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Galaxy Tool Linting and Tests for push and PR

Decoupler Pathway Inference #339

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Decoupler Pathway Inference

Decoupler Pathway Inference #339

Workflow file for this run

.github/workflows/pr.yaml at 9efe1e4
name: Galaxy Tool Linting and Tests for push and PR
on: [pull_request]
env:
GALAXY_FORK: galaxyproject
GALAXY_BRANCH: release_21.01
MAX_CHUNKS: 4
jobs:
# the setup job does two things:
# 1. cache the pip cache and .planemo
# 2. determine the list of changed repositories
# it produces one artifact which contains
# - a file with the latest SHA from the chosen branch of the Galaxy repo
# - a file containing the list of changed repositories
# which are needed in subsequent steps.
setup:
name: Setup cache and determine changed repositories
runs-on: self-hosted
outputs:
galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
repository-list: ${{ steps.discover.outputs.repository-list }}
tool-list: ${{ steps.discover.outputs.tool-list }}
chunk-count: ${{ steps.discover.outputs.chunk-count }}
chunk-list: ${{ steps.discover.outputs.chunk-list }}
strategy:
matrix:
python-version: ['3.8']
steps:
- name: Print github context properties
run: |
echo 'event: ${{ github.event_name }}'
echo 'sha: ${{ github.sha }}'
echo 'ref: ${{ github.ref }}'
echo 'head_ref: ${{ github.head_ref }}'
echo 'base_ref: ${{ github.base_ref }}'
echo 'event.before: ${{ github.event.before }}'
echo 'event.after: ${{ github.event.after }}'
- name: Determine latest commit in the Galaxy repo
id: get-galaxy-sha
run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
- uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v2
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}-${{ secrets.CACHE_VERSION }}
- name: Cache .planemo
uses: actions/cache@v2
id: cache-planemo
with:
path: ~/.planemo
key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}-${{ secrets.CACHE_VERSION }}
# Install the `wheel` package so that when installing other packages which
# are not available as wheels, pip will build a wheel for them, which can be cached.
- name: Install wheel
run: pip install wheel
- name: Install jq
run: sudo apt-get install -yq jq libjq1
- uses: actions/checkout@v2
with:
fetch-depth: 0
- name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
uses: galaxyproject/planemo-ci-action@v1
id: discover
with:
create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}
galaxy-fork: ${{ env.GALAXY_FORK }}
galaxy-branch: ${{ env.GALAXY_BRANCH }}
max-chunks: ${{ env.MAX_CHUNKS }}
python-version: ${{ matrix.python-version }}
- name: Show commit range
run: echo '${{ steps.discover.outputs.commit-range }}'
- name: Show repository list
run: echo '${{ steps.discover.outputs.repository-list }}'
- name: Show tool list
run: echo '${{ steps.discover.outputs.tool-list }}'
- name: Show chunks
run: |
echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
# Planemo lint the changed repositories
lint:
name: Lint tool-list
needs: setup
if: needs.setup.outputs.repository-list != ''
runs-on: self-hosted
strategy:
fail-fast: false
matrix:
python-version: ['3.8']
steps:
# checkout the repository
# and use it as the current working directory
- uses: actions/checkout@v2
with:
fetch-depth: 1
- uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v2
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}-${{ secrets.CACHE_VERSION }}
- name: Install jq
run: sudo apt-get install -yq jq libjq1
- name: Planemo lint
uses: galaxyproject/planemo-ci-action@v1
id: lint
with:
mode: lint
repository-list: ${{ needs.setup.outputs.repository-list }}
tool-list: ${{ needs.setup.outputs.tool-list }}
# Planemo test the changed repositories, each chunk creates an artifact
# containing HTML and JSON reports for the executed tests
test:
name: Test tools
# This job runs on Linux
runs-on: self-hosted
needs: setup
if: needs.setup.outputs.repository-list != ''
strategy:
fail-fast: false
matrix:
chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
python-version: ['3.8']
services:
postgres:
image: postgres:11
env:
POSTGRES_USER: postgres
POSTGRES_PASSWORD: postgres
POSTGRES_DB: postgres
ports:
- 5432:5432
steps:
# checkout the repository
# and use it as the current working directory
- uses: actions/checkout@v2
with:
fetch-depth: 1
- uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v2
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}-${{ secrets.CACHE_VERSION }}
- name: Cache .planemo
uses: actions/cache@v2
id: cache-planemo
with:
path: ~/.planemo
key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}-${{ secrets.CACHE_VERSION }}
- name: Install jq
run: sudo apt-get install -yq jq libjq1
- name: Get test-data for changed repos
run: |
for repo in ${{ needs.setup.outputs.repository-list }}; do
pushd $repo
if [ -f get_test_data.sh ]; then
mkdir -p test-data
chmod u+x get_test_data.sh
./get_test_data.sh
fi
popd
done
- name: Planemo test
uses: galaxyproject/planemo-ci-action@v1
id: test
with:
mode: test
repository-list: ${{ needs.setup.outputs.repository-list }}
galaxy-fork: ${{ env.GALAXY_FORK }}
galaxy-branch: ${{ env.GALAXY_BRANCH }}
chunk: ${{ matrix.chunk }}
chunk-count: ${{ needs.setup.outputs.chunk-count }}
html-report: true
- uses: actions/upload-artifact@v2
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload
# - combine the results of the test chunks (which will never fail due
# to `|| true`) and create a global test report as json and html which
# is provided as artifact
# - check if any tool test actually failed (by lookup in the combined json)
# and fail this step if this is the case
combine_outputs:
name: Combine chunked test results
needs: [setup, test]
strategy:
matrix:
python-version: ['3.8']
# This job runs on Linux
runs-on: self-hosted
steps:
- uses: actions/download-artifact@v2
with:
path: artifacts
- uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v2
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}-${{ secrets.CACHE_VERSION }}
- name: Combine outputs
uses: galaxyproject/planemo-ci-action@v1
id: combine
with:
mode: combine
html-report: true
- uses: actions/upload-artifact@v2
with:
name: 'All tool test results'
path: upload
- name: Check outputs
uses: galaxyproject/planemo-ci-action@v1
id: check
with:
mode: check