Clean up and refactor KmerMinHash::merge in core
#5901
Workflow file for this run
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| # note: to invalidate caches, adjust the pip-v? number below. | |
| name: Python tests | |
| on: | |
| push: | |
| branches: [latest] | |
| pull_request: | |
| schedule: | |
| - cron: "0 0 * * *" # daily | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-22.04, macos-latest] | |
| py: ["3.12", "3.11", "3.10"] | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.py }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.py }} | |
| - name: Get pip cache dir | |
| id: pip-cache | |
| run: | | |
| echo "::set-output name=dir::$(pip cache dir)" | |
| - name: pip cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ steps.pip-cache.outputs.dir }} | |
| key: ${{ runner.os }}-pip-v4-${{ hashFiles('**/pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip-v4- | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install tox tox-gh-actions | |
| - name: Set up Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Set up IPFS | |
| if: startsWith(runner.os, 'Linux') && (matrix.py == '3.10') | |
| uses: ibnesayeed/setup-ipfs@master | |
| with: | |
| ipfs_version: 0.6 | |
| run_daemon: true | |
| - name: Start Redis | |
| if: startsWith(runner.os, 'Linux') && (matrix.py == '3.10') | |
| uses: supercharge/[email protected] | |
| with: | |
| redis-version: 6 | |
| - name: tox cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: .tox/ | |
| key: ${{ runner.os }}-tox-v4-${{ hashFiles('**/pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-tox-v4- | |
| - name: Test with tox | |
| run: tox | |
| env: | |
| PYTHONDEVMODE: 1 | |
| - name: Upload Python coverage to codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| flags: python | |
| fail_ci_if_error: true | |
| files: .tox/coverage.xml |