Update batch_single_subject.sh and process_data.sh to match changes to 2024 SCT Course Slides
#64
Workflow file for this run
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| name: "Run sct_run_batch -s process_data.sh" | |
| # The tl;dr purpose of this workflow is to: | |
| # - A) Run the batch processing script part of the the SCT Course | |
| # - B) If run manually, then take some of 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: | |
| pull_request: | |
| 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 PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH | |
| - name: "Checkout '${{ github.event.repository.name }}'" | |
| uses: actions/checkout@v4 | |
| with: | |
| path: ${{ github.event.repository.name }} | |
| - name: Run sct_run_batch -s process_data.sh | |
| run: | | |
| cd "${{ github.event.repository.name }}/multi_subject" | |
| sct_run_batch -script process_data.sh -config config.yml | |
| - name: Output full log for sanity checking | |
| run: | | |
| cd "${{ github.event.repository.name }}/multi_subject/output/log" | |
| for logfile in process_data_sub-01.log err.process_data_sub-01.log; do | |
| if [[ -e "${logfile}" ]]; then | |
| echo "=== Contents of ${logfile} ===" | |
| cat "${logfile}" | |
| else | |
| echo "=== No file ${logfile} ===" | |
| fi | |
| done | |
| - name: Check that script executed without error | |
| run: | | |
| cd "${{ github.event.repository.name }}/multi_subject/output/log" | |
| [ "$(compgen -G "process_data_sub-0*.log")" ] # Log files should exist | |
| [ ! "$(compgen -G "err.process_data_sub-0*.log")" ] # Error files should NOT exist | |
| grep -iF "warning" process_data_sub-01.log | |
| grep -iF "error" process_data_sub-01.log |