Add tests

.github/workflows/cruft.yml

@@ -0,0 +1,79 @@
+# from https://cruft.github.io/cruft/#automating-updates-with-github-actions
+
+name: Update repository with Cruft
+
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 2 * * 1" # Every Monday at 2am
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - add-paths: .
+            body: Use this to merge the changes to this repository.
+            branch: cruft/update
+            commit-message: "chore: accept new Cruft update"
+            title: New updates detected with Cruft
+          - add-paths: .cruft.json
+            body: Use this to reject the changes in this repository.
+            branch: cruft/reject
+            commit-message: "chore: reject new Cruft update"
+            title: Reject new updates detected with Cruft
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Cruft
+        run: pip3 install cruft
+
+      - name: Check if update is available
+        continue-on-error: false
+        id: check
+        run: |
+          CHANGES=0
+          if [ -f .cruft.json ]; then
+            if ! cruft check; then
+              CHANGES=1
+            fi
+          else
+            echo "No .cruft.json file"
+          fi
+
+          echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
+
+      - name: Run update if available
+        if: steps.check.outputs.has_changes == '1'
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "GitHub"
+
+          cruft update --skip-apply-ask --refresh-private-variables
+          git restore --staged .
+
+      - name: Create pull request
+        if: steps.check.outputs.has_changes == '1'
+        uses: peter-evans/create-pull-request@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          add-paths: ${{ matrix.add-paths }}
+          commit-message: ${{ matrix.commit-message }}
+          branch: ${{ matrix.branch }}
+          delete-branch: true
+          branch-suffix: timestamp
+          title: ${{ matrix.title }}
+          body: |
+            This is an autogenerated PR. ${{ matrix.body }}
+
+            [Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.

.github/workflows/ndex.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@master
       - uses: actions/setup-python@v2
         with:
-          python-version: "3.9"
+          python-version: "3.12"
       - name: Install dependencies
         run: |
           pip install tox

.github/workflows/tests.yml

@@ -0,0 +1,78 @@
+# 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:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  lint:
+    name: Code Quality
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.12", "3.9" ]
+        tox-command: ["manifest", "lint", "pyroma", "mypy"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: "Run command"
+        run: |
+          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@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: Install dependencies
+        run: |
+          sudo apt-get install graphviz
+      - name: Check RST conformity with 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: 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: [ "3.12", "3.9" ]
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: Test with pytest and generate coverage file
+        run:
+          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