Update batch_single_subject.sh and process_data.sh to match changes to 2024 SCT Course Slides
#109
Workflow file for this run
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| name: "Run batch_single_subject.sh" | |
| # The tl;dr purpose of this workflow is to: | |
| # - A) Run all of the commands in the SCT Course | |
| # - B) If the workflow is run manually, then take the output files and package them into tutorial-specific datasets. | |
| # | |
| # In-depth explanation: | |
| # Most of SCT's tutorials depend on files generated by previous steps. (For example, 'sct_register_to_template' | |
| # depends on the segmented spinal cord image file generated by `sct_deepseg`. This creates a dilemma: If we want | |
| # SCT's tutorials to stand alone, we need to provide these intermediate files. But, if we want to run the tutorials | |
| # start to finish in a sequence (e.g. during the SCT Course), it would be confusing if the intermediate files | |
| # were already there. | |
| # | |
| # The solution is to only store the minimally-necessary files in the repository, then generate the intermediate files | |
| # using this workflow. That way, we can provide 2 different downloads: | |
| # - 'sct_course_data.zip': Files required to run the SCT course from start to finish. | |
| # - 'registration.zip', 'segmentation.zip', etc.: Files required by individual tutorials. | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| workflow_dispatch: | |
| inputs: | |
| release_title: | |
| description: 'Release title (e.g. rYYYYMMDD)' | |
| required: true | |
| jobs: | |
| run-course-script: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout spinalcordtoolbox | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: spinalcordtoolbox/spinalcordtoolbox | |
| path: spinalcordtoolbox | |
| # install_sct edits ~/.bashrc, but those environment changes don't get passed to subsequent steps in GH Actions. | |
| # So, we filter through the .bashrc and pass the values to $GITHUB_ENV and $GITHUB_PATH. | |
| # Relevant documentation: https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#environment-files | |
| # This workaround should be replaced by https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3198#discussion_r568225392 | |
| - name: Install spinalcordtoolbox | |
| run: | | |
| cd spinalcordtoolbox | |
| ./install_sct -iy | |
| cat ~/.bashrc | grep "export SCT_DIR" | cut -d " " -f 2 >> $GITHUB_ENV | |
| cat ~/.bashrc | grep "export MPLBACKEND" | cut -d " " -f 2 >> $GITHUB_ENV | |
| cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH | |
| - name: "Checkout '${{ github.event.repository.name }}'" | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ env.GITHUB_SHA }} | |
| path: ${{ github.event.repository.name }} | |
| - name: Run batch_single_subject.sh to generate intermediate files | |
| run: | | |
| cd "${{ github.event.repository.name }}/single_subject" | |
| ./batch_single_subject.sh | |
| - name: "Package data into tutorial-specific .zip files" | |
| run: | | |
| cd ${{ github.event.repository.name }} | |
| awk -F, '{ print $1,$2 }' tutorial-datasets.csv | xargs -l zip -ur | |
| - uses: ncipollo/release-action@v1 | |
| name: Create release ('${{ github.event.inputs.release_title }}') | |
| id: create_release | |
| with: | |
| tag: ${{ github.event.inputs.release_title }} | |
| commit: ${{ env.GITHUB_SHA }} | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| # Only create release if workflow is run manually. (This allows the workflow to double as a PR test.) | |
| if: github.event_name == 'workflow_dispatch' | |
| - uses: xresloader/upload-to-github-release@v1 | |
| name: Attach .zip files to newly-created release | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| file: "${{ github.event.repository.name }}/*.zip" | |
| draft: false | |
| tag_name: ${{ github.event.inputs.release_title }} | |
| release_id: ${{ steps.create_release.outputs.id }} | |
| # 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' |