Generate API documentation using Sphinx.

.github/workflows/sphinx.yml

@@ -0,0 +1,51 @@
+name: Build Documentation
+
+on:
+  push:
+    branches:
+      - 'main'
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+jobs:
+  build:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Set up Python
+        id: setup_python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Cache pip
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ env.pythonLocation }}
+        if: steps.pip-cache.outputs.cache-hit != 'true'
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Build html
+        run: |
+          sphinx-apidoc -o doc src
+          cd doc/
+          make html
+
+      - name: Upload docs artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'doc/_build/html'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

@@ -0,0 +1,36 @@
+# 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
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath(".."))
+
+project = 'TF2.4 IVIM MRI Code Collection'
+copyright = '2024, OSIPI'
+author = 'OSIPI team'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autodoc"]
+
+templates_path = ['_templates']
+exclude_patterns = ['Thumbs.db', '.DS_Store']
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = False
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = False
+
+# -- 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']

doc/index.rst

@@ -0,0 +1,18 @@
+.. TF2.4 IVIM MRI Code Collection documentation master file, created by
+   sphinx-quickstart on Wed Mar  6 00:06:13 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to TF2.4 IVIM MRI Code Collection's documentation!
+==========================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+Indices and tables
+==================
+
+* :ref:`modindex`

requirements.txt

@@ -10,4 +10,6 @@ scienceplots
 cvxpy
 zenodo-get
 pytest
-tqdm
+tqdm
+sphinx
+sphinx_rtd_theme