Samtools fasta #622
Workflow file for this run
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name: Component Testing | |
on: | |
pull_request: | |
push: | |
branches: [ '**' ] | |
jobs: | |
run_ci_check_job: | |
runs-on: ubuntu-latest | |
outputs: | |
run_ci: ${{ steps.github_cli.outputs.check }} | |
steps: | |
- name: 'Check if branch has an existing pull request and the trigger was a push' | |
id: github_cli | |
run: | | |
pull_request=$(gh pr list -R ${{ github.repository }} -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url') | |
# If the branch has a PR and this run was triggered by a push event, do not run | |
if [[ "$pull_request" != "null" && "$GITHUB_REF_NAME" != "main" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then | |
echo "check=false" >> $GITHUB_OUTPUT | |
else | |
echo "check=true" >> $GITHUB_OUTPUT | |
fi | |
env: | |
GH_TOKEN: ${{ github.token }} | |
# phase 1 | |
list: | |
needs: run_ci_check_job | |
runs-on: ubuntu-latest | |
if: ${{ needs.run_ci_check_job.outputs.run_ci == 'true' }} | |
outputs: | |
matrix: ${{ steps.set_matrix.outputs.matrix }} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: Get head git commit message | |
id: get_head_commit_message | |
run: echo "HEAD_COMMIT_MESSAGE=$(git show -s --format=%s ${{ github.event.pull_request.head.sha || github.sha }})" >> "$GITHUB_OUTPUT" | |
- uses: viash-io/viash-actions/setup@v5 | |
- name: Check if all config can be parsed if there is no unicode support | |
run: | | |
LANG=C viash ns list > /dev/null | |
# see https://github.com/viash-io/viash/issues/654 | |
# and https://github.com/viash-io/viash-actions/pull/27 | |
# - name: Get changed files | |
# id: changed-files | |
# uses: tj-actions/changed-files@v42 | |
# with: | |
# separator: ";" | |
# diff_relative: true | |
# - id: ns_list | |
# uses: viash-io/viash-actions/ns-list@v5 | |
# with: | |
# platform: docker | |
# format: json | |
# query: ^(?!workflows) | |
# - id: ns_list_filtered | |
# uses: viash-io/viash-actions/project/detect-changed-components@v5 | |
# with: | |
# input_file: "${{ steps.ns_list.outputs.output_file }}" | |
# - id: set_matrix | |
# run: | | |
# echo "matrix=$(jq -c '[ .[] | | |
# { | |
# "name": (.functionality.namespace + "/" + .functionality.name), | |
# "config": .info.config, | |
# "dir": .info.config | capture("^(?<dir>.*\/)").dir | |
# } | |
# ]' ${{ contains(steps.get_head_commit_message.outputs.HEAD_COMMIT_MESSAGE, 'ci force') && steps.ns_list.outputs.output_file || steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT | |
- id: set_matrix | |
run: | | |
viash ns list --format json > ns_list.json | |
echo "matrix=$(jq -c '[ .[] | | |
{ | |
"name": (.namespace + "/" + .name), | |
"config": .build_info.config, | |
"dir": .build_info.config | capture("^(?<dir>.*\/)").dir | |
} | |
]' ns_list.json )" >> $GITHUB_OUTPUT | |
# phase 2 | |
viash_test: | |
needs: list | |
if: ${{ needs.list.outputs.matrix != '[]' && needs.list.outputs.matrix != '' }} | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
component: ${{ fromJson(needs.list.outputs.matrix) }} | |
steps: | |
# Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' | |
- uses: data-intuitive/reclaim-the-bytes@v2 | |
- uses: actions/checkout@v4 | |
- uses: viash-io/viash-actions/setup@v5 | |
- name: Run test | |
timeout-minutes: 30 | |
run: | | |
viash test \ | |
"${{ matrix.component.config }}" \ | |
--cpus 2 \ | |
--memory "6gb" |