Updating workflows/computational-chemistry/gromacs-dctmd from 0.1.3 to 0.1.4 #1151

Workflow file for this run

.github/workflows/workflow_test.yml at 680621f

	# workflow level env vars cannot be used at the job level
	# https://github.community/t/how-to-set-and-access-a-workflow-variable/17335/15
	name: Galaxy Workflow Tests for push and PR
	on: [push, pull_request]
	env:
	GITHUB_USER: iwc-workflows-bot
	jobs:
	setup:
	name: Setup cache and determine changed repositories
	uses: ./.github/workflows/setup.yml
	with:
	python-version-list: "[\"3.7\"]"
	galaxy-fork: galaxyproject
	galaxy-branch: release_23.1
	max-chunks: 4

	# Planemo lint the changed repositories
	lint:
	name: Lint workflows
	needs: setup
	if: needs.setup.outputs.repository-list != ''
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.7']
	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_${{ needs.setup.outputs.galaxy-head-sha }}
	- name: Install wheel
	run: pip install wheel
	- name: Planemo lint workflows
	uses: galaxyproject/planemo-ci-action@v1
	with:
	mode: lint
	workflows: true
	repository-list: "${{ needs.setup.outputs.repository-list }}"

	test:
	name: Test workflows
	needs: setup
	if: needs.setup.outputs.repository-list != ''
	uses: ./.github/workflows/test_workflows.yml
	with:
	galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }}
	chunk-count: ${{ fromJSON(needs.setup.outputs.chunk-count) }}
	chunk-list: ${{ needs.setup.outputs.chunk-list }}
	python-version-list: "[\"3.7\"]"
	repository-list: ${{ needs.setup.outputs.repository-list }}
	galaxy-fork: galaxyproject
	galaxy-branch: release_23.1
	check-outputs: false

	combine_outputs:
	# same as tool step
	name: Combine chunked test results
	needs: [setup, test]
	strategy:
	matrix:
	python-version: ['3.7']
	runs-on: ubuntu-latest
	steps:
	- 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.outputs.galaxy-head-sha }}
	- name: Combine outputs
	uses: galaxyproject/planemo-ci-action@v1
	id: combine
	with:
	mode: combine
	html-report: true
	markdown-report: true
	- run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
	- uses: actions/upload-artifact@v3
	with:
	name: 'All tool test results'
	path: upload
	- name: Check outputs
	uses: galaxyproject/planemo-ci-action@v1
	id: check
	with:
	mode: check
	- name: Get PR object
	if: failure()
	uses: 8BitJonny/gh-get-current-pr@2.2.0
	id: failed_pr_number
	with:
	sha: ${{ github.event.pull_request.head.sha }}
	- name: Debug GetPR output
	if: failure()
	run: \|
	echo ${{ steps.failed_pr_number.outputs.number }}
	- name: Post comment with test report
	if: failure()
	uses: peter-evans/create-or-update-comment@v3
	with:
	token: ${{ secrets.PAT }}
	issue-number: ${{ steps.failed_pr_number.outputs.number }}
	body-path: upload/tool_test_output.md

	# deploy workflows to organization
	deploy:
	name: Deploy
	needs: [setup,test,combine_outputs]
	strategy:
	matrix:
	python-version: ['3.7']
	runs-on: ubuntu-latest
	if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject'
	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.outputs.galaxy-head-sha }}
	- name: Install requirements for gen_crates.py
	run: pip install -r workflows/requirements.txt
	- name: Generate RO-Crate metadata for workflow repositories
	run: python workflows/gen_crates.py workflows
	- name: Set git user
	run: \|
	git config --global user.email "$GITHUB_USER@galaxyproject.org"
	git config --global user.name "$GITHUB_USER"
	git config --global init.defaultBranch main
	- uses: fusion-engineering/setup-git-credentials@v2
	with:
	credentials: 'https://${{ env.GITHUB_USER }}:${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }}@github.com/'
	- name: Update or create repositories in github namespace
	uses: galaxyproject/planemo-ci-action@v1
	with:
	mode: deploy
	repository-list: ${{ needs.setup.outputs.repository-list }}
	workflows: true
	workflow-namespace: iwc-workflows
	github-token: ${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }}

	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 == 'galaxyproject' }}
	runs-on: ubuntu-latest
	steps:
	# report to the PR if deployment failed
	- name: Get PR object
	uses: 8BitJonny/gh-get-current-pr@2.2.0
	id: getpr
	with:
	sha: ${{ github.event.after }}
	- name: Create comment
	uses: peter-evans/create-or-update-comment@v3
	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 }}

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Updating workflows/computational-chemistry/gromacs-dctmd from 0.1.3 to 0.1.4 #1151

Workflow file

Updating workflows/computational-chemistry/gromacs-dctmd from 0.1.3 to 0.1.4 #1151

Jobs

Run details

Workflow file for this run