feat: complex CDSs within augur ancestral #1806
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| 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@v4 | |
| - 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 ${{ github.workspace }}/bin/augur | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: "${{ 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 } | |
| # Disable mpox CI until pathogen-repo-ci supports custom build directories | |
| # See issue https://github.com/nextstrain/.github/issues/63 | |
| # - { pathogen: mpox } | |
| - { 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: tb } | |
| - { pathogen: zika } | |
| name: pathogen-repo-ci (${{ matrix.pathogen }}) | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| path: ./augur | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| create-args: nextstrain-base | |
| condarc: | | |
| channels: | |
| - nextstrain | |
| - conda-forge | |
| - bioconda | |
| channel_priority: strict | |
| cache-environment: true | |
| environment-name: augur | |
| - run: pip install ./augur | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: nextstrain/${{ 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@v4 | |
| - 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] |