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Direct Zarr IO #693

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Direct Zarr IO

Direct Zarr IO #693

Workflow file for this run

.github/workflows/ci.yml at e635eec
name: CI
on:
merge_group:
pull_request:
push:
branches:
- main
schedule:
# At 04:44 on Monday, see https://crontab.guru/
- cron: "44 4 * * 1"
permissions:
contents: read
jobs:
lint:
name: Lint
runs-on: ubuntu-24.04
steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
with:
persist-credentials: false
- name: Install uv and set the python version
uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
with:
python-version: "3.11"
- name: Install lint group
run: uv sync --locked --only-group lint
- name: Run prek
run: |
uv run --locked --only-group lint \
prek -c prek.toml run --all-files --show-diff-on-failure
python_test:
name: Python tests
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [macos-14, ubuntu-latest, windows-latest]
python-version: ["3.11", "3.13"]
exclude:
# There's a bug in Pyranges which means we need to avoid Windows/3.11
# https://github.com/sgkit-dev/vcztools/issues/290
- os: windows-latest
python-version: "3.11"
steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
with:
fetch-depth: 0
persist-credentials: false
- name: Install bcftools and plink2 (Linux only)
# The bcftools and plink2 validation test files skip cleanly
# via shutil.which on platforms without these binaries, so
# the install runs on Linux only; macOS and Windows leave
# the validation suites as no-ops.
if: runner.os == 'Linux'
run: |
sudo apt-get update
sudo apt-get install -y bcftools plink2
- name: Install uv
uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
with:
python-version: ${{ matrix.python-version }}
- name: Install test dependencies
run: |
uv sync --locked --group test --no-default-groups
# Build the extension module in-place so pytest can find it
uv run python setup.py build_ext --inplace
- name: Run tests
run: |
uv run pytest --cov=vcztools --cov-report=term-missing
c_python_test:
name: CPython interface tests
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
with:
fetch-depth: 0
persist-credentials: false
- name: Install uv and set the python version
uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
with:
python-version: "3.11"
- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y gcovr
- name: Install python dependencies
run: uv sync --locked --group test --no-default-groups
- name: Build module with coverage
run: |
# Build the extension module in-place so pytest can find it
CFLAGS="--coverage" uv run python setup.py build_ext --inplace
- name: Run tests
run: |
uv run pytest -vs tests/test_cpython_interface.py
- name: Show coverage
run: |
gcovr --filter vcztools
c_test:
name: C tests
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
with:
persist-credentials: false
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install -y ninja-build libcunit1-dev valgrind meson gcovr
- name: Build
working-directory: ./lib
run: |
meson setup -Db_coverage=true build
- name: Tests
working-directory: ./lib
run: |
ninja -C build test
- name: Show coverage
working-directory: ./lib
run: |
ninja -C build coverage-text
cat build/meson-logs/coverage.txt
- name: Valgrind
working-directory: ./lib
run: |
valgrind --leak-check=full --error-exitcode=1 ./build/tests
packaging:
name: Packaging
runs-on: ubuntu-24.04
steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
with:
fetch-depth: 0
persist-credentials: false
- name: Install uv and set the python version
uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
with:
python-version: "3.12"
- name: Install packaging deps
run: uv sync --locked --group packaging --no-default-groups
- name: Validate pyproject
run: uv run --locked --group packaging --no-default-groups validate-pyproject pyproject.toml -v
- name: Build artefacts
run: uv build
- name: Twine check
run: uv run --locked --group packaging --no-default-groups twine check --strict dist/*
- name: Install into venv
run: |
uv venv cli-test
uv pip install --python=cli-test dist/*.whl
- name: Check vcztools CLI
run: |
./cli-test/bin/vcztools --help
cd tests
../cli-test/bin/python -m vcztools --help
test-azure-emulator:
name: Test Azure emulator
runs-on: ubuntu-24.04
steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
with:
fetch-depth: 0
persist-credentials: false
- name: Install uv and set the python version
uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
with:
python-version: "3.12"
- name: Set up Node.js
uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
with:
node-version: "22"
- name: Install Azurite
run: npm install -g azurite
- name: Install test dependencies
run: |
uv sync --locked --group test --no-default-groups
- name: Run Azure Icechunk test
run: |
uv run pytest -q tests/test_azure.py