Merge pull request #48 from anissa111/main

First pass at documentation

.gitignore

@@ -13,3 +13,6 @@ cupid.egg-info
 **/*.swp
 
 externals/
+
+# Documentation
+/docs/_build/

build_envs/docs.yml

@@ -0,0 +1,12 @@
+name: cupid-docs
+channels:
+    - conda-forge
+dependencies:
+    - python>=3.9,<3.12
+    - ipykernel
+    - ipython
+    - jupyter_client
+    - sphinx-book-theme
+    - myst-nb
+    - sphinx-design
+    - nbsphinx

docs/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     = .
+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/conf.py

@@ -0,0 +1,113 @@
+# 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
+import datetime
+sys.path.insert(0, os.path.abspath('../..'))
+
+print("sys.path:", sys.path)
+
+# -- Project information -----------------------------------------------------
+
+project = 'CUPiD'
+
+current_year = datetime.datetime.now().year
+copyright = u'{}, University Corporation for Atmospheric Research'.format(
+    current_year)
+
+author = 'NSF NCAR'
+
+# The master toctree document.
+master_doc = 'index'
+
+
+# -- 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 = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'myst_nb',
+    "sphinx_design",
+    "nbsphinx",
+]
+
+intersphinx_mapping = {
+    'dask': ('https://docs.dask.org/en/latest/', None),
+    'python': ('http://docs.python.org/3/', None),
+    'numpy': ("https://numpy.org/doc/stable", None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'xarray': ('http://xarray.pydata.org/en/stable/', None),
+    'pint': ('https://pint.readthedocs.io/en/stable/', None),
+    'cftime': ('https://unidata.github.io/cftime/', None),
+}
+
+autosummary_generate = True
+
+# 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 = ['**.ipynb_checkpoints']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+# source_suffix = ['.rst', '.md']
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.ipynb': 'myst-nb',
+}
+
+
+# -- 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 = "sphinx_book_theme"
+html_title = ""
+
+autosummary_imported_members = True
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = dict(
+    # analytics_id=''  this is configured in rtfd.io
+    # canonical_url="",
+    repository_url="https://github.com/NCAR/CUPiD",
+    repository_branch="main",
+    path_to_docs="docs",
+    use_edit_page_button=True,
+    use_repository_button=True,
+    use_issues_button=True,
+    home_page_in_toc=False,
+    extra_footer=
+    "<em>The National Center for Atmospheric Research is sponsored by the National Science Foundation. Any opinions, findings and conclusions or recommendations expressed in this material do not necessarily reflect the views of the National Science Foundation.</em>",
+)
+
+# 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']
+
+html_logo = '_static/images/logos/logo.png'
+html_favicon = '_static/images/logos/logo.png'
+
+autoclass_content = 'both'

docs/index.rst

@@ -0,0 +1,8 @@
+CUPiD Documentation
+===================
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+    Installation Guide <install.rst>

docs/install.rst

@@ -0,0 +1,2 @@
+Installing CUPiD
+================

docs/make.bat

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