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name: "Run batch_single_subject.sh" |
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# The tl;dr purpose of this workflow is to: |
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# - A) Run all of the commands in the SCT Course |
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# - B) If the workflow is run manually, then take the output files and package them into tutorial-specific datasets. |
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# |
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# In-depth explanation: |
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# Most of SCT's tutorials depend on files generated by previous steps. (For example, 'sct_register_to_template' |
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# depends on the segmented spinal cord image file generated by `sct_deepseg`. This creates a dilemma: If we want |
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# SCT's tutorials to stand alone, we need to provide these intermediate files. But, if we want to run the tutorials |
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# start to finish in a sequence (e.g. during the SCT Course), it would be confusing if the intermediate files |
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# were already there. |
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# |
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# The solution is to only store the minimally-necessary files in the repository, then generate the intermediate files |
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# using this workflow. That way, we can provide 2 different downloads: |
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# - 'sct_course_data.zip': Files required to run the SCT course from start to finish. |
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# - 'registration.zip', 'segmentation.zip', etc.: Files required by individual tutorials. |
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|
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on: |
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push: |
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branches: |
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- master |
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pull_request: |
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workflow_dispatch: |
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inputs: |
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release_title: |
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description: 'Release title (e.g. rYYYYMMDD)' |
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required: true |
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|
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jobs: |
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run-course-script: |
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runs-on: ubuntu-latest |
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steps: |
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|
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- name: Checkout spinalcordtoolbox |
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uses: actions/checkout@v4 |
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with: |
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repository: spinalcordtoolbox/spinalcordtoolbox |
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path: spinalcordtoolbox |
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|
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# install_sct edits ~/.bashrc, but those environment changes don't get passed to subsequent steps in GH Actions. |
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# So, we filter through the .bashrc and pass the values to $GITHUB_ENV and $GITHUB_PATH. |
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# Relevant documentation: https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#environment-files |
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# This workaround should be replaced by https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3198#discussion_r568225392 |
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- name: Install spinalcordtoolbox |
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run: | |
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cd spinalcordtoolbox |
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./install_sct -iy |
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cat ~/.bashrc | grep "export SCT_DIR" | cut -d " " -f 2 >> $GITHUB_ENV |
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cat ~/.bashrc | grep "export MPLBACKEND" | cut -d " " -f 2 >> $GITHUB_ENV |
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cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH |
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|
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- name: "Checkout '${{ github.event.repository.name }}'" |
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uses: actions/checkout@v4 |
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with: |
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ref: ${{ env.GITHUB_SHA }} |
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path: ${{ github.event.repository.name }} |
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|
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- name: Run batch_single_subject.sh to generate intermediate files |
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run: | |
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cd "${{ github.event.repository.name }}/single_subject" |
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./batch_single_subject.sh |
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|
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- name: "Upload QC report for easier output verification" |
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uses: actions/upload-artifact@v4 |
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with: |
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name: batch_single_subject QC (${{ runner.os }}) |
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path: "~/qc_singleSubj" |
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|
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- name: "Upload CSV files for easier tutorial updating" |
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uses: actions/upload-artifact@v4 |
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with: |
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name: Single Subject CSV Files |
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path: ${{ github.event.repository.name }}/single_subject/data/**/*.csv |
|
|
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- name: "Package data into tutorial-specific .zip files" |
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run: | |
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cd ${{ github.event.repository.name }} |
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awk -F, '{ print $1,$2 }' tutorial-datasets.csv | xargs -l zip -ur |
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|
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- uses: ncipollo/release-action@v1 |
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name: Create release ('${{ github.event.inputs.release_title }}') |
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id: create_release |
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with: |
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tag: ${{ github.event.inputs.release_title }} |
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commit: ${{ env.GITHUB_SHA }} |
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token: ${{ secrets.GITHUB_TOKEN }} |
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# Only create release if workflow is run manually. (This allows the workflow to double as a PR test.) |
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if: github.event_name == 'workflow_dispatch' |
|
|
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- uses: xresloader/upload-to-github-release@v1 |
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name: Attach .zip files to newly-created release |
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env: |
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |
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with: |
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file: "${{ github.event.repository.name }}/*.zip" |
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draft: false |
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tag_name: ${{ github.event.inputs.release_title }} |
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release_id: ${{ steps.create_release.outputs.id }} |
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# Only attach to release if workflow is run manually. (This allows the workflow to double as a PR test.) |
|
if: github.event_name == 'workflow_dispatch' |
