ci: Check PRs for semantic labels

.github/dependabot.yml

@@ -0,0 +1,9 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    labels:
+      - no milestone
+      - skip-gpu-ci

.github/workflows/benchmark.yml

@@ -11,7 +11,10 @@ env:
 
 defaults:
   run:
-    shell: bash -el {0}
+    # Add `-l` to GitHub’s default bash options to activate mamba environments
+    # https://docs.github.com/en/actions/reference/workflows-and-actions/workflow-syntax#exit-codes-and-error-action-preference
+    # https://github.com/mamba-org/setup-micromamba/#readme
+    shell: bash -elo pipefail {0}
 
 jobs:
   benchmark:
@@ -29,9 +32,10 @@ jobs:
       ASV_DIR: "./benchmarks"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
+          # no blob filter so asv can checkout other commits
 
       - run: git fetch origin main:main
         if: ${{ github.ref_name != 'main' }}

.github/workflows/check-pr-milestoned.yml → .github/workflows/check-pr.yml

@@ -24,7 +24,7 @@ env:
 
 jobs:
   check-milestone:
-    name: "Triage: Check Milestone"
+    name: "Triage: Check PR title, milestone, and labels"
     runs-on: ubuntu-latest
     steps:
       - name: Check if merging isn’t blocked
@@ -35,3 +35,7 @@ jobs:
         uses: flying-sheep/check@v1
         with:
           success: ${{ github.event.pull_request.user.login == 'pre-commit-ci[bot]' || github.event.pull_request.milestone != null || contains(env.LABELS, 'no milestone') }}
+      - name: Check if PR title is valid
+        uses: amannn/action-semantic-pull-request@v6
+        env: # Needs repo options: “Squash and merge” with commit message set to “PR title”
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish.yml

@@ -11,7 +11,7 @@ jobs:
     permissions:
       id-token: write # to authenticate as Trusted Publisher to pypi.org
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           filter: blob:none

.github/workflows/test-cpu.yml

@@ -10,12 +10,7 @@ on:
 env:
   FORCE_COLOR: "1"
 
-defaults:
-  run:
-    shell: bash -el {0}
-
-# Cancel the job if new commits are pushed
-# https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
+# Cancel the job if new commits are pushed: https://stackoverflow.com/q/66335225/247482
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
@@ -26,11 +21,11 @@ jobs:
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
-      - uses: astral-sh/setup-uv@v5
+      - uses: astral-sh/setup-uv@v6
         with:
           enable-cache: false
       - id: get-envs
@@ -41,6 +36,7 @@ jobs:
               | { name: .key, python: .value.python, args: (.value."extra-args" // [] | join(" ")) }
             )')
           echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
   test:
     needs: get-environments
     runs-on: ubuntu-latest
@@ -51,31 +47,35 @@ jobs:
     env:  # environment variable for use in codecov’s env_vars tagging
       ENV_NAME: ${{ matrix.env.name }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           filter: blob:none
 
       - name: Install system dependencies
         run: sudo apt install -y hdf5-tools
 
-      - name: Set up Python ${{ matrix.env.python }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.env.python }}
-
       - name: Install UV
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
-          cache-dependency-glob: pyproject.toml
+          python-version: ${{ matrix.env.python }}
 
       - name: Install dependencies
         run: uvx hatch -v env create ${{ matrix.env.name }}
 
       - name: Run tests
         run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto --cov --cov-report=xml --junitxml=test-data/test-results.xml -m "${{ matrix.io_mark }}" ${{ matrix.env.args }}
 
+      - name: Upload test results
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          env_vars: ENV_NAME
+          fail_ci_if_error: true
+          file: test-data/test-results.xml
+
       - name: Upload coverage data
         uses: codecov/codecov-action@v5
         with:
@@ -85,17 +85,18 @@ jobs:
           files: test-data/coverage.xml
 
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           filter: blob:none
 
-      - name: Set up Python 3.13
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.13'
+          python-version: '3.x'
+          cache: pip
 
       - name: Install build tools and requirements
         run: |
@@ -123,6 +124,6 @@ jobs:
       - build
     runs-on: ubuntu-latest
     steps:
-        - uses: re-actors/alls-green@release/v1
-          with:
-            jobs: ${{ toJSON(needs) }}
+      - uses: re-actors/alls-green@release/v1
+        with:
+          jobs: ${{ toJSON(needs) }}

.github/workflows/test-gpu.yml

@@ -13,10 +13,6 @@ env:
   PYTEST_ADDOPTS: "-v --color=yes"
   FORCE_COLOR: "1"
 
-defaults:
-  run:
-    shell: bash -el {0}
-
 # Cancel the job if new commits are pushed
 # https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
 concurrency:
@@ -48,7 +44,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           filter: blob:none
@@ -66,28 +62,22 @@ jobs:
           max_version=$(echo "$classifiers" | sort -V | tail -1)
           echo "max_python_version=$max_version" >> $GITHUB_ENV
 
-      - name: Install Python
-        uses: actions/setup-python@v5
-        with:
-          # https://github.com/cupy/cupy/issues/8651 cupy does not support python3.13 yet
-          python-version: "3.12"
-
       - name: Install UV
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
-          cache-dependency-glob: pyproject.toml
+          python-version: ${{ env.max_python_version }}
 
       - name: Install AnnData
         run: uv pip install --system -e ".[dev,test,cu12]" -c ci/constraints.txt
 
       - name: Env list
-        run: pip list
+        run: uv pip list
 
       - name: Run test
         run: coverage run -m pytest -m gpu -n auto --cov --cov-report=xml
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

.readthedocs.yml

@@ -1,6 +1,6 @@
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: "3.13"
   jobs:

pyproject.toml

@@ -250,10 +250,13 @@ single_file = false
 package_dir = "src"
 issue_format = "{{pr}}`{issue}`"
 title_format = "(v{version})=\n### {version} {{small}}`{project_date}`"
-fragment.bugfix.name = "Bug fixes"
-fragment.doc.name = "Documentation"
-fragment.feature.name = "Features"
-fragment.misc.name = "Miscellaneous improvements"
-fragment.performance.name = "Performance"
-fragment.breaking.name = "Breaking changes"
-fragment.dev.name = "Development Process"
+# Valid fragments should be a subset of conventional commit types (except for `breaking`):
+# https://github.com/commitizen/conventional-commit-types/blob/master/index.json
+# style, refactor, test, build, ci: should not go into changelog
+fragment.feat.name = "Features"
+fragment.fix.name = "Bug fixes"
+fragment.docs.name = "Documentation"
+fragment.perf.name = "Performance"
+fragment.chore.name = "Miscellaneous changes"
+fragment.revert.name = "Revert"
+fragment.breaking.name = "Breaking changes"   # add `!` to commit type (e.g. “feature!:”)