arfc · samgdotson · Jun 28, 2023 · Feb 21, 2023 · Feb 21, 2023 · Feb 21, 2023
diff --git a/.github/workflows/test-openmcyclus.yml b/.github/workflows/test-openmcyclus.yml
@@ -6,54 +6,47 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: cyclus/cycamore
+    defaults: 
+      run:
+        shell: bash -l {0}
+
     steps:
       - uses: actions/checkout@v3
       - name: Setup Conda
         uses: conda-incubator/setup-miniconda@v2
         with:
+          miniforge-variant: Mambaforge
           miniforge-version: latest
           activate-environment: openmcyclus-env
+          environment-file: environment.yml
+          use-mamba: true
 
       - name: Conda config
         run: |
           conda config --env --set pip_interop_enabled True 
-
-      - name: Install pytest
-        run: conda install -y pytest
-
-      - name: Build OpenMC 
-        run: |
-          conda install -y python=3.7 cyclus cycamore 
-          HDF5_DIR=$CONDA_PREFIX && pip install h5py
-
-      - name: OpenMC dependencies
+
+      - name: Update Environment
         run: |
-          sudo apt -y update
-          sudo apt install -y libhdf5-dev
-
-      - name: Download OpenMC
-        uses: actions/checkout@v3
-        with: 
-          repository: openmc-dev/openmc
-          path: openmc
-          submodules: recursive
+          pip install pytest
+          mamba env update -n openmcyclus-env -f environment.yml
 
-      - name: Build OpenMC from source
-        run: |
-          run: build-openmc.sh
+      - name: Install OpenMC cross section library
+        run: $GITHUB_WORKSPACE/openmc-xs.bash
 
+      - name: Install OpenMC from Mamba
+        run: mamba install openmc
 
       - name: Install OpenMC cross section library
         run: echo "OPENMC_CROSS_SECTIONS=cross_sections.xml" >> $GITHUB_ENV
 
       - name: Install OpenMCyclus
         run: |
           pip install .
-      
-      - name: Check environment 
-        run: |
-          pip install pytest
+
+#      - name: Check environment
+#        run: |
+#          pip install pytest
 
       - name: Run Tests
         run: |
-          pytest 
+          pytest tests/integration_tests/test_depletereactor.py
diff --git a/README.md b/README.md
@@ -22,7 +22,7 @@ git clone https://github.com/abachma2/cyclus.git
 
 cd cyclus
 
-git checkout 2022-05-maintenance
+git checkout python-api
 
 python install.py
 
@@ -53,12 +53,10 @@ directory. To run tests: ``pytest`` from the main directory.
 
 ## Running
 This archetype assumes that you have a defined reactor model in OpenMC (``.xml``) 
-files and the 
-required microscopic cross sections (``.csv`` file) for the model. The 
-cross 
-section data must be saved as a ``.csv`` file. These files must 
-all be in the same location. Information about 
-these can be found on the [OpenMC docpages](https://docs.openmc.org). 
+files and the required microscopic cross sections (``.csv`` file) for the model. 
+The cross section data must be saved as a ``.csv`` file. These files must 
+all be in the same location. Information about these can be found on the 
+[OpenMC docpages](https://docs.openmc.org). 
 
 This archetype is then called during a Cyclus simulation by calling 
 the ``DepleteReactor`` archetype from the ``openmcyclus.DepleteReactor`` 
@@ -96,15 +94,26 @@ library. The input structure is:
       <n_assem_core>int</n_assem_core>
       <n_assem_batch>int</n_assem_batch>
       <power_cap>double</power_cap>
+      <model_path>string</model_path>
+      <chain_file>string</chain_file>
     </DepleteReactor>
 
-The `fuel_prefs`, `fuel_inrecipes`, and `fuel_outrecipes` state variables are optional.
-But if included, `fuel_prefs` and `fuel_inrecipes` must be equal in length to 
+`fuel_prefs` and `fuel_inrecipes` must be equal in length to 
 `fuel_incommods` and `fuel_outrecipes` must be equal in length to `fuel_outcommods`. 
 
+The fresh fuel recipes (`fuel_increipes`) are to be defined in the main input file but 
+the spent fuel recipes (`fuel_outrecipes`) are to be defined in a separate xml file 
+name `prototype_fuel.xml`, in which `prototype` is the name given to the prototype 
+in the main input file. The spent fuel recipes should be named the same as the 
+fresh fuel recipes, with `spent_` prepended (e.g. `spent_uox` if the inrecipe is 
+named `uox`).  
+
+The `model_path` variable must be an absolute path. The archetype assumes that 
+the OpenMC materials are in the file called `materials.xml`, located in the `model_path`
+directory, and that the cross section data is in a file called `micro_xs.csv`, 
+also located in the `model_path` directory. 
+
 
 ### Outputs
-The compositions for the spent fuel are saved to an ``.xml`` file named 
-``prototype_fuel.xml`` in which ``prototype`` is the prototype name in 
-the Cyclus simulation. The results of the simulation wil be written to `cyclus.sqlite`
+The results of the simulation wil be written to `cyclus.sqlite`
 or the file name provided when Cyclus was called. 
diff --git a/build-cyclus.sh b/build-cyclus.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+# Build cyclus
+cd cyclus 
+conda activate openmcyclus-env
+python install.py
+cd ../
diff --git a/environment.yml b/environment.yml
@@ -3,6 +3,48 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - numpy
+  - openssh 
   - pytest
-  - pip
+  - gxx_linux-64==12.2 
+  - gcc_linux-64==12.2 
+  - cmake 
+  - make 
+  - docker-pycreds 
+  - git 
+  - xo 
+  - python-json-logger 
+  - glib 
+  - libxml2 
+  - libxmlpp 
+  - libblas 
+  - libcblas 
+  - liblapack 
+  - pkg-config 
+  - coincbc 
+  - boost-cpp 
+  - sqlite 
+  - pcre 
+  - gettext 
+  - bzip2 
+  - xz 
+  - setuptools 
+  - pytables 
+  - pandas 
+  - jinja2 
+  - cython 
+  - websockets 
+  - pprintpp 
+  - hdf5==1.12.2 
+  - notebook 
+  - nb_conda_kernels 
+  - requests 
+  - entrypoints 
+  - pyyaml 
+  - vtk 
+  - coverage 
+  - pytest-cov 
+  - colorama 
+  - libpng 
+  - uncertainties 
+  - lxml 
+  - scipy
diff --git a/examples/OneReactor_fuel.xml b/examples/OneReactor_fuel.xml
@@ -0,0 +1,27 @@
+<recipes>
+<recipe>
+  <name>spent_uox</name>
+  <basis>mass</basis>
+  <nuclide>
+    <id>92235</id>
+    <comp>0.05</comp>
+  </nuclide>
+  <nuclide>
+    <id>92238</id>
+    <comp>0.95</comp>
+  </nuclide>
+</recipe>
+
+<recipe>
+  <name>spent_mox</name>
+  <basis>mass</basis>
+  <nuclide>
+    <id>94239</id>
+    <comp>0.05</comp>
+  </nuclide>
+  <nuclide>
+    <id>94241</id>
+    <comp>0.95</comp>
+  </nuclide>
+</recipe>
+</recipes>
diff --git a/tests/chain_endfb71_pwr.xml → examples/chain_endfb71_pwr.xml b/tests/chain_endfb71_pwr.xml → examples/chain_endfb71_pwr.xml
diff --git a/examples/complex.xml b/examples/complex.xml
@@ -1,4 +1,4 @@
-<simulation>
+<simulation xmlns:xi="http://www.w3.org/2001/XInclude">
 
 <control>
     <duration>20</duration>
@@ -105,7 +105,7 @@
             <n_assem_core>3</n_assem_core>
             <n_assem_batch>1</n_assem_batch>
             <power_cap>100</power_cap>
-            <model_path>/home/abachmann/openmcyclus/tests/</model_path>
+            <model_path>./examples/</model_path>
             <chain_file>chain_endfb71_pwr.xml</chain_file>
           </DepleteReactor>
         </config>
@@ -163,20 +163,6 @@
       </nuclide>
     </recipe>
 
-    <recipe>
-      <name>spent_uox</name>
-      <basis>mass</basis>
-      <nuclide>
-        <id>92235</id>
-        <comp>0.05</comp>
-      </nuclide>
-      <nuclide>
-        <id>92238</id>
-        <comp>0.95</comp>
-      </nuclide>
-    </recipe>
-
-
     <recipe>
       <name>mox</name>
       <basis>mass</basis>
@@ -190,17 +176,6 @@
       </nuclide>
     </recipe>
 
-    <recipe>
-      <name>spent_mox</name>
-      <basis>mass</basis>
-      <nuclide>
-        <id>94239</id>
-        <comp>0.05</comp>
-      </nuclide>
-      <nuclide>
-        <id>94241</id>
-        <comp>0.95</comp>
-      </nuclide>
-    </recipe>
+  <xi:include href="examples/OneReactor_fuel.xml#xpointer(/recipes/child::*)"/>
 
  </simulation>
diff --git a/examples/geometry.xml b/examples/geometry.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='utf-8'?>
+<geometry>
+  <cell id="6" material="5" region="-9" universe="2" />
+  <cell id="7" material="6" region="-10" universe="2" />
+  <cell id="8" material="7" region="-11" universe="2" />
+  <cell id="9" material="8" region="9 10 11 -12" universe="2" />
+  <cell id="10" material="void" region="12" universe="2" />
+  <surface boundary="vacuum" coeffs="-15 0.0 0.0 5" id="9" type="sphere" />
+  <surface boundary="vacuum" coeffs="0.0 0.0 0.0 5" id="10" type="sphere" />
+  <surface boundary="vacuum" coeffs="15 0.0 0.0 5" id="11" type="sphere" />
+  <surface boundary="vacuum" coeffs="0.0 0.0 0.0 50" id="12" type="sphere" />
+</geometry>
diff --git a/examples/materials.xml b/examples/materials.xml
@@ -0,0 +1,16 @@
+<materials>
+  <material depletable="true" id="5" name="assembly_1" temperature="900" volume="78.53981633974483">
+    <density units="g/cm3" value="19.1" />
+    <nuclide wo="0.99289" name="U238" /><nuclide wo="0.00711" name="U235" /></material>
+  <material depletable="true" id="6" name="assembly_2" temperature="900" volume="78.53981633974483">
+    <density units="g/cm3" value="19.1" />
+    <nuclide wo="0.99289" name="U238" /><nuclide wo="0.00711" name="U235" /></material>
+  <material depletable="true" id="7" name="assembly_3" temperature="900" volume="78.53981633974483">
+    <density units="g/cm3" value="19.1" />
+    <nuclide wo="0.99289" name="U238" /><nuclide wo="0.00711" name="U235" /></material>
+  <material id="8" name="water" temperature="900" volume="7853.981633974483">
+    <density units="g/cm3" value="1" />
+    <nuclide ao="0.6667" name="H1" />
+    <nuclide ao="0.3333" name="O16" />
+  </material>
+</materials>
diff --git a/tests/micro_xs.csv → examples/micro_xs.csv b/tests/micro_xs.csv → examples/micro_xs.csv
diff --git a/tests/settings.xml → examples/settings.xml b/tests/settings.xml → examples/settings.xml
diff --git a/examples/simple.xml b/examples/simple.xml
@@ -1,4 +1,4 @@
-<simulation>
+<simulation xmlns:xi="http://www.w3.org/2001/XInclude">
 
 <control>
     <duration>10</duration>
@@ -65,7 +65,7 @@
             <n_assem_core>3</n_assem_core>
             <n_assem_batch>1</n_assem_batch>
             <power_cap>100</power_cap>
-            <model_path>/home/abachmann/openmcyclus/tests/</model_path>
+            <model_path>./examples/</model_path>
             <chain_file>chain_endfb71_pwr.xml</chain_file>
           </DepleteReactor>
         </config>
@@ -112,18 +112,6 @@
       </nuclide>
     </recipe>
 
-    <recipe>
-      <name>spent_uox</name>
-      <basis>mass</basis>
-      <nuclide>
-        <id>92235</id>
-        <comp>0.05</comp>
-      </nuclide>
-      <nuclide>
-        <id>92238</id>
-        <comp>0.95</comp>
-      </nuclide>
-    </recipe>
-
+ <xi:include href="examples/OneReactor_fuel.xml#xpointer(/recipes/child::*)"/>
 
  </simulation>
diff --git a/materials.xml b/materials.xml