quicktest #28
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| name: PR quicktest | ||
| # File: quicktest.yaml | ||
| # Author: David Kügler | ||
| # Reworked on: 2024-12-01 | ||
| # Created on: 2023-07-10 by Taha Abdullah | ||
| # 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 (default = "": deep MI/fastsurfer-build:freesurferXXX' and find the version number from Docker/install_fs_pruned.sh) | ||
| 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 == "true" && steps.parse.outputs.docker-image == 'build-cached' }} | ||
| uses: actions/checkout@v4 | ||
| - name: Get the FreeSurfer version | ||
| if: ${{ steps.parse.outputs.continue == "true" && steps.parse.outputs.docker-image == 'build-cached' }} | ||
| shell: bash | ||
| id: parse-version | ||
| run: | | ||
| # get the FreeSurfer version from install_fs_pruned.sh | ||
| { | ||
| eval "$(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 = "true" && 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' | ||
| if: needs.docker-build-latest.outputs.continue == "true" | ||
| 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] }} | ||
