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name: "Run sct_run_batch -s process_data.sh" |
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# The tl;dr purpose of this workflow is to: |
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# - A) Run the batch processing script part of the the SCT Course |
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# - B) If run manually, then take some of 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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pull_request: |
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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 PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH |
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|
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- name: Pre-download necessary models |
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run: | |
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sct_deepseg spinalcord -install |
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|
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- name: "Checkout '${{ github.event.repository.name }}'" |
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uses: actions/checkout@v4 |
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with: |
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path: ${{ github.event.repository.name }} |
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|
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- name: Run sct_run_batch -s process_data.sh |
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run: | |
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cd "${{ github.event.repository.name }}/multi_subject" |
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sct_run_batch -script process_data.sh -config config.yml |
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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: Multi Subject CSV Files |
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path: ${{ github.event.repository.name }}/multi_subject/output/**/*.csv |
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|
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- name: Output full log for sanity checking |
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if: always() |
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run: | |
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cd "${{ github.event.repository.name }}/multi_subject/output/log" |
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for subxx in sub-01 sub-03 sub-05; do |
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for logfile in process_data_${subxx}.log err.process_data_${subxx}.log; do |
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if [[ -e "${logfile}" ]]; then |
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echo "=== Contents of ${logfile} ===" |
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cat "${logfile}" |
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else |
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echo "=== No file ${logfile} ===" |
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fi |
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done |
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done |
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|
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- name: Check results (no error logs) |
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if: always() |
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run: | |
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cd "${{ github.event.repository.name }}/multi_subject/output/log" |
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[ "$(compgen -G "process_data_sub-0*.log")" ] # Log files should exist |
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|
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- name: Check results (no error logs) |
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if: always() |
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run: | |
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cd "${{ github.event.repository.name }}/multi_subject/output/log" |
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[ ! "$(compgen -G "err.process_data_sub-0*.log")" ] # Error files should NOT exist |
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|
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- name: Check results (warnings in log) |
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if: always() |
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run: | |
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cd "${{ github.event.repository.name }}/multi_subject/output/log" |
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# ! grep -iF "warning" process_data_sub-01.log |
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|
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- name: Check results (errors in log) |
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if: always() |
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run: | |
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cd "${{ github.event.repository.name }}/multi_subject/output/log" |
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! grep -iF "error" process_data_sub-01.log |
