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a3684d9594
* ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
103 lines
3.3 KiB
YAML
103 lines
3.3 KiB
YAML
name: Pytest-workflow
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on: [push, pull_request]
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jobs:
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changes:
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name: Check for changes
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runs-on: ubuntu-latest
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outputs:
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# Expose matched filters as job 'modules' output variable
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modules: ${{ steps.filter.outputs.changes }}
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steps:
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- uses: actions/checkout@v2
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- uses: dorny/paths-filter@v2
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id: filter
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with:
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filters: 'tests/config/pytest_software.yml'
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test:
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runs-on: ubuntu-20.04
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name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
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needs: changes
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if: needs.changes.outputs.modules != '[]'
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strategy:
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fail-fast: false
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matrix:
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nxf_version: ['20.11.0-edge', '21.03.0-edge']
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tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
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profile: ['docker', 'singularity', 'conda']
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# FIXME: Remove this when nf-core modules lint stabilizes
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- name: Install nf-core tools development version
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run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
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- name: Lint ${{ matrix.tags }}
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run: nf-core modules lint . -t ${{ matrix.tags }}
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- uses: actions/cache@v2
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with:
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path: /usr/local/bin/nextflow
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key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
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restore-keys: |
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${{ runner.os }}-nextflow-
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Singularity
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if: matrix.profile == 'singularity'
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uses: eWaterCycle/setup-singularity@v5
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with:
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singularity-version: 3.7.1
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- name: Setup miniconda
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if: matrix.profile == 'conda'
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uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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channels: conda-forge,bioconda,defaults
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python-version: ${{ matrix.python-version }}
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- name: Conda clean
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if: matrix.profile == 'conda'
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run: conda clean -a
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# Test the module
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- name: Run pytest-workflow
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# only use one thread for pytest-workflow to avoid race condition on conda cache.
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run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
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- name: Upload logs on failure
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if: failure()
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uses: actions/upload-artifact@v2
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with:
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name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
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path: |
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/home/runner/pytest_workflow_*/*/.nextflow.log
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/home/runner/pytest_workflow_*/*/log.out
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/home/runner/pytest_workflow_*/*/log.err
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/home/runner/pytest_workflow_*/*/work
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