doc updates

docs/conf.py

@@ -0,0 +1,220 @@
+"""
+# 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 = 'Fuse-Med-ML'
+copyright = '2023, Rakesh'
+author = 'Rakesh'
+release = 'latest'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.viewcode',
+ 'sphinx.ext.napoleon'
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+"""
+# 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_file_name = package_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:: "
+ # INCLUDE_TEXT += "../../"
+
+ README_FILE_NAME = "README.md"
+
+ source_code_dir = os.path.join(
+ "..", "..", "causallib"
+ ) # causallib source code directory
+ source_html_dir = "." # sphinx's docs source directory
+
+ for dir_name, subdir_list, file_names in os.walk(source_code_dir):
+ 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:
+ try:
+ include_text = INCLUDE_TEXT + readme_file_path + "\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.dl.rst

@@ -1,4 +1,5 @@
-.. mdinclude:: ../../fuse/dl/README.md
+fuse.dl package
+===============
 
 Subpackages
 -----------

docs/source/fuse.rst

@@ -1,3 +1,5 @@
+.. mdinclude:: ../../fuse/dl/README.md
+
 fuse package
 ============