Weekly global Tool Linting and Tests #18
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name: Weekly global Tool Linting and Tests | |
on: | |
schedule: | |
# Run at midnight every monday | |
- cron: '0 0 * * 1' | |
repository_dispatch: | |
types: [run-all-tool-tests-command] | |
env: | |
GALAXY_FORK: galaxyproject | |
GALAXY_BRANCH: release_23.0 | |
MAX_CHUNKS: 40 | |
jobs: | |
setup: | |
name: Setup cache and determine changed repositories | |
if: ${{ github.repository_owner == 'bernt-matthias' }} | |
runs-on: ubuntu-latest | |
outputs: | |
galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
fork: ${{ steps.get-fork-branch.outputs.fork }} | |
branch: ${{ steps.get-fork-branch.outputs.branch }} | |
repository-list: ${{ steps.discover.outputs.repository-list }} | |
chunk-count: ${{ steps.discover.outputs.chunk-count }} | |
chunk-list: ${{ steps.discover.outputs.chunk-list }} | |
strategy: | |
matrix: | |
python-version: ['3.7'] | |
steps: | |
- name: Add reaction | |
if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
uses: peter-evans/create-or-update-comment@v2 | |
with: | |
token: ${{ secrets.PAT }} | |
repository: ${{ github.event.client_payload.github.payload.repository.full_name }} | |
comment-id: ${{ github.event.client_payload.github.payload.comment.id }} | |
reaction-type: hooray | |
- name: Set galaxy fork and branch | |
id: get-fork-branch | |
run: | | |
TMP="${{ github.event.client_payload.slash_command.args.named.fork }}" | |
echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT | |
TMP="${{ github.event.client_payload.slash_command.args.named.branch }}" | |
echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT | |
- name: Determine latest commit in the Galaxy repo | |
id: get-galaxy-sha | |
run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache .cache/pip | |
uses: actions/cache@v3 | |
id: cache-pip | |
with: | |
path: ~/.cache/pip | |
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
# 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 | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 1 | |
- 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: ${{ steps.get-fork-branch.outputs.fork }} | |
galaxy-branch: ${{ steps.get-fork-branch.outputs.branch }} | |
max-chunks: ${{ env.MAX_CHUNKS }} | |
python-version: ${{ matrix.python-version }} | |
- name: Show repository list | |
run: echo '${{ steps.discover.outputs.repository-list }}' | |
- name: Show chunks | |
run: | | |
echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})' | |
lint: | |
name: Check for missing containers | |
needs: setup | |
if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }} | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ['3.7'] | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 1 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache .cache/pip | |
uses: actions/cache@v3 | |
id: cache-pip | |
with: | |
path: ~/.cache/pip | |
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
- 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 }} | |
additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd | |
- uses: actions/upload-artifact@v3 | |
if: ${{ failure() }} | |
with: | |
name: 'Tool linting output' | |
path: lint_report.txt | |
test: | |
name: Test tools | |
# This job runs on Linux | |
runs-on: ubuntu-latest | |
needs: setup | |
if: ${{ needs.setup.outputs.repository-list != '' }} | |
strategy: | |
fail-fast: false | |
matrix: | |
chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }} | |
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 | |
# and use it as the current working directory | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 1 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache .cache/pip | |
uses: actions/cache@v3 | |
id: cache-pip | |
with: | |
path: ~/.cache/pip | |
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
- name: Get number of CPU cores | |
uses: SimenB/github-actions-cpu-cores@v1 | |
id: cpu-cores | |
- name: Clean dotnet folder for space | |
run: rm -Rf /usr/share/dotnet | |
- name: Planemo test | |
uses: galaxyproject/planemo-ci-action@v1 | |
id: test | |
with: | |
mode: test | |
repository-list: ${{ needs.setup.outputs.repository-list }} | |
galaxy-fork: ${{ needs.setup.outputs.fork }} | |
galaxy-branch: ${{ needs.setup.outputs.branch }} | |
chunk: ${{ matrix.chunk }} | |
chunk-count: ${{ needs.setup.outputs.chunk-count }} | |
galaxy-slots: ${{ steps.cpu-cores.outputs.count }} | |
# Limit each test to 15 minutes | |
test_timeout: 900 | |
- uses: actions/upload-artifact@v3 | |
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: ['3.7'] | |
# This job runs on Linux | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/download-artifact@v3 | |
with: | |
path: artifacts | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache .cache/pip | |
uses: actions/cache@v3 | |
id: cache-pip | |
with: | |
path: ~/.cache/pip | |
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
- name: Combine outputs | |
uses: galaxyproject/planemo-ci-action@v1 | |
id: combine | |
with: | |
mode: combine | |
html-report: true | |
- uses: actions/upload-artifact@v3 | |
with: | |
name: 'All tool test results' | |
path: upload | |
- name: Create URL to the run output | |
if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
id: vars | |
run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT | |
- name: Create comment | |
if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
uses: peter-evans/create-or-update-comment@v2 | |
with: | |
token: ${{ secrets.PAT }} | |
repository: ${{ github.event.client_payload.github.payload.repository.full_name }} | |
issue-number: ${{ github.event.client_payload.github.payload.issue.number }} | |
body: | | |
Summary: | |
${{ steps.combine.outputs.statistics }} | |
[Find all tool test results here][1] | |
[1]: ${{ steps.vars.outputs.run-url }} | |
- name: Check outputs | |
uses: galaxyproject/planemo-ci-action@v1 | |
id: check | |
with: | |
mode: check |