Galaxy Tool Linting and Tests for push and PR

Update filter_assembly.xml #12

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_21.05
	MAX_CHUNKS: 4
	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 }}
	commit_range: ${{ steps.get-commit-range.outputs.commit_range }}
	nchunks: ${{ steps.get-chunks.outputs.nchunks }}
	chunk_list: ${{ steps.get-chunks.outputs.chunk_list }}
	strategy:
	matrix:
	python-version: [3.7]
	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: ${{ github.event.after }}'
	- name: Determine latest commit in the Galaxy repo
	id: get-galaxy-sha
	run: echo "::set-output name=galaxy_head_sha::$(git ls-remote ${{ env.GALAXY_REPO }} refs/heads/${{ env.GALAXY_RELEASE }} \| cut -f1)"
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
	- name: Cache .planemo
	uses: actions/cache@v2
	id: cache-planemo
	with:
	path: ~/.planemo
	key: planemo_cache_py_${{ 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 Planemo and flake8
	run: pip install planemo flake8 flake8-import-order
	- name: Fake a Planemo run to update cache
	if: steps.cache-pip.outputs.cache-hit != 'true' \|\| steps.cache-planemo.outputs.cache-hit != 'true'
	run: \|
	touch tool.xml
	PIP_QUIET=1 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~.." >> $GITHUB_ENV
	- id: get-commit-range
	run: echo "::set-output name=commit_range::$COMMIT_RANGE"
	- name: Planemo ci_find_repos for the commit range
	run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --exclude_from .tt_skip --output repository_list.txt
	- name: Show repository list
	run: cat repository_list.txt
	- uses: actions/upload-artifact@v2
	with:
	name: Workflow artifacts
	path: repository_list.txt
	- name: Planemo ci_find_tools for the repository list
	run: \|
	touch tool_list.txt
	if [ -s repository_list.txt ]; then
	planemo ci_find_tools --output tool_list.txt $(cat repository_list.txt)
	fi
	- name: Show tool list
	run: cat tool_list.txt
	- name: Compute chunks
	id: get-chunks
	run: \|
	nchunks=$(wc -l < tool_list.txt)
	if [ "$nchunks" -gt "$MAX_CHUNKS" ]; then
	nchunks=$MAX_CHUNKS
	elif [ "$nchunks" -eq 0 ]; then
	nchunks=1
	fi
	echo "::set-output name=nchunks::$nchunks"
	echo "::set-output name=chunk_list::[$(seq -s ", " 0 $(($nchunks - 1)))]"
	- name: Show chunks
	run: \|
	echo 'Using ${{ steps.get-chunks.outputs.nchunks }} chunks (${{ steps.get-chunks.outputs.chunk_list }})'

	# Planemo lint the changed repositories
	lint:
	name: Lint tools
	needs: setup
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: [3.7]
	steps:
	# checkout the repository
	# and use it as the current working directory
	- uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v2
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
	- name: Install Planemo
	run: pip install planemo
	- name: Planemo lint
	run: \|
	set -e
	while read -r DIR; do
	planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR";
	done < ../workflow_artifacts/repository_list.txt
	- name: Planemo ci_find_tools for the commit range
	run: planemo ci_find_tools --changed_in_commit_range ${{ needs.setup.outputs.commit_range }} --exclude packages --exclude deprecated --exclude_from .tt_skip --output tool_list.txt
	- name: Check if each changed tool is in the list of changed repositories
	run: \|
	set -e
	while read -r TOOL; do
	# Check if any changed repo dir is a substring of $TOOL
	if ! echo $TOOL \| grep -qf ../workflow_artifacts/repository_list.txt; then
	echo "Tool $TOOL not in changed repositories list: .shed.yml file missing" >&2
	exit 1
	fi
	done < tool_list.txt

	# 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: [3.7]
	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: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v2
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
	- name: Install flake8
	run: pip install flake8 flake8-import-order
	- name: Flake8
	run: \|
	if [ -s ../workflow_artifacts/repository_list.txt ]; then
	flake8 $(cat ../workflow_artifacts/repository_list.txt)
	fi

	lintr:
	name: Lint R scripts
	needs: setup
	runs-on: ubuntu-latest
	strategy:
	matrix:
	r-version: [4.0.1]
	steps:
	# checkout the repository to master
	# and use it as the current working directory
	- uses: actions/checkout@v2
	with:
	fetch-depth: 1
	- uses: actions/download-artifact@v2
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- uses: r-lib/actions/setup-r@master
	with:
	r-version: ${{ matrix.r-version }}
	- name: Cache R packages
	uses: actions/cache@v2
	with:
	path: ${{ env.R_LIBS_USER }}
	key: r_cache_${{ matrix.r-version }}
	- name: Install non-R lintr dependencies
	run: sudo apt-get install libcurl4-openssl-dev
	- name: Install lintr
	run: \|
	install.packages('remotes')
	remotes::install_cran("lintr")
	shell: Rscript {0}
	- name: lintr
	run: \|
	library(lintr)
	linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL,
	object_name_linter = NULL, object_usage_linter=NULL)
	con <- file("../workflow_artifacts/repository_list.txt", "r")
	status <- 0
	while (TRUE) {
	repo <- readLines(con, n = 1)
	if (length(repo) == 0) {
	break
	}
	lnt <- lint_dir(repo, relative_path=T, linters=linters)
	if (length(lnt) > 0) {
	status <- 1
	for (l in lnt) {
	rel_path <- paste(repo, l$filename, sep="/")
	write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), stderr())
	}
	}
	}
	quit(status = status)
	shell: Rscript {0}

	# 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: ${{ 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@v2
	with:
	fetch-depth: 1
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v2
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
	- name: Cache .planemo
	uses: actions/cache@v2
	id: cache-planemo
	with:
	path: ~/.planemo
	key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
	- name: Install Planemo
	run: pip install planemo
	- name: Planemo ci_find_tools for the repository list, chunked
	run: \|
	touch tool_list_chunk.txt
	if [ -s ../workflow_artifacts/repository_list.txt ]; then
	planemo ci_find_tools --chunk_count ${{ needs.setup.outputs.nchunks }} --chunk ${{ matrix.chunk }} --group_tools --output tool_list_chunk.txt $(cat ../workflow_artifacts/repository_list.txt)
	fi
	- name: Show tool list chunk
	run: cat tool_list_chunk.txt
	- name: Planemo test tools
	run: \|
	mkdir json_output
	while read -r TOOL_GROUP; do
	# Check if any of the lines in .tt_biocontainer_skip is a substring of $TOOL_GROUP
	if echo $TOOL_GROUP \| grep -qf .tt_biocontainer_skip; then
	PLANEMO_OPTIONS=""
	else
	PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
	fi
	json=$(mktemp -u -p json_output --suff .json)
	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 ${{ matrix.python-version }} --test_output_json "$json" $TOOL_GROUP \|\| true
	docker system prune --all --force --volumes \|\| true
	done < tool_list_chunk.txt
	if [ ! -s tool_list_chunk.txt ]; then
	echo '{"tests":[]}' > "$(mktemp -u -p json_output --suff .json)"
	fi
	- name: Merge tool_test_output.json files
	run: planemo merge_test_reports json_output/*.json tool_test_output.json
	- 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@v2
	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@v2
	with:
	path: artifacts
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
	- name: Install Planemo
	run: pip install planemo
	- name: Install jq
	run: sudo apt-get install jq
	- name: Combine outputs
	run: find artifacts/ -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" 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@v2
	with:
	name: 'All tool test results'
	path: upload
	- name: Check status of combined outputs
	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: [setup, lint, flake8, lintr, combine_outputs]
	strategy:
	matrix:
	python-version: [3.7]
	runs-on: ubuntu-latest
	if: github.ref == 'refs/heads/master' && github.repository_owner == 'abims-sbr'
	steps:
	- uses: actions/checkout@v2
	with:
	fetch-depth: 1
	- uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/download-artifact@v2
	with:
	name: Workflow artifacts
	path: ../workflow_artifacts/
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.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/repository_list.txt
	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/repository_list.txt

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Update filter_assembly.xml #12

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