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tools.yaml
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on: [push, pull_request]
name: 'Test action for tools'
env:
GALAXY_FORK: galaxyproject
GALAXY_BRANCH: master
MAX_CHUNKS: 4
jobs:
setup-pr-tools:
name: Setup as in PR for tools
runs-on: ubuntu-latest
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: [3.11]
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: ${{ github.event.after }}'
- name: Determine latest commit in the Galaxy repo
id: get-galaxy-sha
run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_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_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
- name: Cache .planemo
uses: actions/cache@v3
id: cache-planemo
with:
path: ~/.planemo
key: planemo_cache_py_${{ 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: 0
- name: Introduce a change on test tool1
run: |
git config --global user.name "Arthur Dent"
git config --global user.email "[email protected]"
echo "" >> test/tools/tool1/tool1.xml
git commit -m bump test/tools/tool1/tool1.xml
- name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
uses: ./
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: ${{ matrix.python-version }}
- name: Check commit range
run: if ! grep "\.\." <<<$(echo ${{ steps.discover.outputs.commit-range }}); then echo "wrong commit range"; exit 1; fi
- name: Check content of repository list
run: |
if ! grep -q "tool1" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool1 must be in repo list"; exit 1; fi
if grep -q "tool2" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool2 must not be in repo list"; exit 1; fi
- name: Check content of tool list
run: |
if ! grep -q "tool1.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool1.xml must be in tool list"; exit 1; fi
if grep -q "tool2.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool2.xml must not be in tool list"; exit 1; fi
- name: Check number of chunks
run: if [ "${{ steps.discover.outputs.chunk-count }}" != "1" ]; then echo "wrong chunk-count"; exit 1; fi
setup-ci-tools:
name: Setup as in CI for tools
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: ${{ steps.discover.outputs.chunk-list }}
strategy:
matrix:
python-version: [3.11]
steps:
- name: Determine latest commit in the Galaxy repo
id: get-galaxy-sha
run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_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: Artificially exclude workflows (because ci_find_repos discovers tool and workflow repos)
run: echo 'test/workflows/' > .tt_skip
- name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
uses: ./
id: discover
env:
GITHUB_EVENT_NAME: schedule
with:
create-cache: true
galaxy-fork: ${{ env.GALAXY_FORK }}
galaxy-branch: ${{ env.GALAXY_BRANCH }}
max-chunks: ${{ env.MAX_CHUNKS }}
python-version: ${{ matrix.python-version }}
github-event-name-override: 'schedule'
- name: Check for empty commit range
run: if [ -n "${{ steps.discover.outputs.commit-range }}" ]; then exit 1; fi
# note: ci_find_repos will find all tools and workflows
- name: Check that all tools an workflows are in the repository list
run: |
if ! grep -q "tool1" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool1 must be in the repo list"; exit 1; fi
if ! grep -q "tool2" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool2 must be in the repo list"; exit 1; fi
if grep -q "example3" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "example3 must not be in the repo list"; exit 1; fi
if grep -q "example4" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "example4 must not be in the repo list"; exit 1; fi
# note: ci_find_tools will find onlytools
- name: Check that all tools are in the tool list
run: |
if ! grep -q "tool1.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool1.xml must be in the repo list"; exit 1; fi
if ! grep -q "tool2.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool2.xml must be in the repo list"; exit 1; fi
# chunk-count will only consider tools/workflows depending on the workflow input to the action
- name: Check that the number of chunks is three, i.e. the number of tools
run: if [ "${{ steps.discover.outputs.chunk-count }}" != "3" ]; then exit 1; fi
lint:
name: Test linting of tools
needs: [setup-ci-tools]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.11]
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-ci-tools.outputs.galaxy-head-sha }}
- name: Install wheel
run: pip install wheel
- name: Planemo lint tools
uses: ./
with:
mode: lint
report-level: all
fail-level: warn
repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }}
tool-list: ${{ needs.setup-ci-tools.outputs.tool-list }}
additional-planemo-options: --report_level all
continue-on-error: true
- name: check if all test tools were linted
run: |
set -x
# check if the ToolIDValid linter is called (no of tools - 1 ) times, i.e. is skipped once
if [ "$(grep -c ToolIDValid ToolIDValid)" != "2" ]; then
echo "expecting exactly 2 tests for ToolIDValid"; exit 1;
fi
grep tool1 lint_report.txt
grep tool2 lint_report.txt
grep "ERROR: Error 'HTTPConnectionPool" lint_report.txt
grep "Applying linter tests... CHECK" lint_report.txt
test-tools:
name: Test testing of tools
needs: [setup-ci-tools]
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
chunk: ${{ fromJson(needs.setup-ci-tools.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@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-ci-tools.outputs.galaxy-head-sha }}
- name: Get number of CPU cores
uses: SimenB/github-actions-cpu-cores@v1
id: cpu-cores
- name: Planemo test tools
uses: ./
id: test-tools
with:
mode: test
repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }}
galaxy-fork: ${{ env.GALAXY_FORK }}
galaxy-branch: ${{ env.GALAXY_BRANCH }}
chunk: ${{ matrix.chunk }}
chunk-count: ${{ needs.setup-ci-tools.outputs.chunk-count }}
additional-planemo-options: --simultaneous_uploads --check_uploads_ok
galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
- uses: actions/upload-artifact@v3
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload
combine_outputs:
name: Test combining 'chunked' test results
needs: [setup-ci-tools, test-tools]
strategy:
matrix:
python-version: [3.11]
# This job runs on Linux
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 1
- 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_${{ needs.setup-ci-tools.outputs.galaxy-head-sha }}
- name: Combine outputs
uses: ./
id: combine
with:
mode: combine
html-report: true
- name: Check statistics
run: if ! grep -q "3\s\+success" <<<$(echo ${{ steps.combine.outputs.statistics }}); then echo "wrong statistics"; exit 1; fi
- uses: actions/upload-artifact@v3
with:
name: 'All tool test results'
path: upload
- name: Check outputs
uses: ./
id: check
with:
mode: check