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Restore correct owner
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.github/workflows/pr.yaml

Lines changed: 14 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -95,7 +95,7 @@ jobs:
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matrix:
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python-version: [3.7]
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steps:
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# checkout the repository to master
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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:
@@ -115,7 +115,7 @@ jobs:
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with:
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path: ~/.cache/pip
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key: pip_cache_python_${{ matrix.python-version }}_${{ env.GALAXY_HEAD_SHA }}
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- name: Setup planemo
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- name: Install Planemo
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run: pip install planemo
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- name: Planemo lint
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run: |
@@ -126,7 +126,7 @@ jobs:
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# flake8 of python scripts in the changed repositories
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flake8:
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name: Lint python scripts
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name: Lint Python scripts
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needs: setup
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runs-on: ubuntu-latest
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strategy:
@@ -154,12 +154,12 @@ jobs:
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with:
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path: ~/.cache/pip
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key: pip_cache_python_${{ matrix.python-version }}_${{ env.GALAXY_HEAD_SHA }}
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- name: Setup flake8
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- name: Install flake8
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run: pip install flake8
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- name: Flake8
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run: |
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if [ -s ../workflow_artifacts/changed_repositories.list ]; then
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flake8 $(cat ../workflow_artifacts/changed_repositories.list)
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flake8 $(cat ../workflow_artifacts/changed_repositories.list)
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fi
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# planemo test the changed repositories, each chunk creates an artifact
@@ -184,7 +184,7 @@ jobs:
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ports:
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- 5432:5432
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steps:
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# checkout the repository to master
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# checkout the repository
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# and use it as the current working directory
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- uses: actions/checkout@v2
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with:
@@ -300,9 +300,9 @@ jobs:
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with:
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path: ~/.cache/pip
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key: pip_cache_python_${{ matrix.python-version }}_${{ env.GALAXY_HEAD_SHA }}
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- name: Setup planemo
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- name: Install Planemo
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run: pip install planemo
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- name: Setup jq
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- name: Install jq
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run: sudo apt-get install jq
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- name: Combine outputs
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run: find . -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
@@ -320,15 +320,14 @@ jobs:
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run: |
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stat=$(jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success" || true)
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if [[ "$(echo -n $stat | wc -l)" -gt "0" ]]; then
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echo "unsuccessful tests found $(sort <<<$stat | uniq -c)"
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echo "Unsuccessful tests found $(sort <<<$stat | uniq -c)"
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exit 1
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fi
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# deploy the tools to the toolsheds (first TTS for testing)
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deploy:
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name: Deploy
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needs: combine_outputs
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# This job runs on Linux
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strategy:
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matrix:
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python-version: [3.7]
@@ -353,21 +352,19 @@ jobs:
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with:
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path: ~/.cache/pip
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key: pip_cache_python_${{ matrix.python-version }}_${{ env.GALAXY_HEAD_SHA }}
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- name: Setup planemo
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- name: Install Planemo
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run: pip install planemo
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# TODO remove --owner
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- name: Deploy on testtoolshed
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env:
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SHED_KEY: ${{ secrets.tts_api_key }}
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run: |
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while read -r DIR;
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do
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planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" --owner matthias || exit 1;
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while read -r DIR; do
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planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
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done < ../workflow_artifacts/changed_repositories.list
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- name: Deploy on toolshed
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env:
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SHED_KEY: ${{ secrets.ts_api_key }}
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run: |
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while read -r DIR;
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do planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
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while read -r DIR; do
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planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
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done < ../workflow_artifacts/changed_repositories.list

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