Galaxy Tool Linting and Tests for push and PR

Update filterFragSpectra.R - update filenames - ensure as character #74

Workflow file for this run

	name: Galaxy Tool Linting and Tests for push and PR
	on: [push, pull_request]
	env:
	GALAXY_REPO: https://github.com/galaxyproject/galaxy
	GALAXY_RELEASE: release_24.0
	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
	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 }}'
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- name: Determine latest galaxy commit
	run: echo "GALAXY_HEAD_SHA=$(git ls-remote ${{ env.GALAXY_REPO }} refs/heads/${{ env.GALAXY_RELEASE }} \| cut -f1)" >> $GITHUB_ENV
	- name: Save latest galaxy commit to artifact file
	run: echo $GALAXY_HEAD_SHA > galaxy.sha
	- uses: actions/upload-artifact@v4
	with:
	name: Workflow artifacts
	path: galaxy.sha
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
	- name: Cache .planemo
	uses: actions/cache@v2
	id: cache-planemo
	with:
	path: ~/.planemo
	key: planemo_cache_py_${{ matrix.python-version }}_gxy1_$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 Planemo and flake8
	run: pip install planemo flake8 flake8-import-order
	- name: Fake a Planemo run to update cache
	continue-on-error: true
	if: steps.cache-pip.outputs.cache-hit != 'true' \|\| steps.cache-planemo.outputs.cache-hit != 'true'
	run: \|
	touch tool.xml
	PIP_QUIET=2 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE
	- uses: actions/checkout@v2
	with:
	fetch-depth: 0
	# The range of commits to check for changes is:
	# - `origin/master...` for all events happening on a feature branch
	# - for events on the master branch we compare against the sha before the event
	# (note that this does not work for feature branch events since we want all
	# commits on the feature branch and not just the commits of the last event)
	# - for pull requests we compare against the 1st ancestor, given the current
	# HEAD is the merge between the PR branch and the base branch
	- name: Set commit range (push to the feature branch)
	if: github.ref != 'refs/heads/master' && github.event_name == 'push'
	run: \|
	git fetch origin master
	echo "COMMIT_RANGE=origin/master..." >> $GITHUB_ENV
	- name: Set commit range (push to the master branch, e.g. merge)
	if: github.ref == 'refs/heads/master' && github.event_name == 'push'
	run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV
	- name: Set commit range (pull request)
	if: github.event_name == 'pull_request'
	run: echo "COMMIT_RANGE=HEAD~.." >> $GITHUB_ENV
	- name: Planemo ci_find_repos
	run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --exclude_from .tt_skip --output changed_repositories.list
	- name: Show repo list
	run: cat changed_repositories.list
	- uses: actions/upload-artifact@v4
	with:
	name: Workflow artifacts
	path: changed_repositories.list

	# Planemo lint the changed repositories
	lint:
	name: Lint tools
	needs: setup
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: [3.11]
	steps:
	# checkout the repository
	# and use it as the current working directory
	- uses: actions/checkout@v2
	with:
	fetch-depth: 1
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v4
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- name: Determine latest galaxy commit
	run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
	- name: Install Planemo
	run: pip install planemo
	- name: Planemo lint
	run: \|
	set -e
	while read -r DIR; do
	planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR";
	done < ../workflow_artifacts/changed_repositories.list

	# flake8 of Python scripts in the changed repositories
	flake8:
	name: Lint Python scripts
	needs: setup
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: [3.11]
	steps:
	# checkout the repository to master
	# and use it as the current working directory
	- uses: actions/checkout@v2
	with:
	fetch-depth: 1
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v4
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- name: Determine latest galaxy commit
	run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
	- name: Install flake8
	run: pip install flake8 flake8-import-order
	- name: Flake8
	run: \|
	if [ -s ../workflow_artifacts/changed_repositories.list ]; then
	flake8 $(cat ../workflow_artifacts/changed_repositories.list)
	fi

	# 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: ubuntu-latest
	needs: setup
	strategy:
	fail-fast: false
	matrix:
	chunk: [0]
	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@v2
	with:
	fetch-depth: 1
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v4
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- name: Determine latest galaxy commit
	run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
	- name: Cache .planemo
	uses: actions/cache@v2
	id: cache-planemo
	with:
	path: ~/.planemo
	key: planemo_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
	- name: Install Planemo
	run: pip install planemo
	- name: Planemo ci_find_tools
	run: \|
	touch changed_repositories_chunk.list changed_tools_chunk.list
	if [ -s ../workflow_artifacts/changed_repositories.list ]; then
	if [ $(wc -l < ../workflow_artifacts/changed_repositories.list) -eq 1 ]; then
	planemo ci_find_tools --chunk_count 1 --chunk ${{ matrix.chunk }} \
	--output changed_tools_chunk.list \
	$(cat ../workflow_artifacts/changed_repositories.list)
	else
	planemo ci_find_repos --chunk_count 1 --chunk ${{ matrix.chunk }} \
	--output changed_repositories_chunk.list \
	$(cat ../workflow_artifacts/changed_repositories.list)
	fi
	fi
	- name: Show changed tools/repositories chunk list
	run: cat changed_tools_chunk.list changed_repositories_chunk.list
	- name: Planemo test tools
	run: \|
	if grep -lqf .tt_biocontainer_skip changed_tools_chunk.list changed_repositories_chunk.list; then
	PLANEMO_OPTIONS=""
	else
	PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
	fi
	if [ -s changed_tools_chunk.list ]; then
	PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json tool_test_output.json $(cat changed_tools_chunk.list) \|\| true
	docker system prune --all --force --volumes \|\| true
	elif [ -s changed_repositories_chunk.list ]; then
	while read -r DIR; do
	if [[ "$DIR" =~ ^data_managers.* ]]; then
	TESTPATH=$(planemo ci_find_tools "$DIR")
	else
	TESTPATH="$DIR"
	fi
	PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json "$DIR"/tool_test_output.json "$TESTPATH" \|\| true
	docker system prune --all --force --volumes \|\| true
	done < changed_repositories_chunk.list
	else
	echo '{"tests":[]}' > tool_test_output.json
	fi
	- name: Merge tool_test_output.json files
	run: find . -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
	- name: Create tool_test_output.html
	run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
	- name: Copy artifacts into place
	run: \|
	mkdir upload
	mv tool_test_output.json tool_test_output.html upload/
	- 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: 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@v1
	with:
	python-version: ${{ matrix.python-version }}
	- name: Determine latest galaxy commit
	run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
	- name: Install Planemo
	run: pip install planemo
	- name: Install jq
	run: sudo apt-get install jq
	- name: Combine outputs
	run: find artifacts/ -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
	- name: Create tool_test_output.html
	run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
	- name: Copy artifacts into place
	run: \|
	mkdir upload
	mv tool_test_output.json tool_test_output.html upload/
	- uses: actions/upload-artifact@v4
	with:
	name: 'All tool test results'
	path: upload
	- name: Check status of combined status
	run: \|
	if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json \| grep -v "success"; then
	echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
	exit 1
	fi

	# deploy the tools to the toolsheds (first TTS for testing)
	deploy:
	name: Deploy
	needs: [lint,flake8,combine_outputs]
	strategy:
	matrix:
	python-version: [3.11]
	runs-on: ubuntu-latest
	if: github.ref == 'refs/heads/master' && github.repository_owner == 'computational-metabolomics'
	steps:
	- uses: actions/checkout@v2
	with:
	fetch-depth: 1
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v4
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- name: Determine latest galaxy commit
	run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy_$GALAXY_HEAD_SHA
	- name: Install Planemo
	run: pip install planemo
	- name: Deploy on testtoolshed
	env:
	SHED_KEY: ${{ secrets.tts_api_key }}
	run: \|
	while read -r DIR; do
	planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" \|\| exit 1;
	done < ../workflow_artifacts/changed_repositories.list
	continue-on-error: true
	- name: Deploy on toolshed
	env:
	SHED_KEY: ${{ secrets.ts_api_key }}
	run: \|
	while read -r DIR; do
	planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" \|\| exit 1;
	done < ../workflow_artifacts/changed_repositories.list

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Update filterFragSpectra.R - update filenames - ensure as character #74

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Update filterFragSpectra.R - update filenames - ensure as character #74

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