Galaxy Tool Linting and Tests for push and PR

Add more collection_type specifiers (#55) #81

Workflow file for this run

	# From https://github.com/galaxyproject/galaxy-tool-repository-template/blob/main/.github/workflows/pr.yaml
	# License (spdx): MIT
	# Last updated: 2022-07-14
	# Search for "MODIFIED" to see modifications from original

	name: Galaxy Tool Linting and Tests for push and PR
	# MODIFIED START
	on:
	push:
	branches: [main]
	paths-ignore:
	# The rendering has 2 phases: 1st is updating distros which issues a PR,
	# that PR has the changes which are then tested by this action.
	- 'distros.yaml'
	- 'repo-utils/**'
	- 'README.md'
	pull_request:
	branches: [main]
	paths-ignore:
	- 'distros.yaml'
	- 'repo-utils/**'
	- 'README.md'
	# MODIFIED END
	env:
	GALAXY_FORK: galaxyproject
	GALAXY_BRANCH: release_23.1 # MODIFIED
	MAX_CHUNKS: 10 # MODIFIED
	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 }}
	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 https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} \| 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 flake8
	run: pip install flake8 flake8-import-order
	- uses: actions/checkout@v2
	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: ['3.7']
	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: ${{ matrix.python-version }}
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
	# - name: 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 }}
	# - uses: actions/upload-artifact@v2
	# 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: ${{ needs.setup.outputs.repository-list != '' }}
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ['3.7']
	steps:
	- uses: actions/checkout@v2
	with:
	fetch-depth: 1
	- 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_${{ needs.setup.outputs.galaxy-head-sha }}
	- name: Install flake8
	run: pip install flake8 flake8-import-order
	- name: Flake8
	run: echo '${{ needs.setup.outputs.repository-list }}' \| xargs -d '\n' flake8 --output-file pylint_report.txt --tee
	- uses: actions/upload-artifact@v2
	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: ['4.0.1']
	steps:
	- uses: actions/checkout@v2
	with:
	fetch-depth: 1
	- uses: r-lib/actions/setup-r@v2
	with:
	r-version: ${{ matrix.r-version }}
	- name: Cache R packages
	uses: actions/cache@v2
	with:
	path: ${{ env.R_LIBS_USER }}
	key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
	- name: Install non-R lintr dependencies
	run: sudo apt-get install libcurl4-openssl-dev
	- name: Install lintr
	run: \|
	install.packages('remotes')
	remotes::install_cran("lintr")
	shell: Rscript {0}
	- name: Save repositories to file
	run: echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
	- name: lintr
	run: \|
	library(lintr)
	linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL)
	con <- file("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())
	write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), "rlint_report.txt", append=TRUE)
	}
	}
	}
	quit(status = status)
	shell: Rscript {0}
	- uses: actions/upload-artifact@v2
	if: ${{ failure() }}
	with:
	name: 'R linting output'
	path: rlint_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: ['3.7']
	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: ${{ matrix.python-version }}
	- name: Cache .cache/pip
	uses: actions/cache@v2
	id: cache-pip
	with:
	path: ~/.cache/pip
	key: pip_cache_py_${{ 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: 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 }}
	chunk: ${{ matrix.chunk }}
	chunk-count: ${{ needs.setup.outputs.chunk-count }}
	- 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]
	if: ${{ needs.setup.outputs.repository-list != '' }}
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.7']
	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: Combine outputs
	uses: galaxyproject/planemo-ci-action@v1
	id: combine
	with:
	mode: combine
	html-report: true
	- uses: actions/upload-artifact@v2
	with:
	name: 'All tool test results'
	path: upload
	- name: Check outputs
	uses: galaxyproject/planemo-ci-action@v1
	id: check
	with:
	mode: check

	# deploy the tools to the toolsheds (first TTS for testing)
	deploy:
	name: Deploy
	needs: [setup, lint, flake8, lintr, combine_outputs]
	if: ${{ (github.ref == 'refs/heads/master' \|\| github.ref == 'refs/heads/main' ) && github.repository_owner == 'qiime2' }} # MODIFIED
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.7']
	steps:
	- uses: actions/checkout@v2
	with:
	fetch-depth: 1
	- 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: 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 }}

	determine-success:
	name: Check workflow success
	needs: [setup, lint, flake8, lintr, 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: Check tool test status
	if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
	run: exit 1

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Add more collection_type specifiers (#55) #81

Workflow file

Add more collection_type specifiers (#55) #81

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Workflow file for this run