Merge pull request #9 from biomarkersParkinson/main

testing workflows

.github/workflows/build-and-test.yml

@@ -34,6 +34,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     # Get the version from pyproject.toml
+    # This will be used to tag the release in the publishing workflow
     - name: Install toml package
       run: pip install toml
     - name: Get version from pyproject.toml
@@ -43,21 +44,38 @@ jobs:
         echo Version: $VERSION
         echo "version=$VERSION" >> $GITHUB_OUTPUT
 
+    # Installation
     - name: Install dependencies
       run: |
         python -m pip install poetry
         poetry install
-    # - name: Build the docs  # just to see whether the build passes
-    #   run: |
-    #     poetry run mkdocs build
+
+    # Testing and checking
     - name: Test with pytest
       run: |
         poetry run pytest
+    # - name: Type check
+    #   run: |
+    #     poetry run pytype .
+
+    # Build the package
     - name: Build the package
       run: |
         poetry build
     - name: Archive build artifacts
       uses: actions/upload-artifact@v4
+      if: github.ref == 'refs/heads/release'
       with:
         name: build-artifacts
         path: dist/
+
+    # Build the docs
+    - name: Build the docs
+      run: |
+        poetry run make html --directory docs
+    - name: Archive documentation
+      uses: actions/upload-artifact@v4
+      if: github.ref == 'refs/heads/release'
+      with:
+        name: docs-html
+        path: docs/_build/html/

.github/workflows/publish.yml

@@ -2,7 +2,7 @@
 # https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/#workflow-definition
 # https://github.com/marketplace/actions/pypi-publish
 
-name: Publish to PyPI
+name: Publish package and docs
 
 on:
   push:
@@ -94,3 +94,22 @@ jobs:
         gh release upload
         "v${VERSION}" dist/**
         --repo '${{ github.repository }}'
+
+
+  publish-docs:
+    name: Publish documentation
+    needs: build-and-test
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Download the documentation
+        uses: actions/download-artifact@v4
+        with:
+          name: docs-html
+          path: docs/
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/

.gitignore

@@ -1,2 +1,3 @@
 dist/
+docs/build/
 *.pyc

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     = source
+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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,27 @@
+# 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
+
+project = 'paradigma'
+copyright = '2024, NLeSC'
+author = 'NLeSC'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

docs/source/index.rst

@@ -0,0 +1,20 @@
+.. paradigma documentation master file, created by
+   sphinx-quickstart on Thu Jul  4 15:25:23 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to paradigma's documentation!
+=====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`