Update project

.github/workflows/tests.yml

@@ -1,3 +1,7 @@
+# This file configures the continuous integration (CI) system on GitHub.
+# Introductory materials can be found here: https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions.
+# Documentation for editing this file can be found here: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions
+
 name: Tests
 
 on:
@@ -8,71 +12,67 @@ on:
 
 jobs:
   lint:
-    name: Lint
+    name: Code Quality
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.9", "3.12" ]
+        python-version: [ "3.12", "3.9" ]
+        tox-command: ["manifest", "lint", "pyroma", "mypy"]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: "Run command"
         run: |
-          sudo apt-get install graphviz
-          pip install tox
-      - name: Check manifest
-        run: tox -e manifest
-      - name: Check code quality with flake8
-        run: tox -e flake8
-      - name: Check package metadata with Pyroma
-        run: tox -e pyroma
-      - name: Check static typing with MyPy
-        run: tox -e mypy
+          uvx -p ${{ matrix.python-version }} --with tox-uv tox -e ${{ matrix.tox-command }}
+
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     strategy:
       matrix:
+        # We only test documentation on the latest version
+        # sphinx 8.0 / sphinx-rtd-theme 3.0 discontinued Python 3.9 support
+        # a year early, which prompted re-thinking about this.
         python-version: [ "3.12" ]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
         with:
-          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
       - name: Install dependencies
         run: |
           sudo apt-get install graphviz
-          pip install tox tox-uv
       - name: Check RST conformity with doc8
-        run: tox -e doc8
-      - name: Check README.rst
-        run: tox -e doc8
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e doc8
+      - name: Check docstring coverage
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e docstr-coverage
       - name: Check documentation build with Sphinx
-        run: tox -e docs-test
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e docs-test
   tests:
     name: Tests
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ "3.9", "3.12" ]
-        exclude:
-          - os: windows-latest
-            python-version: 3.9
+        python-version: [ "3.12", "3.9" ]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          sudo apt-get install graphviz
-          pip install tox tox-uv
-      - name: Test with pytest
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: Test with pytest and generate coverage file
         run:
-          tox -e py
+          uvx -p ${{ matrix.python-version }} --with tox-uv tox -e py
+      - name: Upload coverage report to codecov
+        uses: codecov/codecov-action@v4
+        if: success()
+        with:
+          file: coverage.xml

.readthedocs.yml

@@ -1,15 +1,20 @@
-# See: https://docs.readthedocs.io/en/latest/config-file/v2.html
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 version: 2
 
+# Set the version of Python and other tools you might need
 build:
-  image: latest
+  os: ubuntu-22.04
+  apt_packages:
+    - graphviz
+  tools:
+    python: "3.12"
 
 python:
-  version: "3.8"
   install:
     - method: pip
       path: .
       extra_requirements:
         - docs
-        - rdflib

MANIFEST.in

@@ -1,14 +1,11 @@
 graft src
 graft tests
-prune benchmarking
+prune scripts
+prune notebooks
 prune tests/.pytest_cache
-prune docs/source/api
+prune docs
 
-recursive-include docs/source *.py
-recursive-include docs/source *.rst
-recursive-include docs/source *.png
+global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle .idea/**
 
-global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
-
-exclude .bumpversion.cfg Dockerfile docker-compose.yml
-include *.rst *.yml LICENSE tox.ini
+include README.md LICENSE
+exclude tox.ini .readthedocs.yml