quicktest #26
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| name: PR quicktest | |
| # File: quicktest.yaml | |
| # Author: Taha Abdullah | |
| # Created on: 2023-07-10 | |
| # Functionality: This workflow runs FastSurfer on MRI data and runs pytest to check if the results are acceptable. It | |
| # also checks if the FastSurfer environment and output already exist, and if not, it creates them. | |
| # Usage: This workflow is triggered on a pull request to the dev and main branch. It can also be triggered manually | |
| # with workflow-dispatch. | |
| # Expected Secrets: | |
| # - QUICKTEST_IMAGE_HREF_08mm: URL to a sample 0.8mm image | |
| # - QUICKTEST_IMAGE_HREF_1mm: URL to a sample 1mm image | |
| # - QUICKTEST_TARGET_HREF_08mm: URL to the reference processing of the sample 0.8mm image | |
| # - QUICKTEST_TARGET_HREF_1mm: URL to the reference processing of the sample 1mm image | |
| # - QUICKTEST_LICENSE: content of a FreeSurfer license file | |
| concurrency: | |
| # maybe the group here should actually not depend on the ref (only number would mean there are | |
| # not concurrent runs of the same pr) -- but then we should probably add the branch name (for | |
| # manually triggered workflows) | |
| group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }} | |
| cancel-in-progress: true | |
| on: | |
| pull_request: | |
| types: [labeled, unlabeled] | |
| workflow_dispatch: | |
| inputs: | |
| docker-image: | |
| description: 'Which docker image should be used to run this test (build-cached => build from git)' | |
| default: build-cached | |
| type: string | |
| freesurfer_build_image: | |
| description: 'FreeSurfer build image to build with' | |
| type: string | |
| permissions: read-all | |
| env: | |
| SUBJECTS_DIR: /tmp/subjects | |
| REFERENCE_DIR: /tmp/reference | |
| jobs: | |
| build-docker-latest: | |
| name: 'Check and build the current docker image' | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 180 | |
| outputs: | |
| continue: ${{ steps.parse.outputs.CONTINUE }} | |
| docker-image: ${{ steps.parse.outputs.DOCKER_IMAGE }} | |
| extra-args: ${{ steps.parse.outputs.EXTRA_ARGS }} | |
| fs-build-image: ${{ steps.parse-version.outputs.FS_BUILD_IMAGE }} | |
| fs-version: ${{ steps.parse-version.outputs.FS_VERSION }} | |
| fs-version-short: ${{ steps.parse-version.outputs.FS_VERSION_SHORT }} | |
| fastsurfer-home: ${{ steps.parse-version.outputs.FASTSURFER_HOME }} | |
| steps: | |
| - name: 'Check whether the tests should run' | |
| id: parse | |
| shell: bash | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| h1="Accept: application/vnd.github+json" | |
| h2="X-GitHub-Api-Version: 2022-11-28" | |
| if [[ "${{ github.event_name }}" == "pull_request" ]] | |
| then | |
| if [[ "${{ github.event.action }}" != "labeled" ]] && [[ "${{ github.event.action }}" != "unlabeled" ]] | |
| then | |
| # not a label-related action, should not be triggered | |
| echo "The Workflow '${{ github.workflow }}' was triggered by 'pull_request' of type" | |
| echo " '${{ github.event.action }}' but should only be triggered by 'labeled' or 'unlabeled' actions." | |
| echo "CONTINUE=false" > $GITHUB_OUTPUT | |
| exit | |
| elif [[ "${{ github.event.label.name }}" == "quicktest" ]] | |
| then | |
| echo "CONTINUE=true" > $GITHUB_OUTPUT | |
| else | |
| echo "This is a different label that was attached." | |
| echo "CONTINUE=false" > $GITHUB_OUTPUT | |
| exit | |
| fi | |
| echo "DOCKER_IMAGE=build-cached" >> $GITHUB_OUTPUT | |
| elif [[ "${{ github.event_name }}" == "workflow_dispatch" ]] | |
| then | |
| if [[ "${{ inputs }}" == "{}" ]] || "${{ inputs.docker-image }}" == "" ]] ; then | |
| echo "DOCKER_IMAGE=build-cached" > $GITHUB_OUTPUT | |
| else | |
| echo "DOCKER_IMAGE=${{ inputs.docker-image }}" > $GITHUB_OUTPUT | |
| fi | |
| echo "CONTINUE=true" >> $GITHUB_OUTPUT | |
| exit | |
| else # this event has no specific rules | |
| echo "This workflow is not defined for the event ${{ github.event_name }}!" | |
| exit 1 | |
| fi | |
| if ! gh api -H "$h1" -H "$h2" /repos/${{ github.repository }}/collaborators/${{ github.event.sender.login }} | |
| then | |
| echo "Only collaborators explicitly listed as collaborators can trigger this workflow!" | |
| echo "CONTINUE=false" >> $GITHUB_OUTPUT | |
| exit | |
| fi | |
| # later, we might want to extract additional run options from the pr text or issue comments | |
| # these should just be added here | |
| # https://api.github.com/repos/${{ github.repository }}/issues/${{ github.number }} | |
| # https://api.github.com/repos/${{ github.repository }}/issues/${{ github.number }}/comments | |
| # this may also need adaptations in the test script at the bottom | |
| echo "EXTRA_ARGS=" >> $GITHUB_OUTPUT | |
| - name: Checkout repository | |
| if: ${{ steps.parse.outputs.continue && steps.parse.outputs.docker-image == 'build-cached' }} | |
| uses: actions/checkout@v4 | |
| - name: Get the FreeSurfer version | |
| if: ${{ steps.parse.outputs.continue && steps.parse.outputs.docker-image == 'build-cached' }} | |
| shell: bash | |
| id: parse-version | |
| run: | | |
| # get the FreeSurfer version from install_fs_pruned.sh | |
| { | |
| eval "$(grep "^fslink=" ./Docker/install_fs_pruned.sh)" | |
| fs_version="$(basename "$(dirname "$fslink")")" | |
| fs_version_short="${fs_version//\./}" | |
| echo "FS_VERSION=$fs_version" | |
| echo "FS_VERSION_SHORT=$fs_version_short" | |
| if [[ -n "${{ inputs.freesurfer_build_image }}" ]] ; then | |
| echo "FS_BUILD_IMAGE=${{ inputs.freesurfer_build_image }}" | |
| else | |
| echo "FS_BUILD_IMAGE=deepmi/fastsurfer-build:freesurfer$fs_version_short" | |
| fi | |
| echo "FASTSURFER_HOME=$(pwd)" | |
| } > $GITHUB_OUTPUT | |
| - uses: Deep-MI/FastSurfer/.github/actions/build-docker@dev | |
| if: ${{ steps.parse.outputs.continue && steps.parse.outputs.docker-image == 'build-cached' }} | |
| # This action needs the "full" checkout (located at ${{ inputs.fastsurfer-home }}) | |
| with: | |
| fastsurfer-home: ${{ steps.parse-version.outputs.FASTSURFER_HOME }} | |
| # currently, this image has to be updated and used to circumvent storage limitations in github actions | |
| # and it is also faster to use this prebuilt, reduced-size freesurfer distribution | |
| freesurfer-build-image: "${{ steps.parse-version.outputs.FS_BUILD_IMAGE }}" | |
| fastsurfer: | |
| name: 'Run FastSurfer on sample images' | |
| needs: build-docker-latest | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 180 | |
| strategy: | |
| # the following matrix strategy will result in one run per subject as matrix is "one-dimensional". | |
| # Additional parameters under "include" are then added as additional (dependent) information | |
| matrix: | |
| subject-id: [0.8mm, 1.0mm] | |
| include: | |
| - subject-id: 1.0mm | |
| file-extension: ".mgz" | |
| image-key: QUICKTEST_IMAGE_HREF_1mm | |
| - subject-id: 0.8mm | |
| file-extension: ".nii.gz" | |
| image-key: QUICKTEST_IMAGE_HREF_08mm | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: .github/actions | |
| - name: Run FastSurfer for ${{ matrix.subject-id }} with the previously created docker container | |
| uses: Deep-MI/FastSurfer/.github/actions/run-fastsurfer@dev | |
| with: | |
| subject-id: ${{ matrix.subject-id }} | |
| file-extension: ${{ matrix.file-extension }} | |
| image-href: ${{ secrets[matrix.image-key] }} | |
| license: ${{ secrets.QUICKTEST_LICENSE }} | |
| docker-image: ${{ needs.build-docker-latest.outputs.docker-image }} | |
| extra-args: ${{ needs.build-docker-latest.outputs.extra-args }} | |
| tests: | |
| name: Download data and perform tests (1.0mm) | |
| needs: fastsurfer | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| strategy: | |
| # the following matrix strategy will result in one run per subject as matrix is "one-dimensional". | |
| # Additional parameters under "include" are then added as additional (dependent) information | |
| matrix: | |
| subject-id: [0.8mm, 1.0mm] | |
| include: | |
| - subject-id: 0.8mm | |
| case-key: QUICKTEST_TARGET_HREF_08mm | |
| - subject-id: 1.0mm | |
| case-key: QUICKTEST_TARGET_HREF_1mm | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Run tests | |
| uses: Deep-MI/FastSurfer/.github/actions/run-tests@dev | |
| with: | |
| subject-id: ${{ matrix.subject-id }} | |
| subjects-dir: ${{ env.SUBJECTS_DIR }} | |
| reference-dir: ${{ env.REFERENCE_DIR }} | |
| case-href: ${{ secrets[matrix.case-href] }} |