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Add GitHub actions (#12)
* Add yaml files and remove travis configs * Update badges
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‎.github/workflows/ci.yaml

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name: Weekly global Tool Linting and Tests
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on:
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schedule:
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# Run at midnight every monday
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- cron: '0 0 * * 1'
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repository_dispatch:
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types: [run-all-tool-tests-command]
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env:
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GALAXY_RELEASE: release_20.09
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jobs:
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setup:
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name: Setup cache
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if: github.repository_owner == 'computational-metabolomics'
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7]
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steps:
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- name: Add reaction
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if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
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uses: peter-evans/create-or-update-comment@v1
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with:
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token: ${{ secrets.PAT }}
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repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
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comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
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reaction-type: hooray
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- uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache .cache/pip
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uses: actions/cache@v2
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id: cache-pip
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with:
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path: ~/.cache/pip
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key: pip_cache_${{ matrix.python-version }}_${{ env.GALAXY_RELEASE }}
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# Install the `wheel` package so that when installing other packages which
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# are not available as wheels, pip will build a wheel for them, which can be cached.
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- name: Install wheel
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run: pip install wheel
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- name: Install Planemo
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run: pip install planemo
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- name: Fake a planemo run to update cache
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run: |
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touch tool.xml
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PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_branch $GALAXY_RELEASE
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test:
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name: Test tools
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# This job runs on Linux
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runs-on: ubuntu-latest
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needs: setup
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strategy:
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fail-fast: false
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matrix:
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chunk: [0,1,2,3]
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python-version: [3.7]
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services:
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postgres:
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image: postgres:11
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env:
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POSTGRES_USER: postgres
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POSTGRES_PASSWORD: postgres
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POSTGRES_DB: postgres
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ports:
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- 5432:5432
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steps:
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# checkout the repository
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# and use it as the current working directory
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- uses: actions/checkout@v2
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with:
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fetch-depth: 1
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- uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache .cache/pip
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uses: actions/cache@v2
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id: cache-pip
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with:
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path: ~/.cache/pip
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key: pip_cache_${{ matrix.python-version }}_${{ env.GALAXY_RELEASE }}
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- name: Install Planemo
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run: pip install planemo
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- name: Planemo ci_find_tools
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run: planemo ci_find_tools --chunk_count 4 --chunk ${{ matrix.chunk }} --exclude test_repositories --exclude packages --exclude deprecated --exclude_from .tt_skip --exclude_from .tt_biocontainer_skip --group_tools --output tool.list
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- name: Show repo list
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run: cat tool.list
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- name: Planemo test tools
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run: |
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mkdir json_output/
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while read -r TOOLS; do
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if grep -qf .tt_biocontainer_skip <(echo $TOOLS); then
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PLANEMO_OPTIONS=""
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else
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PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
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fi
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json=$(mktemp -u -p json_output --suff .json)
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PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json $json $TOOLS || true
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docker system prune --all --force --volumes || true
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done < tool.list
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- name: Merge tool_test_output.json files
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run: planemo merge_test_reports json_output/*.json tool_test_output.json
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- name: Create tool_test_output.html
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run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
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- name: Copy artifacts into place
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run: |
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mkdir upload
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mv tool_test_output.json tool_test_output.html upload/
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- uses: actions/[email protected]
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with:
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name: 'Tool test output ${{ matrix.chunk }}'
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path: upload
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combine_outputs:
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name: Combine chunked test results
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needs: test
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strategy:
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matrix:
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python-version: [3.7]
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# This job runs on Linux
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runs-on: ubuntu-latest
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steps:
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- uses: actions/download-artifact@v2
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with:
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path: artifacts
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- uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Planemo
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run: pip install planemo
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- name: Install jq
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run: sudo apt-get install jq
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- name: Combine outputs
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run: find artifacts -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
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- name: Create tool_test_output.html
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run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
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- name: Copy artifacts into place
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run: |
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mkdir upload
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mv tool_test_output.json tool_test_output.html upload/
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- uses: actions/[email protected]
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with:
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name: 'All tool test results'
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path: upload
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- name: Create URL to the run output
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if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
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id: vars
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run: echo ::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID
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- name: Create comment
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if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
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uses: peter-evans/create-or-update-comment@v1
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with:
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token: ${{ secrets.PAT }}
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repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
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issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
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body: |
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[Find all tool test results here][1]
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[1]: ${{ steps.vars.outputs.run-url }}
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- name: Check status of combined outputs
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run: |
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if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
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echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
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exit 1
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fi

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