Create Docs for scripts and standardize the docstrings

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     = docs
+BUILDDIR      = docs/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)

docs/analysis_doc.rst

@@ -0,0 +1,7 @@
+Analysis
+--------
+
+.. automodule:: scripts.analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/conf.py

@@ -0,0 +1,104 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Transition Scenarios'
+copyright = '2024, ARFC'
+author = 'ARFC'
+
+# The full version, including alpha/beta/rc tags
+release = '0.01'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+
+# myst_parser adds support for Markedly Structured Text, includes more features
+# sphinx.ext.napoleon allows for a google/numpy docstring style
+# sphinx.ext.duration represents time durations in a human-readable format
+# sphinx.ext.autosectionlabel labels sections
+# sphinx.ext.autodoc generates docs from docstrings
+# sphinx.ext.autosummary generates summary tables of modules and packages
+# sphinx.ext.intersphinx allows for linking to external documentation sites
+# sphinx.ext.viewcode adds "View Source" links to docs
+# sphinx.ext.mathjax renders mathematical expressions written in LaTeX
+# sphinx.ext.coverage assesses and visualizing the test coverage
+# nbsphinx includes Jupyter Notebooks in docs
+# sphinxcontrib.mermaid create diagrams in markdown
+
+extensions = ["myst_parser",
+              "sphinx.ext.napoleon",
+              "sphinx.ext.duration",
+              "sphinx.ext.autosectionlabel",
+              "sphinx.ext.autodoc",
+              "sphinx.ext.autosummary",
+              "sphinx.ext.intersphinx",
+              "sphinx.ext.viewcode",
+              "sphinx.ext.mathjax",
+              "sphinx.ext.coverage",
+              "nbsphinx",
+              "sphinxcontrib.mermaid"]
+
+# Suffixes that are useable
+# source_suffix = {
+#     '.rst': 'restructuredtext',
+#     '.txt': 'markdown',
+#     '.md': 'markdown',
+# }
+
+# make sure you have a unique autolabelled target
+autosectionlabel_prefix_document = True
+# Sphinx will create explicit targets for all your sections, the name of target
+# has the form {path/to/page}:{title-of-section}.
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# List of modules to be mocked up.
+autodoc_mock_imports = ['pyne', 'd3ploy', 'seaborn', 'xmltodict',
+                        'dataframe_analysis', 'predicting_the_past_import',
+                        'create_AR_DeployInst']
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'pandas': ('https://pandas.pydata.org/docs/', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'astropy': ('https://docs.astropy.org/en/stable/', None),
+    'cyclus': ('https://fuelcycle.org/', None),
+}
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['source/_static']

docs/create_ar_deployinst_doc.rst

@@ -0,0 +1,7 @@
+Create AR DeployInst
+--------------------
+
+.. automodule:: scripts.create_AR_DeployInst
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/create_cyclus_input_doc.rst

@@ -0,0 +1,7 @@
+Create Cyclus Input
+-------------------
+
+.. automodule:: scripts.create_cyclus_input
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/dakota_input_doc.rst

@@ -0,0 +1,7 @@
+Dakota Input
+------------
+
+.. automodule:: scripts.dakota_input
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/dataframe_analysis_doc.rst

@@ -0,0 +1,7 @@
+Dataframe Analysis
+------------------
+
+.. automodule:: scripts.dataframe_analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/index.md

@@ -0,0 +1,55 @@
+<!-- Transition Scenarios documentation master file, created by
+   sphinx-quickstart on Mon Feb 19 13:18:08 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive. -->
+
+# Welcome to Transition Scenarios's documentation!
+
+```{toctree}
+:maxdepth: 1
+
+scripts_outline
+analysis_doc
+create_ar_deployinst_doc
+create_cyclus_input_doc
+dakota_input_doc
+dataframe_analysis_doc
+merge_coordinates_doc
+output_metrics_doc
+predicting_the_past_import_doc
+random_lifetime_extension_doc
+transition_metrics_doc
+transition_plots_doc
+```
+
+# Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
+
+
+# Building the Docs
+To compile the documentation, make sure you have all the requirements
+installed, then run `make html` from the top level of the repository.
+
+```{warning}
+The docs are still in their nascent stage. If you find a
+problem, please open an issue on
+[github](https://github.com/arfc/transition-scenarios/issues).
+```
+
+## Docs Requirements
+* sphinx
+* myst_parser
+* sphinx.ext.napoleon
+* sphinx.ext.duration
+* sphinx.ext.autosectionlabel
+* sphinx.ext.autodoc
+* sphinx.ext.autosummary
+* sphinx.ext.intersphinx
+* sphinx.ext.viewcode
+* sphinx.ext.mathjax
+* sphinx.ext.coverage
+* nbsphinx
+* sphinxcontrib.mermaid

docs/merge_coordinates_doc.rst

@@ -0,0 +1,7 @@
+Merge Coordinates
+-----------------
+
+.. automodule:: scripts.merge_coordinates
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/output_metrics_doc.rst

@@ -0,0 +1,7 @@
+Output Metrics
+--------------
+
+.. automodule:: scripts.output_metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/predicting_the_past_import_doc.rst

@@ -0,0 +1,7 @@
+Predicting the Past
+-------------------
+
+.. automodule:: scripts.predicting_the_past_import
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/random_lifetime_extension_doc.rst

@@ -0,0 +1,7 @@
+Random Lifetime Extension
+-------------------------
+
+.. automodule:: scripts.random_lifetime_extension
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/scripts_outline.md

@@ -0,0 +1,4 @@
+# Scripts Outline
+
+```{include} ../scripts/scripts_README.md
+```

docs/transition_metrics_doc.rst

@@ -0,0 +1,7 @@
+Transition Metrics
+------------------
+
+.. automodule:: scripts.transition_metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/transition_plots_doc.rst

@@ -0,0 +1,7 @@
+Transition Plots
+----------------
+
+.. automodule:: scripts.transition_plots
+   :members:
+   :undoc-members:
+   :show-inheritance:

make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=docs
+set BUILDDIR=docs/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

requirements.txt

@@ -6,3 +6,6 @@ pandas
 pytest
 matplotlib
 tables
+sphinx
+m2r2
+fuzzywuzzy