auto generate docs

Author: bmtgoncalves

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line, and also
 # from the environment for the first two.
 SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
+SPHINXBUILD   ?= sphinx-build 
 SOURCEDIR     = source
 BUILDDIR      = build
 

docs/conf.py

@@ -0,0 +1,61 @@
+# 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
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+import epidemik
+
+project = 'epidemik'
+copyright = '2024, Bruno Gonçalves'
+author = 'Bruno Gonçalves'
+
+# The full version, including alpha/beta/rc tags
+release = epidemik.__version__ 
+
+
+# -- 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.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx_autodoc_typehints',
+]
+
+# 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 = []
+
+
+# -- 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/source/conf.py

@@ -0,0 +1,45 @@
+epidemik package
+================
+
+Submodules
+----------
+
+epidemik.EpiModel module
+------------------------
+
+.. automodule:: epidemik.EpiModel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epidemik.MetaEpiModel module
+----------------------------
+
+.. automodule:: epidemik.MetaEpiModel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epidemik.NetworkEpiModel module
+-------------------------------
+
+.. automodule:: epidemik.NetworkEpiModel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epidemik.utils module
+---------------------
+
+.. automodule:: epidemik.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: epidemik
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/epidemik.rst

@@ -0,0 +1,20 @@
+.. epidemik documentation master file, created by
+   sphinx-quickstart on Sun Mar 30 10:52:07 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to epidemik's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/index.rst

@@ -0,0 +1,7 @@
+src
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   epidemik