API docs

docs/conf.py

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+# 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
+from pathlib import Path
+
+sys.path.insert(0, os.path.abspath(".."))
+
+try:
+ # version > 3.0
+ from sphinx.ext.apidoc import main as apidoc_main
+except ImportError:
+ # sphinx version < 3
+ from sphinx.apidoc import main as apidoc_main
+
+
+# -- Project information -----------------------------------------------------
+
+project = "epimargin"
+copyright = "2021, Satej Soman, Caitlin Loftus, Steven Buschbach, Manasi Phadnis, Luís M. A. Bettencourt"
+author = "Satej Soman, Caitlin Loftus, Steven Buschbach, Manasi Phadnis, Luís M. A. Bettencourt"
+
+
+# -- 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_autodoc_typehints",
+ "sphinx_rtd_theme",
+]
+
+autosectionlabel_prefix_document = True
+autosectionlabel_maxdepth = 2
+
+autoclass_content = "both"
+
+autodoc_default_options = {
+ "member-order": "bysource",
+ "special-members": "__init__",
+ "undoc-members": True,
+ "show_inheritance": True,
+ "inherited-members": True,
+}
+
+# hack to generate apidoc automatically.
+cwd = Path(__file__).parent
+module = cwd / ".." / "epimargin"
+os.environ["SPHINX_APIDOC_OPTIONS"] = ",".join(
+ [f"{k}={v}" for k, v in autodoc_default_options.items()]
+)
+apidoc_main(["-e", "-o", str(cwd), str(module), "--force"])
+
+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 = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- 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_rtd_theme"
+
+# 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"]

docs/index.rst

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+Welcome to epimargin's documentation!
+=====================================
+
+.. image:: https://github.com/COVID-IWG/epimargin/raw/master/docs/logo.svg
+ :width: 300
+
+API Documentation
+==================
+
+
+..
+ comment: module.rst and epimargin.rst are generated by sphinx-build at run time.
+ See conf.py file.
+
+
+.. toctree::
+
+ modules
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/requirements.txt

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+sphinxcontrib-napoleon
+sphinx-autodoc-typehints
+sphinx_rtd_theme
+commonmark
+rst_include