reformatting using black

docs/source/conf.py

@@ -1,4 +1,4 @@
-'''
+"""
 # Configuration file for the Sphinx documentation builder.
 #
 # For the full list of built-in configuration values, see the documentation:
@@ -31,7 +31,7 @@
 
 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
@@ -45,32 +45,37 @@
 # 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('..', '..')))
+
+sys.path.insert(0, os.path.abspath(os.path.join("..", "..")))
 
 
 # -- Project information -----------------------------------------------------
 
+
 # Take from setup.py file
 def grep_value_from_setup(key):
- 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+$', '', value) # rstrip non alphanumeric
- return value
-
-
-project = grep_value_from_setup('name')
-copyright = '2023'
-author = grep_value_from_setup('author')
+ import re
+
+ setup_file = os.path.normpath(
+ os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "..", "setup.py")
+ )
+ with open(setup_file, "r") as setup_file:
+ for line in setup_file.readlines():
+ value = re.search(".*{key}=(.*),*".format(key=key), line)
+ if value:
+ value = value.group(1)
+ value = re.sub(r"^\W+", "", value) # lstrip non alphanumeric
+ value = re.sub(r"\W+$", "", 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'
+release = "latest"
 
 
 # -- General configuration ---------------------------------------------------
@@ -79,128 +84,137 @@ def grep_value_from_setup(key):
 # 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
+ "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)
+ "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'
+autoclass_content = "both"
 
-numpydoc_show_class_members = False  # Suppress sphinx warnings when building numpy-doc
+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']
+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',
+ ".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
+ "*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
+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'
+on_rtd = os.environ.get("READTHEDOCS") == "True"
 if on_rtd:
- html_theme = 'sphinx_rtd_theme'
+ html_theme = "sphinx_rtd_theme"
 else:
- html_theme = 'classic'
+ 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']
+html_static_path = ["_static"]
 
 # # Add content to the navigation side bar:
-html_sidebars = {'**': ['localtoc.html', 'sourcelink.html', 'searchbox.html', 'globaltoc.html']}
+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():
- def get_rst_file_name_from_package_source(package_source_path):
- 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, include_text, remove_original_header=True):
- 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))
+ def get_rst_file_name_from_package_source(package_source_path):
+ 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, include_text, remove_original_header=True
+ ):
+ 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()