[python] Initial work toward PyTorch data loaders #19
Workflow file for this run
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name: python-tiledbsoma-ml | |
on: | |
pull_request: | |
branches: ["*"] | |
paths: | |
- "!**" | |
- "other_packages/python/tiledbsoma_ml/**" | |
- ".github/workflows/python-tiledbsoma-ml.yml" | |
push: | |
branches: [main] | |
paths: | |
- "!**" | |
- "other_packages/python/tiledbsoma_ml/**" | |
- ".github/workflows/python-tiledbsoma-ml.yml" | |
workflow_dispatch: | |
jobs: | |
lint: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
- name: Restore pre-commit cache | |
uses: actions/cache@v4 | |
with: | |
path: ~/.cache/pre-commit | |
key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }} | |
- name: Install pre-commit | |
run: pip -v install pre-commit | |
- name: Run pre-commit hooks on all files | |
run: pre-commit run -v -a | |
tests: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
cache: pip | |
cache-dependency-path: python-spec/requirements-py${{ matrix.python-version }}.txt | |
- name: Install prereqs | |
working-directory: ./other_packages/python/tiledbsoma_ml/ | |
run: | | |
pip install --upgrade pip wheel pytest pytest-cov setuptools | |
pip install . | |
- name: Run tests | |
run: | | |
PYTHONPATH=$(pwd)/other_packages/python/tiledbsoma_ml python -m pytest \ | |
--cov=other_packages/python/tiledbsoma_ml/src \ | |
--cov-report=xml other_packages/python/tiledbsoma_ml/tests \ | |
-v | |
# - name: Report coverage to Codecov | |
# if: ${{ matrix.python-version == '3.11' }} | |
# uses: codecov/codecov-action@v4 | |
# with: | |
# flags: python | |
# # Although Codecov isn't supposed to require an auth token for public repos like this one, | |
# # the uploader can be unreliable without one; see | |
# # https://github.com/codecov/codecov-action/issues/557#issuecomment-1216749652 | |
# # As of this writing (8 Nov 2022) the CODECOV_TOKEN was generated by @aaronwolen in his | |
# # Codecov settings page for this repo, then filled into the GitHub Actions secrets. | |
# token: ${{ secrets.CODECOV_TOKEN }} | |
build: | |
# for now, just do a test build to ensure that it works | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
- name: Do build | |
working-directory: ./other_packages/python/tiledbsoma_ml/ | |
run: | | |
pip install --upgrade build pip wheel setuptools setuptools-scm | |
python -m build . |