Backport PR #1906: (fix): Accelerate tests: migrate to Github Actions… (#1910)

* Backport PR #1906: (fix): Accelerate tests: migrate to Github Actions, remove slow param, parallelize

* (fix): correct min versions

* (fix): notebooks

Author: ilan-gold

.azure-pipelines.yml

@@ -6,12 +6,16 @@ on:
   pull_request:
     branches: [main]
 
+env:
+  FORCE_COLOR: "1"
+
+defaults:
+  run:
+    shell: bash -el {0}
+
 jobs:
   benchmark:
     runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -el {0} # -e to fail on error, -l for mamba
 
     strategy:
       fail-fast: false

.github/workflows/benchmark.yml

@@ -16,7 +16,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Codespell
-        uses: codespell-project/actions-codespell@v2
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+      - uses: codespell-project/actions-codespell@v2

.github/workflows/codespell.yml

@@ -12,6 +12,9 @@ jobs:
       id-token: write # to authenticate as Trusted Publisher to pypi.org
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
       - uses: actions/setup-python@v5
         with:
           python-version: "3.x"

.github/workflows/publish.yml

@@ -0,0 +1,124 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - "*.*.x"
+  pull_request:
+
+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:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - python-version: '3.12'
+            test-type: coverage
+          - python-version: '3.10'
+            test-type: standard
+          - python-version: '3.12'
+            dependencies-version: pre-release
+            test-type: strict-warning
+          - python-version: '3.10'
+            dependencies-version: minimum
+            test-type: coverage
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install UV
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+
+      - name: Install dependencies
+        if: matrix.dependencies-version == null
+        run: uv pip install --system --compile "anndata[dev,test] @ ." -c ci/constraints.txt
+
+      - name: Install minimum dependencies
+        if: matrix.dependencies-version == 'minimum'
+        run: |
+          uv pip install --system --compile tomli packaging
+
+          deps=$(python3 ci/scripts/min-deps.py pyproject.toml --extra dev test)
+          uv pip install --system --compile $deps "anndata @ ."
+
+      - name: Install dependencies release candidates
+        if: matrix.dependencies-version == 'pre-release'
+        run: uv pip install -v --system --compile --pre "anndata[dev,test] @ ." -c ci/constraints.txt
+
+      - name: Display installed versions
+        run: uv pip list
+
+      - name: Run Pytest
+        if: matrix.test-type == 'standard'
+        run: pytest -n auto
+
+      - name: Run Pytest (coverage)
+        if: matrix.test-type == 'coverage'
+        run: coverage run -m pytest -n auto --cov --cov-report=xml
+
+      - name: Run Pytest (treat warnings as errors)
+        if: matrix.test-type == 'strict-warning'
+        run: pytest --strict-warnings -n auto
+
+      - uses: codecov/codecov-action@v4
+        if: matrix.test-type == 'coverage'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          files: test-data/coverage.xml
+
+  check-build:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install build tools and requirements
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Display installed versions
+        run: pip list
+
+      - name: Build & Twine check
+        run: |
+          python -m build --sdist --wheel .
+          twine check dist/*
+
+      - name: Check runtime version
+        run: |
+          pip install dist/*.whl
+          python -c 'import anndata; print(anndata.__version__)'

.github/workflows/test-cpu.yml

@@ -9,6 +9,14 @@ on:
       - opened
       - synchronize
 
+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:
@@ -39,14 +47,11 @@ jobs:
     # At time of writing, a typical run takes about 5 minutes
     timeout-minutes: 30
 
-    defaults:
-      run:
-        shell: bash -el {0}
-
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          filter: blob:none
 
       - name: Nvidia SMI sanity check
         run: nvidia-smi
@@ -67,9 +72,10 @@ jobs:
           python-version: ${{ env.max_python_version }}
 
       - name: Install UV
-        uses: hynek/setup-cached-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
-          cache-dependency-path: pyproject.toml
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
 
       - name: Install AnnData
         run: uv pip install --system -e ".[dev,test,cu12]" -c ci/constraints.txt
@@ -78,13 +84,13 @@ jobs:
         run: pip list
 
       - name: Run test
-        run: pytest -m gpu --cov --cov-report=xml --cov-context=test
+        run: coverage run -m pytest -m gpu -n auto --cov --cov-report=xml
 
       - uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
-          verbose: true
+          files: test-data/coverage.xml
 
       - name: Remove 'run-gpu-ci' Label
         if: always()

.github/workflows/test-gpu.yml

@@ -102,7 +102,7 @@ test = [
     "pytest-mock",
     "anndata[dask]",
 ]
-dev-test = [ "pytest-xdist" ] # local test speedups
+dev-test = [ "pytest-xdist[psutil]" ] # local test speedups
 gpu = [ "cupy" ]
 cu12 = [ "cupy-cuda12x" ]
 cu11 = [ "cupy-cuda11x" ]
@@ -120,6 +120,9 @@ packages = [ "src/anndata", "src/testing" ]
 data_file = "test-data/coverage"
 source_pkgs = [ "anndata" ]
 omit = [ "src/anndata/_version.py", "**/test_*.py" ]
+concurrency = [ "multiprocessing" ]
+parallel = "true"
+
 [tool.coverage.xml]
 output = "test-data/coverage.xml"
 [tool.coverage.paths]
@@ -139,8 +142,8 @@ addopts = [
     "-ptesting.anndata._pytest",
 ]
 filterwarnings = [
-    # all `ignore::anndata.*` entries are in `conftest.py`
-    # See: https://github.com/pytest-dev/pytest-cov/issues/437
+    "ignore::anndata._warnings.OldFormatWarning",
+    "ignore::anndata._warnings.ExperimentalFeatureWarning",
 ]
 # When `--strict-warnings` is used, all warnings are treated as errors, except those:
 filterwarnings_when_strict = [