bug fixing #283
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| # NOTE: this does not run with --run-raxml or --run-generax flags, so these | |
| # tests will be skipped. | |
| name: topiary | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| schedule: | |
| - cron: '0 0 * * *' # Every night at midnight | |
| jobs: | |
| build-nix: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 3 | |
| matrix: | |
| os: [ubuntu-latest,macos-latest] | |
| python-version: ['3.8', '3.9', '3.10' , '3.11', '3.12'] | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3.0.0 | |
| - name: set up miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: topiary | |
| environment-file: environment.yml | |
| channel-priority: strict | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| - name: install topiary | |
| shell: bash -l {0} | |
| run: | | |
| # platform specific packages | |
| conda install -c conda-forge -c bioconda "muscle>=5.0" "raxml-ng==1.1" "generax>=2.0" "blast>=2.2" | |
| python -m pip install mpi4py | |
| python -m pip install . -vv -r requirements.txt | |
| - name: run flake8 | |
| shell: bash -l {0} | |
| run: | | |
| conda install flake8 | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| - name: run pytest | |
| shell: bash -l {0} | |
| run: | | |
| conda install pytest | |
| export PATH=`which conda | xargs dirname`/envs/topiary/bin/:$PATH | |
| pytest | |
| build-windows: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 3 | |
| matrix: | |
| os: [windows-latest] | |
| python-version: ['3.8', '3.9', '3.10' , '3.11', '3.12'] | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3.0.0 | |
| - name: set up miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: topiary | |
| environment-file: environment.yml | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| - name: install topiary | |
| shell: pwsh | |
| run: | | |
| python -m pip install . -vv -r requirements.txt | |
| - name: run flake8 | |
| shell: pwsh | |
| run: | | |
| conda install flake8 | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| - name: run pytest | |
| shell: pwsh | |
| run: | | |
| conda install pytest | |
| $Env:PATH = "C:\Miniconda3\Scripts\;$Env:PATH" | |
| pytest |