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Weekly global Tool Linting and Tests #237

Weekly global Tool Linting and Tests

Weekly global Tool Linting and Tests #237

Workflow file for this run

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_24.0
MAX_CHUNKS: 40
jobs:
setup:
name: Setup cache and determine changed repositories
if: ${{ github.repository_owner == 'galaxyproteomics' }}
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: ['3.11']
steps:
- name: Add reaction
if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
uses: peter-evans/create-or-update-comment@v4
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@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ 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@v4
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: ['3.11']
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ 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 stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion
- uses: actions/upload-artifact@v4
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: ['3.11']
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@v4
with:
fetch-depth: 1
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
- name: Get number of CPU cores
uses: SimenB/github-actions-cpu-cores@v2
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@v4
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: ['3.11']
# This job runs on Linux
runs-on: ubuntu-latest
steps:
- uses: actions/download-artifact@v4
with:
path: artifacts
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ 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@v4
with:
name: 'All tool test results'
path: upload
- run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
- 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@v4
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