Generate API documentation using Sphinx.

.github/workflows/analysis.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - 'main'
       - 'analysis/**'
+      - 'test-docs'
 
 jobs:
   algorithms:

.github/workflows/sphinx.yml

@@ -0,0 +1,80 @@
+name: Build & Deploy Documentation
+
+on:
+  workflow_run:
+    workflows: [Algorithm Analysis]
+    types:
+      - completed
+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: ${{ env.pythonLocation }}
+        if: steps.pip-cache.outputs.cache-hit != 'true'
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      # Action to download artifacts from a different workflow (analysis.yml)
+      - name: 'Download artifact'
+        uses: actions/github-script@v6
+        with:
+          script: |
+            let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               run_id: context.payload.workflow_run.id,
+            });
+            let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
+              return artifact.name == "Figures"
+            })[0];
+            let download = await github.rest.actions.downloadArtifact({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               artifact_id: matchArtifact.id,
+               archive_format: 'zip',
+            });
+            let fs = require('fs');
+            fs.writeFileSync(`${process.env.GITHUB_WORKSPACE}/Figures.zip`, Buffer.from(download.data));
+
+      - name: 'Unzip artifact'
+        run: unzip Figures.zip
+
+      - name: Build html
+        run: |
+          mkdir docs/_static
+          ls
+          mv *.pdf docs/_static/
+          sphinx-apidoc -o docs src
+          cd docs/
+          make html
+
+      - name: Upload docs artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs/_build/html'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

docs/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)

docs/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']

docs/figures.rst

@@ -0,0 +1,45 @@
+Algorithm Analysis Figures
+===========
+
+.. raw:: html
+
+   <!DOCTYPE html>
+   <html lang="en">
+   <head>
+       <meta charset="UTF-8">
+       <meta name="viewport" content="width=device-width, initial-scale=1.0">
+       <title>Algorithm Analysis Figures</title>
+       <style>
+
+           embed {
+               width: 90%;
+               margin-bottom: 4rem;
+               height: 100vh;
+           }
+       </style>
+   </head>
+   <body>
+        <h4>Diffusion grid for limited algorithms:</h4>
+       <embed src="_static/D_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+       <h4>Diffusion grid for all algorithms:</h4>
+       <embed src="_static/D.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+
+       <h4>Perfusion grid for limited algorithms:</h4>
+       <embed src="_static/Dp_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+       <h4>Perfusion grid for all algorithms:</h4>
+       <embed src="_static/Dp.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+
+       <h4>Perfusion fraction grid for limited algorithms:</h4>
+       <embed src="_static/f_limited.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+       <h4>Perfusion fraction grid for all algorithms:</h4>
+       <embed src="_static/f.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+
+      <h4>Fitted curves:</h4>
+       <embed src="_static/fitted_curves.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+      <h4>Curve plot:</h4>
+      <embed src="_static/curve_plot.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+      <h4>Algorithm Fitting duration:</h4>
+      <embed src="_static/durations.pdf" type="application/pdf" frameborder="0" scrolling="auto">
+
+   </body>
+   </html>

docs/index.rst

@@ -0,0 +1,19 @@
+.. 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: 4
+   :caption: Contents:
+
+   figures
+   modules
+
+Indices and tables
+==================
+
+* :ref:`modindex`

requirements.txt

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