Adds Sphinx Documentation (#332)

* Add doxygen, breathe, sphinx documentation first steps

* Add draft readthedocs.yaml file

* Update to use exhale

* try forcing output

* Updated conf.py:

* Added conf.py new location

* Updated to fix typo

* Updated to re-add import

* update RTD.yaml

* Update to use correct doxygen command

* add docs env

* Test

* Remove exhale

* Remove not-working mod from all rst files

Co-authored-by: Kristin Berry <kberry@gyro.wr.usgs.gov>

.readthedocs.yaml

+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+conda:
+  environment: doc_environment.yml
+

doc_environment.yml

+name: usgscsm
+channels:
+  - conda-forge
+  - default
+
+dependencies:
+  - cmake>=3.12
+  - ale
+  - csm
+  - nlohmann_json
+  - breathe

docs/Makefile

+# 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)

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

+# 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 = 'usgscsm'
+copyright = '2021, USGS Astrogeology Software Team'
+author = 'USGS Astrogeology Software Team'
+
+
+# -- 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.
+extensions = ['breathe'] #, 'exhale']
+
+# 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 = []
+
+
+# -- 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 = ['_static']
+
+# breathe (doxygen -> sphinx package) settings
+breathe_projects = { "usgscsm": "../xml/" }
+breathe_default_project = "usgscsm"
+
+import subprocess, os
+
+# build doxygen on readthedocs
+read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
+if read_the_docs_build:
+    subprocess.call('cd ..; doxygen Doxyfile', shell=True)
+
+# Setup the exhale extension
+#exhale_args = {
+#    # These arguments are required
+#    "containmentFolder":     "./library",
+#    "rootFileName":          "index.rst",
+#    "rootFileTitle":         "USGSCSM API",
+#    "doxygenStripFromPath":  "..",
+#    # Suggested optional arguments
+#    "createTreeView":        True,
+#    # TIP: if using the sphinx-bootstrap-theme, you need
+#    # "treeViewIsBootstrap": True,
+#    "exhaleExecutesDoxygen": True,
+#    "exhaleDoxygenStdin":    "INPUT = ../../include"
+#}
+
+# Tell sphinx what the primary language being documented is.
+primary_domain = 'cpp'
+
+# Tell sphinx what the pygments highlight language should be.
+highlight_language = 'cpp'
+

docs/source/index.rst

+Welcome to usgscsm's documentation!
+===================================
+
+:Release: |version|
+:Date: |today|
+
+
+Issues and Version Control
+--------------------------
+This project is hosted on `GitHub`_. If you run into a problem, please open an `issue`_ on our `issue`_ tracker.
+
+
+.. toctree::
+   :maxdepth: 2
+
+   library/index
+
+.. _GitHub: http://github.com/USGS-Astrogeology/usgscsm
+.. _issue: https://github.com/USGS-Astrogeology/usgscsm/issues?state=open

docs/source/library/distortion.rst

+USGSCSM Distortion Class
+==============================================
+
+.. doxygenfile:: Distortion.h
+   :project: usgscsm
+
+

docs/source/library/framer.rst

+USGSCSM Astro Frame Sensor Model Class
+=======================================================
+
+.. doxygenfile:: UsgsAstroFrameSensorModel.h
+   :project: usgscsm
+

docs/source/library/index.rst

+#################
+Library Reference
+#################
+
+:Release: |version|
+:Date: |today|
+
+.. toctree::
+  distortion
+  utilities
+  plugin
+  framer
+  linescanner
+  sar
+
+
+
+   
+   
+   
+   
+   
+   
+   
+   
+   
+   

docs/source/library/linescanner.rst

+USGSCSM Astro Linescan Sensor Model Class
+=============================================================
+
+.. doxygenfile:: UsgsAstroLsSensorModel.h
+   :project: usgscsm
+

docs/source/library/plugin.rst

+USGSCSM Astro Plugin Class
+=====================================================
+
+.. doxygenfile:: UsgsAstroPlugin.h
+   :project: usgscsm
+

docs/source/library/sar.rst

+USGSCSM Astro SAR Sensor Model Class
+=============================================================
+
+.. doxygenfile:: UsgsAstroSarSensorModel.h
+   :project: usgscsm
+

docs/source/library/utilities.rst

+USGSCSM Utilities Class
+==============================================
+
+.. doxygenfile:: Utilities.h
+   :project: usgscsm
+