Galaxy Tool Linting and Tests for push and PR

Fix omero plate #445

Workflow file for this run

	name: Galaxy Tool Linting and Tests for push and PR
	on:
	pull_request:
	paths-ignore:
	- 'deprecated/**'
	- 'docs/**'
	- '*'
	push:
	branches:
	- main
	- master
	paths-ignore:
	- 'deprecated/**'
	- 'docs/**'
	- '*'
	env:
	GALAXY_FORK: galaxyproject
	GALAXY_BRANCH: release_24.1
	MAX_CHUNKS: 4
	MAX_FILE_SIZE: 1M
	concurrency:
	# Group runs by PR, but keep runs on the default branch separate
	# because we do not want to cancel ToolShed uploads
	group: pr-${{ (github.ref == 'refs/heads/master' \|\| github.ref == 'refs/heads/main') && github.run_number \|\| github.ref }}
	cancel-in-progress: true
	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: 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 }}
	commit-range: ${{ steps.discover.outputs.commit-range }}
	strategy:
	matrix:
	python-version: ['3.10']
	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 }}'
	echo 'repository_owner: ${{ github.repository_owner }}'
	- name: Determine latest commit in the Galaxy repo
	id: get-galaxy-sha
	run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} \| cut -f1)" >> $GITHUB_OUTPUT
	- uses: actions/setup-python@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_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
	- name: Cache .planemo
	uses: actions/cache@v4
	id: cache-planemo
	with:
	path: ~/.planemo
	key: planemo_cache_py_${{ 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
	- name: Install flake8
	run: pip install flake8 flake8-import-order
	- uses: actions/checkout@v4
	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 != '' \|\| needs.setup.outputs.tool-list != '' }}
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ['3.10']
	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: Set fail level for pull request
	if: ${{ github.event_name == 'pull_request' }}
	run:
	echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
	- name: Set fail level for merge
	if: ${{ github.event_name != 'pull_request' }}
	run:
	echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
	- name: Planemo lint
	uses: galaxyproject/planemo-ci-action@v1
	id: lint
	with:
	mode: lint
	fail-level: ${{ env.FAIL_LEVEL }}
	repository-list: ${{ needs.setup.outputs.repository-list }}
	tool-list: ${{ needs.setup.outputs.tool-list }}
	- uses: actions/upload-artifact@v4
	if: ${{ failure() }}
	with:
	name: 'Tool linting output'
	path: lint_report.txt

	# flake8 of Python scripts in the changed repositories
	flake8:
	name: Lint Python scripts
	needs: setup
	if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ['3.10']
	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_${{ needs.setup.outputs.galaxy-head-sha }}
	- name: Install flake8
	run: pip install flake8 flake8-import-order
	- name: Flake8
	run: echo '${{ needs.setup.outputs.repository-list }}' \| xargs -d '\n' flake8 --output-file pylint_report.txt --tee
	- uses: actions/upload-artifact@v4
	if: ${{ failure() }}
	with:
	name: 'Python linting output'
	path: pylint_report.txt

	lintr:
	name: Lint R scripts
	needs: setup
	if: ${{ needs.setup.outputs.repository-list != '' }}
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [ubuntu-20.04]
	r-version: ['release']
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- uses: r-lib/actions/setup-r@v2
	with:
	r-version: ${{ matrix.r-version }}
	- name: Cache R packages
	uses: actions/cache@v4
	with:
	path: ${{ env.R_LIBS_USER }}
	key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
	- name: Install packages
	uses: r-lib/actions/setup-r-dependencies@v2
	with:
	packages: \|
	any::argparse
	any::styler
	- name: lintr
	run: \|
	set -eo pipefail
	echo '${{ needs.setup.outputs.repository-list }}' \| xargs -d '\n' -n 1 ./.github/styler.R --dry off
	git status
	git diff --exit-code \| tee rlint_report.txt
	- uses: actions/upload-artifact@v4
	if: ${{ failure() }}
	with:
	name: 'R linting output'
	path: rlint_report.txt

	file_sizes:
	name: Check file sizes
	needs: setup
	if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Check file sizes
	run: \|
	touch file_size_report.txt
	git diff --diff-filter=d --name-only ${{ needs.setup.outputs.commit-range }} > git.diff
	while read line; do
	find "$line" -type f -size +${{ env.MAX_FILE_SIZE }} >> file_size_report.txt
	done < git.diff
	if [[ -s file_size_report.txt ]]; then
	echo "Files larger than ${{ env.MAX_FILE_SIZE }} found"
	cat file_size_report.txt
	exit 1
	fi
	- uses: actions/upload-artifact@v4
	if: ${{ failure() }}
	with:
	name: 'File size report'
	path: file_size_report.txt

	# Planemo test the changed repositories, each chunk creates an artifact
	# containing HTML and JSON reports for the executed tests
	test:
	name: Test tools
	needs: setup
	if: ${{ needs.setup.outputs.repository-list != '' }}
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
	python-version: ['3.10']
	services:
	postgres:
	image: postgres:11
	env:
	POSTGRES_USER: postgres
	POSTGRES_PASSWORD: postgres
	POSTGRES_DB: postgres
	ports:
	- 5432:5432
	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_${{ needs.setup.outputs.galaxy-head-sha }}
	- name: Cache .planemo
	uses: actions/cache@v4
	id: cache-planemo
	with:
	path: ~/.planemo
	key: planemo_cache_py_${{ 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

	# the following 2 steps are needed for testing the scripting tool
	- name: Install Apptainer's singularity
	uses: eWaterCycle/setup-apptainer@v2
	- name: Symlink singularity
	run: ln -s $(which apptainer) $(dirname apptainer)/singularity
	- name: Install containers
	run: \|
	echo "${{ needs.setup.outputs.repository-list }}" > repository_list.txt
	if grep -q scripting repository_list.txt; then
	singularity pull --dir /tmp docker://continuumio/anaconda3
	singularity pull --dir /tmp docker://rocker/tidyverse
	fi

	# Start OMERO
	- name: Start OMERO
	uses: sudo-bot/action-docker-compose@latest
	with:
	cli-args: "-f .github/omero-docker-compose.yml up -d"

	# Setup environment
	- name: Set up Python environment for omero-py
	uses: actions/setup-python@v4
	with:
	python-version: '3.11.0'

	# Upload a dummy dataset in OMERO
	- name: Install dependencies and upload a OMERO dummy dataset
	run: \|
	echo "Waiting for OMERO to be ready..."
	sleep 60
	pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl
	pip install omero-py==5.19.4
	omero login -s localhost -u root -w omero -p 6064
	PID=$(omero obj new Project name='test_prj')
	DID=$(omero obj new Dataset name='test_dts')
	omero obj new ProjectDatasetLink parent=$PID child=$DID
	omero import -d $DID .github/dummy-dts-omero
	omero tag create --name test_tag --desc 'description of my_tag'
	omero tag link Image:1 1
	echo "Created the dummy dataset into OMERO"
	DID_HCS=$(omero obj new Dataset name='test_hcs_dts')
	omero import -d $DID_HCS .github/dummy-hcs-omero
	echo "Created the hcs dummy dataset into OMERO"

	# download or create large test data via script
	- name: Create test data
	run: \|
	set -x
	pip install planemo > /dev/null
	echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
	mapfile -t REPO_ARRAY < repository_list.txt
	planemo ci_find_tools --chunk_count "${{ needs.setup.outputs.chunk-count }}" --chunk "${{ matrix.chunk }}" --output tool_list_chunk.txt "${REPO_ARRAY[@]}"
	cat tool_list_chunk.txt \| sed 's@/[^/]*$@@' \| sort -i > repository_list_chunk.txt
	while read repo
	do
	echo "executing test-data.sh for $repo"
	if [ -x $repo/test-data.sh ]; then
	cd $repo
	./test-data.sh
	fi
	done < repository_list_chunk.txt

	- 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 }}
	additional-planemo-options: --docker_run_extra_arguments '--add-host=host.docker.internal:host-gateway'
	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: 1800
	- 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]
	if: ${{ always() && needs.setup.outputs.repository-list != '' }}
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.10']
	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
	markdown-report: true
	- uses: actions/upload-artifact@v4
	with:
	name: 'All tool test results'
	path: upload
	- run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
	- name: Check outputs
	uses: galaxyproject/planemo-ci-action@v1
	id: check
	with:
	mode: check
	- name: Check if all test chunks succeeded
	run: \|
	NFILES=$(ls artifacts/ \| grep "Tool test output" \| wc -l)
	if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
	exit 1
	fi

	# deploy the tools to the toolsheds (first TTS for testing)
	deploy:
	name: Deploy
	needs: [setup, lint, combine_outputs]
	if: ${{ (github.ref == 'refs/heads/master' \|\| github.ref == 'refs/heads/main' ) && github.repository_owner == 'Helmholtz-UFZ' }}
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.10']
	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: Deploy on testtoolshed
	uses: galaxyproject/planemo-ci-action@v1
	with:
	mode: deploy
	repository-list: ${{ needs.setup.outputs.repository-list }}
	shed-target: testtoolshed
	shed-key: ${{ secrets.TTS_API_KEY }}
	continue-on-error: true
	- name: Deploy on toolshed
	uses: galaxyproject/planemo-ci-action@v1
	with:
	mode: deploy
	repository-list: ${{ needs.setup.outputs.repository-list }}
	shed-target: toolshed
	shed-key: ${{ secrets.TS_API_KEY }}

	deploy-report:
	name: Report deploy status
	needs: [deploy]
	if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' \|\| github.ref == 'refs/heads/main' ) && github.repository_owner == 'Helmholtz-UFZ' }}
	runs-on: ubuntu-latest
	steps:
	# report to the PR if deployment failed
	- name: Get PR object
	uses: 8BitJonny/[email protected]
	id: getpr
	with:
	sha: ${{ github.event.after }}
	- name: Create comment
	uses: peter-evans/create-or-update-comment@v4
	with:
	token: ${{ secrets.PAT }}
	issue-number: ${{ steps.getpr.outputs.number }}
	body: \|
	Attention: deployment ${{ needs.deploy.result }}!

	https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}

	determine-success:
	name: Check workflow success
	needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs]
	if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
	runs-on: ubuntu-latest
	steps:
	- name: Check tool lint status
	if: ${{ needs.lint.result != 'success' && needs.flake8.result != 'skipped' }}
	run: exit 1
	- name: Indicate Python script lint status
	if: ${{ needs.flake8.result != 'success' && needs.flake8.result != 'skipped' }}
	run: exit 1
	- name: Indicate R script lint status
	if: ${{ needs.lintr.result != 'success' && needs.lintr.result != 'skipped' }}
	run: exit 1
	- name: Indicate file size check status
	if: ${{ needs.file_sizes.result != 'success' && needs.file_sizes.result != 'skipped' }}
	run: exit 1
	- name: Check tool test status
	if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
	run: exit 1

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Fix omero plate #445

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Fix omero plate #445

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