TOML configfile & unit tests. Remove old XML code.

NuSpaceSim · Dec 20, 2023 · 3385264 · 3385264
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diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ This is the official release of the *nuspacesim* simulator tool!
 
 This package simulates upward-going extensive air showers caused by neutrino
 interactions with the atmosphere. It calculates the tau neutrino acceptance for the
-Optical Cherenkov technique. The simulation is parameterized by an input XML
+Optical Cherenkov technique. The simulation is parameterized by an input TOML
 configuration file, with settings for detector characteristics and global parameters.
 The package also provides a python3 API for programatic access.
 
@@ -31,18 +31,18 @@ Tau propagation is interpolated using included data tables from [nupyprop](https
 
 ![NuSpaceSim Usage](https://raw.githubusercontent.com/NuSpaceSim/nuSpaceSim/main/docs/_static/run.svg)
 
-### Create an XML configuration script
+### Create an TOML configuration script
 
-The command line simulator uses an XML file to store configuration parameters. To
+The command line simulator uses an TOML file to store configuration parameters. To
 generate a default configuration file run the following, with your choice of file name.
 
-`nuspacesim create-config my_config_file.xml`
+`nuspacesim create-config my_config_file.toml`
 
 ### Run simulator
 
 Simulate neutrino interactions and save the results to a named fits file.
 
-`nuspacesim run my_config_file.xml -o my_nss_sim.fits`
+`nuspacesim run my_config_file.toml -o my_nss_sim.fits`
 
 # Documentation
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -92,7 +92,6 @@
     "click",
     "dask",
     "h5py",
-    "lxml",
     "matplotlib",
     "mpl_toolkits",
     "numpy",

diff --git a/docs/index.rst b/docs/index.rst
@@ -13,7 +13,7 @@ This is the public release of the nuspacesim simulator tool!
 
 This package simulates upward-going electromagnetic air showers caused by neutrino
 interactions with the atmosphere. It calculates the tau neutrino acceptance for the
-Optical Cherenkov technique. The simulation is parameterized by an input XML
+Optical Cherenkov technique. The simulation is parameterized by an input TOML
 configuration file, with settings for detector characteristics and global parameters.
 The package also provides a python3 API for programatic access.
 

diff --git a/docs/quickstart.rst b/docs/quickstart.rst
@@ -27,13 +27,13 @@ Read the nuspacesim help docstring
   python3 -m nuspacesim --help
 
 ----------------------------------
-Create the XML configuration file
+Create the TOML configuration file
 ----------------------------------
 
 Create a configuration file with the ``create-config`` command. This is editable by the
 user for defining different simulation parameters.  ::
 
-  nuspacesim create-config --numtrajs 1e6 --monospectrum 10.25 my_config_file.xml
+  nuspacesim create-config --numtrajs 1e6 --monospectrum 10.25 my_config_file.toml
 
 -----------------
 Run the simulator
@@ -42,11 +42,11 @@ Run the simulator
 Simulate neutrino interactions, and extensive air showers, then save the results to a
 FITS file.  ::
 
-  nuspacesim run my_config_file.xml -output my_nss_sim.fits
+  nuspacesim run my_config_file.toml -output my_nss_sim.fits
 
 Optionally, override the configuration file on the command line.  ::
 
-  nuspacesim run my_config_file.xml 1e5 --powerspectrum 2 6 12 -o my_nss_sim.fits
+  nuspacesim run my_config_file.toml 1e5 --powerspectrum 2 6 12 -o my_nss_sim.fits
 
 
 .. raw:: html

diff --git a/docs/tutorial/command_line.rst b/docs/tutorial/command_line.rst
@@ -12,12 +12,12 @@ in application or module mode.
   nuspacesim --help
 
 
-Create an XML configuration file.
+Create an TOML configuration file.
 
 ::
 
   nuspacesim create-config --help
-  nuspacesim create-config my_config_file.xml
+  nuspacesim create-config my_config_file.TOML
 
 
 Run a simulation.

diff --git a/docs/tutorial/configuration.rst b/docs/tutorial/configuration.rst
@@ -7,14 +7,14 @@ Configuration File
 .. toctree::
    :hidden:
 
-Simulation configuration is governed by an XML file. The File structure is
+Simulation configuration is governed by a TOML file. The File structure is
 separated into 2 primary sections, the DetectorCharacteristics and the
-SimulationParameters. Both XML sections map 1-to-1 to the nuspacesim.config
+SimulationParameters. Both TOML sections map 1-to-1 to the nuspacesim.config
 dataclass objects of the same names.
 
 
 
-DetectorCharacteristics
+Detector
 ***********************
 
 This is a dataclass holding the Detector Characteristics for a given simulation.
@@ -34,7 +34,7 @@ The member attributes are as follows:
   * **det_gain**: Antenna gain in dB: Default = 1.8
 
 
-SimulationParameters
+Simulation
 ********************
 
 This is a dataclass holding the Detector Characteristics for a given simulation.

diff --git a/docs/tutorial/simulation.rst b/docs/tutorial/simulation.rst
@@ -12,7 +12,7 @@ variables determined by the physics modules.
 Configuration File
 ******************
 
-Simulation configuration is governed by an XML file.
+Simulation configuration is governed by a TOML file.
 
 Results File
 ************

diff --git a/recipe/meta.yaml b/recipe/meta.yaml
@@ -37,7 +37,6 @@ requirements:
     - importlib_metadata # [py<38]
     - importlib_resources # [py<39]
     - h5py
-    - lxml
     - matplotlib
     - numpy >=1.20
     - rich

diff --git a/sample_input_file.toml b/sample_input_file.toml
@@ -0,0 +1,45 @@
+title = "NuSpaceSim"
+
+[detector]
+name = "Default Name"
+
+[detector.initial_position]
+altitude = "525.0 km"
+latitude = "0.0 deg"
+longitude = "0.0 deg"
+
+[detector.optical]
+telescope_effective_area = "2.5 m2"
+quantum_efficiency = 0.2
+photo_electron_threshold = 10
+
+[detector.radio]
+low_frequency = "30.0 MHz"
+high_frequency = "300.0 MHz"
+snr_threshold = 5.0
+nantennas = 10
+gain = "1.8 dB"
+
+[simulation]
+mode = "Diffuse"
+thrown_events = 10000
+max_cherenkov_angle = "3.0000000000000004 deg"
+max_azimuth_angle = "360.0 deg"
+angle_from_limb = "7.0 deg"
+cherenkov_light_engine = "Default"
+
+[simulation.ionosphere]
+total_electron_content = 10.0
+total_electron_error = 0.1
+
+[simulation.tau_shower]
+id = "nupyprop"
+etau_frac = 0.5
+table_version = "3"
+
+[simulation.spectrum]
+id = "monospectrum"
+log_nu_energy = 8.0
+
+[simulation.cloud_model]
+id = "no_cloud"
diff --git a/sample_input_file.xml b/sample_input_file.xml
diff --git a/setup.cfg b/setup.cfg
@@ -31,15 +31,16 @@ install_requires =
     dask
     dask[distributed]
     h5py
-    lxml
     matplotlib
     numpy>=1.21
+    pydantic
     rich
     scipy
-    cached-property;python_version<"3.8"
+    tomli-w
     configparser;python_version<"3.8"
     importlib-metadata;python_version<"3.8"
     importlib-resources;python_version<"3.9"
+    tomli;python_version<"3.11"
 python_requires = >=3.8
 ext_package = nuspacesim
 package_dir =

diff --git a/src/nuspacesim/__init__.py b/src/nuspacesim/__init__.py
@@ -74,7 +74,7 @@
    nuspacesim.NssConfig
    nuspacesim.DetectorCharacteristics
    nuspacesim.SimulationParameters
-   nuspacesim.xml_config
+   nuspacesim.config
 
 *****************
 Simulate Function
@@ -131,18 +131,17 @@
 
 """
 
-from . import constants, data, utils, xml_config
+from . import constants, data, utils
 from ._version import version, version_tuple
 from .compute import compute
-from .config import DetectorCharacteristics, NssConfig, SimulationParameters
+from .config import NssConfig, config_from_toml
 from .simulation import eas_optical, geometry, taus
 
 __all__ = [
     # Core
     "constants",
     "NssConfig",
-    "DetectorCharacteristics",
-    "SimulationParameters",
+    "config_from_toml",
     "compute",
     # modules
     "geometry",
@@ -151,7 +150,6 @@
     # other
     "data",
     "utils",
-    "xml_config",
     # version
     "version",
     "version_tuple",

diff --git a/src/nuspacesim/apps/__init__.py b/src/nuspacesim/apps/__init__.py
@@ -15,6 +15,6 @@
 
 """
 
-__all__ = ["cli"]
+__all__ = ["cli", "run", "create_config", "show_plot", "utils"]
 
-from . import cli
+from . import cli, create_config, run, show_plot, utils
diff --git a/src/nuspacesim/apps/__main__.py b/src/nuspacesim/apps/__main__.py
@@ -0,0 +1,3 @@
+from .cli import cli
+
+cli()