/cm3")).value,
             4.8170911e-11 / 13.0**3,
         )
         assert_almost_equal(
-            self.model.density[2].to(u.Unit("g/cm3")).value,
+            self.simulation_state.density[2].to(u.Unit("g/cm3")).value,
             2.5600000e-11 / 13.0**3,
         )
         assert_almost_equal(
-            self.model.density[3].to(u.Unit("g/cm3")).value,
+            self.simulation_state.density[3].to(u.Unit("g/cm3")).value,
             1.4450533e-11 / 13.0**3,
         )
         assert_almost_equal(
-            self.model.density[4].to(u.Unit("g/cm3")).value,
+            self.simulation_state.density[4].to(u.Unit("g/cm3")).value,
             8.5733893e-11 / 13.0**3,
         )
         assert_almost_equal(
-            self.model.density[5].to(u.Unit("g/cm3")).value,
+            self.simulation_state.density[5].to(u.Unit("g/cm3")).value,
             5.3037103e-11 / 13.0**3,
         )
         assert_almost_equal(
-            self.model.density[6].to(u.Unit("g/cm3")).value,
+            self.simulation_state.density[6].to(u.Unit("g/cm3")).value,
             3.3999447e-11 / 13.0**3,
         )
 
@@ -219,7 +231,7 @@ def test_ascii_reader_power_law(example_configuration_dir):
     config = Configuration.from_yaml(
         example_configuration_dir / "tardis_configv1_density_power_law_test.yml"
     )
-    model = Radial1DModel.from_config(config)
+    simulation_state = SimulationState.from_config(config)
 
     expected_densites = [
         3.29072513e-14,
@@ -244,10 +256,10 @@ def test_ascii_reader_power_law(example_configuration_dir):
         1.93928168e-15,
     ]
 
-    assert model.no_of_shells == 20
+    assert simulation_state.no_of_shells == 20
     for i, mdens in enumerate(expected_densites):
         assert_almost_equal(
-            model.density[i].to(u.Unit("g / (cm3)")).value, mdens
+            simulation_state.density[i].to(u.Unit("g / (cm3)")).value, mdens
         )
 
 
@@ -256,7 +268,7 @@ def test_ascii_reader_exponential_law(example_configuration_dir):
         example_configuration_dir
         / "tardis_configv1_density_exponential_test.yml"
     )
-    model = Radial1DModel.from_config(config)
+    simulation_state = SimulationState.from_config(config)
 
     expected_densites = [
         5.18114795e-14,
@@ -282,10 +294,10 @@ def test_ascii_reader_exponential_law(example_configuration_dir):
     ]
     expected_unit = "g / (cm3)"
 
-    assert model.no_of_shells == 20
+    assert simulation_state.no_of_shells == 20
     for i, mdens in enumerate(expected_densites):
-        assert_almost_equal(model.density[i].value, mdens)
-        assert model.density[i].unit == u.Unit(expected_unit)
+        assert_almost_equal(simulation_state.density[i].value, mdens)
+        assert simulation_state.density[i].unit == u.Unit(expected_unit)
 
 
 @pytest.fixture
@@ -301,29 +313,33 @@ def test_model_decay(simple_isotope_abundance, example_configuration_dir):
     config = Configuration.from_yaml(
         example_configuration_dir / "tardis_configv1_verysimple.yml"
     )
-    model = Radial1DModel.from_config(config)
+    simulation_state = SimulationState.from_config(config)
 
-    model.raw_isotope_abundance = simple_isotope_abundance
-    decayed = simple_isotope_abundance.decay(model.time_explosion).as_atoms()
+    simulation_state.raw_isotope_abundance = simple_isotope_abundance
+    decayed = simple_isotope_abundance.decay(
+        simulation_state.time_explosion
+    ).as_atoms()
     norm_factor = 1.4
 
     assert_almost_equal(
-        model.abundance.loc[8][0],
-        model.raw_abundance.loc[8][0] / norm_factor,
+        simulation_state.abundance.loc[8][0],
+        simulation_state.raw_abundance.loc[8][0] / norm_factor,
         decimal=4,
     )
     assert_almost_equal(
-        model.abundance.loc[14][0],
-        (model.raw_abundance.loc[14][0] + decayed.loc[14][0]) / norm_factor,
+        simulation_state.abundance.loc[14][0],
+        (simulation_state.raw_abundance.loc[14][0] + decayed.loc[14][0])
+        / norm_factor,
         decimal=4,
     )
     assert_almost_equal(
-        model._abundance.loc[12][5],
-        (model.raw_abundance.loc[12][5] + decayed.loc[12][5]) / norm_factor,
+        simulation_state._abundance.loc[12][5],
+        (simulation_state.raw_abundance.loc[12][5] + decayed.loc[12][5])
+        / norm_factor,
         decimal=4,
     )
     assert_almost_equal(
-        model.abundance.loc[6][12],
+        simulation_state.abundance.loc[6][12],
         (decayed.loc[6][12]) / norm_factor,
         decimal=4,
     )
@@ -338,7 +354,7 @@ def test_model_decay(simple_isotope_abundance, example_configuration_dir):
     ],
 )
 def test_radial_1D_geometry_volume(simulation_verysimple, index, expected):
-    geometry = simulation_verysimple.model.model_state.geometry
+    geometry = simulation_verysimple.simulation_state.model_state.geometry
     volume = geometry.volume
 
     assert volume.unit == u.Unit("cm3")
@@ -371,7 +387,7 @@ def test_radial_1D_geometry_volume(simulation_verysimple, index, expected):
 def test_composition_elemental_number_density(
     simulation_verysimple, index, expected
 ):
-    comp = simulation_verysimple.model.model_state.composition
+    comp = simulation_verysimple.simulation_state.model_state.composition
 
     assert_almost_equal(
         comp.elemental_number_density.loc[index], expected, decimal=-2
@@ -387,7 +403,7 @@ def test_composition_elemental_number_density(
     ],
 )
 def test_model_state_mass(simulation_verysimple, index, expected):
-    model_state = simulation_verysimple.model.model_state
+    model_state = simulation_verysimple.simulation_state.model_state
 
     assert_almost_equal((model_state.mass).loc[index], expected, decimal=-27)
 
@@ -401,7 +417,7 @@ def test_model_state_mass(simulation_verysimple, index, expected):
     ],
 )
 def test_model_state_number(simulation_verysimple, index, expected):
-    model_state = simulation_verysimple.model.model_state
+    model_state = simulation_verysimple.simulation_state.model_state
 
     assert_almost_equal((model_state.number).loc[index], expected, decimal=-47)
 
@@ -412,7 +428,7 @@ def non_uniform_model_state(atomic_dataset, example_model_file_dir):
         example_model_file_dir / "tardis_configv1_isotope_iabund.yml"
     )
     atom_data = atomic_dataset
-    model = Radial1DModel.from_config(config, atom_data=atom_data)
+    model = SimulationState.from_config(config, atom_data=atom_data)
     return model.model_state
 
 
@@ -469,7 +485,7 @@ def test_number(self, model_state):
 
 @pytest.fixture(scope="module", autouse=True)
 def to_hdf_buffer(hdf_file_path, simulation_verysimple):
-    simulation_verysimple.model.to_hdf(hdf_file_path, overwrite=True)
+    simulation_verysimple.simulation_state.to_hdf(hdf_file_path, overwrite=True)
 
 
 model_scalar_attrs = ["t_inner"]
@@ -479,7 +495,7 @@ def to_hdf_buffer(hdf_file_path, simulation_verysimple):
 def test_hdf_model_scalars(hdf_file_path, simulation_verysimple, attr):
     path = os.path.join("model", "scalars")
     expected = pd.read_hdf(hdf_file_path, path)[attr]
-    actual = getattr(simulation_verysimple.model, attr)
+    actual = getattr(simulation_verysimple.simulation_state, attr)
     if hasattr(actual, "cgs"):
         actual = actual.cgs.value
     assert_almost_equal(actual, expected)
@@ -492,7 +508,7 @@ def test_hdf_model_scalars(hdf_file_path, simulation_verysimple, attr):
 def test_hdf_model_nparray(hdf_file_path, simulation_verysimple, attr):
     path = os.path.join("model", attr)
     expected = pd.read_hdf(hdf_file_path, path)
-    actual = getattr(simulation_verysimple.model, attr)
+    actual = getattr(simulation_verysimple.simulation_state, attr)
     if hasattr(actual, "cgs"):
         actual = actual.cgs.value
     assert_almost_equal(actual, expected.values)
diff --git a/tardis/model/tests/test_csvy_model.py b/tardis/model/tests/test_csvy_model.py
index 93a5b7b2e5f..8e8f69c1b6b 100644
--- a/tardis/model/tests/test_csvy_model.py
+++ b/tardis/model/tests/test_csvy_model.py
@@ -6,7 +6,7 @@
 import os
 from astropy import units as u
 from tardis.io.configuration.config_reader import Configuration
-from tardis.model import Radial1DModel
+from tardis.model import SimulationState
 import pytest
 
 
@@ -35,8 +35,8 @@ def test_compare_models(model_config_fnames):
     csvy_config_file, old_config_file = model_config_fnames
     tardis_config = Configuration.from_yaml(csvy_config_file)
     tardis_config_old = Configuration.from_yaml(old_config_file)
-    csvy_model = Radial1DModel.from_csvy(tardis_config)
-    config_model = Radial1DModel.from_config(tardis_config_old)
+    csvy_model = SimulationState.from_csvy(tardis_config)
+    config_model = SimulationState.from_config(tardis_config_old)
     csvy_model_props = csvy_model.get_properties().keys()
     config_model_props = config_model.get_properties().keys()
     npt.assert_array_equal(csvy_model_props, config_model_props)
@@ -80,7 +80,7 @@ def csvy_model_test_abundances(example_csvy_file_dir):
     """Returns Radial1DModel to use to test abundances dataframes"""
     csvypath = example_csvy_file_dir / "csvy_model_to_test_abundances.yml"
     config = Configuration.from_yaml(csvypath)
-    csvy_model_test_abundances = Radial1DModel.from_csvy(config)
+    csvy_model_test_abundances = SimulationState.from_csvy(config)
     return csvy_model_test_abundances
 
 
diff --git a/tardis/model/tests/test_density.py b/tardis/model/tests/test_density.py
index c9451211088..fd7035ec9f7 100644
--- a/tardis/model/tests/test_density.py
+++ b/tardis/model/tests/test_density.py
@@ -10,11 +10,11 @@
 
 @pytest.fixture(scope="module", autouse=True)
 def to_hdf_buffer(hdf_file_path, simulation_verysimple):
-    simulation_verysimple.model.to_hdf(hdf_file_path, overwrite=True)
+    simulation_verysimple.simulation_state.to_hdf(hdf_file_path, overwrite=True)
 
 
 def test_hdf_density_0(hdf_file_path, simulation_verysimple):
-    actual = simulation_verysimple.model.density
+    actual = simulation_verysimple.simulation_state.density
     if hasattr(actual, "cgs"):
         actual = actual.cgs.value
     path = os.path.join("model", "density")
@@ -23,7 +23,7 @@ def test_hdf_density_0(hdf_file_path, simulation_verysimple):
 
 
 def test_hdf_time_0(hdf_file_path, simulation_verysimple):
-    actual = simulation_verysimple.model.time_explosion
+    actual = simulation_verysimple.simulation_state.time_explosion
     if hasattr(actual, "cgs"):
         actual = actual.cgs.value
     path = os.path.join("model", "scalars")
diff --git a/tardis/montecarlo/montecarlo_numba/tests/conftest.py b/tardis/montecarlo/montecarlo_numba/tests/conftest.py
index 6b2c92b5308..3bf3a2552ac 100644
--- a/tardis/montecarlo/montecarlo_numba/tests/conftest.py
+++ b/tardis/montecarlo/montecarlo_numba/tests/conftest.py
@@ -34,12 +34,14 @@ def verysimple_opacity_state(nb_simulation_verysimple):
 
 @pytest.fixture(scope="package")
 def verysimple_numba_radial_1d_geometry(nb_simulation_verysimple):
-    return nb_simulation_verysimple.model.model_state.geometry.to_numba()
+    return (
+        nb_simulation_verysimple.simulation_state.model_state.geometry.to_numba()
+    )
 
 
 @pytest.fixture(scope="package")
 def verysimple_numba_model(nb_simulation_verysimple):
-    model = nb_simulation_verysimple.model
+    model = nb_simulation_verysimple.simulation_state
     return NumbaModel(
         model.time_explosion.to("s").value,
     )
diff --git a/tardis/plasma/tests/test_nlte_solver.py b/tardis/plasma/tests/test_nlte_solver.py
index b53dbc72fbd..fe47b496e97 100644
--- a/tardis/plasma/tests/test_nlte_solver.py
+++ b/tardis/plasma/tests/test_nlte_solver.py
@@ -6,7 +6,7 @@
 from copy import deepcopy
 from numpy.testing import assert_allclose, assert_almost_equal
 from tardis.io.configuration.config_reader import Configuration
-from tardis.model.base import Radial1DModel
+from tardis.model.base import SimulationState
 from tardis.plasma.properties import NLTERateEquationSolver
 from tardis.io.atom_data.base import AtomData
 from tardis.plasma.properties.ion_population import IonNumberDensity
diff --git a/tardis/plasma/tests/test_tardis_model_density_config.py b/tardis/plasma/tests/test_tardis_model_density_config.py
index 89b4a514502..6bb6ff6dbdf 100644
--- a/tardis/plasma/tests/test_tardis_model_density_config.py
+++ b/tardis/plasma/tests/test_tardis_model_density_config.py
@@ -1,7 +1,7 @@
 import pytest
 
 from tardis.io.configuration.config_reader import Configuration
-from tardis.model import Radial1DModel
+from tardis.model import SimulationState
 from tardis.plasma.standard_plasmas import assemble_plasma
 from numpy.testing import assert_almost_equal
 
@@ -15,7 +15,7 @@ def tardis_model_density_config(example_model_file_dir):
 
 @pytest.fixture()
 def raw_model(tardis_model_density_config):
-    return Radial1DModel.from_config(tardis_model_density_config)
+    return SimulationState.from_config(tardis_model_density_config)
 
 
 @pytest.fixture()
diff --git a/tardis/simulation/base.py b/tardis/simulation/base.py
index be4b8f6eefa..0aee0bb1773 100644
--- a/tardis/simulation/base.py
+++ b/tardis/simulation/base.py
@@ -9,7 +9,7 @@
 from tardis import model
 
 from tardis.montecarlo.base import MontecarloTransport
-from tardis.model import Radial1DModel
+from tardis.model import SimulationState
 from tardis.plasma.standard_plasmas import assemble_plasma
 from tardis.io.util import HDFWriterMixin
 from tardis.io.configuration.config_reader import ConfigurationError
@@ -107,7 +107,7 @@ class Simulation(PlasmaStateStorerMixin, HDFWriterMixin):
     """
 
     hdf_properties = [
-        "model",
+        "simulation_state",
         "plasma",
         "transport",
         "iterations_w",
@@ -120,7 +120,7 @@ class Simulation(PlasmaStateStorerMixin, HDFWriterMixin):
     def __init__(
         self,
         iterations,
-        model,
+        simulation_state,
         plasma,
         transport,
         no_of_packets,
@@ -134,12 +134,14 @@ def __init__(
         convergence_plots_kwargs,
         show_progress_bars,
     ):
-        super(Simulation, self).__init__(iterations, model.no_of_shells)
+        super(Simulation, self).__init__(
+            iterations, simulation_state.no_of_shells
+        )
 
         self.converged = False
         self.iterations = iterations
         self.iterations_executed = 0
-        self.model = model
+        self.simulation_state = simulation_state
         self.plasma = plasma
         self.transport = transport
         self.no_of_packets = no_of_packets
@@ -215,7 +217,7 @@ def _get_convergence_status(
         self, t_rad, w, t_inner, estimated_t_rad, estimated_w, estimated_t_inner
     ):
         # FIXME: Move the convergence checking in its own class.
-        no_of_shells = self.model.no_of_shells
+        no_of_shells = self.simulation_state.no_of_shells
 
         convergence_t_rad = (
             abs(t_rad - estimated_t_rad) / estimated_t_rad
@@ -279,15 +281,15 @@ def advance_state(self):
             estimated_w,
         ) = self.transport.calculate_radiationfield_properties()
         estimated_t_inner = self.estimate_t_inner(
-            self.model.t_inner,
+            self.simulation_state.t_inner,
             self.luminosity_requested,
             t_inner_update_exponent=self.convergence_strategy.t_inner_update_exponent,
         )
 
         converged = self._get_convergence_status(
-            self.model.t_rad,
-            self.model.w,
-            self.model.t_inner,
+            self.simulation_state.t_rad,
+            self.simulation_state.w,
+            self.simulation_state.t_inner,
             estimated_t_rad,
             estimated_w,
             estimated_t_inner,
@@ -296,12 +298,12 @@ def advance_state(self):
         # calculate_next_plasma_state equivalent
         # FIXME: Should convergence strategy have its own class?
         next_t_rad = self.damped_converge(
-            self.model.t_rad,
+            self.simulation_state.t_rad,
             estimated_t_rad,
             self.convergence_strategy.t_rad.damping_constant,
         )
         next_w = self.damped_converge(
-            self.model.w,
+            self.simulation_state.w,
             estimated_w,
             self.convergence_strategy.w.damping_constant,
         )
@@ -309,40 +311,44 @@ def advance_state(self):
             self.iterations_executed + 1
         ) % self.convergence_strategy.lock_t_inner_cycles == 0:
             next_t_inner = self.damped_converge(
-                self.model.t_inner,
+                self.simulation_state.t_inner,
                 estimated_t_inner,
                 self.convergence_strategy.t_inner.damping_constant,
             )
         else:
-            next_t_inner = self.model.t_inner
+            next_t_inner = self.simulation_state.t_inner
 
         if hasattr(self, "convergence_plots"):
             self.convergence_plots.fetch_data(
                 name="t_inner",
-                value=self.model.t_inner.value,
+                value=self.simulation_state.t_inner.value,
                 item_type="value",
             )
             self.convergence_plots.fetch_data(
-                name="t_rad", value=self.model.t_rad, item_type="iterable"
+                name="t_rad",
+                value=self.simulation_state.t_rad,
+                item_type="iterable",
             )
             self.convergence_plots.fetch_data(
-                name="w", value=self.model.w, item_type="iterable"
+                name="w", value=self.simulation_state.w, item_type="iterable"
             )
             self.convergence_plots.fetch_data(
-                name="velocity", value=self.model.velocity, item_type="iterable"
+                name="velocity",
+                value=self.simulation_state.velocity,
+                item_type="iterable",
             )
 
         self.log_plasma_state(
-            self.model.t_rad,
-            self.model.w,
-            self.model.t_inner,
+            self.simulation_state.t_rad,
+            self.simulation_state.w,
+            self.simulation_state.t_inner,
             next_t_rad,
             next_w,
             next_t_inner,
         )
-        self.model.t_rad = next_t_rad
-        self.model.w = next_w
-        self.model.blackbody_packet_source.temperature = next_t_inner
+        self.simulation_state.t_rad = next_t_rad
+        self.simulation_state.w = next_w
+        self.simulation_state.blackbody_packet_source.temperature = next_t_inner
 
         # model.calculate_j_blues() equivalent
         # model.update_plasmas() equivalent
@@ -350,7 +356,9 @@ def advance_state(self):
         if "nlte_data" in self.plasma.outputs_dict:
             self.plasma.store_previous_properties()
 
-        update_properties = dict(t_rad=self.model.t_rad, w=self.model.w)
+        update_properties = dict(
+            t_rad=self.simulation_state.t_rad, w=self.simulation_state.w
+        )
         # A check to see if the plasma is set with JBluesDetailed, in which
         # case it needs some extra kwargs.
         if "j_blue_estimator" in self.plasma.outputs_dict:
@@ -375,7 +383,7 @@ def iterate(self, no_of_packets, no_of_virtual_packets=0):
             f"\n\tStarting iteration {(self.iterations_executed + 1):d} of {self.iterations:d}"
         )
         self.transport.run(
-            self.model,
+            self.simulation_state,
             self.plasma,
             no_of_packets,
             no_of_virtual_packets=no_of_virtual_packets,
@@ -422,10 +430,10 @@ def run_convergence(self):
         while self.iterations_executed < self.iterations - 1:
             self.store_plasma_state(
                 self.iterations_executed,
-                self.model.w,
-                self.model.t_rad,
+                self.simulation_state.w,
+                self.simulation_state.t_rad,
                 self.plasma.electron_densities,
-                self.model.t_inner,
+                self.simulation_state.t_inner,
             )
             self.iterate(self.no_of_packets)
             self.converged = self.advance_state()
@@ -447,10 +455,10 @@ def run_final(self):
         """
         self.store_plasma_state(
             self.iterations_executed,
-            self.model.w,
-            self.model.t_rad,
+            self.simulation_state.w,
+            self.simulation_state.t_rad,
             self.plasma.electron_densities,
-            self.model.t_inner,
+            self.simulation_state.t_inner,
         )
         self.iterate(self.last_no_of_packets, self.no_of_virtual_packets)
 
@@ -458,7 +466,7 @@ def run_final(self):
         if hasattr(self, "convergence_plots"):
             self.convergence_plots.fetch_data(
                 name="t_inner",
-                value=self.model.t_inner.value,
+                value=self.simulation_state.t_inner.value,
                 item_type="value",
             )
             self.convergence_plots.update(
@@ -632,21 +640,23 @@ def from_config(
         # Allow overriding some config structures. This is useful in some
         # unit tests, and could be extended in all the from_config classmethods.
         if "model" in kwargs:
-            model = kwargs["model"]
+            simulation_state = kwargs["model"]
         else:
             if hasattr(config, "csvy_model"):
-                model = Radial1DModel.from_csvy(
+                simulation_state = SimulationState.from_csvy(
                     config, atom_data=kwargs.get("atom_data", None)
                 )
             else:
-                model = Radial1DModel.from_config(
+                simulation_state = SimulationState.from_config(
                     config, atom_data=kwargs.get("atom_data", None)
                 )
         if "plasma" in kwargs:
             plasma = kwargs["plasma"]
         else:
             plasma = assemble_plasma(
-                config, model, atom_data=kwargs.get("atom_data", None)
+                config,
+                simulation_state,
+                atom_data=kwargs.get("atom_data", None),
             )
         if "transport" in kwargs:
             if packet_source is not None:
@@ -694,7 +704,7 @@ def from_config(
 
         return cls(
             iterations=config.montecarlo.iterations,
-            model=model,
+            simulation_state=simulation_state,
             plasma=plasma,
             transport=transport,
             show_convergence_plots=show_convergence_plots,
diff --git a/tardis/simulation/tests/test_simulation.py b/tardis/simulation/tests/test_simulation.py
index e44519281f8..d4f68ff3cc5 100644
--- a/tardis/simulation/tests/test_simulation.py
+++ b/tardis/simulation/tests/test_simulation.py
@@ -54,7 +54,10 @@ def simulation_one_loop(
             "iterations_electron_densities",
             "iterations_t_inner",
         ]
-        simulation.model.hdf_properties = ["t_radiative", "dilution_factor"]
+        simulation.simulation_state.hdf_properties = [
+            "t_radiative",
+            "dilution_factor",
+        ]
         simulation.transport.hdf_properties = [
             "j_estimator",
             "nu_bar_estimator",
@@ -64,7 +67,7 @@ def simulation_one_loop(
         simulation.to_hdf(
             tardis_ref_data, "", "test_simulation", overwrite=True
         )
-        simulation.model.to_hdf(
+        simulation.simulation_state.to_hdf(
             tardis_ref_data, "", "test_simulation", overwrite=True
         )
         simulation.transport.to_hdf(
@@ -88,7 +91,7 @@ def test_plasma_estimates(simulation_one_loop, refdata, name):
     try:
         actual = getattr(simulation_one_loop.transport, name)
     except AttributeError:
-        actual = getattr(simulation_one_loop.model, name)
+        actual = getattr(simulation_one_loop.simulation_state, name)
     if name in ["t_radiative", "output_nu", "output_energy"]:
         # removing the quantitiness of the data
         actual = actual.value
diff --git a/tardis/tests/fixtures/atom_data.py b/tardis/tests/fixtures/atom_data.py
index 68036b900b7..fb506011c8a 100644
--- a/tardis/tests/fixtures/atom_data.py
+++ b/tardis/tests/fixtures/atom_data.py
@@ -4,7 +4,7 @@
 
 from tardis.io.atom_data.base import AtomData
 from tardis.io.configuration.config_reader import Configuration
-from tardis.model.base import Radial1DModel
+from tardis.model.base import SimulationState
 
 DEFAULT_ATOM_DATA_UUID = "864f1753714343c41f99cb065710cace"
 
@@ -84,4 +84,4 @@ def tardis_model_config_nlte(example_configuration_dir):
 
 @pytest.fixture  # (scope="session")
 def nlte_raw_model(tardis_model_config_nlte):
-    return Radial1DModel.from_config(tardis_model_config_nlte)
+    return SimulationState.from_config(tardis_model_config_nlte)
diff --git a/tardis/tests/integration_tests/test_integration.py b/tardis/tests/integration_tests/test_integration.py
index 8f9c97f2acc..a380763e12a 100644
--- a/tardis/tests/integration_tests/test_integration.py
+++ b/tardis/tests/integration_tests/test_integration.py
@@ -176,7 +176,7 @@ def plot_t_rad(self):
         ax.set_ylabel("t_rad")
 
         result_line = ax.plot(
-            self.result.model.t_rad.cgs,
+            self.result.simulation_state.t_rad.cgs,
             color="blue",
             marker=".",
             label="Result",
@@ -192,7 +192,7 @@ def plot_t_rad(self):
         error_line = error_ax.plot(
             (
                 1
-                - self.result.model.t_rad.cgs.value
+                - self.result.simulation_state.t_rad.cgs.value
                 / self.reference["/simulation/model/t_rad"]
             ),
             color="red",
diff --git a/tardis/visualization/tools/sdec_plot.py b/tardis/visualization/tools/sdec_plot.py
index bcd3195c11b..63806535a39 100644
--- a/tardis/visualization/tools/sdec_plot.py
+++ b/tardis/visualization/tools/sdec_plot.py
@@ -165,8 +165,8 @@ def from_simulation(cls, sim, packets_mode):
         lines_df = sim.plasma.atomic_data.lines.reset_index().set_index(
             "line_id"
         )
-        r_inner = sim.model.r_inner
-        t_inner = sim.model.t_inner
+        r_inner = sim.simulation_state.r_inner
+        t_inner = sim.simulation_state.t_inner
         time_of_simulation = sim.transport.time_of_simulation
 
         if packets_mode == "virtual":
diff --git a/tardis/visualization/widgets/custom_abundance.py b/tardis/visualization/widgets/custom_abundance.py
index f5586d75266..6e08567f1ad 100644
--- a/tardis/visualization/widgets/custom_abundance.py
+++ b/tardis/visualization/widgets/custom_abundance.py
@@ -14,7 +14,7 @@
 from tardis.io.model.readers.generic_readers import read_uniform_abundances
 from tardis.util.base import quantity_linspace, is_valid_nuclide_or_elem
 from tardis.io.configuration.config_reader import Configuration
-from tardis.model import Radial1DModel
+from tardis.model import SimulationState
 from tardis.io.model.parse_density_configuration import (
     calculate_power_law_density,
     calculate_exponential_density,
@@ -198,9 +198,9 @@ def from_yml(cls, fpath):
         config = Configuration.from_yaml(fpath)
 
         if hasattr(config, "csvy_model"):
-            model = Radial1DModel.from_csvy(config)
+            model = SimulationState.from_csvy(config)
         else:
-            model = Radial1DModel.from_config(config)
+            model = SimulationState.from_config(config)
 
         velocity = model.velocity
         density_t_0 = model.time_explosion
diff --git a/tardis/visualization/widgets/shell_info.py b/tardis/visualization/widgets/shell_info.py
index 336c8f580cf..5dcc709cd4b 100644
--- a/tardis/visualization/widgets/shell_info.py
+++ b/tardis/visualization/widgets/shell_info.py
@@ -184,8 +184,8 @@ def __init__(self, sim_model):
             TARDIS Simulation object produced by running a simulation
         """
         super().__init__(
-            sim_model.model.t_radiative,
-            sim_model.model.w,
+            sim_model.simulation_state.t_radiative,
+            sim_model.simulation_state.w,
             sim_model.plasma.abundance,
             sim_model.plasma.number_density,
             sim_model.plasma.ion_number_density,
@@ -210,8 +210,8 @@ def __init__(self, hdf_fpath):
         """
         with pd.HDFStore(hdf_fpath, "r") as sim_data:
             super().__init__(
-                sim_data["/simulation/model/t_radiative"],
-                sim_data["/simulation/model/w"],
+                sim_data["/simulation/simulation_state/t_radiative"],
+                sim_data["/simulation/simulation_state/w"],
                 sim_data["/simulation/plasma/abundance"],
                 sim_data["/simulation/plasma/number_density"],
                 sim_data["/simulation/plasma/ion_number_density"],
diff --git a/tardis/visualization/widgets/tests/test_shell_info.py b/tardis/visualization/widgets/tests/test_shell_info.py
index 8d6af014617..4c08233d8d2 100644
--- a/tardis/visualization/widgets/tests/test_shell_info.py
+++ b/tardis/visualization/widgets/tests/test_shell_info.py
@@ -13,8 +13,8 @@
 @pytest.fixture(scope="class")
 def base_shell_info(simulation_verysimple):
     return BaseShellInfo(
-        simulation_verysimple.model.t_radiative,
-        simulation_verysimple.model.w,
+        simulation_verysimple.simulation_state.t_radiative,
+        simulation_verysimple.simulation_state.w,
         simulation_verysimple.plasma.abundance,
         simulation_verysimple.plasma.number_density,
         simulation_verysimple.plasma.ion_number_density,
@@ -39,16 +39,16 @@ class TestBaseShellInfo:
     def test_shells_data(self, base_shell_info, simulation_verysimple):
         shells_data = base_shell_info.shells_data()
         assert shells_data.shape == (
-            len(simulation_verysimple.model.t_radiative),
+            len(simulation_verysimple.simulation_state.t_radiative),
             2,
         )
         assert np.allclose(
             shells_data.iloc[:, 0].map(np.float64),
-            simulation_verysimple.model.t_radiative.value,
+            simulation_verysimple.simulation_state.t_radiative.value,
         )
         assert np.allclose(
             shells_data.iloc[:, 1].map(np.float64),
-            simulation_verysimple.model.w,
+            simulation_verysimple.simulation_state.w,
         )
 
     @pytest.mark.parametrize("shell_num", [1, 20])

From f89e12552f97c35dcd95d4bae30dea68e89e5ad0 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Mon, 2 Oct 2023 09:34:18 -0400
Subject: [PATCH 06/35] rename simulation_state2 (#2421)

* fixup of many files to make them pass the tests

* change model for typo
---
 .../nebular_phase/gammaray_deposition.ipynb   |  4 +--
 docs/io/grid/TardisGridTutorial.ipynb         |  4 +--
 docs/io/optional/callback_example.ipynb       |  4 +--
 docs/io/output/physical_quantities.ipynb      | 10 +++---
 docs/io/output/to_hdf.ipynb                   |  8 ++---
 .../montecarlo_packet_visualization.ipynb     |  8 ++---
 docs/physics/setup/index.rst                  |  2 +-
 docs/physics/setup/model.ipynb                | 32 +++++++++----------
 docs/physics/setup/setup_example.ipynb        |  4 +--
 .../update_and_conv/update_and_conv.ipynb     |  2 +-
 tardis/analysis/opacities.py                  |  2 +-
 tardis/energy_input/gamma_ray_transport.py    |  2 +-
 tardis/grid/base.py                           |  4 +--
 tardis/io/model/hdf.py                        |  4 +--
 tardis/io/model/model_reader.py               |  8 ++---
 tardis/io/model_reader.py                     | 12 +++----
 tardis/model/base.py                          |  8 ++---
 tardis/model/tests/test_csvy_model.py         |  2 +-
 tardis/montecarlo/base.py                     |  8 ++---
 .../montecarlo_numba/formal_integral.py       |  4 +--
 .../tests/test_cuda_formal_integral.py        |  4 +--
 tardis/plasma/standard_plasmas.py             |  4 +--
 tardis/simulation/base.py                     |  2 +-
 tardis/util/base.py                           |  2 +-
 .../visualization/widgets/custom_abundance.py | 10 +++---
 .../widgets/grotrian_mockup.ipynb             |  4 +--
 26 files changed, 79 insertions(+), 79 deletions(-)

diff --git a/docs/contributing/in_progress/nebular_phase/gammaray_deposition.ipynb b/docs/contributing/in_progress/nebular_phase/gammaray_deposition.ipynb
index d3ea13ee1d1..8c36359faea 100644
--- a/docs/contributing/in_progress/nebular_phase/gammaray_deposition.ipynb
+++ b/docs/contributing/in_progress/nebular_phase/gammaray_deposition.ipynb
@@ -42,7 +42,7 @@
     "import numpy as np\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
-    "from tardis.model import Radial1DModel\n",
+    "from tardis.model import SimulationState\n",
     "from tardis.io.config_reader import Configuration\n",
     "\n",
     "from tardis.plasma.properties import Density, Abundance, IsotopeAbundance, IsotopeNumberDensity, AtomicData, AtomicMass, IsotopeMass, NumberDensity, SelectedAtoms\n",
@@ -60,7 +60,7 @@
     "\n",
     "config.atom_data = \"kurucz_cd23_chianti_H_He.h5\"\n",
     "\n",
-    "model = Radial1DModel.from_config(config)\n",
+    "model = SimulationState.from_config(config)\n",
     "\n",
     "# Construct plasma\n",
     "input = [Density, Abundance, IsotopeAbundance, AtomicData, AtomicMass, IsotopeNumberDensity, NumberDensity, SelectedAtoms, IsotopeMass]\n",
diff --git a/docs/io/grid/TardisGridTutorial.ipynb b/docs/io/grid/TardisGridTutorial.ipynb
index 2791937c538..b3eed9f12e8 100644
--- a/docs/io/grid/TardisGridTutorial.ipynb
+++ b/docs/io/grid/TardisGridTutorial.ipynb
@@ -118,7 +118,7 @@
    "source": [
     "## TARDIS Grid Functionality\n",
     "\n",
-    "The TARDIS Grid provides a variety of functions for using the grid to generate new Configurations, return new Radial1DModel objects, or directly run simulations using the parameters specified by the grid. This functionality is particularly useful for running large numbers of simulations and easily works with JobArrays where the row_index is the JobArray index."
+    "The TARDIS Grid provides a variety of functions for using the grid to generate new Configurations, return new SimulationState objects, or directly run simulations using the parameters specified by the grid. This functionality is particularly useful for running large numbers of simulations and easily works with JobArrays where the row_index is the JobArray index."
    ]
   },
   {
@@ -144,7 +144,7 @@
     "# In case a user needs to make more complicated changes\n",
     "# to the base TARDIS model (i.e. using parameters that \n",
     "# are not valid TARDIS Configuration keys), the grid\n",
-    "# can return a Radial1DModel object for a given row.\n",
+    "# can return a SimulationState object for a given row.\n",
     "model = tg.grid_row_to_model(row_index=0)\n",
     "model"
    ]
diff --git a/docs/io/optional/callback_example.ipynb b/docs/io/optional/callback_example.ipynb
index c9b67f2f884..488aa27392f 100644
--- a/docs/io/optional/callback_example.ipynb
+++ b/docs/io/optional/callback_example.ipynb
@@ -25,8 +25,8 @@
    "outputs": [],
    "source": [
     "def average_temp(sim):\n",
-    "    t_rads = sim.model.t_rad\n",
-    "    volumes = sim.model.volume\n",
+    "    t_rads = sim.simulation_state.t_rad\n",
+    "    volumes = sim.simulation_state.volume\n",
     "    avg = sum(t_rads*volumes) / sum(volumes)\n",
     "    print(f\"Average temperature for iteration {sim.iterations_executed}: {avg}\")"
    ]
diff --git a/docs/io/output/physical_quantities.ipynb b/docs/io/output/physical_quantities.ipynb
index 0eb2aee8e83..85f64b1ec48 100644
--- a/docs/io/output/physical_quantities.ipynb
+++ b/docs/io/output/physical_quantities.ipynb
@@ -111,7 +111,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Several important quantities that were setup when the model was defined by the configuration file are located in the `model` section of the simulation. For example, the inner and outer velocity boundaries of the zones in the model is given by `simulation.model.v_inner.cgs` and `simulation.model.v_outer.cgs` respectively. These exist as Astropy [Quantities](http://astropy.readthedocs.org/en/v0.2.1/_generated/astropy.units.quantity.Quantity.html)."
+    "Several important quantities that were setup when the model was defined by the configuration file are located in the `model` section of the simulation. For example, the inner and outer velocity boundaries of the zones in the model is given by `simulation.simulation_state.v_inner.cgs` and `simulation.simulation_state.v_outer.cgs` respectively. These exist as Astropy [Quantities](http://astropy.readthedocs.org/en/v0.2.1/_generated/astropy.units.quantity.Quantity.html)."
    ]
   },
   {
@@ -120,7 +120,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.model.v_inner.cgs"
+    "simulation.simulation_state.v_inner.cgs"
    ]
   },
   {
@@ -129,14 +129,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.model.v_outer.cgs"
+    "simulation.simulation_state.v_outer.cgs"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The average density in the zones is given by `simulation.model.density.cgs`. These also exist as Astropy [Quantities](http://astropy.readthedocs.org/en/v0.2.1/_generated/astropy.units.quantity.Quantity.html)."
+    "The average density in the zones is given by `simulation.simulation_state.density.cgs`. These also exist as Astropy [Quantities](http://astropy.readthedocs.org/en/v0.2.1/_generated/astropy.units.quantity.Quantity.html)."
    ]
   },
   {
@@ -145,7 +145,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.model.density.cgs"
+    "simulation.simulation_state.density.cgs"
    ]
   },
   {
diff --git a/docs/io/output/to_hdf.ipynb b/docs/io/output/to_hdf.ipynb
index ed81072fbfb..0888948c7c7 100644
--- a/docs/io/output/to_hdf.ipynb
+++ b/docs/io/output/to_hdf.ipynb
@@ -108,7 +108,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(data['/simulation/model/density'])"
+    "print(data['/simulation/simulation_state/density'])"
    ]
   },
   {
@@ -127,7 +127,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(data['/simulation/model/scalars']['t_inner'])"
+    "print(data['/simulation/simulation_state/scalars']['t_inner'])"
    ]
   },
   {
@@ -209,7 +209,7 @@
    "metadata": {},
    "source": [
     "### Model\n",
-    "The following call will store properties of the `Radial1DModel` to `/tmp/model_output.hdf` under `/model`."
+    "The following call will store properties of the `SimulationState` to `/tmp/model_output.hdf` under `/simulation_state`."
    ]
   },
   {
@@ -218,7 +218,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.model.to_hdf('/tmp/model_output.hdf', overwrite=True)"
+    "simulation.simulation_state.to_hdf('/tmp/model_output.hdf', overwrite=True)"
    ]
   },
   {
diff --git a/docs/io/visualization/montecarlo_packet_visualization.ipynb b/docs/io/visualization/montecarlo_packet_visualization.ipynb
index c33c7e4b5fd..fe46b67b745 100644
--- a/docs/io/visualization/montecarlo_packet_visualization.ipynb
+++ b/docs/io/visualization/montecarlo_packet_visualization.ipynb
@@ -235,8 +235,8 @@
    "source": [
     "# animated plot\n",
     "\n",
-    "v_shells = sim.model.radius.value * 1e-5 / sim.model.time_explosion.value\n",
-    "xs,ys,ints = get_coordinates_multiple_packets_ints(sim.transport.rpacket_tracker_df,sim.model.time_explosion.value)\n",
+    "v_shells = sim.simulation_state.radius.value * 1e-5 / sim.simulation_state.time_explosion.value\n",
+    "xs,ys,ints = get_coordinates_multiple_packets_ints(sim.transport.rpacket_tracker_df,sim.simulation_state.time_explosion.value)\n",
     "xs,ys,ints,max_size = get_equal_array_size(xs,ys,ints)\n",
     "\n",
     "fig = go.Figure()\n",
@@ -247,7 +247,7 @@
     "\n",
     "# adding the shells\n",
     "shell_shapes={}\n",
-    "for i in range(len(sim.model.radius.value)-2,-2,-1):\n",
+    "for i in range(len(sim.simulation_state.radius.value)-2,-2,-1):\n",
     "    if i==0:\n",
     "        fig.add_shape(type=\"circle\",\n",
     "            xref=\"x\", yref=\"y\",\n",
@@ -256,7 +256,7 @@
     "            fillcolor=\"darkgrey\",\n",
     "            opacity=1\n",
     "        )\n",
-    "    elif i==(len(sim.model.radius.value)-1):\n",
+    "    elif i==(len(sim.simulation_state.radius.value)-1):\n",
     "        fig.add_shape(type=\"circle\",\n",
     "            xref=\"x\", yref=\"y\",\n",
     "            x0=-1*v_shells[i], y0=-1*v_shells[i], x1=v_shells[i], y1=v_shells[i],\n",
diff --git a/docs/physics/setup/index.rst b/docs/physics/setup/index.rst
index fd233499e81..38e716717a6 100644
--- a/docs/physics/setup/index.rst
+++ b/docs/physics/setup/index.rst
@@ -5,7 +5,7 @@ Setting Up the Simulation
 *************************
 
 The first step executed when TARDIS runs is to call an instance of the ``Simulation`` class. This sets up a lot of
-things that TARDIS will need during its run. The main things that are set up are the supernova model (a ``Radial1DModel`` object), the
+things that TARDIS will need during its run. The main things that are set up are the supernova model (a ``SimulationState`` object), the
 initial plasma state (a ``BasePlasma`` object, which may be updated throughout the simulation, see :doc:`../update_and_conv/update_and_conv`),
 and a ``MonteCarloTransport`` object. The pages linked below explain how the former two are calculated (the latter is used mainly in the
 :doc:`next step of the calculation <../montecarlo/index>`), as well as showing this in action by calling an instance of the ``Simulation``
diff --git a/docs/physics/setup/model.ipynb b/docs/physics/setup/model.ipynb
index e2d6d729a8e..355121bd4ca 100644
--- a/docs/physics/setup/model.ipynb
+++ b/docs/physics/setup/model.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "# Model\n",
     "\n",
-    "As shown previously, when `Simulation.from_config()` is called, a `Radial1DModel` object is created. This is done via the class method `Radial1DModel.from_config()`. This model object contains important information about the shell structure, density, abundance, radiative temperature, and dilution factor throughout the supernova.\n",
+    "As shown previously, when `Simulation.from_config()` is called, a `SimulationState` object is created. This is done via the class method `SimulationState.from_config()`. This model object contains important information about the shell structure, density, abundance, radiative temperature, and dilution factor throughout the supernova.\n",
     "\n",
     "Throughout this notebook, we show various configuration inputs into the TARDIS model and the resulting model. In interactive mode, these parameters can be varied to explore how the model changes. Editing configuration parameters in the notebook is explained [here](../../io/configuration/read_configuration.ipynb).\n",
     "\n",
@@ -53,7 +53,7 @@
    "source": [
     "# We import the necessary packages\n",
     "from tardis.io.configuration.config_reader import Configuration\n",
-    "from tardis.model import Radial1DModel\n",
+    "from tardis.model import SimulationState\n",
     "from tardis.io.atom_data.util import download_atom_data\n",
     "from astropy import units as u\n",
     "import matplotlib.pyplot as plt\n",
@@ -79,7 +79,7 @@
    "id": "cee054e9",
    "metadata": {},
    "source": [
-    "In the cell below, we set up a model. We use the [specific structure](../../io/configuration/components/models/index.rst#specific-structure) where we supply $t_\\mathrm{explosion}$, the velocity of the inner and outer boundaries of the supernova (labeled `start` and `stop`), and the number of shells (labeled `num`). The shells are then evenly spaced between the inner and outer boundaries of the supernova. The time after the explosion, the inner and outer velocities, and the number of shells can be varied to get different shell structures. The `Radial1DModel` object stores information about the model in the following attributes: `velocity` shows the velocity of the shell boundaries, `v_inner` shows the velocities of the inner boundaries of each shell, `v_outer` shows the velocity of the outer boundaries of each shell, and `v_middle` shows the velocity of the middle of each shell. Similarly, `radius`, `r_inner`, `r_outer`, and `r_middle` show the radii of each shell boundary, the inner boundaries, the outer boundaries, and the middles of each shell, respectively. `v_boundary_inner` shows the velocity of the inner boundary of the computational domain, and `v_boundary_outer` shows the velocity of the outer boundary of the computational domain. Finally, `volume` shows the volume of each shell, calculated via the formula of the volume of a spherical shell: $V=\\frac{4}{3}\\pi (r_\\mathrm{outer}^3-r_\\mathrm{inner}^3)$."
+    "In the cell below, we set up a model. We use the [specific structure](../../io/configuration/components/models/index.rst#specific-structure) where we supply $t_\\mathrm{explosion}$, the velocity of the inner and outer boundaries of the supernova (labeled `start` and `stop`), and the number of shells (labeled `num`). The shells are then evenly spaced between the inner and outer boundaries of the supernova. The time after the explosion, the inner and outer velocities, and the number of shells can be varied to get different shell structures. The `SimulationState` object stores information about the model in the following attributes: `velocity` shows the velocity of the shell boundaries, `v_inner` shows the velocities of the inner boundaries of each shell, `v_outer` shows the velocity of the outer boundaries of each shell, and `v_middle` shows the velocity of the middle of each shell. Similarly, `radius`, `r_inner`, `r_outer`, and `r_middle` show the radii of each shell boundary, the inner boundaries, the outer boundaries, and the middles of each shell, respectively. `v_boundary_inner` shows the velocity of the inner boundary of the computational domain, and `v_boundary_outer` shows the velocity of the outer boundary of the computational domain. Finally, `volume` shows the volume of each shell, calculated via the formula of the volume of a spherical shell: $V=\\frac{4}{3}\\pi (r_\\mathrm{outer}^3-r_\\mathrm{inner}^3)$."
    ]
   },
   {
@@ -103,7 +103,7 @@
     "shell_config.model.structure.velocity.stop = 2000 * u.km/u.s\n",
     "shell_config.model.structure.velocity.num = 20\n",
     "\n",
-    "shell_model = Radial1DModel.from_config(shell_config)\n",
+    "shell_model = SimulationState.from_config(shell_config)\n",
     "\n",
     "print('velocity:\\n', shell_model.velocity)\n",
     "print('v_inner:\\n', shell_model.v_inner)\n",
@@ -151,7 +151,7 @@
     "\n",
     "Since the state of the ejecta, including the density, is the same throughout the shell, we determine the shell's density by plugging the velocity/radius at the center of the shell into the density function. We now explore the various built-in density profiles. For each profile, we build an example model using the density profile and example parameters (which can be varied in interactive mode), print the densities in each shell, and show a graph of density versus radius (specifically the radius at the center of each shell).\n",
     "\n",
-    "Note that the density in each shell is stored in the `density` attribute of the `Radial1DModel` object.\n",
+    "Note that the density in each shell is stored in the `density` attribute of the `SimulationState` object.\n",
     "\n",
     "### Branch85 W7 Density\n",
     "\n",
@@ -181,7 +181,7 @@
     "\n",
     "w7_density_config.model.structure.density.type = 'branch85_w7'\n",
     "\n",
-    "w7_density_model = Radial1DModel.from_config(w7_density_config)\n",
+    "w7_density_model = SimulationState.from_config(w7_density_config)\n",
     "\n",
     "print('density:\\n', w7_density_model.density)\n",
     "\n",
@@ -209,7 +209,7 @@
     "\n",
     "w7_modified_config.supernova.time_explosion = 12 * u.day\n",
     "\n",
-    "w7_modified_model = Radial1DModel.from_config(w7_modified_config)\n",
+    "w7_modified_model = SimulationState.from_config(w7_modified_config)\n",
     "\n",
     "print('density:\\n', w7_modified_model.density)\n",
     "\n",
@@ -273,7 +273,7 @@
     "uni_density_config.model.structure.density.time_0 = 1 * u.day\n",
     "uni_density_config.model.structure.density.value = 5e-10 * u.kg/u.cm**3\n",
     "\n",
-    "uni_density_model = Radial1DModel.from_config(uni_density_config)\n",
+    "uni_density_model = SimulationState.from_config(uni_density_config)\n",
     "\n",
     "print('density:\\n', uni_density_model.density)\n",
     "\n",
@@ -327,7 +327,7 @@
     "pow_density_config.model.structure.density.v_0 = 500 * u.km/u.s\n",
     "pow_density_config.model.structure.density.exponent = -2\n",
     "\n",
-    "pow_density_model = Radial1DModel.from_config(pow_density_config)\n",
+    "pow_density_model = SimulationState.from_config(pow_density_config)\n",
     "\n",
     "print('density:\\n', pow_density_model.density)\n",
     "\n",
@@ -378,7 +378,7 @@
     "exp_density_config.model.structure.density.rho_0 = 5e-10 * u.kg/u.cm**3\n",
     "exp_density_config.model.structure.density.v_0 = 500 * u.km/u.s\n",
     "\n",
-    "exp_density_model = Radial1DModel.from_config(exp_density_config)\n",
+    "exp_density_model = SimulationState.from_config(exp_density_config)\n",
     "\n",
     "print('density:\\n', exp_density_model.density)\n",
     "\n",
@@ -394,11 +394,11 @@
    "source": [
     "## Abundance\n",
     "\n",
-    "The `Radial1DModel` also carries important information about elemental abundances in each shell. These are mass abundances -- that is, the abundance of oxygen is the fraction of the shell's mass that is made up of oxygen.\n",
+    "The `SimulationState` also carries important information about elemental abundances in each shell. These are mass abundances -- that is, the abundance of oxygen is the fraction of the shell's mass that is made up of oxygen.\n",
     "\n",
     "The only built-in abundance model that TARDIS offers is a uniform abundance, meaning each shell has identical abundances. Like density, however, the [file abundance](../../io/configuration/components/models/index.rst#file-abundance), [CSVY model](../../io/configuration/components/models/index.rst#csvy-model), and [custom abundance widget](../../io/visualization/abundance_widget.ipynb) methods allow users more freedom with assigning different abundances in each shell.\n",
     "\n",
-    "A table of abundances in each shell is stored in the `abundance` attribute of the `Radial1DModel` object.\n",
+    "A table of abundances in each shell is stored in the `abundance` attribute of the `SimulationState` object.\n",
     "\n",
     "In this first example, the abundances in each shell do not depend on the time after the explosion and are identical to those provided in the configuration."
    ]
@@ -423,7 +423,7 @@
     "                                            'Si':.3,\n",
     "                                            'He': .1}\n",
     "\n",
-    "abund_model = Radial1DModel.from_config(abund_config)\n",
+    "abund_model = SimulationState.from_config(abund_config)\n",
     "\n",
     "abund_model.abundance"
    ]
@@ -459,7 +459,7 @@
     "                                            'Ni57':.1,\n",
     "                                            'Cr51':.4}\n",
     "\n",
-    "abund_isotopes_model = Radial1DModel.from_config(abund_isotopes_config)\n",
+    "abund_isotopes_model = SimulationState.from_config(abund_isotopes_config)\n",
     "\n",
     "abund_isotopes_model.abundance"
    ]
@@ -527,7 +527,7 @@
     "t_rad_config.model.structure.velocity.stop = 2000 * u.km/u.s\n",
     "t_rad_config.model.structure.velocity.num = 20\n",
     "\n",
-    "t_rad_model = Radial1DModel.from_config(t_rad_config)\n",
+    "t_rad_model = SimulationState.from_config(t_rad_config)\n",
     "\n",
     "print('t_inner:\\n', t_rad_model.t_inner)\n",
     "print('t_rad:\\n', t_rad_model.t_rad)\n",
@@ -590,7 +590,7 @@
     "w_config.model.structure.velocity.stop = 2000 * u.km/u.s\n",
     "w_config.model.structure.velocity.num = 20\n",
     "\n",
-    "w_model = Radial1DModel.from_config(w_config)\n",
+    "w_model = SimulationState.from_config(w_config)\n",
     "\n",
     "print('w:\\n', w_model.w)\n",
     "\n",
diff --git a/docs/physics/setup/setup_example.ipynb b/docs/physics/setup/setup_example.ipynb
index 287edd18d23..a2c90106a27 100644
--- a/docs/physics/setup/setup_example.ipynb
+++ b/docs/physics/setup/setup_example.ipynb
@@ -72,7 +72,7 @@
    "id": "e3f86364",
    "metadata": {},
    "source": [
-    "When the `Simulation` object is created, a `Radial1DModel`, `BasePlasma`, and `MontecarloTransport` object are created and stored as attributes of the `Simulation` object."
+    "When the `Simulation` object is created, a `SimulationState`, `BasePlasma`, and `MontecarloTransport` object are created and stored as attributes of the `Simulation` object."
    ]
   },
   {
@@ -82,7 +82,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim.model"
+    "sim.simulation_state"
    ]
   },
   {
diff --git a/docs/physics/update_and_conv/update_and_conv.ipynb b/docs/physics/update_and_conv/update_and_conv.ipynb
index 470247bd55b..b92b8f134b0 100644
--- a/docs/physics/update_and_conv/update_and_conv.ipynb
+++ b/docs/physics/update_and_conv/update_and_conv.ipynb
@@ -212,7 +212,7 @@
    "source": [
     "sim = Simulation.from_config(tardis_config)\n",
     "\n",
-    "model = sim.model\n",
+    "model = sim.simulation_state\n",
     "plasma = sim.plasma\n",
     "transport = sim.transport"
    ]
diff --git a/tardis/analysis/opacities.py b/tardis/analysis/opacities.py
index 315c669e40b..e1b383233c1 100644
--- a/tardis/analysis/opacities.py
+++ b/tardis/analysis/opacities.py
@@ -33,7 +33,7 @@ class opacity_calculator(object):
 
     Parameters
     ----------
-    mdl : tardis.model.Radial1DModel
+    mdl : tardis.model.SimulationState
         model object of the Tardis run
     nbins : int
         number of bins of the frequency grid (default 300)
diff --git a/tardis/energy_input/gamma_ray_transport.py b/tardis/energy_input/gamma_ray_transport.py
index e89098e8ca6..6731e97bf60 100644
--- a/tardis/energy_input/gamma_ray_transport.py
+++ b/tardis/energy_input/gamma_ray_transport.py
@@ -281,7 +281,7 @@ def main_gamma_ray_loop(
     ----------
     num_decays : int
         Number of decays requested
-    model : tardis.Radial1DModel
+    model : tardis.SimulationState
         The tardis model to calculate gamma ray propagation through
     plasma : tardis.plasma.BasePlasma
         The tardis plasma with calculated atomic number density
diff --git a/tardis/grid/base.py b/tardis/grid/base.py
index 91599f5833d..25fa32a6ca2 100644
--- a/tardis/grid/base.py
+++ b/tardis/grid/base.py
@@ -95,7 +95,7 @@ def grid_row_to_config(self, row_index):
 
     def grid_row_to_model(self, row_index):
         """
-        Generates a TARDIS Radial1DModel object using the base
+        Generates a TARDIS SimulationState object using the base
         self.config modified by the specified grid row.
 
         Parameters
@@ -105,7 +105,7 @@ def grid_row_to_model(self, row_index):
 
         Returns
         -------
-        model : tardis.model.base.Radial1DModel
+        model : tardis.model.base.SimulationState
         """
         rowconfig = self.grid_row_to_config(row_index)
         model = SimulationState.from_config(rowconfig)
diff --git a/tardis/io/model/hdf.py b/tardis/io/model/hdf.py
index 104bae6d568..2ed9ee1a141 100644
--- a/tardis/io/model/hdf.py
+++ b/tardis/io/model/hdf.py
@@ -6,11 +6,11 @@
 
 def store_model_to_hdf(model, fname):
     """
-    Stores data from Radial1DModel object into a hdf file.
+    Stores data from SimulationState object into a hdf file.
 
     Parameters
     ----------
-    model : tardis.model.Radial1DModel
+    model : tardis.model.SimulationState
     filename : str
     """
     with h5py.File(fname, "a") as f:
diff --git a/tardis/io/model/model_reader.py b/tardis/io/model/model_reader.py
index 989157b620a..8a010ab6dc3 100644
--- a/tardis/io/model/model_reader.py
+++ b/tardis/io/model/model_reader.py
@@ -284,11 +284,11 @@ def transport_from_hdf(fname):
 
 def model_to_dict(model):
     """
-    Retrieves all the data from a Radial1DModel object and returns a dictionary.
+    Retrieves all the data from a SimulationState object and returns a dictionary.
 
     Parameters
     ----------
-    transport : tardis.model.Radial1DModel
+    transport : tardis.model.SimulationState
 
     Returns
     -------
@@ -321,7 +321,7 @@ def model_to_dict(model):
 
 def model_from_hdf(fname):
     """
-    Creates a Radial1DModel object using data stored in a hdf file.
+    Creates a SimulationState object using data stored in a hdf file.
 
     Parameters
     ----------
@@ -329,7 +329,7 @@ def model_from_hdf(fname):
 
     Returns
     -------
-    new_model : tardis.model.Radial1DModel
+    new_model : tardis.model.SimulationState
     """
 
     from tardis.model import SimulationState
diff --git a/tardis/io/model_reader.py b/tardis/io/model_reader.py
index 2d512a65aa2..2ca6236fa3b 100644
--- a/tardis/io/model_reader.py
+++ b/tardis/io/model_reader.py
@@ -810,11 +810,11 @@ def transport_from_hdf(fname):
 
 def model_to_dict(model):
     """
-    Retrieves all the data from a Radial1DModel object and returns a dictionary.
+    Retrieves all the data from a SimulationState object and returns a dictionary.
 
     Parameters
     ----------
-    transport : tardis.model.Radial1DModel
+    transport : tardis.model.SimulationState
 
     Returns
     -------
@@ -847,11 +847,11 @@ def model_to_dict(model):
 
 def store_model_to_hdf(model, fname):
     """
-    Stores data from Radial1DModel object into a hdf file.
+    Stores data from SimulationState object into a hdf file.
 
     Parameters
     ----------
-    model : tardis.model.Radial1DModel
+    model : tardis.model.SimulationState
     filename : str
     """
     with h5py.File(fname, "a") as f:
@@ -870,7 +870,7 @@ def store_model_to_hdf(model, fname):
 
 def model_from_hdf(fname):
     """
-    Creates a Radial1DModel object using data stored in a hdf file.
+    Creates a SimulationState object using data stored in a hdf file.
 
     Parameters
     ----------
@@ -878,7 +878,7 @@ def model_from_hdf(fname):
 
     Returns
     -------
-    new_model : tardis.model.Radial1DModel
+    new_model : tardis.model.SimulationState
     """
 
     from tardis.model import SimulationState
diff --git a/tardis/model/base.py b/tardis/model/base.py
index 4d5e94abeda..65807a27589 100644
--- a/tardis/model/base.py
+++ b/tardis/model/base.py
@@ -541,7 +541,7 @@ def v_boundary_outer_index(self):
     @classmethod
     def from_config(cls, config, atom_data=None):
         """
-        Create a new Radial1DModel instance from a Configuration object.
+        Create a new SimulationState instance from a Configuration object.
 
         Parameters
         ----------
@@ -550,7 +550,7 @@ def from_config(cls, config, atom_data=None):
 
         Returns
         -------
-        Radial1DModel
+        SimulationState
         """
         time_explosion = config.supernova.time_explosion.cgs
 
@@ -668,7 +668,7 @@ def from_config(cls, config, atom_data=None):
     @classmethod
     def from_csvy(cls, config, atom_data=None):
         """
-        Create a new Radial1DModel instance from a Configuration object.
+        Create a new SimulationState instance from a Configuration object.
 
         Parameters
         ----------
@@ -677,7 +677,7 @@ def from_csvy(cls, config, atom_data=None):
 
         Returns
         -------
-        Radial1DModel
+        SimulationState
         """
         CSVY_SUPPORTED_COLUMNS = {
             "velocity",
diff --git a/tardis/model/tests/test_csvy_model.py b/tardis/model/tests/test_csvy_model.py
index 8e8f69c1b6b..52fb2933a62 100644
--- a/tardis/model/tests/test_csvy_model.py
+++ b/tardis/model/tests/test_csvy_model.py
@@ -77,7 +77,7 @@ def test_compare_models(model_config_fnames):
 
 @pytest.fixture(scope="module")
 def csvy_model_test_abundances(example_csvy_file_dir):
-    """Returns Radial1DModel to use to test abundances dataframes"""
+    """Returns SimulationState to use to test abundances dataframes"""
     csvypath = example_csvy_file_dir / "csvy_model_to_test_abundances.yml"
     config = Configuration.from_yaml(csvypath)
     csvy_model_test_abundances = SimulationState.from_csvy(config)
diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 8a6976cb9c8..5924c9c3f66 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -197,7 +197,7 @@ def _initialize_geometry_arrays(self, model):
 
         Parameters
         ----------
-        model : model.Radial1DModel
+        model : model.SimulationState
         """
         self.r_inner_cgs = model.r_inner.to("cm").value
         self.r_outer_cgs = model.r_outer.to("cm").value
@@ -315,7 +315,7 @@ def run(
 
         Parameters
         ----------
-        model : tardis.model.Radial1DModel
+        model : tardis.model.SimulationState
         plasma : tardis.plasma.BasePlasma
         no_of_packets : int
         no_of_virtual_packets : int
@@ -571,7 +571,7 @@ def calculate_luminosity_inner(self, model):
 
         Parameters
         ----------
-        model : model.Radial1DModel
+        model : model.SimulationState
 
         Returns
         -------
@@ -591,7 +591,7 @@ def calculate_time_of_simulation(self, model):
 
         Parameters
         ----------
-        model : model.Radial1DModel
+        model : model.SimulationState
 
         Returns
         -------
diff --git a/tardis/montecarlo/montecarlo_numba/formal_integral.py b/tardis/montecarlo/montecarlo_numba/formal_integral.py
index fbb443e79a1..e27704fbd96 100644
--- a/tardis/montecarlo/montecarlo_numba/formal_integral.py
+++ b/tardis/montecarlo/montecarlo_numba/formal_integral.py
@@ -273,7 +273,7 @@ class FormalIntegrator(object):
 
     Parameters
     ----------
-    model : tardis.model.Radial1DModel
+    model : tardis.model.SimulationState
     plasma : tardis.plasma.BasePlasma
     transport : tardis.montecarlo.MontecarloTransport
     points : int64
@@ -404,7 +404,7 @@ def make_source_function(self):
 
         Parameters
         ----------
-        model : tardis.model.Radial1DModel
+        model : tardis.model.SimulationState
 
         Returns
         -------
diff --git a/tardis/montecarlo/montecarlo_numba/tests/test_cuda_formal_integral.py b/tardis/montecarlo/montecarlo_numba/tests/test_cuda_formal_integral.py
index d3412ff1919..3eab004525a 100644
--- a/tardis/montecarlo/montecarlo_numba/tests/test_cuda_formal_integral.py
+++ b/tardis/montecarlo/montecarlo_numba/tests/test_cuda_formal_integral.py
@@ -349,11 +349,11 @@ def test_full_formal_integral(
     sim = simulation_verysimple
 
     formal_integrator_numba = FormalIntegrator(
-        sim.model, sim.plasma, sim.transport
+        sim.simulation_state, sim.plasma, sim.transport
     )
 
     formal_integrator_cuda = FormalIntegrator(
-        sim.model, sim.plasma, sim.transport
+        sim.simulation_state, sim.plasma, sim.transport
     )
 
     # The function calculate_spectrum sets this property, but in order to test the CUDA.
diff --git a/tardis/plasma/standard_plasmas.py b/tardis/plasma/standard_plasmas.py
index 01e40fde22e..5cf21d431bd 100644
--- a/tardis/plasma/standard_plasmas.py
+++ b/tardis/plasma/standard_plasmas.py
@@ -52,12 +52,12 @@
 def assemble_plasma(config, model, atom_data=None):
     """
     Create a BasePlasma instance from a Configuration object
-    and a Radial1DModel.
+    and a SimulationState.
 
     Parameters
     ----------
     config : io.config_reader.Configuration
-    model : model.Radial1DModel
+    model : model.SimulationState
     atom_data : atomic.AtomData
         If None, an attempt will be made to read the atomic data
         from config.
diff --git a/tardis/simulation/base.py b/tardis/simulation/base.py
index 0aee0bb1773..3c7b67cb761 100644
--- a/tardis/simulation/base.py
+++ b/tardis/simulation/base.py
@@ -94,7 +94,7 @@ class Simulation(PlasmaStateStorerMixin, HDFWriterMixin):
     ----------
     converged : bool
     iterations : int
-    model : tardis.model.Radial1DModel
+    model : tardis.model.SimulationState
     plasma : tardis.plasma.BasePlasma
     transport : tardis.montecarlo.MontecarloTransport
     no_of_packets : int
diff --git a/tardis/util/base.py b/tardis/util/base.py
index a3bcd07422e..68693c3fa6b 100644
--- a/tardis/util/base.py
+++ b/tardis/util/base.py
@@ -194,7 +194,7 @@ def create_synpp_yaml(radial1d_mdl, fname, shell_no=0, lines_db=None):
 
     Parameters
     ----------
-    radial1d_mdl : Radial1DModel
+    radial1d_mdl : SimulationState
         Inputted object that will be read into YAML file
     fname : str
         File name for the synpp yaml
diff --git a/tardis/visualization/widgets/custom_abundance.py b/tardis/visualization/widgets/custom_abundance.py
index 6e08567f1ad..863a750ee2d 100644
--- a/tardis/visualization/widgets/custom_abundance.py
+++ b/tardis/visualization/widgets/custom_abundance.py
@@ -269,8 +269,8 @@ def from_simulation(cls, sim):
         -------
         CustomAbundanceWidgetData
         """
-        abundance = sim.model.raw_abundance.copy()
-        isotope_abundance = sim.model.raw_isotope_abundance.copy()
+        abundance = sim.simulation_state.raw_abundance.copy()
+        isotope_abundance = sim.simulation_state.raw_isotope_abundance.copy()
 
         # integrate element and isotope to one DataFrame
         abundance["mass_number"] = ""
@@ -278,9 +278,9 @@ def from_simulation(cls, sim):
         abundance = pd.concat([abundance, isotope_abundance])
         abundance.sort_index(inplace=True)
 
-        velocity = sim.model.velocity
-        density_t_0 = sim.model.time_explosion
-        density = sim.model.density
+        velocity = sim.simulation_state.velocity
+        density_t_0 = sim.simulation_state.time_explosion
+        density = sim.simulation_state.density
 
         return cls(
             density_t_0=density_t_0,
diff --git a/tardis/visualization/widgets/grotrian_mockup.ipynb b/tardis/visualization/widgets/grotrian_mockup.ipynb
index 07e73cc9b7d..e77d5367382 100644
--- a/tardis/visualization/widgets/grotrian_mockup.ipynb
+++ b/tardis/visualization/widgets/grotrian_mockup.ipynb
@@ -62,7 +62,7 @@
     "from tardis.io.config_reader import Configuration\n",
     "from tardis.simulation import Simulation\n",
     "from tardis.plasma.standard_plasmas import assemble_plasma\n",
-    "from tardis.model import Radial1DModel\n",
+    "from tardis.model import SimulationState\n",
     "from tardis.io.atom_data import AtomData\n",
     "from tardis.visualization.widgets.grotrian import GrotrianWidget\n",
     "from tardis.io.config_internal import get_data_dir\n",
@@ -981,7 +981,7 @@
     "atom_data = AtomData.from_hdf(\n",
     "    os.path.join(get_data_dir(), \"kurucz_cd23_chianti_H_He.h5\")\n",
     ")\n",
-    "model = Radial1DModel.from_config(config, atom_data=atom_data)\n",
+    "model = SimulationState.from_config(config, atom_data=atom_data)\n",
     "plasma = assemble_plasma(config, model, atom_data=atom_data)\n",
     "sim = Simulation.from_config(config, model=model, plasma=plasma)\n",
     "sim.run_convergence()\n",

From 14084ae51e50a4c6566f8a6a7d2c6437ce140feb Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Wed, 4 Oct 2023 21:31:52 +0530
Subject: [PATCH 07/35] Ignore tests in docstr coverage (#2424)

ignore tests in docstr coverage
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 61e061f8aec..aa87db29650 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,7 +41,7 @@ ignore-nested-functions = false
 ignore-nested-classes = true
 ignore-private = true
 ignore-property-decorators = true
-#ignore-regex = ["^get$", "^mock_.*", ".*BaseClass.*"]
+ignore-regex = ["^test"]
 ignore-semiprivate = true
 ignore-setters = true
 omit-covered-files = false

From 255a45b68d02779a83c08695d9125f54cd798a1b Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Wed, 4 Oct 2023 21:05:57 +0200
Subject: [PATCH 08/35] Disabled formal integral for continuum interaction
 (#2426)

Disabled formal integral

Co-authored-by: Alexander Holas <alexander.holas@h-its>
---
 tardis/montecarlo/montecarlo_numba/formal_integral.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/tardis/montecarlo/montecarlo_numba/formal_integral.py b/tardis/montecarlo/montecarlo_numba/formal_integral.py
index e27704fbd96..c97c017360d 100644
--- a/tardis/montecarlo/montecarlo_numba/formal_integral.py
+++ b/tardis/montecarlo/montecarlo_numba/formal_integral.py
@@ -12,6 +12,7 @@
 import pdb
 
 from tardis.montecarlo.montecarlo_numba.numba_config import SIGMA_THOMSON
+from tardis.montecarlo import montecarlo_configuration as mc_config_module
 from tardis.montecarlo.montecarlo_numba import njit_dict, njit_dict_no_parallel
 from tardis.montecarlo.montecarlo_numba.numba_interface import (
     opacity_state_initialize,
@@ -359,6 +360,12 @@ def raise_or_return(message):
                 'and line_interaction_type == "macroatom"'
             )
 
+        if mc_config_module.CONTINUUM_PROCESSES_ENABLED:
+            return raise_or_return(
+                "The FormalIntegrator currently does not work for "
+                "continuum interactions."
+            )
+
         return True
 
     def calculate_spectrum(

From 70fcf0b4e494c3d8cb16794d03c843462351b6d4 Mon Sep 17 00:00:00 2001
From: Joshua Shields <54691495+jvshields@users.noreply.github.com>
Date: Wed, 4 Oct 2023 15:38:52 -0400
Subject: [PATCH 09/35] add linelist exposure to atom data and reader, built on
 current (#2428)

* add linelist exposure to atom data and reader, built on current

* add josh to mailmap
---
 .mailmap                    |  2 ++
 tardis/io/atom_data/base.py | 11 +++++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/.mailmap b/.mailmap
index 0baa7c0c71b..e8de40e3ee3 100644
--- a/.mailmap
+++ b/.mailmap
@@ -104,6 +104,8 @@ John Reichenbach <56849859+jreichenbach-msu@users.noreply.github.com>
 Jordi Eguren <jordi.eguren.brown@gmail.com>
 Jordi Eguren <jordi.eguren.brown@gmail.com> jordi5 <45364266+jordi5@users.noreply.github.com>
 
+Josh Shields <shields.joshua.v@gmail.com>
+
 Karan Desai <karandesai_96@live.com>
 Karan Desai <karandesai_96@live.com> karandesai-96 <karandesai_96@live.com>
 
diff --git a/tardis/io/atom_data/base.py b/tardis/io/atom_data/base.py
index 1db66d58e09..a1cf9e8d449 100644
--- a/tardis/io/atom_data/base.py
+++ b/tardis/io/atom_data/base.py
@@ -138,6 +138,7 @@ class AtomData(object):
         "photoionization_data",
         "yg_data",
         "two_photon_data",
+        "linelist",
     ]
 
     # List of tuples of the related dataframes.
@@ -165,7 +166,6 @@ def from_hdf(cls, fname=None):
         fname = resolve_atom_data_fname(fname)
 
         with pd.HDFStore(fname, "r") as store:
-
             for name in cls.hdf_names:
                 try:
                     dataframes[name] = store.select(name)
@@ -182,7 +182,6 @@ def from_hdf(cls, fname=None):
                     # Checks for various collisional data from Carsus files
                     if "collisions_data" in store:
                         try:
-
                             dataframes["collision_data_temperatures"] = store[
                                 "collisions_metadata"
                             ].temperatures
@@ -211,6 +210,8 @@ def from_hdf(cls, fname=None):
                     raise ValueError(
                         f"Current carsus version, {carsus_version}, is not supported."
                     )
+            if "linelist" in store:
+                dataframes["linelist"] = store["linelist"]
 
             atom_data = cls(**dataframes)
 
@@ -273,8 +274,8 @@ def __init__(
         photoionization_data=None,
         yg_data=None,
         two_photon_data=None,
+        linelist=None,
     ):
-
         self.prepared = False
 
         # CONVERT VALUES TO CGS UNITS
@@ -333,6 +334,9 @@ def __init__(
 
         self.two_photon_data = two_photon_data
 
+        if linelist is not None:
+            self.linelist = linelist
+
         self._check_related()
 
         self.symbol2atomic_number = OrderedDict(
@@ -426,7 +430,6 @@ def prepare_atom_data(
             self.macro_atom_data_all is not None
             and not line_interaction_type == "scatter"
         ):
-
             self.macro_atom_data = self.macro_atom_data_all.loc[
                 self.macro_atom_data_all["atomic_number"].isin(
                     self.selected_atomic_numbers

From 5fffd73fd9c73b41a0f832377172e75989d7de0f Mon Sep 17 00:00:00 2001
From: Anirban <anirbaniamdutta@gmail.com>
Date: Mon, 9 Oct 2023 16:19:40 -0400
Subject: [PATCH 10/35] =?UTF-8?q?Modified=20how=20setup=20input=20energy?=
 =?UTF-8?q?=20takes=20isotope=20name.=20Earlier=20it=20was=20ga=E2=80=A6?=
 =?UTF-8?q?=20(#2425)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Modified how setup input energy takes isotope name. Earlier it was gamma_ray_lines.Isotope
---
 tardis/energy_input/gamma_ray_transport.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/tardis/energy_input/gamma_ray_transport.py b/tardis/energy_input/gamma_ray_transport.py
index 6731e97bf60..b3cb174c1fc 100644
--- a/tardis/energy_input/gamma_ray_transport.py
+++ b/tardis/energy_input/gamma_ray_transport.py
@@ -428,17 +428,13 @@ def main_gamma_ray_loop(
                     parents[c] = isotope
 
         energy, intensity = setup_input_energy(
-            gamma_ray_lines[
-                gamma_ray_lines.Isotope == isotope.replace("-", "")
-            ],
+            gamma_ray_lines[gamma_ray_lines.index == isotope.replace("-", "")],
             "g",
         )
         gamma_ray_line_array_list.append(np.stack([energy, intensity]))
         average_energies_list.append(np.sum(energy * intensity))
         positron_energy, positron_intensity = setup_input_energy(
-            gamma_ray_lines[
-                gamma_ray_lines.Isotope == isotope.replace("-", "")
-            ],
+            gamma_ray_lines[gamma_ray_lines.index == isotope.replace("-", "")],
             "bp",
         )
         average_positron_energies_list.append(

From ecd011c85692771fc0924322e504e008156b3395 Mon Sep 17 00:00:00 2001
From: Anirban <anirbaniamdutta@gmail.com>
Date: Mon, 9 Oct 2023 16:20:05 -0400
Subject: [PATCH 11/35] Added a function to calculate shell masses (#2434)

* Added a function to calculate shell masses

* Added a function to calculate shell masses

* changed shell masses with the new function
---
 tardis/energy_input/gamma_ray_transport.py | 23 +++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/tardis/energy_input/gamma_ray_transport.py b/tardis/energy_input/gamma_ray_transport.py
index b3cb174c1fc..6aea2856080 100644
--- a/tardis/energy_input/gamma_ray_transport.py
+++ b/tardis/energy_input/gamma_ray_transport.py
@@ -260,6 +260,27 @@ def initialize_packets(
     )
 
 
+def calculate_shell_masses(model):
+
+    """Function to calculate shell masses
+    Parameters
+    ----------
+    model : tardis.Radial1DModel
+        The tardis model to calculate gamma ray propagation through
+    Returns
+    -------
+    numpy.ndarray
+        shell masses in units of g
+
+    """
+
+    ejecta_density = model.density.to("g/cm^3").value
+    ejecta_volume = model.volume.to("cm^3").value
+    shell_masses = ejecta_volume * ejecta_density
+
+    return shell_masses
+
+
 def main_gamma_ray_loop(
     num_decays,
     model,
@@ -346,7 +367,7 @@ def main_gamma_ray_loop(
         by=["atomic_number", "mass_number"], ascending=False
     )
 
-    shell_masses = ejecta_volume * ejecta_density
+    shell_masses = calculate_shell_masses(model)
 
     time_start = time_explosion
     time_end *= u.d.to(u.s)

From d2b03068c12db73b98220f172bb67d72d8c5f982 Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Fri, 13 Oct 2023 22:48:04 +0200
Subject: [PATCH 12/35] Fix duplicate entries in continuum line list (#2443)

* Workaround list access

* Formatting

* Added error if duplicate

* Remove duplicates

* Fix typo, add comment

* Remove bandaid fix

* Cleanup

* More cleanup
---
 tardis/plasma/properties/atomic.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/tardis/plasma/properties/atomic.py b/tardis/plasma/properties/atomic.py
index 236edb01ecc..6ade1ae1377 100644
--- a/tardis/plasma/properties/atomic.py
+++ b/tardis/plasma/properties/atomic.py
@@ -467,6 +467,26 @@ def calculate(self, atomic_data):
         level_idxs2line_idx = pd.Series(
             np.arange(len(index)), index=index, name="lines_idx"
         )
+
+        # Check for duplicate indices
+        if level_idxs2line_idx.index.duplicated().any():
+            logger.warn(
+                "Duplicate indices in level_idxs2line_idx. "
+                "Dropping duplicates. "
+                "This is an issue with the atomic data & carsus. "
+                "Once fixed upstream, this warning will be removed. "
+                "This will raise an error in the future instead. "
+                "See https://github.com/tardis-sn/carsus/issues/384"
+            )
+            # This is necessary since pd.DataFrame.drop_duplicates()
+            # does not remove duplicates if the data is different
+            # and only the index is duplicated. See the example given
+            # in the pandas documentation:
+            # https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.drop_duplicates.html
+            level_idxs2line_idx = level_idxs2line_idx[
+                ~level_idxs2line_idx.index.duplicated()
+            ]
+
         return level_idxs2line_idx
 
 

From 50f3c0310af07676f942c98d3d8bf65cbd50b4bb Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Tue, 17 Oct 2023 20:18:06 +0200
Subject: [PATCH 13/35] Fix numba parallel issues (#2447)

* Enabled parallel

* Fix the mistake

* Update docs
---
 docs/io/configuration/index.rst            |  5 -----
 docs/quickstart.ipynb                      | 16 ----------------
 tardis/montecarlo/base.py                  |  6 ------
 tardis/montecarlo/montecarlo_numba/base.py |  2 +-
 4 files changed, 1 insertion(+), 28 deletions(-)

diff --git a/docs/io/configuration/index.rst b/docs/io/configuration/index.rst
index 96483b6b8da..9eae01041a2 100644
--- a/docs/io/configuration/index.rst
+++ b/docs/io/configuration/index.rst
@@ -9,11 +9,6 @@ The necessary parameters for a TARDIS simulation are provided via a `YAML <https
 configuration file. The following sections respectively describes what can or must be included in the
 configuration file, shows an example configuration file, describes how TARDIS checks to make sure a configuration
 file is valid, and demonstrates how a YAML configuration file is read in.
-
-.. caution:: 
-    TARDIS parallelization is not working correctly at the moment and might produce incorrect results.
-    Please avoid using it.
-    For more information, see issue `#2021 <https://github.com/tardis-sn/tardis/issues/2021>`_.
   
 .. toctree::
   :maxdepth: 1
diff --git a/docs/quickstart.ipynb b/docs/quickstart.ipynb
index c15ebfd2365..b694d9dcca1 100644
--- a/docs/quickstart.ipynb
+++ b/docs/quickstart.ipynb
@@ -56,22 +56,6 @@
     "The configuration file [tardis_example.yml](https://github.com/tardis-sn/tardis/tree/master/docs/tardis_example.yml) is used throughout this Quickstart."
    ]
   },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<div class=\"alert alert-warning\">\n",
-    "\n",
-    "**Warning:**\n",
-    "\n",
-    "TARDIS parallelization is not working correctly at the moment and might produce incorrect results.\n",
-    "Please avoid using it.\n",
-    "For more information, see issue [#2021](https://github.com/tardis-sn/tardis/issues/2021).\n",
-    "\n",
-    "</div>\n"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 5924c9c3f66..ba65fb0e8ca 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -134,12 +134,6 @@ def __init__(
 
         # Set number of threads
         self.nthreads = nthreads
-        if self.nthreads != 1:
-            raise ValueError(
-                """TARDIS parallelization is not working correctly at the moment and is hence disabled.
-            Please see issue https://github.com/tardis-sn/tardis/issues/2021.
-            """
-            )
 
         # set up logger based on config
         mc_tracker.DEBUG_MODE = debug_packets
diff --git a/tardis/montecarlo/montecarlo_numba/base.py b/tardis/montecarlo/montecarlo_numba/base.py
index 028a91ff775..4ba3c0dd8d4 100644
--- a/tardis/montecarlo/montecarlo_numba/base.py
+++ b/tardis/montecarlo/montecarlo_numba/base.py
@@ -278,7 +278,7 @@ def montecarlo_main_loop(
             numba_radial_1d_geometry,
             numba_model,
             opacity_state,
-            estimators,
+            local_estimators,
             vpacket_collection,
             rpacket_tracker,
         )

From 74afcedeaaa900888be451d3b53064f69b1b1b90 Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Wed, 18 Oct 2023 23:12:04 +0530
Subject: [PATCH 14/35] Change glob patterns in `setup.cfg`  (#2441)

* Fix package_data in setup.cfg, mainly io and viz

* more folders

* Test pip installation

* Remove test step

* Fix more folders
---
 .github/workflows/tests.yml | 49 ++++++++++++++++++++++++++++---------
 setup.cfg                   | 14 ++++++++---
 2 files changed, 49 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 326b9ee2144..7414b517f28 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -32,20 +32,22 @@ jobs:
     if: github.repository_owner == 'tardis-sn'
     strategy:
       matrix:
+        pip: [true, false]
+        label: [osx-64, linux-64]
         include:
+          - label: osx-64
+            os: macos-latest
+            prefix: /Users/runner/miniconda3/envs/tardis
 
-        - os: ubuntu-latest
-          label: linux-64
-          prefix: /usr/share/miniconda3/envs/tardis
+          - label: linux-64
+            os: ubuntu-latest
+            prefix: /usr/share/miniconda3/envs/tardis
 
-        - os: macos-latest
-          label: osx-64
-          prefix: /Users/runner/miniconda3/envs/tardis
-
-    name: ${{ matrix.label }}
+    name: ${{ matrix.label }}-pip-${{ matrix.pip }}
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v2
+        if: matrix.pip == false
 
       - name: Clone tardis-sn/tardis-refdata
         uses: actions/checkout@v2
@@ -93,6 +95,10 @@ jobs:
             activate-environment: tardis
             use-mamba: true
 
+      - name: Download Lock File
+        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-${{ matrix.label }}.lock
+        if: matrix.pip == true
+
       - uses: actions/cache@v2
         with:
           path: ${{ matrix.prefix }}
@@ -102,12 +108,33 @@ jobs:
       - name: Update environment
         run: mamba update -n tardis --file conda-${{ matrix.label }}.lock
         if: steps.cache-conda.outputs.cache-hit != 'true'
-
-      - name: Install package
-        run: pip install -e .
+      
+      - name: Install package editable
+        run: | 
+          pip install -e .
+          echo "TARDIS_PIP_PATH=tardis" >> $GITHUB_ENV
+        if: matrix.pip == false
+
+      - name: Install package git
+        run: pip install git+https://github.com/tardis-sn/tardis.git@${{ github.ref }}
+        if: matrix.pip == true
+
+      - name: Set pip path
+        if: matrix.pip == true
+        run: |
+          location_line=$(pip show tardis | grep -i -x "Location:.*")
+          directory_path=$(echo $location_line | awk -F " " '{print $2}')
+          echo "TARDIS_PIP_PATH=$directory_path" >> $GITHUB_ENV
+      
+      - name: Set install path
+        if: matrix.pip == false
+        run: |
+          directory_path="."
+          echo "TARDIS_PIP_PATH=$directory_path" >> $GITHUB_ENV
 
       - name: Run tests
         run: pytest tardis ${{ env.PYTEST_FLAGS }}
+        working-directory: ${{ env.TARDIS_PIP_PATH }}
 
       - name: Upload to Codecov
         run: bash <(curl -s https://codecov.io/bash)
diff --git a/setup.cfg b/setup.cfg
index 33f668a2ecb..b22542f996b 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -26,14 +26,22 @@ docs =
     sphinx-astropy
 
 [options.package_data]
-tardis = data/*
-tardis.io = schemas/*.yml
-tardis.io.tests = data/*
+tardis = 
+    data/*
+tardis.grid = 
+    tests/data/*
+    ./*
+tardis.io = 
+    configuration/schemas/*
+    configuration/tests/data/*
+    model/readers/tests/data/*
 tardis.model.tests = data/*
 tardis.montecarlo.tests = data/*
 tardis.plasma.tests = data/*
 tardis.scripts = debug/*
 tardis.tests.integration_tests = **/* 
+tardis.visualization = 
+    tools/tests/data/*
 
 [tool:pytest]
 testpaths = "tardis" # "docs"

From 1503684c1594f3bfb893c39389c7069f5a40a9f5 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 19 Oct 2023 13:34:19 -0400
Subject: [PATCH 15/35] restructure of geometry (#2422)

* restructure of geometry

* add radial1d boundary logic

* black format

* several fixes

* fix epsilon

* add testing of boundaries

* change the r_inner_active

* first integration with `from_config` working

* hunting down density indexing bug

* all model tests (without csvy) pass

* more fixes

* fix of model to simulation_state

* fix inner boundary packet error

* fix some leftovers

* final fix for csvy

* blackify

* restructure to readers and remove some leftover code

* further cleanup

* first start of the restructure

* add comment about removing quantitiness

* add velocity check

* add new abundance functions

* remove default units
---
 tardis/io/model/model_reader.py               |  22 +-
 tardis/io/tests/test_model_reader.py          |  52 +--
 tardis/model/__init__.py                      |   2 +-
 tardis/model/base.py                          | 326 ++++--------------
 tardis/model/geometry/radial1d.py             | 132 ++++++-
 tardis/model/geometry/tests/test_radial1d.py  | 117 +++++++
 tardis/model/parse_input.py                   | 155 +++++++++
 tardis/model/tests/test_base.py               |  24 +-
 tardis/montecarlo/base.py                     |  28 +-
 .../montecarlo_numba/tests/test_base.py       |   1 +
 .../montecarlo_numba/tests/test_vpacket.py    |   6 +-
 tardis/montecarlo/packet_source.py            |   6 +-
 tardis/plasma/standard_plasmas.py             |  41 ++-
 tardis/simulation/tests/test_simulation.py    |   4 +
 .../visualization/tools/convergence_plot.py   |  10 +-
 15 files changed, 576 insertions(+), 350 deletions(-)
 create mode 100644 tardis/model/geometry/tests/test_radial1d.py
 create mode 100644 tardis/model/parse_input.py

diff --git a/tardis/io/model/model_reader.py b/tardis/io/model/model_reader.py
index 8a010ab6dc3..a1c9bd98f52 100644
--- a/tardis/io/model/model_reader.py
+++ b/tardis/io/model/model_reader.py
@@ -42,7 +42,7 @@ def transport_to_dict(transport):
         "input_energy": transport.input_energy,
         "input_mu": transport.input_mu,
         "input_nu": transport.input_nu,
-        "input_r_cgs": transport.input_r,
+        "input_r": transport.input_r,
         "j_blue_estimator": transport.j_blue_estimator,
         "j_estimator": transport.j_estimator,
         "last_interaction_in_nu": transport.last_interaction_in_nu,
@@ -296,23 +296,23 @@ def model_to_dict(model):
     isotope_abundance : dict
     """
     model_dict = {
-        "velocity_cgs": model.velocity,
+        "velocity_cgs": model.velocity.cgs,
         "abundance": model.abundance,
-        "time_explosion_cgs": model.time_explosion,
-        "t_inner_cgs": model.t_inner,
-        "t_radiative_cgs": model.t_radiative,
+        "time_explosion_cgs": model.time_explosion.cgs,
+        "t_inner_cgs": model.t_inner.cgs,
+        "t_radiative_cgs": model.t_radiative.cgs,
         "dilution_factor": model.dilution_factor,
-        "v_boundary_inner_cgs": model.v_boundary_inner,
-        "v_boundary_outer_cgs": model.v_boundary_outer,
+        "v_boundary_inner_cgs": model.v_boundary_inner.cgs,
+        "v_boundary_outer_cgs": model.v_boundary_outer.cgs,
         "w": model.w,
-        "t_rad_cgs": model.t_rad,
-        "r_inner_cgs": model.r_inner,
-        "density_cgs": model.density,
+        "t_rad_cgs": model.t_rad.cgs,
+        "r_inner_cgs": model.r_inner.cgs,
+        "density_cgs": model.density.cgs,
     }
 
     for key, value in model_dict.items():
         if hasattr(value, "unit"):
-            model_dict[key] = [value.cgs.value, value.unit.to_string()]
+            model_dict[key] = [value.cgs.value, value.cgs.unit.to_string()]
 
     isotope_abundance = model.raw_isotope_abundance.__dict__
 
diff --git a/tardis/io/tests/test_model_reader.py b/tardis/io/tests/test_model_reader.py
index 1d3196fe19e..8b283b71c1e 100644
--- a/tardis/io/tests/test_model_reader.py
+++ b/tardis/io/tests/test_model_reader.py
@@ -138,8 +138,10 @@ def test_model_to_dict(simulation_verysimple):
     model_dict, isotope_abundance = model_to_dict(model)
 
     # Check model dictionary
-    assert np.array_equal(model_dict["velocity_cgs"][0], model.velocity.value)
-    assert model_dict["velocity_cgs"][1] == model.velocity.unit.to_string()
+    assert np.array_equal(
+        model_dict["velocity_cgs"][0], model.velocity.cgs.value
+    )
+    assert model_dict["velocity_cgs"][1] == model.velocity.cgs.unit.to_string()
     assert np.array_equal(model_dict["abundance"], model.abundance)
     assert np.array_equal(
         model_dict["time_explosion_cgs"][0], model.time_explosion.value
@@ -148,36 +150,36 @@ def test_model_to_dict(simulation_verysimple):
         model_dict["time_explosion_cgs"][1]
         == model.time_explosion.unit.to_string()
     )
-    assert np.array_equal(model_dict["t_inner_cgs"][0], model.t_inner.value)
+    assert np.array_equal(model_dict["t_inner_cgs"][0], model.t_inner.cgs.value)
     assert model_dict["t_inner_cgs"][1] == model.t_inner.unit.to_string()
     assert np.array_equal(
-        model_dict["t_radiative_cgs"][0], model.t_radiative.value
+        model_dict["t_radiative_cgs"][0], model.t_radiative.cgs.value
     )
     assert (
         model_dict["t_radiative_cgs"][1] == model.t_radiative.unit.to_string()
     )
     assert np.array_equal(model_dict["dilution_factor"], model.dilution_factor)
     assert np.array_equal(
-        model_dict["v_boundary_inner_cgs"][0], model.v_boundary_inner.value
+        model_dict["v_boundary_inner_cgs"][0], model.v_boundary_inner.cgs.value
     )
     assert (
         model_dict["v_boundary_inner_cgs"][1]
-        == model.v_boundary_inner.unit.to_string()
+        == model.v_boundary_inner.cgs.unit.to_string()
     )
     assert np.array_equal(
-        model_dict["v_boundary_outer_cgs"][0], model.v_boundary_outer.value
+        model_dict["v_boundary_outer_cgs"][0], model.v_boundary_outer.cgs.value
     )
     assert (
         model_dict["v_boundary_outer_cgs"][1]
-        == model.v_boundary_outer.unit.to_string()
+        == model.v_boundary_outer.cgs.unit.to_string()
     )
     assert np.array_equal(model_dict["w"], model.w)
-    assert np.array_equal(model_dict["t_rad_cgs"][0], model.t_rad.value)
-    assert model_dict["t_rad_cgs"][1] == model.t_rad.unit.to_string()
-    assert np.array_equal(model_dict["r_inner_cgs"][0], model.r_inner.value)
-    assert model_dict["r_inner_cgs"][1] == model.r_inner.unit.to_string()
-    assert np.array_equal(model_dict["density_cgs"][0], model.density.value)
-    assert model_dict["density_cgs"][1] == model.density.unit.to_string()
+    assert np.array_equal(model_dict["t_rad_cgs"][0], model.t_rad.cgs.value)
+    assert model_dict["t_rad_cgs"][1] == model.t_rad.cgs.unit.to_string()
+    assert np.array_equal(model_dict["r_inner_cgs"][0], model.r_inner.cgs.value)
+    assert model_dict["r_inner_cgs"][1] == model.r_inner.cgs.unit.to_string()
+    assert np.array_equal(model_dict["density_cgs"][0], model.density.cgs.value)
+    assert model_dict["density_cgs"][1] == model.density.cgs.unit.to_string()
 
 
 def test_store_model_to_hdf(simulation_verysimple, tmp_path):
@@ -190,26 +192,26 @@ def test_store_model_to_hdf(simulation_verysimple, tmp_path):
 
     # Check file contents
     with h5py.File(fname) as f:
-        assert np.array_equal(f["model/velocity_cgs"], model.velocity.value)
+        assert np.array_equal(f["model/velocity_cgs"], model.velocity.cgs.value)
         assert np.array_equal(f["model/abundance"], model.abundance)
         assert np.array_equal(
-            f["model/time_explosion_cgs"], model.time_explosion.value
+            f["model/time_explosion_cgs"], model.time_explosion.cgs.value
         )
-        assert np.array_equal(f["model/t_inner_cgs"], model.t_inner.value)
+        assert np.array_equal(f["model/t_inner_cgs"], model.t_inner.cgs.value)
         assert np.array_equal(
-            f["model/t_radiative_cgs"], model.t_radiative.value
+            f["model/t_radiative_cgs"], model.t_radiative.cgs.value
         )
         assert np.array_equal(f["model/dilution_factor"], model.dilution_factor)
         assert np.array_equal(
-            f["model/v_boundary_inner_cgs"], model.v_boundary_inner.value
+            f["model/v_boundary_inner_cgs"], model.v_boundary_inner.cgs.value
         )
         assert np.array_equal(
-            f["model/v_boundary_outer_cgs"], model.v_boundary_outer.value
+            f["model/v_boundary_outer_cgs"], model.v_boundary_outer.cgs.value
         )
         assert np.array_equal(f["model/w"], model.w)
-        assert np.array_equal(f["model/t_rad_cgs"], model.t_rad.value)
-        assert np.array_equal(f["model/r_inner_cgs"], model.r_inner.value)
-        assert np.array_equal(f["model/density_cgs"], model.density.value)
+        assert np.array_equal(f["model/t_rad_cgs"], model.t_rad.cgs.value)
+        assert np.array_equal(f["model/r_inner_cgs"], model.r_inner.cgs.value)
+        assert np.array_equal(f["model/density_cgs"], model.density.cgs.value)
 
 
 def test_transport_to_dict(simulation_verysimple):
@@ -289,9 +291,7 @@ def test_store_transport_to_hdf(simulation_verysimple, tmp_path):
         assert np.array_equal(
             f["transport/input_nu"], transport_data["input_nu"]
         )
-        assert np.array_equal(
-            f["transport/input_r_cgs"], transport_data["input_r"].value
-        )
+        assert np.array_equal(f["transport/input_r"], transport_data["input_r"])
         assert np.array_equal(
             f["transport/j_blue_estimator"], transport_data["j_blue_estimator"]
         )
diff --git a/tardis/model/__init__.py b/tardis/model/__init__.py
index 3399f042e29..4b7881ad71e 100644
--- a/tardis/model/__init__.py
+++ b/tardis/model/__init__.py
@@ -6,4 +6,4 @@
 factor of the model used in the simulation.
 """
 
-from tardis.model.base import *
+from tardis.model.base import SimulationState
diff --git a/tardis/model/base.py b/tardis/model/base.py
index 65807a27589..fb58aacf9ce 100644
--- a/tardis/model/base.py
+++ b/tardis/model/base.py
@@ -8,30 +8,37 @@
 from tardis import constants
 import radioactivedecay as rd
 from radioactivedecay.utils import Z_DICT
-from tardis.io.model.readers.base import read_abundances_file, read_density_file
+from tardis.model.parse_input import (
+    parse_abundance_section,
+    parse_csvy_geometry,
+    parse_structure_config,
+)
+from tardis.util.base import is_valid_nuclide_or_elem
+
+
+from tardis.montecarlo.packet_source import BlackBodySimpleSource
+
+from tardis.radiation_field.base import MonteCarloRadiationFieldState
+
 from tardis.io.model.readers.generic_readers import (
     read_uniform_abundances,
 )
-from tardis.model.geometry.radial1d import Radial1DGeometry
 
-from tardis.util.base import quantity_linspace, is_valid_nuclide_or_elem
-from tardis.io.model.readers.csvy import load_csvy
 from tardis.io.model.readers.csvy import (
     parse_csv_abundances,
+    load_csvy,
 )
+
+
 from tardis.io.configuration.config_validator import validate_dict
 from tardis.io.configuration.config_reader import Configuration
 from tardis.io.util import HDFWriterMixin
 from tardis.io.decay import IsotopeAbundances
 
 from tardis.io.model.parse_density_configuration import (
-    parse_config_v1_density,
     parse_csvy_density,
     calculate_density_after_time,
 )
-from tardis.montecarlo.packet_source import BlackBodySimpleSource
-
-from tardis.radiation_field.base import MonteCarloRadiationFieldState
 
 logger = logging.getLogger(__name__)
 
@@ -119,11 +126,9 @@ def __init__(self, composition, geometry, time_explosion):
     def mass(self):
         """Mass calculated using the formula:
         mass_fraction * density * volume"""
-        return (
-            self.composition.elemental_mass_fraction
-            * self.composition.density
-            * self.geometry.volume
-        )
+
+        total_mass = (self.geometry.volume * self.composition.density).to(u.g)
+        return self.composition.elemental_mass_fraction * total_mass.value
 
     @property
     def number(self):
@@ -200,7 +205,7 @@ class SimulationState(HDFWriterMixin):
 
     def __init__(
         self,
-        velocity,
+        geometry,
         density,
         abundance,
         isotope_abundance,
@@ -210,26 +215,17 @@ def __init__(
         luminosity_requested=None,
         t_radiative=None,
         dilution_factor=None,
-        v_boundary_inner=None,
-        v_boundary_outer=None,
         electron_densities=None,
     ):
-        self._v_boundary_inner = None
-        self._v_boundary_outer = None
-        self._velocity = None
-        self.raw_velocity = velocity
-        self.v_boundary_inner = v_boundary_inner
-        self.v_boundary_outer = v_boundary_outer
+        self.geometry = geometry
+
         self._abundance = abundance
         self.time_explosion = time_explosion
         self._electron_densities = electron_densities
-        v_outer = self.velocity[1:]
-        v_inner = self.velocity[:-1]
-        if len(density) != len(self.velocity) - 1:
+
+        if len(density) != len(self.geometry.v_inner_active):
             density = density[
-                self.v_boundary_inner_index
-                + 1 : self.v_boundary_outer_index
-                + 1
+                self.geometry.v_inner_boundary_index : self.geometry.v_outer_boundary_index
             ]
 
         self.raw_abundance = self._abundance
@@ -275,12 +271,6 @@ def __init__(
             elemental_mass_fraction=self.abundance,
             atomic_mass=atomic_mass,
         )
-        geometry = Radial1DGeometry(
-            r_inner=self.time_explosion * v_inner,
-            r_outer=self.time_explosion * v_outer,
-            v_inner=v_inner,
-            v_outer=v_outer,
-        )
         self.model_state = ModelState(
             composition=composition,
             geometry=geometry,
@@ -308,12 +298,17 @@ def __init__(
             )
             t_radiative = constants.b_wien / (
                 lambda_wien_inner
-                * (1 + (self.v_middle - self.v_boundary_inner) / constants.c)
+                * (
+                    1
+                    + (self.v_middle - self.geometry.v_inner_boundary)
+                    / constants.c
+                )
             )
-        elif len(t_radiative) != self.no_of_shells:
+
+        elif len(t_radiative) == self.no_of_shells + 1:
             t_radiative = t_radiative[
-                self.v_boundary_inner_index
-                + 1 : self.v_boundary_outer_index
+                self.geometry.v_inner_boundary_index
+                + 1 : self.geometry.v_outer_boundary_index
                 + 1
             ]
         else:
@@ -328,9 +323,7 @@ def __init__(
             )
         elif len(dilution_factor) != self.no_of_shells:
             dilution_factor = dilution_factor[
-                self.v_boundary_inner_index
-                + 1 : self.v_boundary_outer_index
-                + 1
+                self.geometry.v_inner_boundary_index : self.geometry.v_outer_boundary_index
             ]
             assert len(dilution_factor) == self.no_of_shells
 
@@ -393,13 +386,21 @@ def t_radiative(self, value):
     def radius(self):
         return self.time_explosion * self.velocity
 
+    @property
+    def v_boundary_inner(self):
+        return self.geometry.v_inner_boundary
+
+    @property
+    def v_boundary_outer(self):
+        return self.geometry.v_outer_boundary
+
     @property
     def r_inner(self):
-        return self.model_state.geometry.r_inner
+        return self.model_state.geometry.r_inner_active
 
     @property
     def r_outer(self):
-        return self.model_state.geometry.r_outer
+        return self.model_state.geometry.r_outer_active
 
     @property
     def r_middle(self):
@@ -407,21 +408,16 @@ def r_middle(self):
 
     @property
     def velocity(self):
-        if self._velocity is None:
-            self._velocity = self.raw_velocity[
-                self.v_boundary_inner_index : self.v_boundary_outer_index + 1
-            ]
-            self._velocity[0] = self.v_boundary_inner
-            self._velocity[-1] = self.v_boundary_outer
-        return self._velocity
+        velocity = self.geometry.v_outer_active.copy()
+        return velocity.insert(0, self.geometry.v_inner_active[0])
 
     @property
     def v_inner(self):
-        return self.model_state.geometry.v_inner
+        return self.model_state.geometry.v_inner_active
 
     @property
     def v_outer(self):
-        return self.model_state.geometry.v_outer
+        return self.model_state.geometry.v_outer_active
 
     @property
     def v_middle(self):
@@ -437,8 +433,9 @@ def abundance(self):
             self._abundance = self.raw_isotope_abundance.decay(
                 self.time_explosion
             ).merge(self.raw_abundance)
-        abundance = self._abundance.loc[
-            :, self.v_boundary_inner_index : self.v_boundary_outer_index - 1
+        abundance = self._abundance.iloc[
+            :,
+            self.geometry.v_inner_boundary_index : self.geometry.v_outer_boundary_index,
         ]
         abundance.columns = range(len(abundance.columns))
         return abundance
@@ -449,94 +446,11 @@ def volume(self):
 
     @property
     def no_of_shells(self):
-        return len(self.velocity) - 1
+        return self.geometry.no_of_shells
 
     @property
     def no_of_raw_shells(self):
-        return len(self.raw_velocity) - 1
-
-    @property
-    def v_boundary_inner(self):
-        if self._v_boundary_inner is None:
-            return self.raw_velocity[0]
-        if self._v_boundary_inner < 0 * u.km / u.s:
-            return self.raw_velocity[0]
-        return self._v_boundary_inner
-
-    @v_boundary_inner.setter
-    def v_boundary_inner(self, value):
-        if value is not None:
-            if value > 0 * u.km / u.s:
-                value = u.Quantity(value, self.v_boundary_inner.unit)
-                if value > self.v_boundary_outer:
-                    raise ValueError(
-                        f"v_boundary_inner ({value}) must not be higher than "
-                        f"v_boundary_outer ({self.v_boundary_outer})."
-                    )
-                if value > self.raw_velocity[-1]:
-                    raise ValueError(
-                        f"v_boundary_inner ({value}) is outside of the model range ({self.raw_velocity[-1]})."
-                    )
-                if value < self.raw_velocity[0]:
-                    raise ValueError(
-                        f"v_boundary_inner ({value}) is lower than the lowest shell ({self.raw_velocity[0]}) in the model."
-                    )
-        self._v_boundary_inner = value
-        # Invalidate the cached cut-down velocity array
-        self._velocity = None
-
-    @property
-    def v_boundary_outer(self):
-        if self._v_boundary_outer is None:
-            return self.raw_velocity[-1]
-        if self._v_boundary_outer < 0 * u.km / u.s:
-            return self.raw_velocity[-1]
-        return self._v_boundary_outer
-
-    @v_boundary_outer.setter
-    def v_boundary_outer(self, value):
-        if value is not None:
-            if value > 0 * u.km / u.s:
-                value = u.Quantity(value, self.v_boundary_outer.unit)
-                if value < self.v_boundary_inner:
-                    raise ValueError(
-                        f"v_boundary_outer ({value}) must not be smaller than v_boundary_inner ({self.v_boundary_inner})."
-                    )
-                if value < self.raw_velocity[0]:
-                    raise ValueError(
-                        f"v_boundary_outer ({value}) is outside of the model range ({self.raw_velocity[0]})."
-                    )
-                if value > self.raw_velocity[-1]:
-                    raise ValueError(
-                        f"v_boundary_outer ({value}) is larger than the largest shell in the model ({self.raw_velocity[-1]})."
-                    )
-        self._v_boundary_outer = value
-        # Invalidate the cached cut-down velocity array
-        self._velocity = None
-
-    @property
-    def v_boundary_inner_index(self):
-        if self.v_boundary_inner in self.raw_velocity:
-            v_inner_ind = np.argwhere(
-                self.raw_velocity == self.v_boundary_inner
-            )[0][0]
-        else:
-            v_inner_ind = (
-                np.searchsorted(self.raw_velocity, self.v_boundary_inner) - 1
-            )
-        return v_inner_ind
-
-    @property
-    def v_boundary_outer_index(self):
-        if self.v_boundary_outer in self.raw_velocity:
-            v_outer_ind = np.argwhere(
-                self.raw_velocity == self.v_boundary_outer
-            )[0][0]
-        else:
-            v_outer_ind = np.searchsorted(
-                self.raw_velocity, self.v_boundary_outer
-            )
-        return v_outer_ind
+        return self.geometry.no_of_shells
 
     @classmethod
     def from_config(cls, config, atom_data=None):
@@ -554,50 +468,18 @@ def from_config(cls, config, atom_data=None):
         """
         time_explosion = config.supernova.time_explosion.cgs
 
-        structure = config.model.structure
-        electron_densities = None
-        temperature = None
-        if structure.type == "specific":
-            velocity = quantity_linspace(
-                structure.velocity.start,
-                structure.velocity.stop,
-                structure.velocity.num + 1,
-            ).cgs
-            density = parse_config_v1_density(config)
-
-        elif structure.type == "file":
-            if os.path.isabs(structure.filename):
-                structure_fname = structure.filename
-            else:
-                structure_fname = os.path.join(
-                    config.config_dirname, structure.filename
-                )
-
-            (
-                time_0,
-                velocity,
-                density_0,
-                electron_densities,
-                temperature,
-            ) = read_density_file(structure_fname, structure.filetype)
-            density_0 = density_0.insert(0, 0)
-
-            density = calculate_density_after_time(
-                density_0, time_0, time_explosion
-            )
-
-        else:
-            raise NotImplementedError
-
-        # Note: This is the number of shells *without* taking in mind the
-        #       v boundaries.
-        no_of_shells = len(velocity) - 1
+        (
+            electron_densities,
+            temperature,
+            geometry,
+            density,
+        ) = parse_structure_config(config, time_explosion)
 
         if temperature is not None:
             t_radiative = temperature
         elif config.plasma.initial_t_rad > 0 * u.K:
             t_radiative = (
-                np.ones(no_of_shells + 1) * config.plasma.initial_t_rad
+                np.ones(geometry.no_of_shells + 1) * config.plasma.initial_t_rad
             )
         else:
             t_radiative = None
@@ -611,46 +493,12 @@ def from_config(cls, config, atom_data=None):
             luminosity_requested = None
             t_inner = config.plasma.initial_t_inner
 
-        abundances_section = config.model.abundances
-        isotope_abundance = pd.DataFrame()
-
-        if abundances_section.type == "uniform":
-            abundance, isotope_abundance = read_uniform_abundances(
-                abundances_section, no_of_shells
-            )
-
-        elif abundances_section.type == "file":
-            if os.path.isabs(abundances_section.filename):
-                abundances_fname = abundances_section.filename
-            else:
-                abundances_fname = os.path.join(
-                    config.config_dirname, abundances_section.filename
-                )
-
-            index, abundance, isotope_abundance = read_abundances_file(
-                abundances_fname, abundances_section.filetype
-            )
-
-        abundance = abundance.replace(np.nan, 0.0)
-        abundance = abundance[abundance.sum(axis=1) > 0]
-
-        norm_factor = abundance.sum(axis=0) + isotope_abundance.sum(axis=0)
-
-        if np.any(np.abs(norm_factor - 1) > 1e-12):
-            logger.warning(
-                "Abundances have not been normalized to 1." " - normalizing"
-            )
-            abundance /= norm_factor
-            isotope_abundance /= norm_factor
-
-        isotope_abundance = IsotopeAbundances(isotope_abundance)
-
-        elemental_mass = None
-        if atom_data is not None:
-            elemental_mass = atom_data.atom_data.mass
+        isotope_abundance, abundance, elemental_mass = parse_abundance_section(
+            config, atom_data, geometry
+        )
 
         return cls(
-            velocity=velocity,
+            geometry=geometry,
             density=density,
             abundance=abundance,
             isotope_abundance=isotope_abundance,
@@ -660,8 +508,6 @@ def from_config(cls, config, atom_data=None):
             elemental_mass=elemental_mass,
             luminosity_requested=luminosity_requested,
             dilution_factor=None,
-            v_boundary_inner=structure.get("v_inner_boundary", None),
-            v_boundary_outer=structure.get("v_outer_boundary", None),
             electron_densities=electron_densities,
         )
 
@@ -733,35 +579,9 @@ def from_csvy(cls, config, atom_data=None):
         electron_densities = None
         temperature = None
 
-        if hasattr(config, "model"):
-            if hasattr(config.model, "v_inner_boundary"):
-                v_boundary_inner = config.model.v_inner_boundary
-            else:
-                v_boundary_inner = None
-
-            if hasattr(config.model, "v_outer_boundary"):
-                v_boundary_outer = config.model.v_outer_boundary
-            else:
-                v_boundary_outer = None
-        else:
-            v_boundary_inner = None
-            v_boundary_outer = None
-
-        if hasattr(csvy_model_config, "velocity"):
-            velocity = quantity_linspace(
-                csvy_model_config.velocity.start,
-                csvy_model_config.velocity.stop,
-                csvy_model_config.velocity.num + 1,
-            ).cgs
-        else:
-            velocity_field_index = [
-                field["name"] for field in csvy_model_config.datatype.fields
-            ].index("velocity")
-            velocity_unit = u.Unit(
-                csvy_model_config.datatype.fields[velocity_field_index]["unit"]
-            )
-            velocity = csvy_model_data["velocity"].values * velocity_unit
-            velocity = velocity.to("cm/s")
+        geometry = parse_csvy_geometry(
+            config, csvy_model_config, csvy_model_data, time_explosion
+        )
 
         if hasattr(csvy_model_config, "density"):
             density = parse_csvy_density(csvy_model_config, time_explosion)
@@ -780,7 +600,7 @@ def from_csvy(cls, config, atom_data=None):
                 density_0, time_0, time_explosion
             )
 
-        no_of_shells = len(velocity) - 1
+        no_of_shells = geometry.no_of_shells
 
         # TODO -- implement t_radiative
         # t_radiative = None
@@ -808,7 +628,9 @@ def from_csvy(cls, config, atom_data=None):
                 )
 
         elif config.plasma.initial_t_rad > 0 * u.K:
-            t_radiative = np.ones(no_of_shells) * config.plasma.initial_t_rad
+            t_radiative = (
+                np.ones(geometry.no_of_shells) * config.plasma.initial_t_rad
+            )
         else:
             t_radiative = None
 
@@ -822,7 +644,7 @@ def from_csvy(cls, config, atom_data=None):
         if hasattr(csvy_model_config, "abundance"):
             abundances_section = csvy_model_config.abundance
             abundance, isotope_abundance = read_uniform_abundances(
-                abundances_section, no_of_shells
+                abundances_section, geometry.no_of_shells
             )
         else:
             index, abundance, isotope_abundance = parse_csv_abundances(
@@ -857,7 +679,7 @@ def from_csvy(cls, config, atom_data=None):
             elemental_mass = atom_data.atom_data.mass
 
         return cls(
-            velocity=velocity,
+            geometry=geometry,
             density=density,
             abundance=abundance,
             isotope_abundance=isotope_abundance,
@@ -867,7 +689,5 @@ def from_csvy(cls, config, atom_data=None):
             elemental_mass=elemental_mass,
             luminosity_requested=luminosity_requested,
             dilution_factor=dilution_factor,
-            v_boundary_inner=v_boundary_inner,
-            v_boundary_outer=v_boundary_outer,
             electron_densities=electron_densities,
         )
diff --git a/tardis/model/geometry/radial1d.py b/tardis/model/geometry/radial1d.py
index db0a064884a..c870b817882 100644
--- a/tardis/model/geometry/radial1d.py
+++ b/tardis/model/geometry/radial1d.py
@@ -2,9 +2,10 @@
 from numba.experimental import jitclass
 import numpy as np
 from astropy import units as u
+import warnings
 
 
-class Radial1DGeometry:
+class HomologousRadial1DGeometry:
     """
     Holds information about model geometry for radial 1D models.
 
@@ -21,17 +22,132 @@ class Radial1DGeometry:
         Volume in each shell
     """
 
-    def __init__(self, r_inner, r_outer, v_inner, v_outer):
-        self.r_inner = r_inner
-        self.r_outer = r_outer
+    def __init__(
+        self,
+        v_inner,
+        v_outer,
+        v_inner_boundary,
+        v_outer_boundary,
+        time_explosion,
+    ):
+        self.time_explosion = time_explosion
+
+        # ensuring that the cells are continuous
+        assert np.allclose(v_inner[1:], v_outer[:-1])
+
+        assert "velocity" in v_inner.unit.physical_type
+        assert "velocity" in v_outer.unit.physical_type
+
         self.v_inner = v_inner
         self.v_outer = v_outer
 
+        # ensuring that the boundaries are within the simulation area
+
+        if v_inner_boundary is None:
+            self.v_inner_boundary = self.v_inner[0]
+        elif v_inner_boundary < 0:
+            warnings.warn(
+                "v_inner_boundary < 0, assuming default value",
+                DeprecationWarning,
+            )
+            self.v_inner_boundary = self.v_inner[0]
+        else:
+            self.v_inner_boundary = v_inner_boundary
+
+        if v_outer_boundary is None:
+            self.v_outer_boundary = self.v_outer[-1]
+        elif v_outer_boundary < 0:
+            warnings.warn(
+                "v_outer_boundary < 0, assuming default value",
+                DeprecationWarning,
+            )
+            self.v_outer_boundary = self.v_outer[-1]
+        else:
+            self.v_outer_boundary = v_outer_boundary
+
+        assert self.v_inner_boundary < self.v_outer_boundary
+        if self.v_inner_boundary < self.v_inner[0]:
+            warnings.warn(
+                "Requesting inner boundary below inner shell. Extrapolating the inner cell"
+            )
+
+        if self.v_outer_boundary > self.v_outer[-1]:
+            warnings.warn(
+                "Requesting inner boundary below inner shell. Extrapolating the inner cell"
+            )
+
+    @property
+    def v_inner_boundary_index(self):
+        return np.clip(
+            np.searchsorted(self.v_inner, self.v_inner_boundary, side="right")
+            - 1,
+            0,
+            None,
+        )
+
+    @property
+    def v_outer_boundary_index(self):
+        return np.clip(
+            np.searchsorted(self.v_outer, self.v_outer_boundary, side="left")
+            + 1,
+            None,
+            len(self.v_outer),
+        )
+
+    @property
+    def v_inner_active(self):
+        v_inner_active = self.v_inner[
+            self.v_inner_boundary_index : self.v_outer_boundary_index
+        ].copy()
+        v_inner_active[0] = self.v_inner_boundary
+        return v_inner_active
+
+    @property
+    def v_outer_active(self):
+        v_outer_active = self.v_outer[
+            self.v_inner_boundary_index : self.v_outer_boundary_index
+        ].copy()
+        v_outer_active[-1] = self.v_outer_boundary
+        return v_outer_active
+
+    @property
+    def r_inner(self):
+        return (self.v_inner * self.time_explosion).cgs
+
+    @property
+    def r_inner_active(self):
+        return (self.v_inner_active * self.time_explosion).cgs
+
+    @property
+    def r_outer(self):
+        return (self.v_outer * self.time_explosion).cgs
+
+    @property
+    def r_outer_active(self):
+        return (self.v_outer_active * self.time_explosion).cgs
+
     @property
     def volume(self):
         """Volume in shell computed from r_outer and r_inner"""
         return (4.0 / 3) * np.pi * (self.r_outer**3 - self.r_inner**3)
 
+    @property
+    def volume_active(self):
+        """Volume in shell computed from r_outer and r_inner"""
+        return (
+            (4.0 / 3)
+            * np.pi
+            * (self.r_outer_active**3 - self.r_inner_active**3)
+        )
+
+    @property
+    def no_of_shells(self):
+        return len(self.r_inner)
+
+    @property
+    def no_of_shells_active(self):
+        return len(self.r_inner_active)
+
     def to_numba(self):
         """
         Returns a new NumbaRadial1DGeometry object
@@ -42,10 +158,10 @@ def to_numba(self):
             Numba version of Radial1DGeometry with properties in cgs units
         """
         return NumbaRadial1DGeometry(
-            self.r_inner.to(u.cm).value,
-            self.r_outer.to(u.cm).value,
-            self.v_inner.to(u.cm / u.s).value,
-            self.v_outer.to(u.cm / u.s).value,
+            self.r_inner_active.to(u.cm).value,
+            self.r_outer_active.to(u.cm).value,
+            self.v_inner_active.to(u.cm / u.s).value,
+            self.v_outer_active.to(u.cm / u.s).value,
         )
 
 
diff --git a/tardis/model/geometry/tests/test_radial1d.py b/tardis/model/geometry/tests/test_radial1d.py
new file mode 100644
index 00000000000..e6c887180d0
--- /dev/null
+++ b/tardis/model/geometry/tests/test_radial1d.py
@@ -0,0 +1,117 @@
+from astropy import units as u
+import numpy as np
+import numpy.testing as npt
+
+from tardis.model.geometry.radial1d import HomologousRadial1DGeometry
+
+import pytest
+
+
+@pytest.fixture(scope="function")
+def homologous_radial1d_geometry():
+    velocity = np.arange(8000, 21000, 1000) * u.km / u.s
+    v_inner = velocity[:-1]
+    v_outer = velocity[1:]
+    time_explosion = 5 * u.day
+    geometry = HomologousRadial1DGeometry(
+        v_inner, v_outer, v_inner[0], v_outer[-1], time_explosion
+    )
+    return geometry
+
+
+def test_vb_indices(homologous_radial1d_geometry):
+    # Testing if the indices returned are correct when inner and outer
+    # boundary are on the innermost and outermost shell
+
+    homologous_radial1d_geometry.v_inner_boundary = (
+        homologous_radial1d_geometry.v_inner[0]
+    )
+    homologous_radial1d_geometry.v_outer_boundary = (
+        homologous_radial1d_geometry.v_outer[-1]
+    )
+    assert homologous_radial1d_geometry.v_inner_boundary_index == 0
+    assert homologous_radial1d_geometry.v_outer_boundary_index == len(
+        homologous_radial1d_geometry.v_inner
+    )
+    vib_index = homologous_radial1d_geometry.v_inner_boundary_index
+    vob_index = homologous_radial1d_geometry.v_outer_boundary_index
+    assert np.all(
+        homologous_radial1d_geometry.v_inner[vib_index:vob_index]
+        == homologous_radial1d_geometry.v_inner
+    )
+    EPSILON_VELOCITY_SHIFT = 1 * u.km / u.s
+    # pivoting around the inner boundary of the simulation
+
+    homologous_radial1d_geometry.v_inner_boundary = (
+        homologous_radial1d_geometry.v_inner[0] + EPSILON_VELOCITY_SHIFT
+    )
+    assert homologous_radial1d_geometry.v_inner_boundary_index == 0
+    homologous_radial1d_geometry.v_inner_boundary = (
+        homologous_radial1d_geometry.v_inner[0] - EPSILON_VELOCITY_SHIFT
+    )
+    assert homologous_radial1d_geometry.v_inner_boundary_index == 0
+
+    # pivoting around the first shell boundary of the simulation
+    homologous_radial1d_geometry.v_inner_boundary = (
+        homologous_radial1d_geometry.v_inner[1] - EPSILON_VELOCITY_SHIFT
+    )
+    assert homologous_radial1d_geometry.v_inner_boundary_index == 0
+    homologous_radial1d_geometry.v_inner_boundary = (
+        homologous_radial1d_geometry.v_inner[1] + EPSILON_VELOCITY_SHIFT
+    )
+    assert homologous_radial1d_geometry.v_inner_boundary_index == 1
+
+    # pivoting around the outer boundary of the simulation
+    homologous_radial1d_geometry.v_outer_boundary = (
+        homologous_radial1d_geometry.v_outer[-1] + EPSILON_VELOCITY_SHIFT
+    )
+    assert homologous_radial1d_geometry.v_outer_boundary_index == 12
+    homologous_radial1d_geometry.v_outer_boundary = (
+        homologous_radial1d_geometry.v_outer[-1] - EPSILON_VELOCITY_SHIFT
+    )
+    assert homologous_radial1d_geometry.v_outer_boundary_index == 12
+
+    # pivoting around the second to outer boundary of the simulation
+    homologous_radial1d_geometry.v_outer_boundary = (
+        homologous_radial1d_geometry.v_outer[-2] + EPSILON_VELOCITY_SHIFT
+    )
+    assert homologous_radial1d_geometry.v_outer_boundary_index == 12
+    homologous_radial1d_geometry.v_outer_boundary = (
+        homologous_radial1d_geometry.v_outer[-2] - EPSILON_VELOCITY_SHIFT
+    )
+    assert homologous_radial1d_geometry.v_outer_boundary_index == 11
+
+
+def test_velocity_boundary(homologous_radial1d_geometry):
+    # testing the active cell boundaries when setting the boundaries
+
+    homologous_radial1d_geometry.v_inner_boundary = 7999 * u.km / u.s
+    npt.assert_almost_equal(
+        homologous_radial1d_geometry.v_inner_active[0].value, 7999
+    )
+    assert len(homologous_radial1d_geometry.v_inner_active) == len(
+        homologous_radial1d_geometry.v_inner
+    )
+
+    homologous_radial1d_geometry.v_inner_boundary = 8001 * u.km / u.s
+    npt.assert_almost_equal(
+        homologous_radial1d_geometry.v_inner_active[0].value, 8001
+    )
+    assert len(homologous_radial1d_geometry.v_inner_active) == len(
+        homologous_radial1d_geometry.v_inner
+    )
+
+    homologous_radial1d_geometry.v_inner_boundary = 9001 * u.km / u.s
+    npt.assert_almost_equal(
+        homologous_radial1d_geometry.v_inner_active[0].value, 9001
+    )
+    assert len(homologous_radial1d_geometry.v_inner_active) == (
+        len(homologous_radial1d_geometry.v_inner) - 1
+    )
+    homologous_radial1d_geometry.v_inner_boundary = 9000 * u.km / u.s
+    npt.assert_almost_equal(
+        homologous_radial1d_geometry.v_inner_active[0].value, 9000
+    )
+    assert len(homologous_radial1d_geometry.v_inner_active) == (
+        len(homologous_radial1d_geometry.v_inner) - 1
+    )
diff --git a/tardis/model/parse_input.py b/tardis/model/parse_input.py
new file mode 100644
index 00000000000..7d3f93bf0e1
--- /dev/null
+++ b/tardis/model/parse_input.py
@@ -0,0 +1,155 @@
+import logging
+import os
+
+from astropy import units as u
+from tardis.io.decay import IsotopeAbundances
+import numpy as np
+import pandas as pd
+from tardis.io.model.parse_density_configuration import (
+    calculate_density_after_time,
+    parse_config_v1_density,
+)
+from tardis.io.model.readers.base import read_abundances_file, read_density_file
+from tardis.io.model.readers.generic_readers import read_uniform_abundances
+from tardis.model.geometry.radial1d import HomologousRadial1DGeometry
+from tardis.util.base import quantity_linspace
+
+logger = logging.getLogger(__name__)
+
+
+def parse_structure_config(config, time_explosion, enable_homology=True):
+    electron_densities = None
+    temperature = None
+    structure_config = config.model.structure
+    if structure_config.type == "specific":
+        velocity = quantity_linspace(
+            structure_config.velocity.start,
+            structure_config.velocity.stop,
+            structure_config.velocity.num + 1,
+        ).cgs
+        density = parse_config_v1_density(config)
+
+    elif structure_config.type == "file":
+        if os.path.isabs(structure_config.filename):
+            structure_config_fname = structure_config.filename
+        else:
+            structure_config_fname = os.path.join(
+                config.config_dirname, structure_config.filename
+            )
+
+        (
+            time_0,
+            velocity,
+            density_0,
+            electron_densities,
+            temperature,
+        ) = read_density_file(structure_config_fname, structure_config.filetype)
+        density_0 = density_0.insert(0, 0)
+
+        density = calculate_density_after_time(
+            density_0, time_0, time_explosion
+        )
+
+    else:
+        raise NotImplementedError
+
+    # Note: This is the number of shells *without* taking in mind the
+    #       v boundaries.
+    if len(density) == len(velocity):
+        logger.warning(
+            "Number of density points larger than number of shells. Assuming inner point irrelevant"
+        )
+        density = density[1:]
+    geometry = HomologousRadial1DGeometry(
+        velocity[:-1],  # r_inner
+        velocity[1:],  # r_outer
+        v_inner_boundary=structure_config.get("v_inner_boundary", None),
+        v_outer_boundary=structure_config.get("v_outer_boundary", None),
+        time_explosion=time_explosion,
+    )
+    return electron_densities, temperature, geometry, density
+
+
+def parse_csvy_geometry(
+    config, csvy_model_config, csvy_model_data, time_explosion
+):
+    if hasattr(config, "model"):
+        if hasattr(config.model, "v_inner_boundary"):
+            v_boundary_inner = config.model.v_inner_boundary
+        else:
+            v_boundary_inner = None
+
+        if hasattr(config.model, "v_outer_boundary"):
+            v_boundary_outer = config.model.v_outer_boundary
+        else:
+            v_boundary_outer = None
+    else:
+        v_boundary_inner = None
+        v_boundary_outer = None
+
+    if hasattr(csvy_model_config, "velocity"):
+        velocity = quantity_linspace(
+            csvy_model_config.velocity.start,
+            csvy_model_config.velocity.stop,
+            csvy_model_config.velocity.num + 1,
+        ).cgs
+    else:
+        velocity_field_index = [
+            field["name"] for field in csvy_model_config.datatype.fields
+        ].index("velocity")
+        velocity_unit = u.Unit(
+            csvy_model_config.datatype.fields[velocity_field_index]["unit"]
+        )
+        velocity = csvy_model_data["velocity"].values * velocity_unit
+        velocity = velocity.to("cm/s")
+
+    geometry = HomologousRadial1DGeometry(
+        velocity[:-1],  # r_inner
+        velocity[1:],  # r_outer
+        v_inner_boundary=v_boundary_inner,
+        v_outer_boundary=v_boundary_outer,
+        time_explosion=time_explosion,
+    )
+    return geometry
+
+
+def parse_abundance_section(config, atom_data, geometry):
+    abundances_section = config.model.abundances
+    isotope_abundance = pd.DataFrame()
+
+    if abundances_section.type == "uniform":
+        abundance, isotope_abundance = read_uniform_abundances(
+            abundances_section, geometry.no_of_shells
+        )
+
+    elif abundances_section.type == "file":
+        if os.path.isabs(abundances_section.filename):
+            abundances_fname = abundances_section.filename
+        else:
+            abundances_fname = os.path.join(
+                config.config_dirname, abundances_section.filename
+            )
+
+        index, abundance, isotope_abundance = read_abundances_file(
+            abundances_fname, abundances_section.filetype
+        )
+
+    abundance = abundance.replace(np.nan, 0.0)
+    abundance = abundance[abundance.sum(axis=1) > 0]
+
+    norm_factor = abundance.sum(axis=0) + isotope_abundance.sum(axis=0)
+
+    if np.any(np.abs(norm_factor - 1) > 1e-12):
+        logger.warning(
+            "Abundances have not been normalized to 1." " - normalizing"
+        )
+        abundance /= norm_factor
+        isotope_abundance /= norm_factor
+
+    isotope_abundance = IsotopeAbundances(isotope_abundance)
+
+    elemental_mass = None
+    if atom_data is not None:
+        elemental_mass = atom_data.atom_data.mass
+
+    return isotope_abundance, abundance, elemental_mass
diff --git a/tardis/model/tests/test_base.py b/tardis/model/tests/test_base.py
index f86fd982204..44f6c4393a3 100644
--- a/tardis/model/tests/test_base.py
+++ b/tardis/model/tests/test_base.py
@@ -59,8 +59,9 @@ def setup(self, example_model_file_dir):
         self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
-        assert_almost_equal(self.simulation_state.v_inner[0].value, 1e4 * 1e5)
+        assert_almost_equal(
+            self.simulation_state.v_inner.to(u.cm / u.s).value[0], 1e4 * 1e5
+        )
 
     def test_abundances(self):
         oxygen_abundance = self.config.model.abundances.O
@@ -78,9 +79,9 @@ def setup(self, example_model_file_dir):
         self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
         assert_almost_equal(
-            self.simulation_state.v_inner[0].value, 1.259375e03 * 1e5
+            self.simulation_state.v_inner[0].to(u.cm / u.s).value,
+            1.259375e03 * 1e5,
         )
 
     def test_abundances(self):
@@ -102,9 +103,9 @@ def setup(self, example_model_file_dir):
         self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
         assert_almost_equal(
-            self.simulation_state.v_inner[0].value, 1.259375e03 * 1e5
+            self.simulation_state.v_inner[0].to(u.cm / u.s).value,
+            1.259375e03 * 1e5,
         )
 
     def test_abundances(self):
@@ -116,7 +117,6 @@ def test_abundances(self):
 class TestModelFromArtisDensityAbundancesVSlice:
     @pytest.fixture(autouse=True)
     def setup(self, example_model_file_dir):
-
         self.config = Configuration.from_yaml(
             example_model_file_dir / "tardis_configv1_artis_density_v_slice.yml"
         )
@@ -126,7 +126,6 @@ def setup(self, example_model_file_dir):
         self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
         assert_almost_equal(
             self.simulation_state.v_inner[0].to(u.km / u.s).value, 9000
         )
@@ -175,7 +174,9 @@ def setup(self, example_model_file_dir):
         self.simulation_state = SimulationState.from_config(self.config)
 
     def test_velocities(self):
-        assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
+        # unclear why we are testing this
+        # assert self.simulation_state.v_inner.unit == u.Unit("cm/s")
+        assert hasattr(self.simulation_state.v_inner, "unit")
         assert_almost_equal(
             self.simulation_state.v_inner[0].to(u.km / u.s).value, 11000
         )
@@ -357,8 +358,9 @@ def test_radial_1D_geometry_volume(simulation_verysimple, index, expected):
     geometry = simulation_verysimple.simulation_state.model_state.geometry
     volume = geometry.volume
 
-    assert volume.unit == u.Unit("cm3")
-    assert_almost_equal(volume[index].value, expected, decimal=-40)
+    assert_almost_equal(
+        volume[index].to(u.cm**3).value, expected, decimal=-40
+    )
 
 
 @pytest.mark.parametrize(
diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index ba65fb0e8ca..32fdc6fa88d 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -185,7 +185,7 @@ def _initialize_continuum_estimator_arrays(self, gamma_shape):
             gamma_shape, dtype=np.int64
         )
 
-    def _initialize_geometry_arrays(self, model):
+    def _initialize_geometry_arrays(self, simulation_state):
         """
         Generate the cgs like geometry arrays for the montecarlo part
 
@@ -193,10 +193,10 @@ def _initialize_geometry_arrays(self, model):
         ----------
         model : model.SimulationState
         """
-        self.r_inner_cgs = model.r_inner.to("cm").value
-        self.r_outer_cgs = model.r_outer.to("cm").value
-        self.v_inner_cgs = model.v_inner.to("cm/s").value
-        self.v_outer_cgs = model.v_outer.to("cm/s").value
+        self.r_inner_cgs = simulation_state.r_inner.to("cm").value
+        self.r_outer_cgs = simulation_state.r_outer.to("cm").value
+        self.v_inner_cgs = simulation_state.v_inner.to("cm/s").value
+        self.v_outer_cgs = simulation_state.v_outer.to("cm/s").value
 
     def _initialize_packets(self, model, no_of_packets, iteration):
         # the iteration (passed as seed_offset) is added each time to preserve randomness
@@ -214,7 +214,7 @@ def _initialize_packets(self, model, no_of_packets, iteration):
             no_of_packets
         )
 
-        self.input_r = radii
+        self.input_r = radii.to(u.cm).value
         self.input_nu = nus
         self.input_mu = mus
         self.input_energy = energies
@@ -296,7 +296,7 @@ def integrator(self):
 
     def run(
         self,
-        model,
+        simulation_state,
         plasma,
         no_of_packets,
         no_of_virtual_packets=0,
@@ -323,8 +323,10 @@ def run(
 
         set_num_threads(self.nthreads)
 
-        self.time_of_simulation = self.calculate_time_of_simulation(model)
-        self.volume = model.volume
+        self.time_of_simulation = self.calculate_time_of_simulation(
+            simulation_state
+        )
+        self.volume = simulation_state.volume
 
         # Initializing estimator array
         self._initialize_estimator_arrays(plasma.tau_sobolevs.shape)
@@ -336,17 +338,17 @@ def run(
 
         self._initialize_continuum_estimator_arrays(gamma_shape)
 
-        self._initialize_geometry_arrays(model)
+        self._initialize_geometry_arrays(simulation_state)
 
         self._initialize_packets(
-            model,
+            simulation_state,
             no_of_packets,
             iteration,
         )
 
         configuration_initialize(self, no_of_virtual_packets)
         montecarlo_radial1d(
-            model,
+            simulation_state,
             plasma,
             iteration,
             no_of_packets,
@@ -354,7 +356,7 @@ def run(
             show_progress_bars,
             self,
         )
-        self._integrator = FormalIntegrator(model, plasma, self)
+        self._integrator = FormalIntegrator(simulation_state, plasma, self)
 
     def legacy_return(self):
         return (
diff --git a/tardis/montecarlo/montecarlo_numba/tests/test_base.py b/tardis/montecarlo/montecarlo_numba/tests/test_base.py
index 4e069fee394..cf10aa19bd2 100644
--- a/tardis/montecarlo/montecarlo_numba/tests/test_base.py
+++ b/tardis/montecarlo/montecarlo_numba/tests/test_base.py
@@ -33,6 +33,7 @@ def test_montecarlo_main_loop(
     config_montecarlo_1e5_verysimple.montecarlo.no_of_virtual_packets = 0
     config_montecarlo_1e5_verysimple.montecarlo.iterations = 1
     config_montecarlo_1e5_verysimple.plasma.line_interaction_type = "macroatom"
+
     del config_montecarlo_1e5_verysimple["config_dirname"]
 
     sim = Simulation.from_config(
diff --git a/tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py b/tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py
index 21ad8647d40..6e156982820 100644
--- a/tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py
+++ b/tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py
@@ -66,7 +66,8 @@ def test_trace_vpacket_within_shell(
     )
 
     npt.assert_almost_equal(tau_trace_combined, 8164850.891288479)
-    npt.assert_almost_equal(distance_boundary, 843684056256104.1)
+    # changed from almost equal to allclose. Now seems to work.
+    npt.assert_allclose(distance_boundary, 843684056256104.1)
     assert delta_shell == 1
 
 
@@ -92,7 +93,8 @@ def test_trace_vpacket(
     )
 
     npt.assert_almost_equal(tau_trace_combined, 8164850.891288479)
-    npt.assert_almost_equal(v_packet.r, 1286064000000000.0)
+    # change from almost_equal to allclose. Now seems to work.
+    npt.assert_allclose(v_packet.r, 1286064000000000.0)
     npt.assert_almost_equal(v_packet.nu, 4.0e15)
     npt.assert_almost_equal(v_packet.energy, 0.0)
     npt.assert_almost_equal(v_packet.mu, 0.8309726858508629)
diff --git a/tardis/montecarlo/packet_source.py b/tardis/montecarlo/packet_source.py
index 095fca194c4..f6a069dac0e 100644
--- a/tardis/montecarlo/packet_source.py
+++ b/tardis/montecarlo/packet_source.py
@@ -123,12 +123,12 @@ def __init__(self, radius=None, temperature=None, **kwargs):
         self.temperature = temperature
         super().__init__(**kwargs)
 
-    def set_state_from_model(self, model):
+    def set_state_from_model(self, simulation_state):
         """
         Set state of packet source (correct state should be ensured before creating packets)
         """
-        self.radius = model.r_inner[0]
-        self.temperature = model.t_inner.value
+        self.radius = simulation_state.r_inner[0]
+        self.temperature = simulation_state.t_inner.value
 
     def create_packets(self, no_of_packets, *args, **kwargs):
         if self.radius is None or self.temperature is None:
diff --git a/tardis/plasma/standard_plasmas.py b/tardis/plasma/standard_plasmas.py
index 5cf21d431bd..63c6ac2324e 100644
--- a/tardis/plasma/standard_plasmas.py
+++ b/tardis/plasma/standard_plasmas.py
@@ -1,3 +1,4 @@
+from astropy import units as u
 import os
 import logging
 
@@ -49,7 +50,7 @@
 logger = logging.getLogger(__name__)
 
 
-def assemble_plasma(config, model, atom_data=None):
+def assemble_plasma(config, simulation_state, atom_data=None):
     """
     Create a BasePlasma instance from a Configuration object
     and a SimulationState.
@@ -106,7 +107,7 @@ def assemble_plasma(config, model, atom_data=None):
             raise
 
     atom_data.prepare_atom_data(
-        model.abundance.index,
+        simulation_state.abundance.index,
         line_interaction_type=config.plasma.line_interaction_type,
         nlte_species=nlte_species,
     )
@@ -135,12 +136,12 @@ def assemble_plasma(config, model, atom_data=None):
     ]
 
     kwargs = dict(
-        t_rad=model.t_radiative,
-        abundance=model.abundance,
-        density=model.density,
+        t_rad=simulation_state.t_radiative,
+        abundance=simulation_state.abundance,
+        density=simulation_state.density,
         atomic_data=atom_data,
-        time_explosion=model.time_explosion,
-        w=model.dilution_factor,
+        time_explosion=simulation_state.time_explosion,
+        w=simulation_state.dilution_factor,
         link_t_rad_t_electron=config.plasma.link_t_rad_t_electron,
         continuum_interaction_species=continuum_interaction_species,
         nlte_ionization_species=nlte_ionization_species,
@@ -213,9 +214,9 @@ def assemble_plasma(config, model, atom_data=None):
             bf_heating_coeff_estimator=None,
             stim_recomb_cooling_coeff_estimator=None,
             alpha_stim_estimator=None,
-            volume=model.volume,
-            r_inner=model.r_inner,
-            t_inner=model.t_inner,
+            volume=simulation_state.volume,
+            r_inner=simulation_state.r_inner.to(u.cm),
+            t_inner=simulation_state.t_inner,
         )
     if config.plasma.radiative_rates_type == "blackbody":
         plasma_modules.append(JBluesBlackBody)
@@ -224,9 +225,9 @@ def assemble_plasma(config, model, atom_data=None):
     elif config.plasma.radiative_rates_type == "detailed":
         plasma_modules += detailed_j_blues_properties + detailed_j_blues_inputs
         kwargs.update(
-            r_inner=model.r_inner,
-            t_inner=model.t_inner,
-            volume=model.volume,
+            r_inner=simulation_state.r_inner.to(u.cm),
+            t_inner=simulation_state.t_inner,
+            volume=simulation_state.volume,
             j_blue_estimator=None,
         )
         property_kwargs[JBluesDetailed] = {"w_epsilon": config.plasma.w_epsilon}
@@ -278,8 +279,10 @@ def assemble_plasma(config, model, atom_data=None):
     else:
         plasma_modules += helium_lte_properties
 
-    if model._electron_densities is not None:
-        electron_densities = pd.Series(model._electron_densities.cgs.value)
+    if simulation_state._electron_densities is not None:
+        electron_densities = pd.Series(
+            simulation_state._electron_densities.cgs.value
+        )
         if config.plasma.helium_treatment == "numerical-nlte":
             property_kwargs[IonNumberDensityHeNLTE] = dict(
                 electron_densities=electron_densities
@@ -289,10 +292,12 @@ def assemble_plasma(config, model, atom_data=None):
                 electron_densities=electron_densities
             )
 
-    if not model.raw_isotope_abundance.empty:
+    if not simulation_state.raw_isotope_abundance.empty:
         plasma_modules += isotope_properties
-        isotope_abundance = model.raw_isotope_abundance.loc[
-            :, model.v_boundary_inner_index : model.v_boundary_outer_index - 1
+        isotope_abundance = simulation_state.raw_isotope_abundance.loc[
+            :,
+            simulation_state.geometry.v_inner_boundary_index : simulation_state.geometry.v_outer_boundary_index
+            - 1,
         ]
         kwargs.update(isotope_abundance=isotope_abundance)
 
diff --git a/tardis/simulation/tests/test_simulation.py b/tardis/simulation/tests/test_simulation.py
index d4f68ff3cc5..258787c612f 100644
--- a/tardis/simulation/tests/test_simulation.py
+++ b/tardis/simulation/tests/test_simulation.py
@@ -112,6 +112,10 @@ def test_plasma_estimates(simulation_one_loop, refdata, name):
 def test_plasma_state_iterations(simulation_one_loop, refdata, name):
     actual = getattr(simulation_one_loop, name)
 
+    # removing the quantitiness of the data as it will screw up the comparison via pandas
+    if hasattr(actual, "value"):
+        actual = actual.value
+
     try:
         actual = pd.Series(actual)
     except Exception:
diff --git a/tardis/visualization/tools/convergence_plot.py b/tardis/visualization/tools/convergence_plot.py
index 5417b85e2a8..16e588f5e76 100644
--- a/tardis/visualization/tools/convergence_plot.py
+++ b/tardis/visualization/tools/convergence_plot.py
@@ -310,10 +310,12 @@ def build(self, display_plot=True):
     def update_plasma_plots(self):
         """Update plasma convergence plots every iteration."""
         # convert velocity to km/s
-        x = self.iterable_data["velocity"].to(u.km / u.s).value.tolist()
+        velocity_km_s = (
+            self.iterable_data["velocity"].to(u.km / u.s).value.tolist()
+        )
 
         # add luminosity data in hover data in plasma plots
-        customdata = len(x) * [
+        customdata = len(velocity_km_s) * [
             "<br>"
             + "Emitted Luminosity: "
             + f'{self.value_data["Emitted"][-1]:.4g}'
@@ -327,7 +329,7 @@ def update_plasma_plots(self):
 
         # add a radiation temperature vs shell velocity trace to the plasma plot
         self.plasma_plot.add_scatter(
-            x=x,
+            x=velocity_km_s,
             y=self.iterable_data["t_rad"],
             line_color=self.plasma_colorscale[self.current_iteration - 1],
             row=1,
@@ -341,7 +343,7 @@ def update_plasma_plots(self):
 
         # add a dilution factor vs shell velocity trace to the plasma plot
         self.plasma_plot.add_scatter(
-            x=x,
+            x=velocity_km_s,
             y=self.iterable_data["w"],
             line_color=self.plasma_colorscale[self.current_iteration - 1],
             row=1,

From d32f3230b611e79a41dac2850626a1e3fd036b8c Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Fri, 20 Oct 2023 04:05:03 +0200
Subject: [PATCH 16/35] Add FAQ section to documentation (#2450)

* Add faq

* Added Overview

* Fix typo
---
 docs/faq.rst   | 39 +++++++++++++++++++++++++++++++++++++++
 docs/index.rst |  1 +
 2 files changed, 40 insertions(+)
 create mode 100644 docs/faq.rst

diff --git a/docs/faq.rst b/docs/faq.rst
new file mode 100644
index 00000000000..de5f9e737cc
--- /dev/null
+++ b/docs/faq.rst
@@ -0,0 +1,39 @@
+.. _installation:
+
+**************************
+Frequently Asked Questions
+**************************
+
+Overview
+--------
+
+Welcome to the FAQ section! Here, you'll find answers to common questions about TARDIS.
+
+- :ref:`faq-usage`
+
+     - :ref:`faq-usage-memory`
+
+
+.. _faq-usage:
+
+Usage
+-----
+
+.. _faq-usage-memory:
+
+My simulation seems to consume excessive amounts of memory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+High memory usage can have many reasons. Both your model
+and certain simulation settings can increase the memory
+usage significantly
+
+1. Enabling ``track_rpacket: true`` will take up substantial
+   amounts of memory, in particular for higher packet counts.
+   Consider turning this feature off or only use it with a
+   small amount of packets.
+2. Both the number of shells and the number of packets
+   increase the memory requirements. Consider using only
+   as many shells/ packets as are required to converge
+   on a result.
diff --git a/docs/index.rst b/docs/index.rst
index 08d84b4a09d..67a202eff2b 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -59,6 +59,7 @@ Mission Statement
     installation
     quickstart
     tutorials
+    faq
     API <api/modules>
 
 

From 4b7d92faae763e2b4a62db1cfba56637f96ebc62 Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Fri, 20 Oct 2023 17:53:32 +0530
Subject: [PATCH 17/35] Remove lock file creation from pre release workflow
 (#2432)

* Install latest version of mamba

* Unpin conda lock installatiion

* Split lockfilee creation to separate workflow

* change docs installation- put a warning for conda forge installation and comment out install from package

* fix

* delete create lockfiles

* download llock file
---
 .github/workflows/pre-release.yml | 40 ++++---------------------------
 docs/installation.rst             | 24 +++++++++++++------
 2 files changed, 22 insertions(+), 42 deletions(-)

diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
index b79a2eed2b3..600076e9994 100644
--- a/.github/workflows/pre-release.yml
+++ b/.github/workflows/pre-release.yml
@@ -15,36 +15,6 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  lock:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Setup environment
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-            miniforge-variant: Mambaforge
-            miniforge-version: latest
-            auto-activate-base: true
-            activate-environment: ""
-            use-mamba: true
-
-      - name: Install conda-lock
-        run: mamba install -c conda-forge conda-lock=1.0.5
-
-      - name: Generate lockfiles
-        run: |
-          conda-lock -f tardis_env3.yml -p linux-64 -p osx-64
-          conda lock render conda-lock.yml
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: lockfiles
-          path: |
-              conda-linux-64.lock
-              conda-osx-64.lock
-              conda-lock.yml
-
   zenodo:
     runs-on: ubuntu-latest
     steps:
@@ -58,6 +28,9 @@ jobs:
         env:
           KEY_SECRET_JSON: ${{ secrets.ZENODO_KEY_SECRET_JSON }}
 
+      - name: Download Lock File
+        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
+        
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -80,7 +53,7 @@ jobs:
           path: .zenodo.json
 
   pull_request:
-    needs: [lock, zenodo]
+    needs: zenodo
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -89,11 +62,8 @@ jobs:
         with:
           path: /tmp
 
-      - name: Copy files to repository
+      - name: Copy zenodo.json to repository
         run: |
-          cp /tmp/lockfiles/conda-linux-64.lock .
-          cp /tmp/lockfiles/conda-osx-64.lock .
-          cp /tmp/lockfiles/conda-lock.yml .
           cp /tmp/zenodo_json/.zenodo.json .
 
       - name: Get current date
diff --git a/docs/installation.rst b/docs/installation.rst
index ed998c3c067..8c2c54a956b 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -41,6 +41,16 @@ this method by following the steps described below.
 
 3. a. Non-developers can install the latest release from ``conda-forge`` with the ``--no-deps`` flag,
 
+      .. warning::
+
+        Currently the conda forge installation doesn't work. It's recommended to install from the specific releases using pip-
+        
+        `$ pip install git+https://github.com/tardis-sn/tardis.git@{tag}`
+
+        For example- 
+        
+        `pip install git+https://github.com/tardis-sn/tardis.git@release-2023.09.17`
+    
       ::
 
         $ conda install tardis-sn --channel conda-forge --no-deps
@@ -82,16 +92,16 @@ You have successfully installed TARDIS! 🎉 Please refer to `Quickstart for TAR
 to start running simulations.
 
 
-Install from package
-====================
+.. Install from package
+.. ====================
 
-It's also possible to install TARDIS by pulling the `conda-forge package <https://anaconda.org/conda-forge/tardis-sn>`_
-into a clean environment. However, we still encourage using lockfiles to ensure
-reproducibility of scientific results.
+.. It's also possible to install TARDIS by pulling the `conda-forge package <https://anaconda.org/conda-forge/tardis-sn>`_
+.. into a clean environment. However, we still encourage using lockfiles to ensure
+.. reproducibility of scientific results.
 
-::
+.. ::
 
-    $ conda create --name tardis-forge tardis-sn --channel conda-forge
+..     $ conda create --name tardis-forge tardis-sn --channel conda-forge
 
 
 Environment update

From cfce38d0d8945fea0f8ebcde8e22639ec8e71872 Mon Sep 17 00:00:00 2001
From: tardis-bot <60989672+tardis-bot@users.noreply.github.com>
Date: Fri, 20 Oct 2023 09:48:23 -0400
Subject: [PATCH 18/35] Pre-release 2023.10.20 (#2452)

Automated changes for pre-release 2023.10.20
---
 .zenodo.json | 58 ++++++++++++++++++++++++++++------------------------
 1 file changed, 31 insertions(+), 27 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index ee0b1896bbe..38bbf9ae996 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -138,38 +138,36 @@
     },
     {
       "name": "Gillanders, James",
-      "orcid": "0000-0002-8094-6108"
+      "orcid": "0000-0002-8094-6108",
+      "affiliation": "University of Oxford"
     },
     {
       "name": "Shields, Joshua"
     },
-    {
-      "name": "Singh, Shreyas"
-    },
     {
       "name": "Savel, Arjun"
     },
     {
-      "name": "Reinecke, Martin"
+      "name": "Singh, Shreyas"
     },
     {
       "name": "Eweis, Youssef"
     },
     {
-      "name": "Bylund, Tomas"
+      "name": "Reinecke, Martin"
     },
     {
-      "name": "Black, William"
+      "name": "Bylund, Tomas"
     },
     {
       "name": "Bentil, Laud"
     },
     {
-      "name": "Eguren, Jordi",
-      "orcid": "0000-0002-2328-8030"
+      "name": "Black, William"
     },
     {
-      "name": "Bartnik, Matthew"
+      "name": "Eguren, Jordi",
+      "orcid": "0000-0002-2328-8030"
     },
     {
       "name": "Alam, Arib"
@@ -177,6 +175,12 @@
     {
       "name": "Kumar, Ansh"
     },
+    {
+      "name": "Bartnik, Matthew"
+    },
+    {
+      "name": "Holas, Alexander"
+    },
     {
       "name": "Varma Buddaraju, Rohith"
     },
@@ -190,21 +194,24 @@
       "name": "Kambham, Satwik"
     },
     {
-      "name": "Daksh, Ayushi"
+      "name": "Mishra, Sashank",
+      "orcid": "0000-0001-8302-1584"
     },
     {
       "name": "Rajagopalan, Srinath"
     },
     {
-      "name": "Mishra, Sashank",
-      "orcid": "0000-0001-8302-1584"
+      "name": "Daksh, Ayushi"
     },
     {
-      "name": "Actions, GitHub"
+      "name": "Bhakar, Jayant"
     },
     {
       "name": "Floers, Andreas"
     },
+    {
+      "name": "Actions, GitHub"
+    },
     {
       "name": "Reichenbach, John"
     },
@@ -212,19 +219,16 @@
       "name": "Jain, Rinkle"
     },
     {
-      "name": "Bhakar, Jayant"
+      "name": "Singh, Sourav"
     },
     {
       "name": "Chaumal, Aarya"
     },
     {
-      "name": "Holas, Alexander"
-    },
-    {
-      "name": "Singh, Sourav"
+      "name": "Brar, Antreev"
     },
     {
-      "name": "Brar, Antreev"
+      "name": "Kumar, Aman"
     },
     {
       "name": "Matsumura, Yuki"
@@ -236,20 +240,20 @@
       "name": "Kowalski, Nathan"
     },
     {
-      "name": "Kumar, Aman"
-    },
-    {
-      "name": "Talegaonkar, Chinmay"
+      "name": "Dutta, Anirban"
     },
     {
       "name": "Selsing, Jonatan"
     },
     {
-      "name": "Gupta, Harshul"
+      "name": "Talegaonkar, Chinmay"
     },
     {
       "name": "Sofiatti, Caroline"
     },
+    {
+      "name": "Gupta, Harshul"
+    },
     {
       "name": "Prasad, Shilpi"
     },
@@ -260,7 +264,7 @@
       "name": "Yap, Kevin"
     },
     {
-      "name": "Martinez, Laureano"
+      "name": "Truong, Le"
     },
     {
       "name": "Sandler, Morgan"
@@ -311,7 +315,7 @@
       "name": "PATIDAR, ABHISHEK"
     },
     {
-      "name": "Truong, Le"
+      "name": "Martinez, Laureano"
     },
     {
       "name": "Kolliboyina, Chaitanya"

From a16acb9b8d29ab1e2fc200bdea52a00a2da01a80 Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Wed, 1 Nov 2023 03:44:36 +0100
Subject: [PATCH 19/35] Add verbose assert to NLTE rate equation (#2457)

* add verbose assert

* formatting
---
 tardis/plasma/properties/nlte_rate_equation_solver.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tardis/plasma/properties/nlte_rate_equation_solver.py b/tardis/plasma/properties/nlte_rate_equation_solver.py
index d76817b9a77..9718efc266f 100644
--- a/tardis/plasma/properties/nlte_rate_equation_solver.py
+++ b/tardis/plasma/properties/nlte_rate_equation_solver.py
@@ -125,7 +125,9 @@ def calculate(
                 ),
                 jac=True,
             )
-            assert solution.success
+            assert (
+                solution.success
+            ), "No solution for NLTE population equation found or solver takes too long to converge"
             ion_number_density_nlte[shell] = solution.x[:-1]
             electron_densities_nlte[shell] = solution.x[-1]
         # TODO: change the jacobian and rate matrix to use shell id and get coefficients from the attribute of the class.

From 33bea127a021c03f1a3c307481e0febf38aca98d Mon Sep 17 00:00:00 2001
From: Christian Vogl <cvogl@mpa-garching.mpg.de>
Date: Wed, 1 Nov 2023 14:48:15 +0100
Subject: [PATCH 20/35] Fix bug in relativistic packet source (#2453)

* Fix bug in relativistic packet source

* Add initial test for BlackBodySimpleSourceRelativistic

* Remove incorrect docstring

* Update tardis/montecarlo/tests/test_packet_source.py

Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>

* Update tardis/montecarlo/tests/test_packet_source.py

Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>

* Rename all occurences of blackbodysimplesourcerelativistic

* Do not hardcore blackbody_simplesource_relativistic.beta

---------

Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
---
 tardis/montecarlo/packet_source.py            |  4 +-
 tardis/montecarlo/tests/test_packet_source.py | 68 ++++++++++++++++++-
 2 files changed, 67 insertions(+), 5 deletions(-)

diff --git a/tardis/montecarlo/packet_source.py b/tardis/montecarlo/packet_source.py
index f6a069dac0e..0bd63ea1f90 100644
--- a/tardis/montecarlo/packet_source.py
+++ b/tardis/montecarlo/packet_source.py
@@ -313,7 +313,7 @@ def create_packets(self, no_of_packets):
         self.beta = ((self.radius / self.time_explosion) / const.c).to("")
         return super().create_packets(no_of_packets)
 
-    def create_packet_nus(self, no_of_packets):
+    def create_packet_mus(self, no_of_packets):
         """
         Create zero-limb-darkening packet :math:`\mu^\prime` distributed
         according to :math:`\\mu^\\prime=2 \\frac{\\mu^\\prime + \\beta}{2 \\beta + 1}`.
@@ -327,7 +327,7 @@ def create_packet_nus(self, no_of_packets):
 
         Returns
         -------
-        array of frequencies
+        Directions for packets
             numpy.ndarray
         """
         z = self.rng.random(no_of_packets)
diff --git a/tardis/montecarlo/tests/test_packet_source.py b/tardis/montecarlo/tests/test_packet_source.py
index 43338903967..a18850d4129 100644
--- a/tardis/montecarlo/tests/test_packet_source.py
+++ b/tardis/montecarlo/tests/test_packet_source.py
@@ -3,8 +3,12 @@
 import numpy as np
 import pandas as pd
 import pytest
+from numpy.testing import assert_allclose
 
-from tardis.montecarlo.packet_source import BlackBodySimpleSource
+from tardis.montecarlo.packet_source import (
+    BlackBodySimpleSource,
+    BlackBodySimpleSourceRelativistic,
+)
 from tardis.montecarlo import (
     montecarlo_configuration as montecarlo_configuration,
 )
@@ -43,6 +47,22 @@ def blackbodysimplesource(self, request):
         yield cls.bb
         montecarlo_configuration.LEGACY_MODE_ENABLED = False
 
+    @pytest.fixture(scope="class")
+    def blackbody_simplesource_relativistic(self, request):
+        """
+        Create BlackBodySimpleSourceRelativistic instance.
+
+        Yields
+        -------
+        tardis.montecarlo.packet_source.BlackBodySimpleSourceRelativistic
+        """
+        montecarlo_configuration.LEGACY_MODE_ENABLED = True
+        bb_rel = BlackBodySimpleSourceRelativistic(
+            base_seed=1963, legacy_second_seed=2508
+        )
+        yield bb_rel
+        montecarlo_configuration.LEGACY_MODE_ENABLED = False
+
     def test_bb_packet_sampling(
         self,
         request,
@@ -51,8 +71,6 @@ def test_bb_packet_sampling(
         blackbodysimplesource,
     ):
         """
-        Test generate_plot_mpl method.
-
         Parameters
         ----------
         request : _pytest.fixtures.SubRequest
@@ -75,3 +93,47 @@ def test_bb_packet_sampling(
         assert np.all(np.isclose(nus, ref_df["nus"]))
         assert np.all(np.isclose(mus, ref_df["mus"]))
         assert np.all(np.isclose(unif_energies, ref_df["energies"]))
+
+    def test_bb_packet_sampling_relativistic(
+        self,
+        tardis_ref_data,
+        blackbody_simplesource_relativistic,
+    ):
+        """
+        Parameters
+        ----------
+        tardis_ref_data : pd.HDFStore
+        blackbody_simplesource_relativistic : tardis.montecarlo.packet_source.BlackBodySimpleSourceRelativistic
+        """
+        blackbody_simplesource_relativistic.temperature = 10000
+        blackbody_simplesource_relativistic.beta = 0.25
+
+        nus = blackbody_simplesource_relativistic.create_packet_nus(100)
+        unif_energies = (
+            blackbody_simplesource_relativistic.create_packet_energies(100)
+        )
+        blackbody_simplesource_relativistic._reseed(2508)
+        mus = blackbody_simplesource_relativistic.create_packet_mus(10)
+
+        gamma = np.sqrt(1 - blackbody_simplesource_relativistic.beta**2) ** -1
+        ref_df = tardis_ref_data["/packet_unittest/blackbody"]
+        expected_nus = ref_df["nus"]
+        expected_unif_energies = ref_df["energies"] * 1.6 / gamma
+        expected_mus = np.array(
+            [
+                0.60420546,
+                0.49899691,
+                0.69583288,
+                0.96812652,
+                0.01544154,
+                0.93562304,
+                0.44306545,
+                0.77010037,
+                0.896973,
+                0.67876489,
+            ]
+        )
+
+        assert_allclose(nus, expected_nus)
+        assert_allclose(unif_energies, expected_unif_energies)
+        assert_allclose(mus, expected_mus, rtol=1e-6)

From 1931b91e3d4f15d3d9fa63cf0785d5977417602b Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Wed, 1 Nov 2023 20:19:32 +0100
Subject: [PATCH 21/35] Enable nlte ionization as plasma component (#2458)

* Rename nlte ion and electron

* Enable NLTE

* Fix typo

* Add docs

* Fix transitionprob dtype

* dtype conversion

* dtype for sparse matrix

* Typing in numba

* Fix test variable name

* Add missing electron density case

* Fix typo
---
 docs/io/configuration/components/plasma.rst   | 13 +++++-
 docs/physics/setup/plasma/index.rst           |  3 ++
 .../montecarlo_numba/numba_interface.py       |  4 +-
 .../properties/nlte_rate_equation_solver.py   |  2 +-
 .../properties/transition_probabilities.py    | 12 +++++-
 tardis/plasma/standard_plasmas.py             | 42 ++++++++++++++++++-
 tardis/plasma/tests/test_nlte_solver.py       |  2 +-
 7 files changed, 71 insertions(+), 7 deletions(-)

diff --git a/docs/io/configuration/components/plasma.rst b/docs/io/configuration/components/plasma.rst
index bf0b5b3579d..448d0a48545 100644
--- a/docs/io/configuration/components/plasma.rst
+++ b/docs/io/configuration/components/plasma.rst
@@ -44,4 +44,15 @@ NLTE
 The NLTE configuration currently allows setting ``coronal_approximation``, which sets all :math:`J_\textrm{blue}` to 0.
 This is useful for debugging with :term:`chianti` for example. Furthermore, one can enable 'classical_nebular' to set all
 :math:`\beta_\textrm{Sobolev}` to 1. Both options are used for checking with other codes and should not be enabled in
-normal operations.
\ No newline at end of file
+normal operations.
+
+NLTE Ionization
+^^^^^^^^^^^^^^^
+
+.. code-block:: yaml
+
+    plasma:
+        nlte_ionization_species: [H I, H II, He I, He II]
+    
+This option allows the user to specify which species should be included in the NLTE ionization treatment. Note that the
+species must be present in the continuum interaction species as well.
diff --git a/docs/physics/setup/plasma/index.rst b/docs/physics/setup/plasma/index.rst
index 6d0c26ad7ff..06c4a2203c9 100644
--- a/docs/physics/setup/plasma/index.rst
+++ b/docs/physics/setup/plasma/index.rst
@@ -73,6 +73,9 @@ The next more complex class is `LTEPlasma` which will calculate the ionization b
 
 TARDIS also allows for NLTE treatments of specified species, as well as special NLTE treatments for Helium.
 
+.. note::
+    The NLTE treatment of specified species is currently incompatible with the NLTE treatment for helium and cannot be used simulataneously.
+
 .. toctree::
     :maxdepth: 2
 
diff --git a/tardis/montecarlo/montecarlo_numba/numba_interface.py b/tardis/montecarlo/montecarlo_numba/numba_interface.py
index 848ba3cfe10..50be58a6d8f 100644
--- a/tardis/montecarlo/montecarlo_numba/numba_interface.py
+++ b/tardis/montecarlo/montecarlo_numba/numba_interface.py
@@ -217,7 +217,9 @@ def opacity_state_initialize(plasma, line_interaction_type):
         ].values
 
         phot_nus = phot_nus.values
-        ff_opacity_factor = plasma.ff_cooling_factor / np.sqrt(t_electrons)
+        ff_opacity_factor = (
+            plasma.ff_cooling_factor / np.sqrt(t_electrons)
+        ).astype(np.float64)
         emissivities = plasma.fb_emission_cdf.loc[
             plasma.level2continuum_idx.index
         ].values
diff --git a/tardis/plasma/properties/nlte_rate_equation_solver.py b/tardis/plasma/properties/nlte_rate_equation_solver.py
index 9718efc266f..a2e8b5f028f 100644
--- a/tardis/plasma/properties/nlte_rate_equation_solver.py
+++ b/tardis/plasma/properties/nlte_rate_equation_solver.py
@@ -11,7 +11,7 @@
 
 
 class NLTERateEquationSolver(ProcessingPlasmaProperty):
-    outputs = ("ion_number_density_nlte", "electron_densities_nlte")
+    outputs = ("ion_number_density", "electron_densities")
 
     def calculate(
         self,
diff --git a/tardis/plasma/properties/transition_probabilities.py b/tardis/plasma/properties/transition_probabilities.py
index 9def7e650df..e69d655ef6b 100644
--- a/tardis/plasma/properties/transition_probabilities.py
+++ b/tardis/plasma/properties/transition_probabilities.py
@@ -41,10 +41,16 @@ def normalize_trans_probs(p):
         all probabilites with the same source_level_idx sum to one.
         Indexed by source_level_idx, destination_level_idx.
     """
-    p_summed = p.groupby(level=0).sum()
+    # Dtype conversion is needed for pandas to return nan instead of
+    # a ZeroDivisionError in cases where the sum is zero.
+    p = p.astype(np.float64)
+    p_summed = p.groupby(level=0).sum().astype(np.float64)
     index = p.index.get_level_values("source_level_idx")
     p_norm = p / p_summed.loc[index].values
     p_norm = p_norm.fillna(0.0)
+    # Convert back to original dtypes to avoid typing problems later on
+    # in the numba code.
+    p_norm = p_norm.convert_dtypes()
     return p_norm
 
 
@@ -78,7 +84,9 @@ def series2matrix(series, idx2reduced_idx):
             idx2reduced_idx.loc[q_indices[1]].values,
         )
         max_idx = idx2reduced_idx.max() + 1
-        matrix = sp.coo_matrix((series, q_indices), shape=(max_idx, max_idx))
+        matrix = sp.coo_matrix(
+            (series.astype(np.float64), q_indices), shape=(max_idx, max_idx)
+        )
         return matrix
 
     @staticmethod
diff --git a/tardis/plasma/standard_plasmas.py b/tardis/plasma/standard_plasmas.py
index 63c6ac2324e..82bbc54a263 100644
--- a/tardis/plasma/standard_plasmas.py
+++ b/tardis/plasma/standard_plasmas.py
@@ -6,6 +6,10 @@
 import pandas as pd
 
 from tardis.io.atom_data import AtomData
+from tardis.plasma.properties.level_population import LevelNumberDensity
+from tardis.plasma.properties.nlte_rate_equation_solver import (
+    NLTERateEquationSolver,
+)
 from tardis.plasma.properties.rate_matrix_index import NLTEIndexHelper
 from tardis.util.base import species_string_to_tuple
 from tardis.plasma import BasePlasma
@@ -265,6 +269,26 @@ def assemble_plasma(config, simulation_state, atom_data=None):
             delta_treatment=config.plasma.delta_treatment
         )
 
+    if (
+        config.plasma.helium_treatment == "recomb-nlte"
+        or config.plasma.helium_treatment == "numerical-nlte"
+    ) and (
+        config.plasma.nlte_ionization_species
+        or config.plasma.nlte_excitation_species
+    ):
+        # Prevent the user from using helium NLTE treatment with
+        # NLTE ionization and excitation treatment. This is because
+        # the helium_nlte_properties could overwrite the NLTE ionization
+        # and excitation ion number and electron densities.
+        # helium_numerical_nlte_properties is also included here because
+        # it is currently in the same if else block, and thus may block
+        # the addition of the components from the else block.
+        raise PlasmaConfigError(
+            "Helium NLTE treatment is incompatible with the NLTE eonization and excitation treatment."
+        )
+
+    # TODO: Disentangle these if else block such that compatible components
+    # can be added independently.
     if config.plasma.helium_treatment == "recomb-nlte":
         plasma_modules += helium_nlte_properties
     elif config.plasma.helium_treatment == "numerical-nlte":
@@ -277,7 +301,16 @@ def assemble_plasma(config, simulation_state, atom_data=None):
                 heating_rate_data_file=config.plasma.heating_rate_data_file
             )
     else:
-        plasma_modules += helium_lte_properties
+        # If nlte ionization species are present, we don't want to add the
+        # IonNumberDensity from helium_lte_properties, since we want
+        # to use the IonNumberDensity provided by the NLTE solver.
+        if (
+            config.plasma.nlte_ionization_species
+            or config.plasma.nlte_excitation_species
+        ):
+            plasma_modules += [LevelNumberDensity]
+        else:
+            plasma_modules += helium_lte_properties
 
     if simulation_state._electron_densities is not None:
         electron_densities = pd.Series(
@@ -287,6 +320,13 @@ def assemble_plasma(config, simulation_state, atom_data=None):
             property_kwargs[IonNumberDensityHeNLTE] = dict(
                 electron_densities=electron_densities
             )
+        elif (
+            config.plasma.nlte_ionization_species
+            or config.plasma.nlte_excitation_species
+        ):
+            property_kwargs[NLTERateEquationSolver] = dict(
+                electron_densities=electron_densities
+            )
         else:
             property_kwargs[IonNumberDensity] = dict(
                 electron_densities=electron_densities
diff --git a/tardis/plasma/tests/test_nlte_solver.py b/tardis/plasma/tests/test_nlte_solver.py
index fe47b496e97..beeb345cf6d 100644
--- a/tardis/plasma/tests/test_nlte_solver.py
+++ b/tardis/plasma/tests/test_nlte_solver.py
@@ -260,7 +260,7 @@ def nlte_raw_plasma_w0(
 
 def test_critical_case_w1(nlte_raw_plasma_w1):
     """Check that the LTE and NLTE solution agree for w=1.0."""
-    ion_number_density_nlte = nlte_raw_plasma_w1.ion_number_density_nlte.values
+    ion_number_density_nlte = nlte_raw_plasma_w1.ion_number_density.values
     ion_number_density_nlte[ion_number_density_nlte < 1e-10] = 0.0
 
     ind = IonNumberDensity(nlte_raw_plasma_w1)

From dce9041d64d4df192e631807cc047b51ca73c6c9 Mon Sep 17 00:00:00 2001
From: Andrew <andrewgfullard@gmail.com>
Date: Thu, 2 Nov 2023 00:16:51 -0400
Subject: [PATCH 22/35] Update docstr-cov.yml to fix failing action (#2462)

* Update docstr-cov.yml to fix failing action

* Explicitly install setuptools
---
 .github/workflows/docstr-cov.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docstr-cov.yml b/.github/workflows/docstr-cov.yml
index 8a741e5267b..645d285bffd 100644
--- a/.github/workflows/docstr-cov.yml
+++ b/.github/workflows/docstr-cov.yml
@@ -31,12 +31,12 @@ jobs:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.x
 
       - name: Install interrogate
-        run: pip install interrogate==1.5.0 parse==1.19.0
+        run: pip install interrogate==1.5.0 parse==1.19.0 setuptools
 
       - name: Get SHAs
         run: |

From 98c19eee870adc2c9a11fcf9fbdfe04729fc72b4 Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Thu, 2 Nov 2023 22:37:44 +0100
Subject: [PATCH 23/35] NLTE Ionization solver polish (#2461)

* assertion for first guess

* Add checks to decay

* Fix greater equal

* Fix deprecated series index
---
 tardis/io/decay.py                                  | 13 ++++++++++++-
 .../plasma/properties/nlte_rate_equation_solver.py  |  6 +++++-
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/tardis/io/decay.py b/tardis/io/decay.py
index a61a54a3cb8..7005fa50e6e 100644
--- a/tardis/io/decay.py
+++ b/tardis/io/decay.py
@@ -2,10 +2,12 @@
 from radioactivedecay import Nuclide, Inventory
 from radioactivedecay.utils import Z_to_elem
 from astropy import units as u
+import logging
 
+logger = logging.getLogger(__name__)
 
-class IsotopeAbundances(pd.DataFrame):
 
+class IsotopeAbundances(pd.DataFrame):
     _metadata = ["time_0"]
 
     def __init__(self, *args, **kwargs):
@@ -92,9 +94,18 @@ def decay(self, t):
         t_second = (
             u.Quantity(t, u.day).to(u.s).value - self.time_0.to(u.s).value
         )
+        logger.info(f"Decaying abundances for {t_second} seconds")
+        if t_second < 0:
+            logger.warning(
+                f"Decay time {t_second} is negative. This could indicate a miss-specified input model."
+                f" A negative decay time can potentially lead to negative abundances."
+            )
         decayed_inventories = [item.decay(t_second) for item in inventories]
         df = IsotopeAbundances.from_inventories(decayed_inventories)
         df.sort_index(inplace=True)
+        assert (
+            df.ge(0.0).all().all()
+        ), "Negative abundances detected. Please make sure your input abundances are correct."
         return df
 
     def as_atoms(self):
diff --git a/tardis/plasma/properties/nlte_rate_equation_solver.py b/tardis/plasma/properties/nlte_rate_equation_solver.py
index a2e8b5f028f..487b93ad5a3 100644
--- a/tardis/plasma/properties/nlte_rate_equation_solver.py
+++ b/tardis/plasma/properties/nlte_rate_equation_solver.py
@@ -110,6 +110,10 @@ def calculate(
                 number_density[shell],
                 initial_electron_densities[shell],
             )
+            # All first guess values have to be positive
+            assert (
+                np.greater_equal(first_guess, 0.0).all()
+            ).all(), "First guess for NLTE solver has negative values, something went wrong."
             solution = root(
                 self.population_objective_function,
                 first_guess,
@@ -591,7 +595,7 @@ def prepare_first_guess(
         """
         first_guess = pd.Series(0.0, index=rate_matrix_index)
         for atomic_number in atomic_numbers:
-            first_guess.loc[(atomic_number, 1)][0] = number_density.loc[
+            first_guess.loc[(atomic_number, 1)].iloc[0] = number_density.loc[
                 atomic_number
             ]
         # TODO: After the first iteration, the new guess can be the old solution.

From 28c01269e3d5e7f2164ae7185823b43b0c949bbe Mon Sep 17 00:00:00 2001
From: tardis-bot <60989672+tardis-bot@users.noreply.github.com>
Date: Sat, 4 Nov 2023 22:34:14 -0400
Subject: [PATCH 24/35] Pre-release 2023.11.05 (#2466)

Automated changes for pre-release 2023.11.05
---
 .zenodo.json | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index 38bbf9ae996..6385dd3064f 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -116,10 +116,10 @@
       "name": "Barbosa, Talytha"
     },
     {
-      "name": "Sondhi, Dhruv"
+      "name": "O'Brien, Jack"
     },
     {
-      "name": "O'Brien, Jack"
+      "name": "Sondhi, Dhruv"
     },
     {
       "name": "Yu, Jenny"
@@ -151,19 +151,22 @@
       "name": "Singh, Shreyas"
     },
     {
-      "name": "Eweis, Youssef"
+      "name": "Reinecke, Martin"
     },
     {
-      "name": "Reinecke, Martin"
+      "name": "Eweis, Youssef"
     },
     {
       "name": "Bylund, Tomas"
     },
+    {
+      "name": "Black, William"
+    },
     {
       "name": "Bentil, Laud"
     },
     {
-      "name": "Black, William"
+      "name": "Holas, Alexander"
     },
     {
       "name": "Eguren, Jordi",
@@ -178,9 +181,6 @@
     {
       "name": "Bartnik, Matthew"
     },
-    {
-      "name": "Holas, Alexander"
-    },
     {
       "name": "Varma Buddaraju, Rohith"
     },

From 87e8f3a8b6fd7fc0caf1d03698841f231f688735 Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Mon, 6 Nov 2023 21:41:31 +0530
Subject: [PATCH 25/35] Tests Plasma Using Syrupy (#2413)

* Add syrupy classes to conftest

* Add syrupy to env file

* Another folder for syrupy data

* Save as npy instead of txt

* Use syrupy fixtures

* Different assertion functions for pandas dataframes and series

* Zeta data fix

* Blackify

* Blackify conftest

* test_hdf_plasmas using syrupy

* Install syrupy with conda

* Remove additional line adding syrupy as a plugin

* Set update snapshots config option when generate reference is selected

* Remove old refdata code from test plasmas complete

* Create plasma conftest file

* Text based snapshot fixture with custom location

* Snapshot path

* tardis regressions my fork

* Refactor test_hdf_plasmas.py

* Format using black

* test nlte excitation using syrupy

* nlte solver

* plasma continuum

* test tardis model density config

* Lock files

* Increase cache no

* format using black

* cleanup- sort dependencies, delete comments

* Documentation to run these tests

* remove commented out fixtures which are not used anywhere

* docs code render fix

* tests final cleanup

* renaming files, yet to deal with ambr snapshot extension and curly brackets

* renaming snapshots

* Add comments
---
 .github/workflows/tests.yml                   |  10 +-
 conda-linux-64.lock                           | 102 +--
 conda-lock.yml                                | 775 ++++++++++--------
 conda-osx-64.lock                             |  94 +--
 .../development/running_tests.rst             |  12 +
 tardis/conftest.py                            |  49 +-
 tardis/plasma/tests/conftest.py               |  42 +
 tardis/plasma/tests/test_complete_plasmas.py  |  54 +-
 tardis/plasma/tests/test_hdf_plasma.py        |  56 +-
 tardis/plasma/tests/test_nlte_excitation.py   |  65 +-
 tardis/plasma/tests/test_nlte_solver.py       |  39 +-
 tardis/plasma/tests/test_plasma_contiuum.py   |   8 +-
 tardis/plasma/tests/test_plasma_vboundary.py  |   6 +-
 .../tests/test_tardis_model_density_config.py |  23 +-
 tardis/util/syrupy_extensions.py              | 129 +++
 tardis_env3.yml                               |   2 +
 16 files changed, 819 insertions(+), 647 deletions(-)
 create mode 100644 tardis/plasma/tests/conftest.py
 create mode 100644 tardis/util/syrupy_extensions.py

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 7414b517f28..699837c9b4f 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -15,8 +15,8 @@ on:
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually
-  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata
-                --cov=tardis --cov-report=xml --cov-report=html
+  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-snapshot-data=${{ github.workspace }}/tardis-regressions
+                --cov=tardis --cov-report=xml --cov-report=html 
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
 concurrency:
@@ -86,6 +86,12 @@ jobs:
         with:
           path: tardis-refdata/.git/lfs
           key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1
+      
+      - name: Clone tardis-sn/tardis-regressions
+        uses: actions/checkout@v4
+        with:
+          repository: tardis-sn/tardis-regressions
+          path: tardis-regressions
 
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v2
diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index 1aaa04b654c..fd93c9a7bf8 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 31d323d670a8deec16e2186403aa54ab8464102ac712829e12e62d80bc50f272
+# input_hash: c282095367763377f64134aabe34418215a97ab21d09982800cc95beb98ebaa9
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
@@ -10,15 +10,15 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2#19410c3df09dfb12d1206132a1d357c5
 https://conda.anaconda.org/conda-forge/linux-64/git-lfs-3.4.0-ha770c72_0.conda#8b8aef0a35f5b98937a65b67b7d3b536
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_1.conda#acfb4817400db5804030a3a7ef7909a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
 https://conda.anaconda.org/conda-forge/noarch/nomkl-1.0-h5ca1d4c_0.tar.bz2#9a66894dfd07c4510beb6b3f9672ccc0
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-3_cp311.conda#c2e2630ddb68cf52eec74dc7dfab20b5
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-4_cp311.conda#d786502c97404c94d7d58d258a445a65
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_1.conda#8bb001683321dcbde117a7337b5aace7
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_1.conda#ff8999574b465089ba0aa25a5e865bd0
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.19.1-hd590300_0.conda#e8c18d865be43e2fb3f7a145b6adf1f5
 https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8
@@ -36,10 +36,10 @@ https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.19-hd590300_0.conda
 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#6305a3dd2752c76335295da4e581f2fd
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_1.conda#a0d27fd5c6f05aa45e9602b1db49581c
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_2.conda#78fdab09d9138851dde2b5fe2a11019e
 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2#b62b52da46c39ee2bc3c162ac7f1804d
 https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-hd590300_1.conda#323e90742f0f48fc22bea908735f55e6
-https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-hd590300_1.conda#854e3e1623b39777140f199c5f9ab952
 https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.18-h36c2ea0_1.tar.bz2#c3788462a6fbddafdb413a9f9053e58d
 https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda#f204c8ba400ec475452737094fb81d52
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
@@ -48,9 +48,9 @@ https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
 https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h516909a_1000.tar.bz2#bb14fcb13341b81d5eb386423b9d2bac
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda#681105bccc2a3f7f1a837d47d39c9179
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.2-hd590300_0.conda#e5ac5227582d6c83ccf247288c0eb095
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.3-hd590300_0.conda#7bb88ce04c8deb9f7d763ae04a1da72f
 https://conda.anaconda.org/conda-forge/linux-64/pcre-8.45-h9c3ff4c_0.tar.bz2#c05d1820a6d34ff07aaaab7a9b7eddaa
-https://conda.anaconda.org/conda-forge/linux-64/pixman-0.40.0-h36c2ea0_0.tar.bz2#660e72c82f2e75a6b3fe6a6e75c79f19
+https://conda.anaconda.org/conda-forge/linux-64/pixman-0.42.2-h59595ed_0.conda#700edd63ccd5fc66b70b1c028cea9a68
 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036
 https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.10-h9fff704_0.conda#e6d228cd0bb74a51dd18f5bfce0b4115
 https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a
@@ -67,7 +67,7 @@ https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda#8b9
 https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.1.0-hd590300_0.conda#43017394a280a42b48d11d2a6e169901
 https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hd590300_0.conda#8e3e1cb77c4b355a3776bdfb74095bed
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_1.conda#394218a92951499aed2ab1bafb30b570
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_2.conda#e75a75a6eaf6f318dae2631158c46575
 https://conda.anaconda.org/conda-forge/linux-64/libllvm14-14.0.6-hcd5def8_4.conda#73301c133ded2bf71906aa2104edae8b
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.52.0-h61bc06f_0.conda#613955a50485812985c059e7b269f42e
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+https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.2.1-h3d44ed6_0.conda#98db5f8813f45e2b29766aff0e4a499c
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@@ -261,34 +262,35 @@ https://conda.anaconda.org/conda-forge/noarch/pytest-cov-4.1.0-pyhd8ed1ab_0.cond
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+https://conda.anaconda.org/conda-forge/noarch/setuptools-scm-8.0.3-pyhd8ed1ab_0.conda#23929f6e32fba28210bf0c329a8cf941
 https://conda.anaconda.org/conda-forge/noarch/stack_data-0.6.2-pyhd8ed1ab_0.conda#e7df0fdd404616638df5ece6e69ba7af
+https://conda.anaconda.org/conda-forge/noarch/syrupy-4.5.0-pyhd8ed1ab_0.conda#23a01c37640f9a8ec3872752c7ff80aa
 https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.6-pyhd8ed1ab_0.conda#078979d33523cb477bd1916ce41aacc9
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+https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.1.1-py311h9547e67_1.conda#52d3de443952d33c5cee6b24b172ce96
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+https://conda.anaconda.org/conda-forge/noarch/jsonschema-with-format-nongpl-4.19.1-pyhd8ed1ab_0.conda#daca0665e6fe8a376e48b9f0b5865326
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+https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.8.0-py311h54ef318_1.conda#20d79e2fe53b49b399f3d36977b05abb
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@@ -299,8 +301,8 @@ https://conda.anaconda.org/conda-forge/noarch/nbclient-0.8.0-pyhd8ed1ab_0.conda#
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+https://conda.anaconda.org/conda-forge/linux-64/pygraphviz-1.11-py311h72a77b7_1.conda#7044cd923985abb6e3b976e5ac0542b8
+https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_1.conda#0123f934221b023ddc7443e85cac9023
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@@ -308,7 +310,7 @@ https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.8.0-pyhd8ed1ab_0.conda
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-https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.3-pyhd8ed1ab_0.conda#1f2d368cde97926b5e351d1a0286bb1e
+https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.4-pyhd8ed1ab_0.conda#9fe0b0f2e8a6dbae64947e90079ea54c
 https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda#fe79dfe7d51794d665ec3c2fdd4e47c3
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diff --git a/conda-lock.yml b/conda-lock.yml
index 7b25a11453c..def78a5fb0e 100644
--- a/conda-lock.yml
+++ b/conda-lock.yml
@@ -9,20 +9,21 @@
 # To update a single package to the latest version compatible with the version constraints in the source:
 #     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
 # To re-solve the entire environment, e.g. after changing a version constraint in the source file:
-#     conda-lock -f tardis_env3.yml -f /Users/wkerzend/python/tardis/tardis_env3.yml --lockfile conda-lock.yml
+#     conda-lock -f tardis_env3.yml -f /Users/wkerzend/python/tardis/tardis_env3.yml -f /home/atharva/workspace/code/tardis-main/tardis/tardis_env3.yml --lockfile conda-lock.yml
 metadata:
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     used_env_vars: []
   content_hash:
-    linux-64: 31d323d670a8deec16e2186403aa54ab8464102ac712829e12e62d80bc50f272
-    osx-64: a32c45fe2a9272de47a9c858b1b632bb1de0c3a0cd55bffe7df61cc7ef21eecd
+    linux-64: c282095367763377f64134aabe34418215a97ab21d09982800cc95beb98ebaa9
+    osx-64: e0b8122702e46d054c30bc66450a0041530cf14a3c2f3dcc4daed538bb8c0785
   platforms:
   - linux-64
   - osx-64
   sources:
   - tardis_env3.yml
   - /Users/wkerzend/python/tardis/tardis_env3.yml
+  - /home/atharva/workspace/code/tardis-main/tardis/tardis_env3.yml
 package:
 - category: main
   dependencies: {}
@@ -115,13 +116,13 @@ package:
 - category: main
   dependencies: {}
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-    sha256: b4ee92e483b24dbcdbaab0928e14bf338342268e3c413111413ee36284006d56
+    md5: 9172c297304f2a20134fc56c97fbe229
+    sha256: ab22ecdc974cdbe148874ea876d9c564294d5eafa760f403ed4fd495307b4243
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   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_1.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda
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@@ -137,13 +138,13 @@ package:
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+    md5: d786502c97404c94d7d58d258a445a65
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   optional: false
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-  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-3_cp311.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-4_cp311.conda
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@@ -175,13 +176,13 @@ package:
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-    sha256: cc9b25e3a0329326936164ca666861738e2833460cd1e0bb2086acb5781a7795
+    md5: e2042154faafe61969556f28bade94b9
+    sha256: e1e82348f8296abfe344162b3b5f0ddc2f504759ebeb8b337ba99beaae583b15
   manager: conda
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   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_1.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda
   version: 13.2.0
 - category: main
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@@ -213,13 +214,13 @@ package:
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     _openmp_mutex: '>=4.5'
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+    md5: c28003b0be0494f9a7664389146716ff
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   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_1.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda
   version: 13.2.0
 - category: main
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@@ -434,13 +435,13 @@ package:
   dependencies:
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   hash:
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-    sha256: 30b4194151c1d6cdede3da8c33aabb848cde4db2fc68e7f5607f2e4a38d881d7
+    md5: 78fdab09d9138851dde2b5fe2a11019e
+    sha256: 55ecf5c46c05a98b4822a041d6e1cb196a7b0606126eb96b24131b7d2c8ca561
   manager: conda
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   optional: false
   platform: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_1.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_2.conda
   version: 13.2.0
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@@ -468,15 +469,15 @@ package:
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 - category: main
   dependencies:
-    libgcc-ng: '>=9.4.0'
+    libgcc-ng: '>=12'
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+    md5: 854e3e1623b39777140f199c5f9ab952
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   manager: conda
   name: libnsl
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   url: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
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-    sha256: 2264ee0dbb0bac37d9fe36867f06eb0169fdeb158696cd41d83c4b0bdc503541
+    md5: 390e0db0f04fabd7330fa626c398b16f
+    sha256: cb2711d7a9d34a5954939737a38ebcb4916279c0a49d7cd7272d2e28b2b94b97
   manager: conda
   name: matplotlib-base
   optional: false
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-  url: https://conda.anaconda.org/conda-forge/osx-64/matplotlib-base-3.7.2-py311haff9b01_0.conda
-  version: 3.7.2
+  url: https://conda.anaconda.org/conda-forge/osx-64/matplotlib-base-3.8.0-py311haff9b01_0.conda
+  version: 3.8.0
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@@ -8454,17 +8509,17 @@ package:
   version: 7.8.0
 - category: main
   dependencies:
-    graphviz: '>=8.0.5,<9.0a0'
+    graphviz: '>=8.1.0,<9.0a0'
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     python_abi: 3.11.* *_cp311
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-    sha256: 131fbc18d15252389162c11718bb4fcb5091ae8ab270c283ab5f4e63afab3482
+    md5: 17602bac3f0091fc1383741385b1c1b1
+    sha256: b0e97e9a5bbd65edddaa9147bfb2410bbbc8105cf02dbd0c7a717355dc81ded3
   manager: conda
   name: pygraphviz
   optional: false
   platform: osx-64
-  url: https://conda.anaconda.org/conda-forge/osx-64/pygraphviz-1.11-py311hc6eba27_0.conda
+  url: https://conda.anaconda.org/conda-forge/osx-64/pygraphviz-1.11-py311hc6eba27_1.conda
   version: '1.11'
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@@ -8507,13 +8562,13 @@ package:
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     websocket-client: ''
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-    sha256: c90bc6f842a37dd99e32b35f0f40214040756949fe5a7abc1256a227bb8ba90e
+    md5: 0123f934221b023ddc7443e85cac9023
+    sha256: 47913d8bda9f0cd5cf2a2d27039436a55a74eec51f1ad2b374a88fbf99fd46b3
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-  url: https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_0.conda
+  url: https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_1.conda
   version: 2.7.3
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-    sha256: b94a8838af82d0d986627439f64bbe85a4806fcc1cdd300bba685df934fbd33b
+    md5: 9fe0b0f2e8a6dbae64947e90079ea54c
+    sha256: 3ee5870402d41db9d93af61cc15ca7b8ccfccc6a024d564d764aabd4ac8ce908
   manager: conda
   name: notebook
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-  url: https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.3-pyhd8ed1ab_0.conda
-  version: 7.0.3
+  url: https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.4-pyhd8ed1ab_0.conda
+  version: 7.0.4
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diff --git a/conda-osx-64.lock b/conda-osx-64.lock
index 00013efcb38..c911a33d163 100644
--- a/conda-osx-64.lock
+++ b/conda-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: a32c45fe2a9272de47a9c858b1b632bb1de0c3a0cd55bffe7df61cc7ef21eecd
+# input_hash: e0b8122702e46d054c30bc66450a0041530cf14a3c2f3dcc4daed538bb8c0785
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-https://conda.anaconda.org/conda-forge/osx-64/python_abi-3.11-3_cp311.conda#5e0a069a585445333868d2c6651c3b3f
+https://conda.anaconda.org/conda-forge/osx-64/python_abi-3.11-4_cp311.conda#fef7a52f0eca6bae9e8e2e255bc86394
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+https://conda.anaconda.org/conda-forge/osx-64/openssl-3.1.3-h8a1eda9_0.conda#26f9b58f905547e658e9587f8e8cfe43
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+https://conda.anaconda.org/conda-forge/osx-64/tk-8.6.13-hef22860_0.conda#0c25eedcc888b6d765948ab62a18c03e
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+https://conda.anaconda.org/conda-forge/noarch/colored-1.4.4-pyhd8ed1ab_0.conda#46762cf2ddf6a1498eec36167d719fcc
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+https://conda.anaconda.org/conda-forge/osx-64/debugpy-1.8.0-py311hdf8f085_1.conda#7f20ef8a63be62d1bcdaa8136ec09647
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+https://conda.anaconda.org/conda-forge/osx-64/docutils-0.17.1-py311h6eed73b_4.conda#55af8a4ccd7f6154a179a4fcaff78381
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@@ -113,16 +114,16 @@ https://conda.anaconda.org/conda-forge/noarch/imagesize-1.4.1-pyhd8ed1ab_0.tar.b
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-https://conda.anaconda.org/conda-forge/osx-64/jsonpointer-2.4-py311h6eed73b_2.conda#39de3020498c7ca47a9ef62c4523032c
+https://conda.anaconda.org/conda-forge/osx-64/jsonpointer-2.4-py311h6eed73b_3.conda#ed1c23d0e55abd27d8b9e31c58105140
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+https://conda.anaconda.org/conda-forge/osx-64/kiwisolver-1.4.5-py311h5fe6e05_1.conda#24305b23f7995de72bbd53b7c01242a2
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+https://conda.anaconda.org/conda-forge/osx-64/markupsafe-2.1.3-py311h2725bcf_1.conda#52ee86f482b552e547e2b1d6c01adf55
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+https://conda.anaconda.org/conda-forge/osx-64/scipy-1.11.3-py311h16c3c4d_0.conda#bd195650c219e5e90f45413cd0bacfa8
 https://conda.anaconda.org/conda-forge/osx-64/astropy-5.3.3-py311h4a70a88_0.conda#067a1e7c5fc33393399dc5c1969469a0
 https://conda.anaconda.org/conda-forge/osx-64/graphviz-8.1.0-hc7f41f9_0.conda#a840f2eb891fdc5c39c762e16ee09600
 https://conda.anaconda.org/conda-forge/noarch/ipython-8.15.0-pyh31c8845_0.conda#24e68bbee62de3c9c6d051d59e9ea87b
 https://conda.anaconda.org/conda-forge/noarch/jupyter_events-0.7.0-pyhd8ed1ab_2.conda#088f0493279a7f7eebd514df47d65851
-https://conda.anaconda.org/conda-forge/osx-64/matplotlib-base-3.7.2-py311haff9b01_0.conda#bd9520e9015e70f3de839ce48c9061ea
+https://conda.anaconda.org/conda-forge/osx-64/matplotlib-base-3.8.0-py311haff9b01_0.conda#390e0db0f04fabd7330fa626c398b16f
 https://conda.anaconda.org/conda-forge/noarch/nbclient-0.8.0-pyhd8ed1ab_0.conda#e78da91cf428faaf05701ce8cc8f2f9b
 https://conda.anaconda.org/conda-forge/osx-64/pytables-3.8.0-py311h21e7aa0_3.conda#fe8ff91c89febadc989bc9e88c53e5a2
 https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.25.2-pyh1050b4e_0.conda#a643e6f6c33ed821664f2a69f6e4e89f
 https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.8.0-pyhd8ed1ab_0.conda#62345c9e24f898bf492979be84a6eb0a
-https://conda.anaconda.org/conda-forge/osx-64/pygraphviz-1.11-py311hc6eba27_0.conda#fed0a15be9e09c83aba369a5049655c1
+https://conda.anaconda.org/conda-forge/osx-64/pygraphviz-1.11-py311hc6eba27_1.conda#17602bac3f0091fc1383741385b1c1b1
 https://conda.anaconda.org/conda-forge/noarch/radioactivedecay-0.4.21-pyhd8ed1ab_0.conda#673319f48d9b160c8056783d301e090c
-https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_0.conda#969249eb7c2f7a9b820520a355dc7d04
+https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_1.conda#0123f934221b023ddc7443e85cac9023
 https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.8.0-pyhd8ed1ab_0.conda#1dba1a577df2625a24667612a069e91c
 https://conda.anaconda.org/conda-forge/noarch/jupyter-lsp-2.2.0-pyhd8ed1ab_0.conda#38589f4104d11f2a59ff01a9f4e3bfb3
 https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.25.0-pyhd8ed1ab_0.conda#a52834fa7e3d12abc5efdf06b2097a05
@@ -293,7 +295,7 @@ https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.8.0-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.3-pyhd8ed1ab_0.conda#67e0fe74c156267d9159e9133df7fd37
 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.6-pyhd8ed1ab_0.conda#80bb1cc3b540790cb5afecd73c2d4d1f
 https://conda.anaconda.org/conda-forge/noarch/nbclassic-1.0.0-pyhb4ecaf3_1.conda#a0be31e9bd84d6eae87cdbf74c56b90b
-https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.3-pyhd8ed1ab_0.conda#1f2d368cde97926b5e351d1a0286bb1e
+https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.4-pyhd8ed1ab_0.conda#9fe0b0f2e8a6dbae64947e90079ea54c
 https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda#fe79dfe7d51794d665ec3c2fdd4e47c3
 https://conda.anaconda.org/conda-forge/noarch/ipywidgets-7.8.0-pyhd8ed1ab_0.conda#518b05adab6cfe6ea249319932d9d4a3
 https://conda.anaconda.org/conda-forge/noarch/qgrid-1.3.1-pyhd8ed1ab_4.tar.bz2#fff68c7404813a1eb2678425f00e9917
diff --git a/docs/contributing/development/running_tests.rst b/docs/contributing/development/running_tests.rst
index e299cb8febc..d5d1a0e4c59 100644
--- a/docs/contributing/development/running_tests.rst
+++ b/docs/contributing/development/running_tests.rst
@@ -70,6 +70,18 @@ Or, to run tests for a particular file or directory
     You can check if cache was generated by looking in the ``Restore LFS Cache`` step of the workflow run. 
     Cache can also be found under the "Management" Section under "Actions" tab.
 
+
+Running Syrupy Tests
+======================
+The tests module is currently being restructured to use `Syrupy <https://github.com/tophat/syrupy>`_. 
+These tests generate individual HDF(for Pandas) and ``.npy`` or ``.npz`` (for NumPy) files(or snapshots) for each test case.
+For other objects, the plugin serialises them and saves them as ``.ambr`` files. There is a custom extension in the 
+main local `conftest <https://github.com/tardis-sn/tardis/blob/master/tardis/conftest.py>`_ file to get this to work.
+The plugin currently only supports ``assert_allclose`` for NumPy and ``assert_series_equal`` and ``assert_frame_equal`` for 
+Pandas. Snapshots can be generated by using the same ``--generate-reference`` flag and are compared automatically.
+You however need to provide the location to your snapshot directory using the ``--tardis-snapshot-data`` flag.
+The snapshots are also saved in `tardis-sn/tardis-regressions <https://github.com/tardis-sn/tardis-regressions>`_.
+
 Generating Plasma Reference
 ===========================
 
diff --git a/tardis/conftest.py b/tardis/conftest.py
index eb64d686fda..00bcb0ec413 100644
--- a/tardis/conftest.py
+++ b/tardis/conftest.py
@@ -39,7 +39,6 @@ def pytest_configure(config):
 
     """
     if ASTROPY_HEADER:
-
         config.option.astropy_header = True
 
         # Customize the following lines to add/remove entries from the list of
@@ -78,11 +77,19 @@ def pytest_configure(config):
 # Here the TARDIS testing stuff begins
 # -------------------------------------------------------------------------
 
+import re
 import pytest
 import pandas as pd
 from tardis.io.util import yaml_load_file, YAMLLoader
 from tardis.io.configuration.config_reader import Configuration
 from tardis.simulation import Simulation
+from tardis.util.syrupy_extensions import (
+    SingleFileSanitizedNames,
+    NumpySnapshotExtenstion,
+    PandasSnapshotExtenstion,
+)
+
+pytest_plugins = "syrupy"
 
 
 def pytest_addoption(parser):
@@ -101,6 +108,13 @@ def pytest_addoption(parser):
         default=False,
         help="generate reference data instead of testing",
     )
+
+    parser.addoption(
+        "--tardis-snapshot-data",
+        default=None,
+        help="Path to Tardis Snapshot Folder",
+    )
+
     parser.addoption(
         "--less-packets",
         action="store_true",
@@ -116,6 +130,8 @@ def pytest_collection_modifyitems(config, items):
         for item in items:
             if "ignore_generate" in item.keywords:
                 item.add_marker(skip_generate)
+        # automatically set update snapshots to true
+        config.option.update_snapshots = True
 
 
 # -------------------------------------------------------------------------
@@ -141,6 +157,17 @@ def tardis_ref_path(request):
         return Path(os.path.expandvars(os.path.expanduser(tardis_ref_path)))
 
 
+@pytest.fixture(scope="session")
+def tardis_snapshot_path(request):
+    tardis_snapshot_path = request.config.getoption("--tardis-snapshot-data")
+    if tardis_snapshot_path is None:
+        pytest.skip("--tardis-snapshot-data was not specified")
+    else:
+        return Path(
+            os.path.expandvars(os.path.expanduser(tardis_snapshot_path))
+        )
+
+
 from tardis.tests.fixtures.atom_data import *
 
 
@@ -211,3 +238,23 @@ def simulation_verysimple(config_verysimple, atomic_dataset):
     sim = Simulation.from_config(config_verysimple, atom_data=atomic_data)
     sim.iterate(4000)
     return sim
+
+
+# -------------------------------------------------------------------------
+# fixtures and plugins for syrupy/regression data testing
+# -------------------------------------------------------------------------
+
+
+@pytest.fixture
+def pandas_snapshot_extention():
+    return PandasSnapshotExtenstion
+
+
+@pytest.fixture
+def numpy_snapshot_extension():
+    return NumpySnapshotExtenstion
+
+
+@pytest.fixture
+def singlefilesanitized():
+    return SingleFileSanitizedNames
diff --git a/tardis/plasma/tests/conftest.py b/tardis/plasma/tests/conftest.py
new file mode 100644
index 00000000000..dab8927219e
--- /dev/null
+++ b/tardis/plasma/tests/conftest.py
@@ -0,0 +1,42 @@
+from pathlib import Path
+
+import pytest
+from syrupy.location import PyTestLocation
+
+SNAPSHOT_LOCATION = "plasma"
+
+
+@pytest.fixture
+def snapshot_pd(snapshot, tardis_snapshot_path, pandas_snapshot_extention):
+    refpath = tardis_snapshot_path.joinpath(SNAPSHOT_LOCATION)
+
+    class PandasSnapshotExtenstionRefdata(pandas_snapshot_extention):
+        @classmethod
+        def dirname(cls, *, test_location: "PyTestLocation") -> str:
+            return str(Path(test_location.filepath).parent.joinpath(refpath))
+
+    return snapshot.use_extension(PandasSnapshotExtenstionRefdata)
+
+
+@pytest.fixture
+def snapshot_np(snapshot, tardis_snapshot_path, numpy_snapshot_extension):
+    refpath = tardis_snapshot_path.joinpath(SNAPSHOT_LOCATION)
+
+    class NumpySnapshotExtenstionRefdata(numpy_snapshot_extension):
+        @classmethod
+        def dirname(cls, *, test_location: "PyTestLocation") -> str:
+            return str(Path(test_location.filepath).parent.joinpath(refpath))
+
+    return snapshot.use_extension(NumpySnapshotExtenstionRefdata)
+
+
+@pytest.fixture
+def snapshot(snapshot, tardis_snapshot_path, singlefilesanitized):
+    refpath = tardis_snapshot_path.joinpath(SNAPSHOT_LOCATION)
+
+    class SingleFileSanitizedRefdata(singlefilesanitized):
+        @classmethod
+        def dirname(cls, *, test_location: "PyTestLocation") -> str:
+            return str(Path(test_location.filepath).parent.joinpath(refpath))
+
+    return snapshot.use_extension(SingleFileSanitizedRefdata)
diff --git a/tardis/plasma/tests/test_complete_plasmas.py b/tardis/plasma/tests/test_complete_plasmas.py
index 4320f0d8284..6231eb11e06 100644
--- a/tardis/plasma/tests/test_complete_plasmas.py
+++ b/tardis/plasma/tests/test_complete_plasmas.py
@@ -2,11 +2,8 @@
 import warnings
 
 import pandas as pd
-import pandas.testing as pdt
 import pytest
 
-import numpy as np
-from numpy.testing import assert_almost_equal
 from tardis.io.configuration.config_reader import Configuration
 from tardis.simulation import Simulation
 
@@ -72,7 +69,6 @@ def idfn(fixture_value):
 
 
 class TestPlasma(object):
-
     general_properties = [
         "beta_rad",
         "g_electron",
@@ -157,18 +153,13 @@ def config(self, request):
         return config
 
     @pytest.fixture(scope="class")
-    def plasma(self, request, chianti_he_db_fpath, config, tardis_ref_data):
+    def plasma(self, chianti_he_db_fpath, config):
         config["atom_data"] = chianti_he_db_fpath
         sim = Simulation.from_config(config)
-        if request.config.getoption("--generate-reference"):
-            sim.plasma.to_hdf(
-                tardis_ref_data, path=config.plasma.save_path, overwrite=True
-            )
-            pytest.skip(f"Reference data saved at {tardis_ref_data}")
         return sim.plasma
 
     @pytest.mark.parametrize("attr", combined_properties)
-    def test_plasma_properties(self, plasma, tardis_ref_data, config, attr):
+    def test_plasma_properties(self, plasma, attr, snapshot_pd, snapshot_np):
         if hasattr(plasma, attr):
             actual = getattr(plasma, attr)
             if hasattr(actual, "unit"):
@@ -177,42 +168,35 @@ def test_plasma_properties(self, plasma, tardis_ref_data, config, attr):
                 actual = pd.Series(actual)
             else:
                 actual = pd.DataFrame(actual)
-            key = os.path.join(config.plasma.save_path, "plasma", attr)
-            expected = tardis_ref_data[key]
-            if type(actual) == pd.DataFrame:
-                pdt.assert_frame_equal(actual, expected)
-            elif type(actual) == pd.Series:
-                pdt.assert_series_equal(actual, expected)
+            if isinstance(actual, (pd.DataFrame, pd.Series)):
+                assert snapshot_pd == actual
             else:
-                raise TypeError(f"Unexpected type {type(actual)}")
-            # we used this before - assert_almost_equal(actual.values, expected.values)
+                assert snapshot_np == actual
         else:
             warnings.warn(f'Property "{attr}" not found')
 
-    def test_levels(self, plasma, tardis_ref_data, config):
+    def test_levels(self, plasma, snapshot_pd, snapshot_np):
         actual = pd.DataFrame(plasma.levels)
-        key = os.path.join(config.plasma.save_path, "plasma", "levels")
-        expected = tardis_ref_data[key]
-        pdt.assert_frame_equal(actual, expected)
+        if isinstance(actual, (pd.DataFrame, pd.Series)):
+            assert snapshot_pd == actual
+        else:
+            assert snapshot_np == actual
 
     @pytest.mark.parametrize("attr", scalars_properties)
-    def test_scalars_properties(self, plasma, tardis_ref_data, config, attr):
+    def test_scalars_properties(self, plasma, attr, snapshot_pd, snapshot_np):
         actual = getattr(plasma, attr)
         if hasattr(actual, "cgs"):
             actual = actual.cgs.value
-        key = os.path.join(config.plasma.save_path, "plasma", "scalars")
-        expected = tardis_ref_data[key][attr]
-        assert_almost_equal(actual, expected)
+        if isinstance(actual, (pd.DataFrame, pd.Series)):
+            assert snapshot_pd == actual
+        else:
+            assert snapshot_np == actual
 
-    def test_helium_treatment(self, plasma, tardis_ref_data, config):
+    def test_helium_treatment(self, plasma, snapshot):
         actual = plasma.helium_treatment
-        key = os.path.join(config.plasma.save_path, "plasma", "scalars")
-        expected = tardis_ref_data[key]["helium_treatment"]
-        assert actual == expected
+        assert snapshot == actual
 
-    def test_zeta_data(self, plasma, tardis_ref_data, config):
+    def test_zeta_data(self, plasma, snapshot_np):
         if hasattr(plasma, "zeta_data"):
             actual = plasma.zeta_data
-            key = os.path.join(config.plasma.save_path, "plasma", "zeta_data")
-            expected = tardis_ref_data[key]
-            assert_almost_equal(actual, expected.values)
+            assert snapshot_np == actual.values
diff --git a/tardis/plasma/tests/test_hdf_plasma.py b/tardis/plasma/tests/test_hdf_plasma.py
index 00edec980d2..01c91cb386b 100644
--- a/tardis/plasma/tests/test_hdf_plasma.py
+++ b/tardis/plasma/tests/test_hdf_plasma.py
@@ -1,21 +1,11 @@
-import os
 import pandas as pd
 import pytest
 
-from numpy.testing import assert_almost_equal
-import pandas.testing as pdt
-from tardis.plasma.properties import property_collections
-
 ###
 # saving and loading of plasma properties in the HDF file
 ###
 
 
-@pytest.fixture(scope="module", autouse=True)
-def to_hdf_buffer(hdf_file_path, simulation_verysimple):
-    simulation_verysimple.plasma.to_hdf(hdf_file_path, overwrite=True)
-
-
 plasma_properties_list = [
     "number_density",
     "beta_rad",
@@ -53,70 +43,48 @@ def to_hdf_buffer(hdf_file_path, simulation_verysimple):
 
 
 @pytest.mark.parametrize("attr", plasma_properties_list)
-def test_hdf_plasma(hdf_file_path, simulation_verysimple, attr):
+def test_hdf_plasma(simulation_verysimple, attr, snapshot_np):
     if hasattr(simulation_verysimple.plasma, attr):
         actual = getattr(simulation_verysimple.plasma, attr)
         if hasattr(actual, "cgs"):
             actual = actual.cgs.value
-        path = os.path.join("plasma", attr)
-        expected = pd.read_hdf(hdf_file_path, path)
-        assert_almost_equal(actual, expected.values)
+        assert snapshot_np == actual
 
 
-def test_hdf_levels(hdf_file_path, simulation_verysimple):
+def test_hdf_levels(simulation_verysimple, snapshot_pd):
     actual = getattr(simulation_verysimple.plasma, "levels")
     if hasattr(actual, "cgs"):
         actual = actual.cgs.value
-    path = os.path.join("plasma", "levels")
-    expected = pd.read_hdf(hdf_file_path, path)
-    pdt.assert_frame_equal(pd.DataFrame(actual), expected)
+    assert snapshot_pd == pd.DataFrame(actual)
 
 
 scalars_list = ["time_explosion", "link_t_rad_t_electron"]
 
 
 @pytest.mark.parametrize("attr", scalars_list)
-def test_hdf_scalars(hdf_file_path, simulation_verysimple, attr):
+def test_hdf_scalars(simulation_verysimple, attr, snapshot_np):
     actual = getattr(simulation_verysimple.plasma, attr)
     if hasattr(actual, "cgs"):
         actual = actual.cgs.value
-    path = os.path.join("plasma", "scalars")
-    expected = pd.read_hdf(hdf_file_path, path)[attr]
-    assert_almost_equal(actual, expected)
+    assert snapshot_np == actual
 
 
-def test_hdf_helium_treatment(hdf_file_path, simulation_verysimple):
+def test_hdf_helium_treatment(simulation_verysimple, snapshot):
     actual = getattr(simulation_verysimple.plasma, "helium_treatment")
-    path = os.path.join("plasma", "scalars")
-    expected = pd.read_hdf(hdf_file_path, path)["helium_treatment"]
-    assert actual == expected
+    assert snapshot == actual
 
 
-def test_atomic_data_uuid(hdf_file_path, simulation_verysimple):
+def test_atomic_data_uuid(simulation_verysimple, snapshot):
     actual = getattr(simulation_verysimple.plasma.atomic_data, "uuid1")
-    path = os.path.join("plasma", "scalars")
-    expected = pd.read_hdf(hdf_file_path, path)["atom_data_uuid"]
-    assert actual == expected
-
-
-@pytest.fixture(scope="module", autouse=True)
-def to_hdf_collection_buffer(hdf_file_path, simulation_verysimple):
-    simulation_verysimple.plasma.to_hdf(
-        hdf_file_path,
-        name="collection",
-        collection=property_collections.basic_inputs,
-        overwrite=True,
-    )
+    assert snapshot == actual
 
 
 collection_properties = ["t_rad", "w", "density"]
 
 
 @pytest.mark.parametrize("attr", collection_properties)
-def test_collection(hdf_file_path, simulation_verysimple, attr):
+def test_collection(simulation_verysimple, attr, snapshot_np):
     actual = getattr(simulation_verysimple.plasma, attr)
     if hasattr(actual, "cgs"):
         actual = actual.cgs.value
-    path = os.path.join("collection", attr)
-    expected = pd.read_hdf(hdf_file_path, path)
-    assert_almost_equal(actual, expected.values)
+    assert snapshot_np == actual
diff --git a/tardis/plasma/tests/test_nlte_excitation.py b/tardis/plasma/tests/test_nlte_excitation.py
index 657d49711c0..884f28af20a 100644
--- a/tardis/plasma/tests/test_nlte_excitation.py
+++ b/tardis/plasma/tests/test_nlte_excitation.py
@@ -1,18 +1,14 @@
-import pandas as pd
 import numpy as np
+import pandas as pd
 import pytest
-from numpy.testing import assert_allclose
-
 
+from tardis.plasma.properties.nlte_excitation_data import NLTEExcitationData
 from tardis.plasma.properties.nlte_rate_equation_solver import (
     NLTERateEquationSolver,
 )
-from tardis.plasma.properties.nlte_excitation_data import NLTEExcitationData
 
 
-def test_prepare_bound_bound_rate_matrix(
-    nlte_atomic_dataset,
-):
+def test_prepare_bound_bound_rate_matrix(nlte_atomic_dataset, snapshot_np):
     """
     Using a simple case of nlte_exc for HI, checks if prepare_bound_bound_rate_matrix generates the correct data.
     """
@@ -73,50 +69,10 @@ def test_prepare_bound_bound_rate_matrix(
         r_lu_matrix,
         simple_beta_sobolev,
     )
-    desired_rate_matrix = [
-        [
-            [-4.41229578e10],
-            [1.09803977e10],
-            [8.87031593e08],
-            [1.83520728e08],
-            [5.71742068e07],
-        ],
-        [
-            [3.54409576e10],
-            [-3.64473689e11],
-            [1.32571818e11],
-            [1.04228424e10],
-            [2.27047121e09],
-        ],
-        [
-            [5.71505717e09],
-            [2.97836962e11],
-            [-1.41199954e12],
-            [6.39719360e11],
-            [5.08905487e10],
-        ],
-        [
-            [2.00818482e09],
-            [4.15382182e10],
-            [1.13720607e12],
-            [-3.74593514e12],
-            [1.98120242e12],
-        ],
-        [
-            [9.58758249e08],
-            [1.41181112e10],
-            [1.41334621e11],
-            [3.09560941e12],
-            [-2.03442061e12],
-        ],
-    ]
     # if this test fails the first thing to check is if the reshape in the
     # methods made a view or a copy. If it's a copy rewrite the function.
-    assert_allclose(
-        desired_rate_matrix,
-        np.array(actual_rate_matrix),
-        rtol=1e-6,
-    )
+    # TODO: allow rtol=1e-6
+    assert snapshot_np == np.array(actual_rate_matrix)
 
 
 @pytest.mark.parametrize(
@@ -124,24 +80,17 @@ def test_prepare_bound_bound_rate_matrix(
         "coll_exc_coeff_values",
         "coll_deexc_coeff_values",
         "number_of_levels",
-        "desired_coeff_matrix",
     ],
     [
         (
             [1, -2, 3],
             [4, 9, 10],
             3,
-            [[1.0, 4.0, 9.0], [1.0, -7.0, 10.0], [-2.0, 3.0, -19.0]],
         ),
         (
             [0.21, 0.045, 0.1234],
             [0.7865, 0.987, 0.00123],
             3,
-            [
-                [-0.255, 0.7865, 0.987],
-                [0.21, -0.9099, 0.00123],
-                [0.045, 0.1234, -0.98823],
-            ],
         ),
     ],
 )
@@ -149,7 +98,7 @@ def test_coll_exc_deexc_matrix(
     coll_exc_coeff_values,
     coll_deexc_coeff_values,
     number_of_levels,
-    desired_coeff_matrix,
+    snapshot_np,
 ):
     """
     Checks the NLTERateEquationSolver.create_coll_exc_deexc_matrix for simple values of species with 3 levels.
@@ -164,4 +113,4 @@ def test_coll_exc_deexc_matrix(
     obtained_coeff_matrix = NLTERateEquationSolver.create_coll_exc_deexc_matrix(
         exc_coeff, deexc_coeff, number_of_levels
     )
-    assert_allclose(obtained_coeff_matrix, desired_coeff_matrix)
+    assert snapshot_np == obtained_coeff_matrix
diff --git a/tardis/plasma/tests/test_nlte_solver.py b/tardis/plasma/tests/test_nlte_solver.py
index beeb345cf6d..fa89a9aab52 100644
--- a/tardis/plasma/tests/test_nlte_solver.py
+++ b/tardis/plasma/tests/test_nlte_solver.py
@@ -1,14 +1,9 @@
-import os
-
-import pytest
 import numpy as np
 import pandas as pd
-from copy import deepcopy
-from numpy.testing import assert_allclose, assert_almost_equal
-from tardis.io.configuration.config_reader import Configuration
-from tardis.model.base import SimulationState
+import pytest
+from numpy.testing import assert_allclose
+
 from tardis.plasma.properties import NLTERateEquationSolver
-from tardis.io.atom_data.base import AtomData
 from tardis.plasma.properties.ion_population import IonNumberDensity
 from tardis.plasma.standard_plasmas import assemble_plasma
 
@@ -144,6 +139,7 @@ def test_rate_matrix(
     simple_total_rad_recomb_coefficients,
     simple_total_col_ion_coefficients,
     simple_total_col_recomb_coefficients,
+    snapshot_np,
 ):
     """
     Using a simple case of nlte_ion for HI and HeII, checks if the calculate_rate_matrix generates the correct data.
@@ -159,18 +155,9 @@ def test_rate_matrix(
         simple_total_col_ion_coefficients,
         simple_total_col_recomb_coefficients,
     )
-    desired_rate_matrix = [
-        [-0.077601, 0.099272, 0.000000, 0.000000, 0.000000, 0.0],
-        [1.000000, 1.000000, 0.000000, 0.000000, 0.000000, 0.0],
-        [0.000000, 0.000000, -0.157263, 0.221960, 0.000000, 0.0],
-        [0.000000, 0.000000, 0.000000, -0.834623, 0.161479, 0.0],
-        [0.000000, 0.000000, 1.000000, 1.000000, 1.000000, 0.0],
-        [0.000000, 1.000000, 0.000000, 1.000000, 2.000000, -1.0],
-    ]
-
-    assert_almost_equal(
-        desired_rate_matrix, np.array(actual_rate_matrix), decimal=6
-    )
+    # TODO: decimal=6
+    # allow for assert_almost_equal
+    assert snapshot_np == np.array(actual_rate_matrix)
 
 
 def test_jacobian_matrix(
@@ -181,6 +168,7 @@ def test_jacobian_matrix(
     simple_total_rad_recomb_coefficients,
     simple_total_col_ion_coefficients,
     simple_total_col_recomb_coefficients,
+    snapshot_np,
 ):
     """
     Using a simple case of nlte_ion for HI and HeII,
@@ -217,15 +205,8 @@ def test_jacobian_matrix(
         simple_total_col_recomb_coefficients,
     )
 
-    desired_jacobian_matrix = [
-        [-0.07760098, 0.09927163, 0.0, 0.0, 0.0, 0.23467404],
-        [1.0, 1.0, 0.0, 0.0, 0.0, 0.0],
-        [0.0, 0.0, -0.15726292, 0.22196045, 0.0, 0.04022076],
-        [0.0, 0.0, 0.0, -0.8346228, 0.16147935, 0.20061248],
-        [0.0, 0.0, 1.0, 1.0, 1.0, 0.0],
-        [0.0, 1.0, 0.0, 1.0, 2.0, -1.0],
-    ]
-    assert_almost_equal(actual_jacobian_matrix, desired_jacobian_matrix)
+    # TODO: allow for assert_almost_equal
+    assert snapshot_np == actual_jacobian_matrix
 
 
 @pytest.fixture
diff --git a/tardis/plasma/tests/test_plasma_contiuum.py b/tardis/plasma/tests/test_plasma_contiuum.py
index 083e5fd65cd..633b47a8036 100644
--- a/tardis/plasma/tests/test_plasma_contiuum.py
+++ b/tardis/plasma/tests/test_plasma_contiuum.py
@@ -1,11 +1,9 @@
-import pytest
 import numpy as np
-from numpy.testing import assert_allclose
+
 from tardis.plasma.properties import YgData
 
 
-def test_exp1_times_exp():
+def test_exp1_times_exp(snapshot_np):
     x = np.array([499.0, 501.0, 710.0])
-    desired = np.array([0.00200000797, 0.0019920397, 0.0014064725])
     actual = YgData.exp1_times_exp(x)
-    assert_allclose(actual, desired)
+    assert snapshot_np == actual
diff --git a/tardis/plasma/tests/test_plasma_vboundary.py b/tardis/plasma/tests/test_plasma_vboundary.py
index 3ea2a53f7f5..af48ac49355 100644
--- a/tardis/plasma/tests/test_plasma_vboundary.py
+++ b/tardis/plasma/tests/test_plasma_vboundary.py
@@ -1,10 +1,10 @@
-import tardis
-import pytest
 import os
+
 import astropy.units as u
+import pytest
 
+import tardis
 from tardis.io.configuration.config_reader import Configuration
-from tardis.io.atom_data.base import AtomData
 from tardis.simulation import Simulation
 
 DATA_PATH = os.path.join(tardis.__path__[0], "plasma", "tests", "data")
diff --git a/tardis/plasma/tests/test_tardis_model_density_config.py b/tardis/plasma/tests/test_tardis_model_density_config.py
index 6bb6ff6dbdf..f3d37dc35a0 100644
--- a/tardis/plasma/tests/test_tardis_model_density_config.py
+++ b/tardis/plasma/tests/test_tardis_model_density_config.py
@@ -3,7 +3,6 @@
 from tardis.io.configuration.config_reader import Configuration
 from tardis.model import SimulationState
 from tardis.plasma.standard_plasmas import assemble_plasma
-from numpy.testing import assert_almost_equal
 
 
 @pytest.fixture
@@ -25,20 +24,16 @@ def raw_plasma(tardis_model_density_config, raw_model, kurucz_atomic_data):
     )
 
 
-def test_electron_densities(raw_plasma):
-    assert_almost_equal(raw_plasma.electron_densities[8], 2.72e14)
-    assert_almost_equal(raw_plasma.electron_densities[3], 2.6e14)
+def test_electron_densities(raw_plasma, snapshot_np):
+    assert snapshot_np == raw_plasma.electron_densities[8]
+    assert snapshot_np == raw_plasma.electron_densities[3]
 
 
-def test_isotope_number_densities(raw_plasma):
-    assert_almost_equal(
-        raw_plasma.isotope_number_density.loc[(28, 56), 0], 9688803936.317898
-    )
-    assert_almost_equal(
-        raw_plasma.isotope_number_density.loc[(28, 58), 1], 13097656958.746628
-    )
+def test_isotope_number_densities(raw_plasma, snapshot_np):
+    assert snapshot_np == raw_plasma.isotope_number_density.loc[(28, 56), 0]
+    assert snapshot_np == raw_plasma.isotope_number_density.loc[(28, 58), 1]
 
 
-def test_t_rad(raw_plasma):
-    assert_almost_equal(raw_plasma.t_rad[5], 76459.592)
-    assert_almost_equal(raw_plasma.t_rad[3], 76399.042)
+def test_t_rad(raw_plasma, snapshot_np):
+    assert snapshot_np == raw_plasma.t_rad[5]
+    assert snapshot_np == raw_plasma.t_rad[3]
diff --git a/tardis/util/syrupy_extensions.py b/tardis/util/syrupy_extensions.py
new file mode 100644
index 00000000000..050fca3a1bc
--- /dev/null
+++ b/tardis/util/syrupy_extensions.py
@@ -0,0 +1,129 @@
+import re
+from typing import Any, List, Tuple
+
+import numpy as np
+import pandas as pd
+from syrupy.data import SnapshotCollection
+from syrupy.extensions.single_file import SingleFileSnapshotExtension, WriteMode
+from syrupy.location import PyTestLocation
+from syrupy.types import SerializableData, SnapshotIndex
+
+
+class SingleFileSanitizedNames(SingleFileSnapshotExtension):
+    # changing write mode to text helps avoid an error message
+    # that comes when files are serialised in syrupy in bytes
+    # either way we won't be serialising files in most cases in bytes
+    _write_mode = WriteMode.TEXT
+    _file_extension = "txt"
+
+    # would change names of all snapshots generated
+    # that use this class- making filenames compliant with python standards.
+    @classmethod
+    def get_snapshot_name(
+        cls, *, test_location: "PyTestLocation", index: "SnapshotIndex"
+    ) -> str:
+        original_name = SingleFileSnapshotExtension.get_snapshot_name(
+            test_location=test_location, index=index
+        )
+        double_under = r"[:\[\]{}]"
+        no_space = r'[,"\']'  # quotes and commas
+
+        name = re.sub(double_under, "__", original_name)
+        name = re.sub(no_space, "", name)
+
+        return f"{name}"
+
+
+class NumpySnapshotExtenstion(SingleFileSanitizedNames):
+    _file_extension = "npy"
+
+    def matches(self, *, serialized_data, snapshot_data):
+        try:
+            if (
+                np.testing.assert_allclose(
+                    np.array(snapshot_data), np.array(serialized_data)
+                )
+                is not None
+            ):
+                return False
+            else:
+                return True
+
+        except:
+            return False
+
+    def _read_snapshot_data_from_location(
+        self, *, snapshot_location: str, snapshot_name: str, session_id: str
+    ):
+        # see https://github.com/tophat/syrupy/blob/f4bc8453466af2cfa75cdda1d50d67bc8c4396c3/src/syrupy/extensions/base.py#L139
+        try:
+            return np.load(snapshot_location)
+
+        except OSError:
+            return None
+
+    @classmethod
+    def _write_snapshot_collection(
+        cls, *, snapshot_collection: SnapshotCollection
+    ) -> None:
+        # see https://github.com/tophat/syrupy/blob/f4bc8453466af2cfa75cdda1d50d67bc8c4396c3/src/syrupy/extensions/base.py#L161
+
+        filepath, data = (
+            snapshot_collection.location,
+            next(iter(snapshot_collection)).data,
+        )
+
+        np.save(filepath, data)
+
+    def serialize(self, data: SerializableData, **kwargs: Any) -> str:
+        return data
+
+
+class PandasSnapshotExtenstion(SingleFileSanitizedNames):
+    _file_extension = "h5"
+
+    def matches(self, *, serialized_data, snapshot_data):
+        try:
+            comparer = {
+                pd.Series: pd.testing.assert_series_equal,
+                pd.DataFrame: pd.testing.assert_frame_equal,
+            }
+            try:
+                comp_func = comparer[type(serialized_data)]
+            except KeyError:
+                raise ValueError(
+                    "Can only compare Series and Dataframes with PandasSnapshotExtenstion."
+                )
+
+            if comp_func(serialized_data, snapshot_data) is not None:
+                return False
+            else:
+                return True
+
+        except:
+            return False
+
+    def _read_snapshot_data_from_location(
+        self, *, snapshot_location: str, snapshot_name: str, session_id: str
+    ):
+        # see https://github.com/tophat/syrupy/blob/f4bc8453466af2cfa75cdda1d50d67bc8c4396c3/src/syrupy/extensions/base.py#L139
+        try:
+            data = pd.read_hdf(snapshot_location)
+            return data
+
+        except OSError:
+            return None
+
+    @classmethod
+    def _write_snapshot_collection(
+        cls, *, snapshot_collection: SnapshotCollection
+    ) -> None:
+        # see https://github.com/tophat/syrupy/blob/f4bc8453466af2cfa75cdda1d50d67bc8c4396c3/src/syrupy/extensions/base.py#L161
+        filepath, data = (
+            snapshot_collection.location,
+            next(iter(snapshot_collection)).data,
+        )
+        data.to_hdf(filepath, "/data")
+
+    def serialize(self, data: SerializableData, **kwargs: Any) -> str:
+        return data
diff --git a/tardis_env3.yml b/tardis_env3.yml
index efa0e7b399e..99224c10a23 100644
--- a/tardis_env3.yml
+++ b/tardis_env3.yml
@@ -68,9 +68,11 @@ dependencies:
   - pytest-html
   - python-dokuwiki
   - coverage
+  - syrupy
 
   # Code quality
   - black =22.3
 
   # Other
   - git-lfs
+

From 84cf2e63fb9d9ccddca5dd3efdd4c29998508bc2 Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Wed, 15 Nov 2023 17:10:19 +0100
Subject: [PATCH 26/35] Add astropy import guard (#2470)

* Add astropy import guard

* mailmap
---
 .mailmap           |  1 +
 tardis/__init__.py | 13 ++++++++++---
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/.mailmap b/.mailmap
index e8de40e3ee3..0525b2ec384 100644
--- a/.mailmap
+++ b/.mailmap
@@ -5,6 +5,7 @@ Alexander Holas <alexander.holas@h-its.org>
 Alexander Holas <alex.holas@gmx.de>
 Alexander Holas <alexander.holas@h-its.org> AlexHls <70367168+AlexHls@users.noreply.github.com>
 Alexander Holas <alexander.holas@h-its.org> AlexHls <alexander.holas@h-its.org>
+Alexander Holas <70367168+AlexHls@users.noreply.github.com>
 
 Alice Harpole <aliceharpole@gmail.com>
 Alice Harpole <aliceharpole@gmail.com> Alice Harpole <harpolea@users.noreply.github.com>
diff --git a/tardis/__init__.py b/tardis/__init__.py
index 14980a8dfed..5d2ec94e90b 100644
--- a/tardis/__init__.py
+++ b/tardis/__init__.py
@@ -12,13 +12,20 @@
 # ----------------------------------------------------------------------------
 
 import sys
+import warnings
 
 # ----------------------------------------------------------------------------
 
-from astropy import physical_constants, astronomical_constants
+if ("astropy.units" in sys.modules) or ("astropy.constants" in sys.modules):
+    warnings.warn(
+        "Astropy is already imported externally. Astropy should be imported"
+        " after TARDIS."
+    )
+else:
+    from astropy import physical_constants, astronomical_constants
 
-physical_constants.set("codata2014")
-astronomical_constants.set("iau2012")
+    physical_constants.set("codata2014")
+    astronomical_constants.set("iau2012")
 
 # ----------------------------------------------------------------------------
 

From 0599113adbadba9f076cbb4e66a3818737cf0cae Mon Sep 17 00:00:00 2001
From: Anirban <anirbaniamdutta@gmail.com>
Date: Mon, 20 Nov 2023 17:16:34 -0500
Subject: [PATCH 27/35] Reading in decay radiation data in atom data (#2471)

* Reading in decay radiation data in atom data

* Added docstring

* Fixes the checksum
---
 tardis/data/atomic_data_repo.yml |  2 +-
 tardis/io/atom_data/base.py      | 11 +++++++++++
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/tardis/data/atomic_data_repo.yml b/tardis/data/atomic_data_repo.yml
index fb746d36fa0..0309eb1ffc9 100644
--- a/tardis/data/atomic_data_repo.yml
+++ b/tardis/data/atomic_data_repo.yml
@@ -6,4 +6,4 @@ kurucz_cd23_chianti_H_He:
     - https://dev.azure.com/tardis-sn/TARDIS/_apis/git/repositories/tardis-refdata/items?path=atom_data/kurucz_cd23_chianti_H_He.h5&resolveLfs=true
     - https://media.githubusercontent.com/media/tardis-sn/tardis-refdata/master/atom_data/kurucz_cd23_chianti_H_He.h5
   uuid: NA
-  md5: 69a304e1e85e06508fe02dd8c5ba9397
+  md5: b95b862ef9f06ac20ad4fa70070af59d
diff --git a/tardis/io/atom_data/base.py b/tardis/io/atom_data/base.py
index a1cf9e8d449..d5cc7dc79ce 100644
--- a/tardis/io/atom_data/base.py
+++ b/tardis/io/atom_data/base.py
@@ -93,6 +93,12 @@ class AtomData(object):
         index: atomic_number, ion_number, level_number_lower, level_number_upper
         columns: A_ul[1/s], nu0[Hz], alpha, beta, gamma
 
+    decay_radiation_data : pandas.DataFrame
+    A dataframe containing the *decay radiation data* with:
+        index: Isotope names
+        columns: atomic_number, element, Rad energy, Rad intensity decay mode.
+        Curated from nndc
+
     Attributes
     ----------
     prepared : bool
@@ -108,6 +114,7 @@ class AtomData(object):
     atomic_number2symbol : OrderedDict
     photoionization_data : pandas.DataFrame
     two_photon_data : pandas.DataFrame
+    decay_radiation_data : pandas.DataFrame
 
     Methods
     -------
@@ -139,6 +146,7 @@ class AtomData(object):
         "yg_data",
         "two_photon_data",
         "linelist",
+        "decay_radiation_data",
     ]
 
     # List of tuples of the related dataframes.
@@ -275,6 +283,7 @@ def __init__(
         yg_data=None,
         two_photon_data=None,
         linelist=None,
+        decay_radiation_data=None,
     ):
         self.prepared = False
 
@@ -337,6 +346,8 @@ def __init__(
         if linelist is not None:
             self.linelist = linelist
 
+        if decay_radiation_data is not None:
+            self.decay_radiation_data = decay_radiation_data
         self._check_related()
 
         self.symbol2atomic_number = OrderedDict(

From 8e0b34936ab3257fd5f5d9fb5e8459937dc09fe3 Mon Sep 17 00:00:00 2001
From: tardis-bot <60989672+tardis-bot@users.noreply.github.com>
Date: Sun, 26 Nov 2023 10:41:06 -0500
Subject: [PATCH 28/35] Pre-release 2023.11.26 (#2477)

Automated changes for pre-release 2023.11.26
---
 .zenodo.json | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index 6385dd3064f..06827c53e3b 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -113,13 +113,13 @@
       "orcid": "0000-0002-8310-0829"
     },
     {
-      "name": "Barbosa, Talytha"
+      "name": "Sondhi, Dhruv"
     },
     {
-      "name": "O'Brien, Jack"
+      "name": "Barbosa, Talytha"
     },
     {
-      "name": "Sondhi, Dhruv"
+      "name": "O'Brien, Jack"
     },
     {
       "name": "Yu, Jenny"
@@ -128,10 +128,10 @@
       "name": "Patel, Maryam"
     },
     {
-      "name": "Rathi, Shikha"
+      "name": "Varanasi, Kaushik"
     },
     {
-      "name": "Varanasi, Kaushik"
+      "name": "Rathi, Shikha"
     },
     {
       "name": "Chitchyan, Sona"
@@ -207,13 +207,13 @@
       "name": "Bhakar, Jayant"
     },
     {
-      "name": "Floers, Andreas"
+      "name": "Reichenbach, John"
     },
     {
-      "name": "Actions, GitHub"
+      "name": "Floers, Andreas"
     },
     {
-      "name": "Reichenbach, John"
+      "name": "Actions, GitHub"
     },
     {
       "name": "Jain, Rinkle"
@@ -222,13 +222,13 @@
       "name": "Singh, Sourav"
     },
     {
-      "name": "Chaumal, Aarya"
+      "name": "Brar, Antreev"
     },
     {
-      "name": "Brar, Antreev"
+      "name": "Dutta, Anirban"
     },
     {
-      "name": "Kumar, Aman"
+      "name": "Chaumal, Aarya"
     },
     {
       "name": "Matsumura, Yuki"
@@ -240,7 +240,10 @@
       "name": "Kowalski, Nathan"
     },
     {
-      "name": "Dutta, Anirban"
+      "name": "Kumar, Aman"
+    },
+    {
+      "name": "Gupta, Harshul"
     },
     {
       "name": "Selsing, Jonatan"
@@ -251,9 +254,6 @@
     {
       "name": "Sofiatti, Caroline"
     },
-    {
-      "name": "Gupta, Harshul"
-    },
     {
       "name": "Prasad, Shilpi"
     },

From a7534c1a556fa214bd87e743d854103d3bd06b5c Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Mon, 27 Nov 2023 18:06:42 +0100
Subject: [PATCH 29/35] Update plasma configuration documentation (#2459)

* update plasma docs

* Update mailmap

* Fix typo
---
 docs/io/configuration/components/plasma.rst | 23 +++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/docs/io/configuration/components/plasma.rst b/docs/io/configuration/components/plasma.rst
index 448d0a48545..4a27598d2fe 100644
--- a/docs/io/configuration/components/plasma.rst
+++ b/docs/io/configuration/components/plasma.rst
@@ -16,10 +16,10 @@ ionization equilibrium and level population calculations (see :ref:`plasma` for
 The radiative rates describe how to calculate the :math:`J_\textrm{blue}` needed for the :ref:`nlte` calculations and
 :ref:`macroatom` calculations. There are three options for ``radiative_rates_type``: 
  
-1) ``lte``, in which
+1) ``blackbody``, in which
 :math:`J_\textrm{blue} = \textrm{Blackbody}(T_\textrm{rad})`
  
-2) ``nebular`` in which
+2) ``dilute-blackbody`` in which
 :math:`J_\textrm{blue} = W \times \textrm{Blackbody}(T_\textrm{rad})`
  
 3) ``detailed`` in which the :math:`J_\textrm{blue}`
@@ -32,6 +32,25 @@ version of ``macroatom`` in which only downward transitions are allowed (see :re
 Finally, ``w_epsilon`` describes the dilution factor to use to calculate :math:`J_\textrm{blue}` that are 0, which
 causes problems with the code (so :math:`J_\textrm{blue}` are set to a very small number).
 
+Continuum Interaction
+^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: yaml
+
+    plasma:
+        link_t_rad_t_electron: 1.0
+        continuum_interaction:
+            species:
+                - H I
+                - H II
+                - He I
+                - He II 
+            enable_adiabatic_cooling: True
+
+This will add continuum interactions for all specified species. Setting :math:`T_\textrm{rad} = T_\textrm{electron}` through 
+``link_t_rad_t_electron: 1.0`` is recommended to enforce LTE (unless the simulation uses NLTE treatment). 
+``enable_adiabatic_cooling`` enables adiabatic cooling.
+
 NLTE
 ^^^^
 

From a3fb19fd0a3f912d4f57b8b034dfbfa7b777b2c7 Mon Sep 17 00:00:00 2001
From: Alexander Holas <70367168+AlexHls@users.noreply.github.com>
Date: Mon, 27 Nov 2023 23:52:38 +0100
Subject: [PATCH 30/35] Add ruff rules and docs (#2478)

* Add ruff rules and docs

* Update pyproject.toml

Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>

* rebuild docs

---------

Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
---
 .ruff.toml                                    | 230 ++++++++++++++++++
 .../contributing/development/code_quality.rst |  17 ++
 pyproject.toml                                |  80 ++++++
 3 files changed, 327 insertions(+)
 create mode 100644 .ruff.toml

diff --git a/.ruff.toml b/.ruff.toml
new file mode 100644
index 00000000000..0a6e49c83ae
--- /dev/null
+++ b/.ruff.toml
@@ -0,0 +1,230 @@
+# Ruff configuration file adapted from astropy
+extend = "pyproject.toml"
+lint.ignore = [
+    # NOTE: to find a good code to fix, run:
+    # ruff --select="ALL" --statistics astropy/<subpackage>
+
+    # flake8-annotations (ANN) : static typing
+    "ANN001",  # Function argument without type annotation
+    "ANN003",  # `**kwargs` without type annotation
+    "ANN201",  # Public function without return type annotation
+    "ANN202",  # Private function without return type annotation
+    "ANN401",  # Use of `Any` type
+
+    # flake8-unused-arguments (ARG)
+    "ARG001",  # unused-function-argument
+    "ARG002",  # unused-method-argument
+    "ARG003",  # unused-class-method-argument
+    "ARG004",  # unused-static-method-argument
+    "ARG005",  # unused-lambda-argument
+
+    # flake8-bugbear (B)
+    "B006",  # MutableArgumentDefault
+    "B007",  # UnusedLoopControlVariable
+    "B023",  # FunctionUsesLoopVariable
+    "B028",  # No-explicit-stacklevel
+    "B904",  # RaiseWithoutFromInsideExcept
+    "B905",  # ZipWithoutExplicitStrict   # requires 3.10+
+
+    # flake8-blind-except (BLE)
+    "BLE001",  # blind-except
+
+    # mccabe (C90) : code complexity
+    # TODO: configure maximum allowed complexity.
+    "C901",  # McCabeComplexity
+
+    # pydocstyle (D)
+    # Missing Docstrings
+    "D100",  # undocumented-public-module
+    "D101",  # undocumented-public-class
+    "D103",  # undocumented-public-function
+    "D104",  # undocumented-public-package
+    "D205",  # blank-line-after-summary
+    # Quotes Issues
+    "D300",  # triple-single-quotes
+    "D301",  # escape-sequence-in-docstring
+    # Docstring Content Issues
+    "D403",  # first-line-capitalized
+    "D404",  # docstring-starts-with-this
+    "D401",  # non-imperative-mood.
+    "D414",  # empty-docstring-section
+    "D419",  # docstring is empty
+
+    # flake8-datetimez (DTZ)
+    "DTZ001",  # call-datetime-without-tzinfo
+    "DTZ005",  # call-datetime-now-without-tzinfo
+
+    # pycodestyle (E, W)
+    "E501",  # line-too-long
+    "E721",  # type-comparison
+    "E731",  # lambda-assignment
+
+    # flake8-errmsg (EM)  : nicer error tracebacks
+    "EM101",   # raw-string-in-exception
+    "EM102",   # f-string-in-exception
+    "EM103",   # dot-format-in-exception
+
+    # eradicate (ERA)
+    # NOTE: be careful that developer notes are kept.
+    "ERA001",  # commented-out-code
+
+    # flake8-executable (EXE)
+    "EXE002",  # shebang-missing-executable-file
+
+    # Pyflakes (F)
+    "F841",  # unused-variable
+
+    # flake8-boolean-trap (FBT)  : boolean flags should be kwargs, not args
+    # NOTE: a good thing to fix, but changes API.
+    "FBT001",  # boolean-positional-arg-in-function-definition
+    "FBT002",  # boolean-default-value-in-function-definition
+    "FBT003",  # boolean-positional-value-in-function-call
+
+    # flake8-fixme (FIX)
+    "FIX001",  # Line contains FIXME.  this should be fixed or at least FIXME replaced with TODO
+    "FIX004",  # Line contains HACK. replace HACK with NOTE.
+
+    # flake8-import-conventions (ICN)  : use conventional import aliases
+    "ICN001",  # import-conventions
+
+    # pep8-naming (N)
+    # NOTE: some of these can/should be fixed, but this changes the API.
+    "N801",  # invalid-class-name
+    "N802",  # invalid-function-name
+    "N803",  # invalid-argument-name
+    "N804",  # invalid-first-argument-name-for-class-method
+    "N805",  # invalid-first-argument-name-for-method
+    "N807",  # dunder-function-name
+    "N813",  # camelcase-imported-as-lowercase
+    "N815",  # mixed-case-variable-in-class-scope
+    "N816",  # mixed-case-variable-in-global-scope
+    "N818",  # error-suffix-on-exception-name
+
+    # NumPy-specific rules (NPY)
+    "NPY002", # Replace legacy `np.random.rand` call with `np.random.Generator`  (2023-05-03)
+
+    # Perflint (PERF)
+    "PERF203",  # `try`-`except` within a loop incurs performance overhead
+    "PERF401",  # Use a list comprehension to create a transformed list
+
+    # pygrep-hooks (PGH)
+    "PGH001",  # eval
+
+    # Pylint (PLC, PLE, PLR, PLW)
+    "PLE0101",  # return-in-init
+    "PLR0124",  # Name compared with itself
+    "PLR0402",  # ConsiderUsingFromImport
+    "PLR0911",  # too-many-return-statements
+    "PLR0912",  # too-many-branches
+    "PLR0913",  # too-many-args
+    "PLR0915",  # too-many-statements
+    "PLR1714",  # Consider merging multiple comparisons
+    "PLR2004",  # MagicValueComparison
+    "PLR5501",  # collapsible-else-if
+    "PLW0603",  # global-statement
+    "PLW2901",  # redefined-loop-name
+
+    # flake8-pytest-style (PT)
+    "PT001",   # pytest-fixture-incorrect-parentheses-style
+    "PT003",   # pytest-extraneous-scope-function
+    "PT004",   # pytest-missing-fixture-name-underscore
+    "PT006",   # pytest-parametrize-names-wrong-type
+    "PT007",   # pytest-parametrize-values-wrong-type
+    "PT011",   # pytest-raises-too-broad
+    "PT012",   # pytest-raises-with-multiple-statements
+    "PT017",   # pytest-assert-in-exceptinstead
+    "PT018",   # pytest-composite-assertion
+    "PT022",   # pytest-useless-yield-fixture
+    "PT023",   # pytest-incorrect-mark-parentheses-style
+
+    # flake8-use-pathlib (PTH)
+    "PTH100",  # os-path-abspath
+    "PTH101",  # os-chmod
+    "PTH102",  # os-mkdir
+    "PTH103",  # os-makedirs
+    "PTH104",  # os-rename
+    "PTH107",  # os-remove
+    "PTH108",  # os-unlink
+    "PTH109",  # os-getcwd
+    "PTH110",  # os-path-exists
+    "PTH111",  # os-path-expanduser
+    "PTH112",  # os-path-isdir
+    "PTH113",  # os-path-isfile
+    "PTH118",  # os-path-join
+    "PTH119",  # os-path-basename
+    "PTH120",  # os-path-dirname
+    "PTH122",  # os-path-splitext
+    "PTH123",  # builtin-open
+    "PTH202",  # `os.path.getsize` should be replaced by `Path.stat().st_size`
+    "PTH207",  # Replace `glob` with `Path.glob` or `Path.rglob`
+
+    # flake8-return (RET)
+    "RET501",  # unnecessary-return-none
+    "RET502",  # implicit-return-value
+    "RET503",  # implicit-return
+    "RET504",  # unnecessary-assign
+    "RET505",  # superfluous-else-return
+    "RET506",  # superfluous-else-raise
+    "RET507",  # superfluous-else-continue
+
+    # flake8-raise (RSE)
+    "RSE102",  # unnecessary-paren-on-raise-exception
+
+    # Ruff-specific rules (RUF)
+    "RUF001",  # ambiguous-unicode-character-string
+    "RUF002",  # ambiguous-unicode-character-docstring
+    "RUF010",  # use conversion in f-string
+    "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar`
+
+    # flake8-bandit (S)
+    "S101",  # Use of `assert` detected
+    "S105",  # hardcoded-password-string
+    "S110",  # try-except-pass
+    "S112",  # try-except-continue
+    "S301",  # suspicious-pickle-usage
+    "S307",  # Use of possibly insecure function; consider using `ast.literal_eval`
+    "S311",  # suspicious-non-cryptographic-randomness
+    "S324",  # hashlib-insecure-hash-function
+    "S506",  # UnsafeYAMLLoad
+    "S310",  # Suspicious-url-open-usage
+    "S603",  # `subprocess` call: check for execution of untrusted input
+    "S607",  # Starting a process with a partial executable path
+
+    # flake8-simplify (SIM)
+    "SIM102",  # NestedIfStatements
+    "SIM105",  # UseContextlibSuppress
+    "SIM108",  # UseTernaryOperator
+    "SIM114",  # if-with-same-arms
+    "SIM115",  # OpenFileWithContextHandler
+    "SIM117",  # MultipleWithStatements
+    "SIM118",  # KeyInDict
+    "SIM201",  # NegateEqualOp
+    "SIM300",  # yoda condition
+
+    # flake8-print (T20)
+    "T201",  # PrintUsed
+
+    # flake8-todos (TD)
+    "TD001",  # Invalid TODO tag
+    "TD003",  # Missing issue link on the line following this TODO
+    "TD004",  # Missing colon in TODO
+    "TD007",  # Missing space after colon in TODO
+
+    # tryceratops (TRY)
+    "TRY002",  # raise-vanilla-class
+    "TRY003",  # raise-vanilla-args
+    "TRY004",  # prefer-type-error
+    "TRY200",  # reraise-no-cause
+    "TRY201",  # verbose-raise
+    "TRY300",  # Consider `else` block
+    "TRY301",  # raise-within-try
+
+    # flake8-quotes (Q)
+    "Q000",  # use double quotes
+]
+lint.unfixable = [
+    "E711"  # NoneComparison. Hard to fix b/c numpy has it's own None.
+]
+
+[lint.extend-per-file-ignores]
+"docs/*" = []
diff --git a/docs/contributing/development/code_quality.rst b/docs/contributing/development/code_quality.rst
index cd5ae10bc6d..71f8196315c 100644
--- a/docs/contributing/development/code_quality.rst
+++ b/docs/contributing/development/code_quality.rst
@@ -26,6 +26,23 @@ A better method is to run Black automatically - first `integrate it within the c
 
 .. warning :: If your code doesn't follow the Black code style, then the Black-check action on your PR will fail.
 
+Ruff
+----
+`Ruff <https://docs.astral.sh/ruff/>`_ is a code linter and formatter that checks for common mistakes and automatically fixes them. It is currently not installed in the TARDIS conda environment, so you will have to install it manually: ::
+
+    conda install -c conda-forge ruff
+
+To run Ruff, use the following command: ::
+
+    ruff check <source_file_or_directory> # Lints the code
+    ruff check <source_file_or_directory> --fix # Lints and fixes any fixable errors
+
+Currently, Ruff is not integrated with the TARDIS CI and is not a requirement for merging a PR. However, it is recommended to run Ruff on your code before commiting it to ensure that new code already follows these rules.
+
+.. note :: We adopt the linting rules utilized by astropy. Permanent rules are defined in the ``pyproject.toml``, non-permanent rules are defined in the ``.ruff.toml`` file. If you want to add a new rule, please add it to the ``.ruff.toml`` file. If you want to add a permanent rule, please open a PR to the ``pyproject.toml``.
+
+.. note :: Ruff can also be used for formatting code, but for now we recommend using Black for this purpose as the CI is configured to run Black on all PRs.
+
 Naming Conventions
 ------------------
 
diff --git a/pyproject.toml b/pyproject.toml
index aa87db29650..0c71b4acb60 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -48,3 +48,83 @@ omit-covered-files = false
 quiet = false
 verbose = 0
 #whitelist-regex = []
+
+[tool.ruff]
+lint.select = ["ALL"]
+exclude=[]
+lint.ignore = [  # NOTE: non-permanent exclusions should be added to `.ruff.toml` instead.
+
+    # flake8-builtins (A) : shadowing a Python built-in.
+    # New ones should be avoided and is up to maintainers to enforce.
+    "A00",
+
+    # flake8-annotations (ANN)
+    "ANN101",  # No annotation for `self`.
+    "ANN102",  # No annotation for `cls`.
+
+    # flake8-bugbear (B)
+    "B008",  # FunctionCallArgumentDefault
+
+    # flake8-commas (COM)
+    "COM812",  # TrailingCommaMissing
+    "COM819",  # TrailingCommaProhibited
+
+    # pydocstyle (D)
+    # Missing Docstrings
+    "D102",  # Missing docstring in public method. Don't check b/c docstring inheritance.
+    "D105",  # Missing docstring in magic method. Don't check b/c class docstring.
+    # Whitespace Issues
+    "D200",  # FitsOnOneLine
+    # Docstring Content Issues
+    "D410",  # BlankLineAfterSection. Using D412 instead.
+    "D400",  # EndsInPeriod.  NOTE: might want to revisit this.
+
+    # pycodestyle (E, W)
+    "E711",  # NoneComparison  (see unfixable)
+    "E741",  # AmbiguousVariableName. Physics variables are often poor code variables
+
+    # flake8-fixme (FIX)
+    "FIX002",  # Line contains TODO | notes for improvements are OK iff the code works
+
+    # pep8-naming (N)
+    "N803",  # invalid-argument-name. Physics variables are often poor code variables
+    "N806",  # non-lowercase-variable-in-function. Physics variables are often poor code variables
+
+    # pandas-vet (PD)
+    "PD",
+
+    # flake8-self (SLF)
+    "SLF001", # private member access
+
+    # flake8-todos (TD)
+    "TD002",  # Missing author in TODO
+
+    # Ruff-specific rules (RUF)
+    "RUF005",  # unpack-instead-of-concatenating-to-collection-literal -- it's not clearly faster.
+]
+
+[tool.ruff.lint.extend-per-file-ignores]
+"setup.py" = ["INP001"]  # Part of configuration, not a package.
+".github/workflows/*.py" = ["INP001"]
+"test_*.py" = [
+    "B018",  # UselessExpression
+    "D",  # pydocstyle
+    "E402",  # Module level import not at top of file
+    "PGH001",  # No builtin eval() allowed
+    "S101",  # Use of assert detected
+]
+".pyinstaller/*.py" = ["INP001"]  # Not a package.
+"conftest.py" = ["INP001"]  # Part of configuration, not a package.
+"docs/*.py" = [
+    "INP001",  # implicit-namespace-package. The examples are not a package.
+]
+
+[tool.ruff.lint.flake8-annotations]
+ignore-fully-untyped = true
+mypy-init-return = true
+
+[tool.ruff.lint.isort]
+known-first-party = ["tardis", "carsus", "stardis"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"

From 799e35ba7f333c15b9ab451dac3a287f4d73f4d5 Mon Sep 17 00:00:00 2001
From: Anirban <anirbaniamdutta@gmail.com>
Date: Mon, 27 Nov 2023 17:54:32 -0500
Subject: [PATCH 31/35] Decay energy chain (#2448)

* Added a function to calculate shell masses

* Added a function to calculate shell masses

* changed shell masses with the new function

* Changed mass fraction to masses in to_inventories()

* Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@users.noreply.github.com>

* Added a function to calculate total decays

* Added a function to calculate energies from gamma rays and positrons.

* added a function to calculate average energies of gamma rays and positrons

* Added a fucntion to calculate each decay chain energies

* Added dictionaries to handle multiple isotopes

* Changed value to values

* added tests for gamma_ray_transport

* Added tests for calculating activity

* Added test for activity

* Added tests for two isotope

* Changed Ni_isotope_mass

* Added pytest paramterize

* Added test for calculating shell masses

* Ran test for checking activity of parent nuclide with analytical solution.

* The function test_activity matches with the radioactivedecay output upto 14 decimal places. The Avogadro's number used in radioactivedecay is not from astropy.

* Added tests for checking if iso_dict is returning the right key.

* Added test for inventories dictionary.

* Added a test to check if the calculate_average_energy function passes the right list ahead.

* Added new function for testing energy budget from each decay chain.

* Added a new function for energy per mass

* Reading in decay radiation data in atom data

* Add

* Added tests for gamma ray transport.

* Added tests for all functions for gamma_ray_transport. Added docstrings.

* Changing decay energy chain

* Added a function to get taus

* Added tests for multiple isotopes

* Fixes the test calculate shell masses with hand calculated values
---
 tardis/energy_input/energy_source.py          |   2 +-
 tardis/energy_input/gamma_ray_transport.py    | 580 +++++++-----------
 .../tests/test_gamma_ray_transport.py         | 306 +++++++++
 ...sity_exponential_nebular_multi_isotope.yml |  52 ++
 tardis/io/decay.py                            |   9 +-
 5 files changed, 594 insertions(+), 355 deletions(-)
 create mode 100644 tardis/energy_input/tests/test_gamma_ray_transport.py
 create mode 100644 tardis/io/configuration/tests/data/tardis_configv1_density_exponential_nebular_multi_isotope.yml

diff --git a/tardis/energy_input/energy_source.py b/tardis/energy_input/energy_source.py
index 1be7f6e5a74..4fa33734944 100644
--- a/tardis/energy_input/energy_source.py
+++ b/tardis/energy_input/energy_source.py
@@ -190,7 +190,7 @@ def get_nuclear_lines_database(
     pandas DataFrame
         The decay radiation lines
     """
-    decay_radiation_db = pd.read_hdf(path, "decay_data")
+    decay_radiation_db = pd.read_hdf(path, "decay_radiation_data")
     return decay_radiation_db
 
 
diff --git a/tardis/energy_input/gamma_ray_transport.py b/tardis/energy_input/gamma_ray_transport.py
index 6aea2856080..7542572ce2b 100644
--- a/tardis/energy_input/gamma_ray_transport.py
+++ b/tardis/energy_input/gamma_ray_transport.py
@@ -178,7 +178,6 @@ def initialize_packets(
 
     packet_index = 0
     for k, shell in enumerate(decays_per_shell):
-
         initial_radii = initial_packet_radius(
             shell, inner_velocities[k], outer_velocities[k]
         )
@@ -261,7 +260,6 @@ def initialize_packets(
 
 
 def calculate_shell_masses(model):
-
     """Function to calculate shell masses
     Parameters
     ----------
@@ -274,186 +272,162 @@ def calculate_shell_masses(model):
 
     """
 
-    ejecta_density = model.density.to("g/cm^3").value
-    ejecta_volume = model.volume.to("cm^3").value
-    shell_masses = ejecta_volume * ejecta_density
-
-    return shell_masses
-
-
-def main_gamma_ray_loop(
-    num_decays,
-    model,
-    plasma,
-    time_steps=10,
-    time_end=80.0,
-    grey_opacity=-1,
-    spectrum_bins=500,
-    time_space="log",
-    photoabsorption_opacity="tardis",
-    pair_creation_opacity="tardis",
-    seed=1,
-    path_to_decay_data="~/Downloads/tardisnuclear/decay_radiation.h5",
-    positronium_fraction=0.0,
-):
-    """Main loop that determines the gamma ray propagation
+    ejecta_density = model.density.to("g/cm^3")
+    ejecta_volume = model.volume.to("cm^3")
+    return (ejecta_volume * ejecta_density).to(u.g)
 
+
+def calculate_total_decays(inventories, time_delta):
+    """Function to create inventories of isotope
     Parameters
     ----------
-    num_decays : int
-        Number of decays requested
-    model : tardis.SimulationState
+    model : tardis.Radial1DModel
         The tardis model to calculate gamma ray propagation through
-    plasma : tardis.plasma.BasePlasma
-        The tardis plasma with calculated atomic number density
-    time_steps : int
-        Number of time steps requested
+
     time_end : float
         End time of simulation in days
-    grey_opacity : float
-        Grey photoabsorption opacity for gamma-rays in cm^2 g^-1, set to -1 to turn off
-    spectrum_bins : int
-        Number of energy bins for the gamma-ray spectrum
-    time_space : str
-        `'log'` for log-space time steps, otherwise time steps will be linear
-    photoabsorption_opacity : str
-        Set the photoabsorption opacity calculation.
-        Defaults to Ambwani & Sutherland (1988) approximation.
-        `'kasen'` uses the Kasen et al. 2006 method.
-    pair_creation_opacity : str
-        Set the pair creation opacity calculation. Defaults to Ambwani & Sutherland (1988) approximation.
-        `'artis'` uses the ARTIS implementation of the Ambwani & Sutherland (1988) approximation.
-    seed : int
-        Sets the seed for the random number generator. Uses deprecated methods.
-    path_to_decay_data : str
-        The path to a decay radiation file from the `nuclear` package.
+    Returns
+    -------
+        Total decay list : List
+            list of total decays for x g of isotope for time 't'
 
+    """
+
+    time_delta = u.Quantity(time_delta, u.s)
+
+    total_decays_list = []
+    for inv in inventories:
+        total_decays = inv.cumulative_decays(time_delta.value)
+        total_decays_list.append(total_decays)
+
+    return total_decays_list
+
+
+def create_isotope_dicts(raw_isotope_abundance, shell_masses):
+    """
+    Function to create a dictionary of isotopes for each shell with their masses.
+    Parameters
+    ----------
+    raw_isotope_abundance : pd.DataFrame
+        isotope abundance in mass fractions.
+    shell_masses : numpy.ndarray
+        shell masses in units of g
     Returns
     -------
-    pandas.DataFrame
-        Energy per shell per time in units of eV/s/cm^-3
-    pandas.DataFrame
-        Columns:
-        packet index,
-        Energy input per packet,
-        radius of deposition,
-        time of deposition,
-        compton opacity,
-        photoabsorption opacity,
-        pair creation opacity
-    pandas.DataFrame
-        Energy of escaping packets
-    numpy.ndarray
-        Packets emitted per shell
-    pandas.DataFrame
-        Energy from positrons
-    pandas.DataFrame
-        Estimated energy deposition in units of keV/s/cm^-3
+        isotope_dicts : Dict
+            dictionary of isotopes for each shell with their ``masses``.
+            For eg: {0: {(28, 56): {'Ni56': 0.0001}, (27, 57): {'Co56': 0.0001}}
+                    {1: {(28, 56): {'Ni56': 0.0001}, (27, 57): {'Co56': 0.0001}}} etc
+
     """
-    # Note: not best numpy practice, but works better in numba than the alternatives
-    np.random.seed(seed)
-
-    # Enforce cgs
-    outer_velocities = model.v_outer.to("cm/s").value
-    inner_velocities = model.v_inner.to("cm/s").value
-    ejecta_density = model.density.to("g/cm^3").value
-    ejecta_volume = model.volume.to("cm^3").value
-    ejecta_velocity_volume = (
-        4 * np.pi / 3 * (outer_velocities**3.0 - inner_velocities**3.0)
-    )
-    time_explosion = model.time_explosion.to("s").value
-    number_of_shells = model.no_of_shells
-    raw_isotope_abundance = model.raw_isotope_abundance.sort_values(
-        by=["atomic_number", "mass_number"], ascending=False
-    )
+    isotope_dicts = {}
+    for i in range(len(raw_isotope_abundance.columns)):
+        isotope_dicts[i] = {}
+        for (
+            atomic_number,
+            mass_number,
+        ), abundances in raw_isotope_abundance.iterrows():
+            isotope_dicts[i][atomic_number, mass_number] = {}
+            nuclear_symbol = f"{rd.utils.Z_to_elem(atomic_number)}{mass_number}"
+            isotope_dicts[i][atomic_number, mass_number][nuclear_symbol] = (
+                abundances[i] * shell_masses[i].to(u.g).value
+            )
 
-    shell_masses = calculate_shell_masses(model)
+    return isotope_dicts
 
-    time_start = time_explosion
-    time_end *= u.d.to(u.s)
 
-    assert (
-        time_start < time_end
-    ), "Error, simulation start time greater than end time!"
+def create_inventories_dict(isotope_dict):
+    """Function to create dictionary of inventories for each shell
+    Parameters
+    ----------
+    isotope_dict : Dict
+        dictionary of isotopes for each shell with their ``masses``.
+    Returns
+    -------
+        inv : Dict
+            dictionary of inventories for each shell
+            For eg: {0: {'Ni56': <radioactivedecay.Inventory at 0x7f7d2c0d0e50>,
+                         'Co56': <radioactivedecay.Inventory at 0x7f7d2c0d0e50>},
+                    {1: {'Ni56': <radioactivedecay.Inventory at 0x7f7d2c0d0e50>,
+                         'Co56': <radioactivedecay.Inventory at 0x7f7d2c0d0e50>}} etc
+    """
+    inv = {}
+    for shell, isotopes in isotope_dict.items():
+        inv[shell] = {}
+        for isotope, name in isotopes.items():
+            inv[shell][isotope] = rd.Inventory(name, "g")
 
-    if time_space == "log":
-        times = np.geomspace(time_start, time_end, time_steps + 1)
-    else:
-        times = np.linspace(time_start, time_end, time_steps + 1)
+    return inv
 
-    dt_array = np.diff(times)
-    effective_time_array = np.array(
-        [np.sqrt(times[i] * times[i + 1]) for i in range(time_steps)]
-    )
 
-    # Use isotopic number density
-    for atom_number in plasma.isotope_number_density.index.get_level_values(0):
-        values = plasma.isotope_number_density.loc[atom_number].values
-        if values.shape[1] > 1:
-            plasma.number_density.loc[atom_number] = np.sum(values, axis=0)
-        else:
-            plasma.number_density.loc[atom_number] = values
-
-    # Calculate electron number density
-    electron_number_density = (
-        plasma.number_density.mul(plasma.number_density.index, axis=0)
-    ).sum()
-
-    electron_number_density_time = np.zeros(
-        (len(ejecta_velocity_volume), len(effective_time_array))
-    )
+def calculate_total_decays(inventory_dict, time_delta):
+    """
+    Function to calculate total decays for each isotope in each shell
+    Parameters
+    ----------
+    inventory_dict : Dict
+        dictionary of inventories for each shell
+    time_delta : float
+        time interval in units of time (days/mins/secs etc)
+    Returns
+    -------
+        total_decays : Dict
+            dictionary of total decays for each isotope in each shell
 
-    mass_density_time = np.zeros(
-        (len(ejecta_velocity_volume), len(effective_time_array))
-    )
+    """
+    time_delta = u.Quantity(time_delta, u.s)
+    total_decays = {}
+    for shell, isotopes in inventory_dict.items():
+        total_decays[shell] = {}
+        for isotope, name in isotopes.items():
+            total_decays[shell][isotope] = name.cumulative_decays(
+                time_delta.value
+            )
 
-    electron_number = (electron_number_density * ejecta_volume).to_numpy()
+    return total_decays
 
-    inv_volume_time = np.zeros(
-        (len(ejecta_velocity_volume), len(effective_time_array))
-    )
 
-    # Pre-calculate quantities as they change with time
-    for i, t in enumerate(effective_time_array):
-        inv_volume_time[:, i] = (1.0 / ejecta_velocity_volume) / (t**3.0)
-        mass_density_time[:, i] = shell_masses * inv_volume_time[:, i]
-        electron_number_density_time[:, i] = (
-            electron_number * inv_volume_time[:, i]
-        )
+def calculate_average_energies(raw_isotope_abundance, gamma_ray_lines):
+    """
+    Function to calculate average energies of positrons and gamma rays
+    from a list of gamma ray lines from nndc.
+    Parameters
+    ----------
+    raw_isotope_abundance : pd.DataFrame
+        isotope abundance in mass fractions
+    gamma_ray_lines : pd.DataFrame
+        decay data
 
-    energy_df_rows = np.zeros((number_of_shells, time_steps))
+    Returns
+    -------
+    average_energies_list : List
+        list of gamma ray energies
+    average_positron_energies_list : List
+        list of positron energies
+    gamma_ray_line_array_list : List
+        list of gamma ray lines
 
-    # Calculate number of packets per shell based on the mass of isotopes
-    number_of_isotopes = plasma.isotope_number_density * ejecta_volume
-    total_number_isotopes = number_of_isotopes.sum(axis=1)
+    """
 
-    inventories = raw_isotope_abundance.to_inventories()
     all_isotope_names = get_all_isotopes(raw_isotope_abundance)
     all_isotope_names.sort()
 
-    gamma_ray_lines = get_nuclear_lines_database(path_to_decay_data)
-
-    taus = {}
-    parents = {}
     gamma_ray_line_array_list = []
     average_energies_list = []
     average_positron_energies_list = []
 
-    for i, isotope in enumerate(all_isotope_names):
-        nuclide = rd.Nuclide(isotope)
-        taus[isotope] = nuclide.half_life() / np.log(2)
-        child = nuclide.progeny()
-        if child is not None:
-            for c in child:
-                if rd.Nuclide(c).half_life("readable") != "stable":
-                    parents[c] = isotope
+    gamma_ray_line_dict = {}
+    average_energies = {}
+    average_positron_energies = {}
 
+    for i, isotope in enumerate(all_isotope_names):
         energy, intensity = setup_input_energy(
             gamma_ray_lines[gamma_ray_lines.index == isotope.replace("-", "")],
             "g",
         )
+        average_energies_list.append(np.sum(energy * intensity))  # keV
         gamma_ray_line_array_list.append(np.stack([energy, intensity]))
-        average_energies_list.append(np.sum(energy * intensity))
+
         positron_energy, positron_intensity = setup_input_energy(
             gamma_ray_lines[gamma_ray_lines.index == isotope.replace("-", "")],
             "bp",
@@ -462,13 +436,8 @@ def main_gamma_ray_loop(
             np.sum(positron_energy * positron_intensity)
         )
 
-    # Construct Numba typed dicts
-    gamma_ray_line_arrays = {}
-    average_energies = {}
-    average_positron_energies = {}
-
     for iso, lines in zip(all_isotope_names, gamma_ray_line_array_list):
-        gamma_ray_line_arrays[iso] = lines
+        gamma_ray_line_dict[iso] = lines
 
     for iso, energy, positron_energy in zip(
         all_isotope_names, average_energies_list, average_positron_energies_list
@@ -476,222 +445,129 @@ def main_gamma_ray_loop(
         average_energies[iso] = energy
         average_positron_energies[iso] = positron_energy
 
-    # urilight chooses to have 0 as the baseline for this calculation
-    # but time_start may also be valid in which case decay time is time_end - time_start
-    total_energy_list = []
-
-    for shell, inv in enumerate(inventories):
-        decayed_energy = {}
-        total_decays = inv.cumulative_decays(time_end)
-        for nuclide in total_decays:
-            if nuclide in parents and nuclide != "Co-56" and nuclide != "Co-57":
-                parent = parents[nuclide]
-                if parent in parents:
-                    parent = parents[parent]
-                decayed_energy[parent] += (
-                    total_decays[nuclide]
-                    * average_energies[nuclide]
-                    * shell_masses[shell]
-                )
-            else:
-                decayed_energy[nuclide] = (
-                    total_decays[nuclide]
-                    * average_energies[nuclide]
-                    * shell_masses[shell]
-                )
-
-        total_energy_list.append(decayed_energy)
-
-    total_energy = pd.DataFrame(total_energy_list)
-
-    total_energy_columns = total_energy.columns.to_list()
-
-    total_energy = total_energy[
-        sorted(
-            total_energy_columns, key=get_nuclide_atomic_number, reverse=True
-        )
-    ]
-
-    energy_per_mass = total_energy.divide(
-        (raw_isotope_abundance * shell_masses).T.to_numpy(),
-        axis=0,
-    )
-
-    # Time averaged energy per mass for constant packet count
-    average_power_per_mass = energy_per_mass / (time_end - time_start)
-
-    energy_per_mass_norm = energy_per_mass.divide(
-        energy_per_mass.sum(axis=1), axis=0
-    )  # .cumsum(axis=1)
-
-    decayed_packet_count = num_decays * number_of_isotopes.divide(
-        total_number_isotopes, axis=0
-    )
-
-    packets_per_isotope = (
-        (energy_per_mass_norm * decayed_packet_count.T.values)
-        .round()
-        .fillna(0)
-        .astype(int)
+    return (
+        average_energies,
+        average_positron_energies,
+        gamma_ray_line_dict,
     )
 
-    print("Total gamma-ray energy")
-    print(total_energy.sum().sum() * u.keV.to("erg"))
 
-    print("Total positron energy")
-    print(total_energy["Co-56"].sum(axis=0) * 0.0337 * u.keV.to("erg"))
-
-    # Taking iron group to be elements 21-30
-    # Used as part of the approximations for photoabsorption and pair creation
-    # Dependent on atomic data
-    iron_group_fraction_per_shell = model.abundance.loc[(21):(30)].sum(axis=0)
+def get_taus(raw_isotope_abundance):
+    """
+    Function to calculate taus for each isotope
+    Parameters
+    ----------
+    raw_isotope_abundance : pd.DataFrame
+        isotope abundance in mass fractions
 
-    number_of_packets = packets_per_isotope.sum().sum()
-    print("Total packets:", number_of_packets)
+    Returns
+    -------
+    taus : Dict
+        dictionary of taus for each isotope
+    parents : Dict
+        dictionary of parents for each isotope
+    """
+    all_isotope_names = get_all_isotopes(raw_isotope_abundance)
+    all_isotope_names.sort()
 
-    packet_energy = total_energy.sum().sum() / number_of_packets
+    taus = {}
+    parents = {}
+    for isotope in all_isotope_names:
+        nuclide = rd.Nuclide(isotope)
+        taus[isotope] = nuclide.half_life() / np.log(2)
+        child = nuclide.progeny()
+        if child is not None:
+            for c in child:
+                if rd.Nuclide(c).half_life("readable") != "stable":
+                    parents[isotope] = c
 
-    print("Energy per packet", packet_energy)
+    return taus, parents
 
-    # Need to update volume for positron deposition to be time-dependent
-    print("Initializing packets")
-    (
-        packets,
-        energy_df_rows,
-        energy_plot_df_rows,
-        energy_plot_positron_rows,
-    ) = initialize_packets(
-        packets_per_isotope,
-        packet_energy,
-        gamma_ray_line_arrays,
-        positronium_fraction,
-        inner_velocities,
-        outer_velocities,
-        inv_volume_time,
-        times,
-        energy_df_rows,
-        effective_time_array,
-        taus,
-        parents,
-        average_positron_energies,
-        inventories,
-        average_power_per_mass,
-    )
 
-    print("Total positron energy from packets")
-    print((energy_df_rows).sum().sum() * u.eV.to("erg"))
+def decay_chain_energies(
+    average_energies,
+    total_decays,
+):
+    """
+    Function to calculate decay chain energies.
+    Parameters
+    ----------
+    raw_isotope_abundance : pd.DataFrame
+        isotope abundance in mass fractions
+    average_energies_list : List
+        list of gamma ray energies
+    average_positron_energies_list : List
+        list of positron energies
+    gamma_ray_line_array_list : List
+        list of gamma ray lines
+    total_decays : Dict
+        dictionary of total decays for each isotope in each shell
+    Returns
+    -------
+    decay_energy : Dict
+        dictionary of decay chain energies for each isotope in each shell
 
-    total_cmf_energy = 0
-    total_rf_energy = 0
+    """
+    decay_energy = {}
+    for shell, isotopes in total_decays.items():
+        decay_energy[shell] = {}
+        for name, isotope in isotopes.items():
+            decay_energy[shell][name] = {}
+            for iso, dps in isotope.items():
+                decay_energy[shell][name][iso] = dps * average_energies[iso]
 
-    for p in packets:
-        total_cmf_energy += p.energy_cmf
-        total_rf_energy += p.energy_rf
+    return decay_energy
 
-    print("Total CMF energy")
-    print(total_cmf_energy)
 
-    # Below is the Artis compensation for their method of packet rejection
+def calculate_energy_per_mass(
+    decay_energy, raw_isotope_abundance, shell_masses
+):
     """
-    energy_ratio = total_energy.sum().sum() / total_cmf_energy
-
-    print("Energy ratio")
-    print(energy_ratio)
-    
-    for p in packets:
-        p.energy_cmf *= energy_ratio
-        p.energy_rf *= energy_ratio
-
-    for e in energy_df_rows:
-        e *= energy_ratio
-    
-    for row in energy_plot_df_rows:
-        row[1] *= energy_ratio
+    Function to calculate decay energy per mass for each isotope chain.
+    Parameters
+    ----------
+    decay_energy : Dict
+        dictionary of decay chain energies for each isotope in each shell
+    raw_isotope_abundance : pd.DataFrame
+        isotope abundance in mass fractions.
+    shell_masses : numpy.ndarray
+        shell masses in units of g
+    Returns
+    -------
+    energy_per_mass : pd.DataFrame
+        decay energy per mass for each isotope chain
+        For e.g Ni56 has 2 decay chains:
+        Ni56 -> Co56 -> Fe56. It will calculate the decay energy per mass for each chain
+        and store as a dataframe.
     """
-    print("Total RF energy")
-    print(total_rf_energy)
-
-    energy_bins = np.logspace(2, 3.8, spectrum_bins)
-    energy_out = np.zeros((len(energy_bins - 1), time_steps))
-
-    # Process packets
-    (
-        energy_df_rows,
-        energy_plot_df_rows,
-        energy_out,
-        deposition_estimator,
-    ) = gamma_packet_loop(
-        packets,
-        grey_opacity,
-        photoabsorption_opacity,
-        pair_creation_opacity,
-        electron_number_density_time,
-        mass_density_time,
-        inv_volume_time,
-        iron_group_fraction_per_shell.to_numpy(),
-        inner_velocities,
-        outer_velocities,
-        times,
-        dt_array,
-        effective_time_array,
-        energy_bins,
-        energy_df_rows,
-        energy_plot_df_rows,
-        energy_out,
-    )
-
-    # DataFrame of energy information
-    energy_plot_df = pd.DataFrame(
-        data=energy_plot_df_rows,
-        columns=[
-            "packet_index",
-            "energy_input",
-            "energy_input_r",
-            "energy_input_time",
-            "energy_input_type",
-            "compton_opacity",
-            "photoabsorption_opacity",
-            "total_opacity",
-        ],
-    )
+    energy_dict = {}
+    for shell, isotopes in decay_energy.items():
+        energy_dict[shell] = {}
+        for name, isotope in isotopes.items():
+            energy_dict[shell][name] = sum(isotope.values())
+
+    energy_list = []
+    for shell, isotopes in energy_dict.items():
+        for isotope, energy in isotopes.items():
+            energy_list.append(
+                {
+                    "shell": shell,
+                    "atomic_number": isotope[0],
+                    "mass_number": isotope[1],
+                    "value": energy,
+                }
+            )
 
-    # DataFrame of positron energies
-    energy_plot_positrons = pd.DataFrame(
-        data=energy_plot_positron_rows,
-        columns=[
-            "packet_index",
-            "energy_input",
-            "energy_input_r",
-            "energy_input_time",
-        ],
+    df = pd.DataFrame(energy_list)
+    energy_df = pd.pivot_table(
+        df,
+        values="value",
+        index=["atomic_number", "mass_number"],
+        columns="shell",
     )
 
-    # DataFrame of estimated deposition
-    # Multiply dataframes by inv_volume_time array
-    # if per unit volume is needed
-    energy_estimated_deposition = (
-        pd.DataFrame(data=deposition_estimator, columns=times[:-1])
-    ) / dt_array
-
-    # Energy is eV/s
-    energy_df = pd.DataFrame(data=energy_df_rows, columns=times[:-1]) / dt_array
-
-    final_energy = 0
-    for p in packets:
-        final_energy += p.energy_rf
-
-    print("Final energy to test for conservation")
-    print(final_energy)
-
-    escape_energy = pd.DataFrame(
-        data=energy_out, columns=times[:-1], index=energy_bins
+    energy_per_mass = energy_df.divide(
+        (raw_isotope_abundance * shell_masses).to_numpy(), axis=0
     )
 
-    return (
-        energy_df,
-        energy_plot_df,
-        escape_energy,
-        decayed_packet_count,
-        energy_plot_positrons,
-        energy_estimated_deposition,
-    )
+    return energy_per_mass, energy_df
diff --git a/tardis/energy_input/tests/test_gamma_ray_transport.py b/tardis/energy_input/tests/test_gamma_ray_transport.py
new file mode 100644
index 00000000000..da17889fe13
--- /dev/null
+++ b/tardis/energy_input/tests/test_gamma_ray_transport.py
@@ -0,0 +1,306 @@
+import os
+import pytest
+import numpy as np
+import pandas as pd
+import numpy.testing as npt
+from pathlib import Path
+import radioactivedecay as rd
+from radioactivedecay import converters
+
+import tardis
+from tardis.model import SimulationState
+from tardis.io.configuration import config_reader
+from tardis.io.util import yaml_load_file, YAMLLoader
+from tardis.energy_input.energy_source import (
+    get_nuclear_lines_database,
+    get_all_isotopes,
+    setup_input_energy,
+)
+from tardis.energy_input.gamma_ray_transport import (
+    calculate_shell_masses,
+    create_isotope_dicts,
+    create_inventories_dict,
+    calculate_total_decays,
+    calculate_average_energies,
+    decay_chain_energies,
+    calculate_energy_per_mass,
+)
+import astropy.units as u
+import astropy.constants as c
+
+
+@pytest.fixture(scope="module")
+def gamma_ray_config(example_configuration_dir: Path):
+    """
+    Parameters
+    ----------
+    example_configuration_dir: Path to the configuration directory.
+
+    Returns
+    -------
+    Tardis configuration
+    """
+    yml_path = (
+        example_configuration_dir
+        / "tardis_configv1_density_exponential_nebular_multi_isotope.yml"
+    )
+
+    return config_reader.Configuration.from_yaml(yml_path)
+
+
+@pytest.fixture(scope="module")
+def simulation_setup(gamma_ray_config):
+    """
+    Parameters
+    ----------
+    gamma_ray_config:
+
+    Returns
+    -------
+    Tardis model
+    """
+    gamma_ray_config.model.structure.velocity.start = 1.0 * u.km / u.s
+    gamma_ray_config.model.structure.density.rho_0 = 5.0e2 * u.g / (u.cm**3)
+    gamma_ray_config.supernova.time_explosion = 1.0 * (u.d)
+    model = SimulationState.from_config(gamma_ray_config)
+    return model
+
+
+def test_calculate_shell_masses(simulation_setup):
+    """Function to test calculation of shell masses.
+    Parameters
+    ----------
+    simulation_setup: A simulation setup which returns a model.
+    """
+    model = simulation_setup
+    volume = 2.70936170e39  # cm^3
+    density = 5.24801665e-09  # g/cm^3
+    desired = volume * density
+
+    shell_masses = calculate_shell_masses(model)[0].value
+    npt.assert_allclose(shell_masses, desired)
+
+
+@pytest.mark.parametrize("nuclide_name", ["Ni-56", "Fe-52", "Cr-48"])
+def test_activity(simulation_setup, nuclide_name):
+    """
+    Function to test the decay of an atom in radioactivedecay with an analytical solution.
+    Parameters
+    ----------
+    simulation_setup: A simulation setup which returns a model.
+    nuclide_name: Name of the nuclide.
+    """
+    nuclide = rd.Nuclide(nuclide_name)
+    model = simulation_setup
+    t_half = nuclide.half_life() * u.s
+    decay_constant = np.log(2) / t_half
+    time_delta = 1.0 * u.s
+    shell_masses = calculate_shell_masses(model)
+    raw_isotope_abundance = model.raw_isotope_abundance
+    raw_isotope_abundance_mass = raw_isotope_abundance.apply(
+        lambda x: x * shell_masses, axis=1
+    )
+    mass = raw_isotope_abundance_mass.loc[nuclide.Z, nuclide.A][0]
+    iso_dict = create_isotope_dicts(raw_isotope_abundance, shell_masses)
+    inv_dict = create_inventories_dict(iso_dict)
+
+    total_decays = calculate_total_decays(inv_dict, time_delta)
+    actual = total_decays[0][nuclide.Z, nuclide.A][nuclide_name]
+
+    isotopic_mass = nuclide.atomic_mass * (u.g)
+    number_of_moles = mass * (u.g) / isotopic_mass
+    number_of_atoms = (number_of_moles * c.N_A).value
+    N1 = number_of_atoms * np.exp(-decay_constant * time_delta)
+    expected = number_of_atoms - N1.value
+
+    npt.assert_allclose(actual, expected)
+
+
+@pytest.mark.parametrize("nuclide_name", ["Ni-56", "Fe-52", "Cr-48"])
+def test_activity_chain(simulation_setup, nuclide_name):
+    """
+    Function to test two atom decay chain in radioactivedecay with an analytical solution.
+    Parameters
+    ----------
+    simulation_setup: A simulation setup which returns a model.
+    nuclide_name: Name of the nuclide.
+    """
+    nuclide = rd.Nuclide(nuclide_name)
+    model = simulation_setup
+    t_half = nuclide.half_life()
+    decay_constant = np.log(2) / t_half
+    time_delta = 1.0 * (u.d).to(u.s)
+    progeny = rd.Nuclide(nuclide.progeny()[0])
+    decay_constant_progeny = np.log(2) / progeny.half_life()
+    shell_masses = calculate_shell_masses(model)
+    raw_isotope_abundance = model.raw_isotope_abundance
+    raw_isotope_abundance_mass = raw_isotope_abundance.apply(
+        lambda x: x * shell_masses, axis=1
+    )
+    mass = raw_isotope_abundance_mass.loc[nuclide.Z, nuclide.A][0]
+    iso_dict = create_isotope_dicts(raw_isotope_abundance, shell_masses)
+    inv_dict = create_inventories_dict(iso_dict)
+    total_decays = calculate_total_decays(inv_dict, time_delta)
+    actual_parent = total_decays[0][nuclide.Z, nuclide.A][nuclide_name]
+    actual_progeny = total_decays[0][nuclide.Z, nuclide.A][nuclide.progeny()[0]]
+    isotopic_mass = nuclide.atomic_mass
+    number_of_moles = mass / isotopic_mass
+    number_of_atoms = number_of_moles * converters.AVOGADRO
+    decayed_parent = number_of_atoms * np.exp(-decay_constant * time_delta)
+    expected_parent = number_of_atoms * (
+        1 - np.exp(-decay_constant * time_delta)
+    )
+
+    npt.assert_almost_equal(expected_parent, actual_parent)
+    # npt.assert_allclose(actual_progeny, expected_progeny, rtol=1e-3)
+
+
+@pytest.mark.parametrize("nuclide_name", ["Ni-56", "Fe-52", "Cr-48"])
+def test_isotope_dicts(simulation_setup, nuclide_name):
+    """
+    Function to test if the right names for the isotopes are present as dictionary keys.
+    Parameters
+    ----------
+    simulation_setup: A simulation setup which returns a model.
+    nuclide_name: Name of the nuclide.
+    """
+    model = simulation_setup
+    nuclide = rd.Nuclide(nuclide_name)
+    raw_isotope_abundance = model.raw_isotope_abundance
+    shell_masses = calculate_shell_masses(model)
+    iso_dict = create_isotope_dicts(raw_isotope_abundance, shell_masses)
+
+    Z, A = nuclide.Z, nuclide.A
+
+    for shell_number, isotope_dict in iso_dict.items():
+        isotope_dict_key = isotope_dict[Z, A]
+        assert nuclide_name.replace("-", "") in isotope_dict_key.keys()
+
+
+@pytest.mark.parametrize("nuclide_name", ["Ni-56", "Fe-52", "Cr-48"])
+def test_inventories_dict(simulation_setup, nuclide_name):
+    """
+    Function to test if the inventories dictionary is created correctly.
+    Parameters
+    ----------
+    simulation_setup: A simulation setup which returns a model.
+    nuclide_name: Name of the nuclide.
+    """
+    model = simulation_setup
+    nuclide = rd.Nuclide(nuclide_name)
+    raw_isotope_abundance = model.raw_isotope_abundance
+    shell_masses = calculate_shell_masses(model)
+    iso_dict = create_isotope_dicts(raw_isotope_abundance, shell_masses)
+    inventories_dict = create_inventories_dict(iso_dict)
+
+    Z, A = nuclide.Z, nuclide.A
+    raw_isotope_abundance_mass = raw_isotope_abundance.apply(
+        lambda x: x * shell_masses, axis=1
+    )
+
+    mass = raw_isotope_abundance_mass.loc[Z, A][0]
+    inventory = rd.Inventory({nuclide.nuclide: mass}, "g")
+    assert inventories_dict[0][Z, A] == inventory
+
+
+def test_average_energies(simulation_setup, atomic_dataset):
+    """
+    Function to test if the energy from each isotope is there in the list.
+    Parameters
+    ----------
+    simulation_setup: A simulation setup which returns a model.
+    atomic_dataset: Tardis atomic and nuclear dataset.
+    """
+
+    model = simulation_setup
+    raw_isotope_abundance = model.raw_isotope_abundance
+    gamma_ray_lines = atomic_dataset.decay_radiation_data
+
+    all_isotope_names = get_all_isotopes(raw_isotope_abundance)
+
+    average_energies_list = []
+
+    for isotope_name in all_isotope_names:
+        energy, intensity = setup_input_energy(
+            gamma_ray_lines[
+                gamma_ray_lines.index == isotope_name.replace("-", "")
+            ],
+            "g",
+        )
+        average_energies_list.append(np.sum(energy * intensity))  # keV
+
+    assert len(average_energies_list) == len(all_isotope_names)
+
+
+@pytest.mark.parametrize("nuclide_name", ["Ni-56", "Fe-52", "Cr-48"])
+def test_decay_energy_chain(simulation_setup, atomic_dataset, nuclide_name):
+    """
+    This function tests if the decay energy is calculated correctly for a decay chain.
+    Parameters
+    ----------
+    simulation_setup: A simulation setup which returns a model.
+    atomic_dataset: Tardis atomic and nuclear dataset.
+    nuclide_name: Name of the nuclide.
+    """
+    model = simulation_setup
+    nuclide = rd.Nuclide(nuclide_name)
+    raw_isotope_abundance = model.raw_isotope_abundance
+    shell_masses = calculate_shell_masses(model)
+    iso_dict = create_isotope_dicts(raw_isotope_abundance, shell_masses)
+    inventories_dict = create_inventories_dict(iso_dict)
+    gamma_ray_lines = atomic_dataset.decay_radiation_data
+    all_isotope_names = get_all_isotopes(raw_isotope_abundance)
+    Z, A = nuclide.Z, nuclide.A
+
+    total_decays = calculate_total_decays(inventories_dict, 1.0 * u.s)
+
+    (
+        average_energies,
+        average_positron_energies,
+        gamma_ray_line_dict,
+    ) = calculate_average_energies(raw_isotope_abundance, gamma_ray_lines)
+
+    decay_chain_energy = decay_chain_energies(
+        average_energies,
+        total_decays,
+    )
+
+    expected = (
+        total_decays[0][Z, A][nuclide_name] * average_energies[nuclide_name]
+    )
+    actual = decay_chain_energy[0][Z, A][nuclide_name]
+
+    npt.assert_almost_equal(expected, actual)
+
+
+def test_energy_per_mass(simulation_setup, atomic_dataset):
+    """
+    This function tests if the energy per mass has the same dimensions as the raw_isotope_abundance.
+    This means for each decay chain we are calculating the energy per mass, by summing the energy from each isotope.
+    Parameters
+    ----------
+    simulation_setup: A simulation setup which returns a model.
+    atomic_dataset: Tardis atomic and nuclear dataset.
+    """
+    model = simulation_setup
+    raw_isotope_abundance = model.raw_isotope_abundance
+    shell_masses = calculate_shell_masses(model)
+    iso_dict = create_isotope_dicts(raw_isotope_abundance, shell_masses)
+    inventories_dict = create_inventories_dict(iso_dict)
+    total_decays = calculate_total_decays(inventories_dict, 1.0 * u.s)
+
+    gamma_ray_lines = atomic_dataset.decay_radiation_data
+    average_energies = calculate_average_energies(
+        raw_isotope_abundance, gamma_ray_lines
+    )
+    decay_energy = decay_chain_energies(
+        average_energies[0],
+        total_decays,
+    )
+    energy_per_mass = calculate_energy_per_mass(
+        decay_energy, raw_isotope_abundance, shell_masses
+    )
+    # If the shape is not same that means the code is not working with multiple isotopes
+    assert (
+        energy_per_mass[0].shape == (raw_isotope_abundance * shell_masses).shape
+    )
diff --git a/tardis/io/configuration/tests/data/tardis_configv1_density_exponential_nebular_multi_isotope.yml b/tardis/io/configuration/tests/data/tardis_configv1_density_exponential_nebular_multi_isotope.yml
new file mode 100644
index 00000000000..4786784264a
--- /dev/null
+++ b/tardis/io/configuration/tests/data/tardis_configv1_density_exponential_nebular_multi_isotope.yml
@@ -0,0 +1,52 @@
+tardis_config_version: v1.0
+
+supernova:
+    luminosity_requested: 9.44 log_lsun
+    time_explosion: 150 day
+
+atom_data: kurucz_atom_pure.h5
+
+model:
+    structure:
+        type: specific
+
+        velocity:
+            start: 1.1e4 km/s
+            stop: 20000 km/s
+            num: 20
+
+        density:
+            type: exponential
+            time_0: 20. second
+            rho_0: 3.e2 g/cm^3
+            v_0: 3000.  km/s
+
+    abundances:
+        type: uniform
+        O: 0.19
+        Mg: 0.03
+        Si: 0.12
+        S: 0.09
+        Ar: 0.02
+        Ca: 0.03
+        Ni56: 0.5
+        Fe52: 0.01
+        Cr48: 0.01
+
+plasma:
+    ionization: nebular
+    excitation: dilute-lte
+    radiative_rates_type: dilute-blackbody
+    line_interaction_type: scatter
+
+montecarlo:
+    seed: 23111963
+    no_of_packets: 2.0e+5
+    iterations: 30
+    last_no_of_packets: 5.0e+5
+    no_of_virtual_packets: 5
+
+spectrum:
+    start: 500 angstrom
+    stop: 20000 angstrom
+    num: 10000
diff --git a/tardis/io/decay.py b/tardis/io/decay.py
index 7005fa50e6e..5b652f460a7 100644
--- a/tardis/io/decay.py
+++ b/tardis/io/decay.py
@@ -57,7 +57,7 @@ def id_to_tuple(atomic_id):
         nuclide = Nuclide(atomic_id)
         return nuclide.Z, nuclide.A
 
-    def to_inventories(self):
+    def to_inventories(self, shell_masses=None):
         """
         Convert DataFrame to a list of inventories interpreting the MultiIndex as
         atomic_number and mass_number
@@ -72,7 +72,12 @@ def to_inventories(self):
         for (atomic_number, mass_number), abundances in self.iterrows():
             nuclear_symbol = f"{Z_to_elem(atomic_number)}{mass_number}"
             for i in range(len(self.columns)):
-                comp_dicts[i][nuclear_symbol] = abundances[i]
+                if shell_masses is None:
+                    comp_dicts[i][nuclear_symbol] = abundances[i]
+                else:
+                    comp_dicts[i][nuclear_symbol] = (
+                        abundances[i] * shell_masses[i].to(u.g).value
+                    )
         return [Inventory(comp_dict, "g") for comp_dict in comp_dicts]
 
     def decay(self, t):

From 60429749a6b132794c7076f7a4e9cfb9e7015d86 Mon Sep 17 00:00:00 2001
From: atharva-2001 <aryaa_1@rknec.edu>
Date: Thu, 26 Oct 2023 11:59:52 +0530
Subject: [PATCH 32/35] Use Mamba instead of conda

---
 .github/workflows/benchmarks.yml | 16 +++++++++++++---
 asv.conf.json                    |  2 +-
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 38a9e82572d..7389b587a8d 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -41,7 +41,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
           fetch-depth: 0
         if: github.event_name == 'pull_request_target'
-      
+     
       - name: Restore Atom Data
         uses: actions/cache/restore@v3
         id: atom-data-restore
@@ -62,9 +62,19 @@ jobs:
         with:
           path: benchmarks/data/kurucz_cd23_chianti_H_He.h5
           key: atom-data
+      
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: benchmark
+          init-shell: >-
+            bash
+          create-args: >-
+            python
+            asv
+            mamba
 
       - name: Install asv
-        run: pip install asv==0.5.*
+        run: pip install asv
 
       - name: Accept all asv questions
         run: asv machine --yes
@@ -79,7 +89,7 @@ jobs:
             echo "Some benchmarks have failed!"
             exit 1
           fi
-          
+
       - name: Generate Graphs and HTML
         if: github.event_name != 'pull_request_target'
         run: asv publish
diff --git a/asv.conf.json b/asv.conf.json
index 8cff9285f8c..ab19c67ff26 100644
--- a/asv.conf.json
+++ b/asv.conf.json
@@ -10,7 +10,7 @@
         "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"
     ],
     "branches": ["master"],
-    "environment_type": "conda",
+    "environment_type": "mamba",
     "show_commit_url": "https://github.com/tardis-sn/tardis/commit",
     "conda_environment_file": "tardis_env3.yml",
     "benchmark_dir": "benchmarks",

From 249969993e855f3dba6e5d90e68f33c3a41d1b7f Mon Sep 17 00:00:00 2001
From: atharva-2001 <aryaa_1@rknec.edu>
Date: Thu, 26 Oct 2023 14:20:44 +0530
Subject: [PATCH 33/35] Run asv for last 5 commits

---
 .github/workflows/benchmarks.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 7389b587a8d..9382d4cc4e0 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -80,7 +80,7 @@ jobs:
         run: asv machine --yes
       
       - name: Run benchmarks for last 5 commits if not PR
-        if: github.event_name != 'pull_request_target'
+        # if: github.event_name != 'pull_request_target'
         continue-on-error: true
         run: |
           git log -n 5  --pretty=format:"%H" >> tag_commits.txt

From e79e1b5b4918caf4b11b2a714188cec632a2f769 Mon Sep 17 00:00:00 2001
From: atharva-2001 <aryaa_1@rknec.edu>
Date: Tue, 28 Nov 2023 16:15:26 +0530
Subject: [PATCH 34/35] Add pull request trigger temporarily

---
 .github/workflows/benchmarks.yml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 9382d4cc4e0..efdb9d7f22c 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -4,9 +4,13 @@ on:
   push:
     branches:
       - master
+
   pull_request_target:
     branches:
       - '*'
+  pull_request:
+    branches:
+      - '*'
     types:
       - opened
       - reopened
@@ -38,7 +42,7 @@ jobs:
       - name: Checkout pull/${{ github.event.number }}
         uses: actions/checkout@v3
         with:
-          ref: ${{ github.event.pull_request.head.sha }}
+          ref: ${{ github.sha }}
           fetch-depth: 0
         if: github.event_name == 'pull_request_target'
      
@@ -63,7 +67,8 @@ jobs:
           path: benchmarks/data/kurucz_cd23_chianti_H_He.h5
           key: atom-data
       
-      - uses: mamba-org/setup-micromamba@v1
+      - name: Setup Mamba
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: benchmark
           init-shell: >-
@@ -81,7 +86,6 @@ jobs:
       
       - name: Run benchmarks for last 5 commits if not PR
         # if: github.event_name != 'pull_request_target'
-        continue-on-error: true
         run: |
           git log -n 5  --pretty=format:"%H" >> tag_commits.txt
           asv run HASHFILE:tag_commits.txt | tee asv-output.log  

From ee7e25138979c36664186c4d08455fb78fdf6ac9 Mon Sep 17 00:00:00 2001
From: atharva-2001 <aryaa_1@rknec.edu>
Date: Tue, 28 Nov 2023 16:29:52 +0530
Subject: [PATCH 35/35] Reset

---
 .github/workflows/benchmarks.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index efdb9d7f22c..657cd972b84 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -7,10 +7,8 @@ on:
 
   pull_request_target:
     branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
+      - master
+
     types:
       - opened
       - reopened
@@ -85,7 +83,7 @@ jobs:
         run: asv machine --yes
       
       - name: Run benchmarks for last 5 commits if not PR
-        # if: github.event_name != 'pull_request_target'
+        if: github.event_name != 'pull_request_target'
         run: |
           git log -n 5  --pretty=format:"%H" >> tag_commits.txt
           asv run HASHFILE:tag_commits.txt | tee asv-output.log