Added readthedocs documentation support (#339)

* readthedocs config added

* index.rst change

* a

* a

* rst files

* a

* a

* all

* all

* all

* all

* all

* all

* all

* all

* all

* readthedocs configured

* reformatting using black

* mypy updates

* mypy updates

* doc update

* doc update

* doc update

* doc update

* doc update

* doc update

* doc update

* doc updates

* doc updatess

* doc updates

* doc updates

* doc updates

* black changes

* conf update

* path updates to conf.py

* module updates

* conf update

.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: "2"
+
+build:
+ os: "ubuntu-22.04"
+ tools:
+ python: "3.10"
+
+python:
+ install:
+ - requirements: docs/requirements.txt
+
+sphinx:
+ configuration: docs/source/conf.py

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)

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/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

docs/requirements.txt

@@ -0,0 +1,4 @@
+sphinx==7.1.2
+sphinx-rtd-theme==1.3.0rc1
+m2r2
+

docs/source/conf.py

@@ -0,0 +1,186 @@
+# 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:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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(os.path.join("..", "..")))
+
+
+# -- Project information -----------------------------------------------------
+
+
+# Take from setup.py file
+def grep_value_from_setup(key: str) -> str:
+ import re
+
+ setup_file = os.path.normpath(
+ os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "..", "setup.py")
+ )
+ with open(setup_file, "r") as setup_file:
+ for line in setup_file.readlines():
+ value = re.search(".*{key}=(.*),*".format(key=key), line)
+ if value:
+ value = value.group(1)
+ value = re.sub(r"^\W+", "", value) # lstrip non alphanumeric
+ value = re.sub(r"\W+$", "", value) # rstrip non alphanumeric
+ return value
+
+
+project = grep_value_from_setup("name")
+copyright = "2023"
+author = grep_value_from_setup("author")
+
+# The full version, including alpha/beta/rc tags
+
+release = "latest"
+
+
+# -- 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.doctest",
+ "sphinx.ext.coverage",
+ "sphinx.ext.viewcode",
+ "sphinx.ext.intersphinx", # link to other documentations
+ # 'nbsphinx', # work with jupyter notebook. requires pip install nbsphinx
+ # 'sphinx.ext.mathjax', # required for math in Jupyter Notebook
+ "m2r2", # work with markdown files. requires pip install m2r2
+ "sphinx.ext.napoleon", # parse Google/numpy docstring
+ # 'sphinx.ext.autosummary', # Automated index.rst toctreee
+]
+
+# autosummary_generate = True # create api docs with autosummary
+
+
+intersphinx_mapping = {
+ "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+ "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
+ "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+ "python": ("https://docs.python.org/{}.{}".format(*sys.version_info), None),
+}
+
+autoclass_content = "both"
+
+numpydoc_show_class_members = False # Suppress sphinx warnings when building numpy-doc
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+source_suffix = {
+ ".rst": "restructuredtext",
+ ".txt": "restructuredtext",
+ ".md": "markdown",
+}
+
+# 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 = [
+ "*estimation.*_.rst", # estimation old files which kept locally
+ "*tests.*", # remove tests from documentation
+]
+
+# https://www.sphinx-doc.org/en/master/usage/configuration.html?highlight=master_doc#confval-master_doc
+master_doc = "index" # what file includes the root toctree. Needed explicitly for readthedocs.org
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+on_rtd = os.environ.get("READTHEDOCS") == "True"
+if on_rtd:
+ html_theme = "sphinx_rtd_theme"
+else:
+ html_theme = "classic"
+
+# 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"]
+
+# # Add content to the navigation side bar:
+html_sidebars = {
+ "**": ["localtoc.html", "sourcelink.html", "searchbox.html", "globaltoc.html"]
+}
+
+
+# -- Custom scripts -------------------------------------------------
+
+
+# Add module's README for each module HTML page
+def add_modules_readme() -> str:
+ def get_rst_file_name_from_package_source(package_source_path: str) -> str:
+ rst_source_path = os.path.relpath(package_source_path, os.getcwd())
+ rst_file_name = rst_source_path.split(os.sep)
+ rst_file_name = [
+ directory for directory in rst_file_name if not directory.startswith(".")
+ ]
+ rst_file_name += ["rst"]
+ rst_file_name = ".".join(rst_file_name)
+ rst_file_name = os.path.join(source_html_dir, rst_file_name)
+ return rst_file_name
+
+ def get_edited_rast_file(
+ rst_source_path: str, include_text: str, remove_original_header: bool = True
+ ) -> str:
+ with open(rst_source_path, "r") as fh:
+ rst_source_lines = fh.read().splitlines()
+ if not any([include_text in line for line in rst_source_lines]):
+ # Add link to readme only if not already exists
+ rst_source_lines.insert(3, include_text)
+ if remove_original_header:
+ rst_source_lines = rst_source_lines[2:] # remove existing header
+
+ return rst_source_lines
+
+ INCLUDE_TEXT = ".. mdinclude:: "
+
+ README_FILE_NAME = "README.md"
+
+ # source_code_dir = os.path.join("..", "..", "fuse-med-ml")
+ source_html_dir = os.getcwd() + "/docs/source/" # sphinx's docs source directory
+
+ for dir_name, subdir_list, file_names in os.walk(os.getcwd()):
+ if README_FILE_NAME in file_names: # Current dir has a readme file
+ # Get README file path:
+ # source_path = os.path.relpath(dir_name, os.path.join(source_code_dir, ".."))
+ source_path = os.path.normpath(dir_name)
+
+ readme_file_path = os.path.join(source_path, README_FILE_NAME)
+
+ # Construct the corresponding module rst file:
+ rst_source_file = get_rst_file_name_from_package_source(source_path)
+
+ # Edit the rst file to include the path to the readme:
+ path_to_be_added = os.path.relpath(readme_file_path, os.getcwd())
+
+ try:
+ include_text = INCLUDE_TEXT + "../../" + path_to_be_added + "\n"
+ content = get_edited_rast_file(rst_source_file, include_text, True)
+
+ with open(rst_source_file, "w") as f:
+ for line in content:
+ f.write("{}\n".format(line))
+
+ except FileNotFoundError:
+ print("Could not find file {}".format(rst_source_file))
+
+
+add_modules_readme()

docs/source/fuse.data.datasets.caching.rst

@@ -0,0 +1,37 @@
+fuse.data.datasets.caching package
+==================================
+
+Subpackages
+-----------
+
+.. toctree::
+ :maxdepth: 4
+
+ fuse.data.datasets.caching.tests
+
+Submodules
+----------
+
+fuse.data.datasets.caching.object\_caching\_handlers module
+-----------------------------------------------------------
+
+.. automodule:: fuse.data.datasets.caching.object_caching_handlers
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+fuse.data.datasets.caching.samples\_cacher module
+-------------------------------------------------
+
+.. automodule:: fuse.data.datasets.caching.samples_cacher
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: fuse.data.datasets.caching
+ :members:
+ :undoc-members:
+ :show-inheritance:

docs/source/fuse.data.datasets.caching.tests.rst

@@ -0,0 +1,21 @@
+fuse.data.datasets.caching.tests package
+========================================
+
+Submodules
+----------
+
+fuse.data.datasets.caching.tests.test\_sample\_caching module
+-------------------------------------------------------------
+
+.. automodule:: fuse.data.datasets.caching.tests.test_sample_caching
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: fuse.data.datasets.caching.tests
+ :members:
+ :undoc-members:
+ :show-inheritance:

docs/source/fuse.data.datasets.rst

@@ -0,0 +1,54 @@
+fuse.data.datasets package
+==========================
+
+Subpackages
+-----------
+
+.. toctree::
+ :maxdepth: 4
+
+ fuse.data.datasets.caching
+ fuse.data.datasets.tests
+
+Submodules
+----------
+
+fuse.data.datasets.dataset\_base module
+---------------------------------------
+
+.. automodule:: fuse.data.datasets.dataset_base
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+fuse.data.datasets.dataset\_default module
+------------------------------------------
+
+.. automodule:: fuse.data.datasets.dataset_default
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+fuse.data.datasets.dataset\_wrap\_seq\_to\_dict module
+------------------------------------------------------
+
+.. automodule:: fuse.data.datasets.dataset_wrap_seq_to_dict
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+fuse.data.datasets.sample\_caching\_audit module
+------------------------------------------------
+
+.. automodule:: fuse.data.datasets.sample_caching_audit
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: fuse.data.datasets
+ :members:
+ :undoc-members:
+ :show-inheritance: