Merge pull request #1317 from nextstrain/export-root-aa-sequences-fro… #1737
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| # Routinely check that tests pass with new versions of dependencies. | |
| schedule: | |
| # Every day at 17:42 UTC / 9:42 Seattle (winter) / 10:42 Seattle (summer) | |
| - cron: "42 17 * * *" | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| pytest-cram: | |
| name: test (python=${{ matrix.python-version }} biopython=${{ matrix.biopython-version || 'latest' }}) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - '3.8' | |
| - '3.9' | |
| - '3.10' | |
| - '3.11' | |
| biopython-version: | |
| # list of Biopython versions with support for a new Python version | |
| # from https://github.com/biopython/biopython/blob/master/NEWS.rst | |
| - '1.76' # first to support Python 3.8 | |
| - '1.79' # first to support Python 3.9 | |
| - '1.80' # first to support Python 3.10 and 3.11 | |
| - '' # latest | |
| exclude: | |
| # some older Biopython versions are incompatible with later Python versions | |
| - { biopython-version: '1.76', python-version: '3.9' } | |
| - { biopython-version: '1.76', python-version: '3.10' } | |
| - { biopython-version: '1.76', python-version: '3.11' } | |
| - { biopython-version: '1.79', python-version: '3.10' } | |
| - { biopython-version: '1.79', python-version: '3.11' } | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| COVERAGE_FILE: ${{ github.workspace }}/.coverage@python=${{ matrix.python-version }},biopython=${{ matrix.biopython-version || 'latest' }} | |
| COVERAGE_RCFILE: ${{ github.workspace }}/.coveragerc | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| - run: | | |
| mamba install \ | |
| mafft \ | |
| raxml \ | |
| fasttree \ | |
| iqtree \ | |
| vcftools \ | |
| biopython=${{ matrix.biopython-version }} | |
| - run: pip install .[dev] | |
| - run: conda info | |
| - run: conda list | |
| - run: pytest -c pytest.python3.ini --cov=augur | |
| - run: cram tests/ | |
| env: | |
| AUGUR: coverage run -a ${{ github.workspace }}/bin/augur | |
| - run: bash tests/builds/runner.sh | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: "${{ env.COVERAGE_FILE }}" | |
| # TODO: Use the central pathogen-repo-ci workflow¹. Currently, this is not | |
| # possible because it only supports "stock" docker and conda runtimes. | |
| # ¹ https://github.com/nextstrain/.github/blob/-/.github/workflows/pathogen-repo-ci.yaml | |
| pathogen-repo-ci: | |
| runs-on: ubuntu-latest | |
| continue-on-error: true | |
| env: | |
| repodata_use_zst: true | |
| strategy: | |
| matrix: | |
| include: | |
| - { pathogen: avian-flu, build-args: auspice/flu_avian_h5n1_ha.json } | |
| - { pathogen: ebola } | |
| - { pathogen: lassa } | |
| - { pathogen: monkeypox } | |
| - { pathogen: mumps } | |
| - { | |
| pathogen: ncov, | |
| build-args: all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci, | |
| } | |
| - { pathogen: rsv } | |
| - { | |
| pathogen: seasonal-flu, | |
| build-args: --configfile profiles/ci/builds.yaml -p, | |
| } | |
| - { pathogen: zika } | |
| name: pathogen-repo-ci (${{ matrix.pathogen }}) | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| path: ./augur | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| create-args: nextstrain-base | |
| condarc: | | |
| channels: | |
| - nextstrain | |
| - conda-forge | |
| - bioconda | |
| channel_priority: strict | |
| cache-environment: true | |
| environment-name: augur | |
| - run: pip install ./augur | |
| - uses: actions/checkout@v3 | |
| with: | |
| repository: nextstrain/${{ matrix.pathogen }} | |
| path: ./pathogen-repo | |
| - name: Copy example data | |
| working-directory: ./pathogen-repo | |
| run: | | |
| if [[ -d example_data ]]; then | |
| mkdir -p data/ | |
| cp -r -v example_data/* data/ | |
| else | |
| echo No example data to copy. | |
| fi | |
| - run: nextstrain build --ambient ./pathogen-repo ${{ matrix.build-args }} | |
| - if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: output-${{ matrix.pathogen }} | |
| path: | | |
| ./pathogen-repo/auspice/ | |
| ./pathogen-repo/results/ | |
| ./pathogen-repo/benchmarks/ | |
| ./pathogen-repo/logs/ | |
| ./pathogen-repo/.snakemake/log/ | |
| codecov: | |
| if: github.repository == 'nextstrain/augur' | |
| needs: [pytest-cram] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| - run: pip install coverage | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: coverage | |
| - run: coverage combine .coverage@* | |
| - run: coverage xml | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| fail_ci_if_error: false | |
| build-docs: | |
| uses: nextstrain/.github/.github/workflows/docs-ci.yaml@master | |
| with: | |
| docs-directory: docs/ | |
| pip-install-target: .[dev] |