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Add cronjob that tests entire tools-iuc repo every monday morning
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@mvdbeek
mvdbeek committed Jan 29, 2020
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239 changes: 239 additions & 0 deletions .github/workflows/ci.yaml
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name: Run Galaxy Tool Linting and Tests
on:
schedule:
# Run at midnight every monday
- cron: '0 * * * 1'
env:
GALAXY_RELEASE: release_20.01
jobs:
setup:
name: Cache planemo setup
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.7]
steps:
- uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
architecture: 'x64' # (x64 or x86)
- name: setup planemo
run: 'git clone --recursive --depth 1 https://github.com/galaxyproject/planemo && python -m pip install --pre planemo/ && rm -rf planemo'
- name: fake a planemo run to update cache
run: 'touch tool.xml && PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_branch $GALAXY_RELEASE'
- name: Cache .cache/pip
uses: actions/cache@v1
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_${{ matrix.python-version }}_${{ env.GALAXY_RELEASE }}
test:
name: Lint & test tools
# This job runs on Linux
runs-on: ubuntu-latest
needs: setup
strategy:
fail-fast: false
matrix:
chunk: [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39]
python-version: [3.7]
services:
postgres:
image: postgres:11
env:
POSTGRES_USER: postgres
POSTGRES_PASSWORD: postgres
POSTGRES_DB: postgres
ports:
- 5432:5432
steps:
# checkout the repository to master
# and use it as the current working directory
- uses: actions/checkout@v1
with:
fetch-depth: 1
- uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
architecture: 'x64' # (x64 or x86)
- name: Cache .cache/pip
uses: actions/cache@v1
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_${{ matrix.python-version }}_${{ env.GALAXY_RELEASE }}
- name: setup planemo
run: 'git clone --recursive --depth 1 https://github.com/galaxyproject/planemo && python -m pip install --pre planemo/ && rm -rf planemo'
- name: planemo ci_find_tools
run: 'planemo ci_find_repos --chunk_count 40 --chunk ${{ matrix.chunk }} --exclude test_repositories --exclude packages --exclude deprecated --exclude_from .tt_skip --exclude_from .tt_biocontainer_skip --output tool.list'
- name: set tool list
id: tools
run: echo "::set-output name=tool_list::$(tr '\n' ' ' < tool.list)"
- name: show repo list
run: 'cat tool.list'
- name: planemo test tools biocontainers
run: |
while read -r DIR; do
if [[ "$DIR" =~ ^data_managers.* ]]; then
TESTPATH=$(planemo ci_find_tools "$DIR")
else
TESTPATH="$DIR"
fi
PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy --no_conda_auto_init --galaxy_branch $GALAXY_RELEASE --biocontainers --galaxy_python_version ${{ matrix.python-version }} --test_output_json "$DIR"/tool_test_output.json "$TESTPATH" || true
docker system prune --all --force --volumes || true
done < tool.list
- name: Merge tool_test_output.json files
run: |
find . -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
- name: Create tool_test_output.html
run: 'planemo test_reports tool_test_output.json --test_output tool_test_output.html'
- name: Copy artifacts into place
run: mkdir upload && mv tool_test_output.json tool_test_output.html upload
- uses: actions/upload-artifact@v1
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload

combine_outputs:
name: Combine chunked test results
needs: test
# This job runs on Linux
runs-on: ubuntu-latest
steps:
- uses: actions/download-artifact@v1
with:
name: Tool test output 0
- uses: actions/download-artifact@v1
with:
name: Tool test output 1
- uses: actions/download-artifact@v1
with:
name: Tool test output 2
- uses: actions/download-artifact@v1
with:
name: Tool test output 3
- uses: actions/download-artifact@v1
with:
name: Tool test output 4
- uses: actions/download-artifact@v1
with:
name: Tool test output 5
- uses: actions/download-artifact@v1
with:
name: Tool test output 6
- uses: actions/download-artifact@v1
with:
name: Tool test output 7
- uses: actions/download-artifact@v1
with:
name: Tool test output 8
- uses: actions/download-artifact@v1
with:
name: Tool test output 9
- uses: actions/download-artifact@v1
with:
name: Tool test output 10
- uses: actions/download-artifact@v1
with:
name: Tool test output 11
- uses: actions/download-artifact@v1
with:
name: Tool test output 12
- uses: actions/download-artifact@v1
with:
name: Tool test output 13
- uses: actions/download-artifact@v1
with:
name: Tool test output 14
- uses: actions/download-artifact@v1
with:
name: Tool test output 15
- uses: actions/download-artifact@v1
with:
name: Tool test output 16
- uses: actions/download-artifact@v1
with:
name: Tool test output 17
- uses: actions/download-artifact@v1
with:
name: Tool test output 18
- uses: actions/download-artifact@v1
with:
name: Tool test output 19
- uses: actions/download-artifact@v1
with:
name: Tool test output 20
- uses: actions/download-artifact@v1
with:
name: Tool test output 21
- uses: actions/download-artifact@v1
with:
name: Tool test output 22
- uses: actions/download-artifact@v1
with:
name: Tool test output 23
- uses: actions/download-artifact@v1
with:
name: Tool test output 24
- uses: actions/download-artifact@v1
with:
name: Tool test output 25
- uses: actions/download-artifact@v1
with:
name: Tool test output 26
- uses: actions/download-artifact@v1
with:
name: Tool test output 27
- uses: actions/download-artifact@v1
with:
name: Tool test output 28
- uses: actions/download-artifact@v1
with:
name: Tool test output 29
- uses: actions/download-artifact@v1
with:
name: Tool test output 30
- uses: actions/download-artifact@v1
with:
name: Tool test output 31
- uses: actions/download-artifact@v1
with:
name: Tool test output 32
- uses: actions/download-artifact@v1
with:
name: Tool test output 33
- uses: actions/download-artifact@v1
with:
name: Tool test output 34
- uses: actions/download-artifact@v1
with:
name: Tool test output 35
- uses: actions/download-artifact@v1
with:
name: Tool test output 36
- uses: actions/download-artifact@v1
with:
name: Tool test output 37
- uses: actions/download-artifact@v1
with:
name: Tool test output 38
- uses: actions/download-artifact@v1
with:
name: Tool test output 39
- uses: actions/setup-python@v1
with:
python-version: '3.7'
architecture: 'x64'
- name: setup planemo
run: 'git clone --recursive --depth 1 https://github.com/galaxyproject/planemo && python -m pip install --pre planemo/ && rm -rf planemo'
- name: combine outputs
run: |
find . -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
- name: Create tool_test_output.html
run: 'planemo test_reports tool_test_output.json --test_output tool_test_output.html'
- name: Copy artifacts into place
run: mkdir upload && mv tool_test_output.json tool_test_output.html upload
- uses: actions/upload-artifact@v1
with:
name: 'All tool test results'
path: upload
2 changes: 2 additions & 0 deletions .tt_biocontainer_skip
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tools/maker
tools/qiime

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