Creates Sphinx doc files for python music_box module in docs/sphinx_f…

…iles (#154)

* added documentations to missing functions

* adds sphinx doc files in docs directory

doc/sphinx_files/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/sphinx_files/docs/source/modules.rst

@@ -0,0 +1,6 @@
+docs
+====
+
+.. toctree::
+   :maxdepth: 4
+

doc/sphinx_files/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/sphinx_files/source/acom_music_box.rst

@@ -0,0 +1,117 @@
+acom\_music\_box package
+========================
+
+Submodules
+----------
+
+acom\_music\_box.music\_box module
+----------------------------------
+
+.. automodule:: acom_music_box.music_box
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_conditions module
+----------------------------------------------
+
+.. automodule:: acom_music_box.music_box_conditions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_evolving\_conditions module
+--------------------------------------------------------
+
+.. automodule:: acom_music_box.music_box_evolving_conditions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_model\_options module
+--------------------------------------------------
+
+.. automodule:: acom_music_box.music_box_model_options
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_product module
+-------------------------------------------
+
+.. automodule:: acom_music_box.music_box_product
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_reactant module
+--------------------------------------------
+
+.. automodule:: acom_music_box.music_box_reactant
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_reaction module
+--------------------------------------------
+
+.. automodule:: acom_music_box.music_box_reaction
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_reaction\_list module
+--------------------------------------------------
+
+.. automodule:: acom_music_box.music_box_reaction_list
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_reaction\_rate module
+--------------------------------------------------
+
+.. automodule:: acom_music_box.music_box_reaction_rate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_species module
+-------------------------------------------
+
+.. automodule:: acom_music_box.music_box_species
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_species\_concentration module
+----------------------------------------------------------
+
+.. automodule:: acom_music_box.music_box_species_concentration
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.music\_box\_species\_list module
+-------------------------------------------------
+
+.. automodule:: acom_music_box.music_box_species_list
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+acom\_music\_box.utils module
+-----------------------------
+
+.. automodule:: acom_music_box.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: acom_music_box
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/sphinx_files/source/conf.py

@@ -0,0 +1,30 @@
+import sys
+import os
+sys.path.insert(0, os.path.abspath('..'))
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'acom_music_box'
+copyright = '2024, NCAR'
+author = 'NCAR'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc']
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

doc/sphinx_files/source/index.rst

@@ -0,0 +1,22 @@
+.. acom_music_box documentation master file, created by
+   sphinx-quickstart on Mon Apr 29 18:31:30 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to acom_music_box's documentation!
+==========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/sphinx_files/source/modules.rst

@@ -0,0 +1,7 @@
+acom_music_box
+==============
+
+.. toctree::
+   :maxdepth: 4
+
+   acom_music_box

src/acom_music_box/music_box.py

@@ -601,6 +601,18 @@ def readFromUIJsonString(self, data):
         self.evolving_conditions = EvolvingConditions.from_UI_JSON(data, self.species_list, self.reaction_list)    
 
     def readConditionsFromJson(self, path_to_json):
+        """
+        Reads and parses a JSON file from the CAMP JSON file to set up the box model simulation.
+
+        Args:
+            path_to_json (str): The JSON path to the JSON file.
+
+        Returns:
+            None
+
+        Raises:
+            ValueError: If the JSON string cannot be parsed.
+        """
 
         with open(path_to_json, 'r') as json_file:
             data = json.load(json_file)

src/acom_music_box/music_box_reaction_list.py

@@ -98,6 +98,20 @@ def add_reaction(self, reaction):
 
     @classmethod
     def get_reactants_from_JSON(self, reaction, species_list):
+        """
+        Retrieves reactants from a JSON object.
+
+        This method iterates over the 'reactants' field of the provided JSON object,
+        matches each reactant with a species from the provided species list, and
+        creates a Reactant object for each one.
+
+        Args:
+            reaction (dict): A dictionary representing a reaction, as parsed from JSON.
+            species_list (SpeciesList): A list of all possible species.
+
+        Returns:
+            list: A list of Reactant objects representing the reactants of the reaction.
+        """
         reactants = []
 
         for reactant, reactant_info in reaction['reactants'].items():
@@ -110,6 +124,21 @@ def get_reactants_from_JSON(self, reaction, species_list):
 
     @classmethod
     def get_products_from_JSON(self, reaction, species_list):
+        """
+        Extracts products from a JSON object.
+
+        This method checks if the 'products' field is present in the provided JSON object.
+        If it is, the method iterates over the 'products' field, matches each product with
+        a species from the provided species list, and creates a Product object for each one.
+
+        Args:
+            reaction (dict): A dictionary representing a reaction, as parsed from JSON.
+            species_list (SpeciesList): A list of all possible species.
+
+        Returns:
+            list: A list of Product objects representing the products of the reaction, or
+                an empty list if the 'products' field is not present in the JSON object.
+        """
         products = []
         if 'products' in reaction:
                 for product, product_info in reaction['products'].items():