Merge pull request #21 from RECETOX/copilot/extend-readthedocs-api-docs

Add Sphinx autodoc API reference to ReadTheDocs

Author: hechth

.readthedocs.yaml

@@ -10,4 +10,5 @@ sphinx:
 
 python:
   install:
+    - requirements: requirements/base.txt
     - requirements: requirements/docs.txt

docs/api/cli.rst

@@ -0,0 +1,7 @@
+CLI
+===
+
+.. automodule:: src.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api/data_sources.rst

@@ -0,0 +1,32 @@
+Data Sources
+============
+
+.. automodule:: src.data_sources
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.data_sources.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.data_sources.pypi
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.data_sources.cran
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.data_sources.conda
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.data_sources.github
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api/index.rst

@@ -0,0 +1,10 @@
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 2
+
+   cli
+   utils
+   data_sources
+   reports

docs/api/reports.rst

@@ -0,0 +1,32 @@
+Reports
+=======
+
+.. automodule:: src.reports
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.reports.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.reports.pypi
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.reports.cran
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.reports.bioconda
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.reports.github
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api/utils.rst

@@ -0,0 +1,7 @@
+Utilities
+=========
+
+.. automodule:: src.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/conf.py

@@ -3,6 +3,12 @@
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+import os
+import sys
+
+# Add the repository root to sys.path so that autodoc can import the source modules.
+sys.path.insert(0, os.path.abspath(".."))
+
 # -- Project information -----------------------------------------------------
 project = "specdatri_reporting"
 copyright = "2024, RECETOX"
@@ -11,11 +17,26 @@
 # -- General configuration ---------------------------------------------------
 extensions = [
     "myst_parser",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
 ]
 
 templates_path = ["_templates"]
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
+# -- Autodoc configuration ---------------------------------------------------
+autodoc_member_order = "bysource"
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "show-inheritance": True,
+}
+
+# -- Napoleon configuration (Google-style docstrings) -------------------------
+napoleon_google_docstring = True
+napoleon_numpy_docstring = False
+
 # -- Options for HTML output -------------------------------------------------
 html_theme = "sphinx_rtd_theme"
 html_static_path = ["_static"]

docs/index.md

@@ -2,3 +2,11 @@
 
 ```{include} ../README.md
 ```
+
+```{toctree}
+:maxdepth: 2
+:caption: API Reference
+:hidden:
+
+api/index
+```