Update workflows to be able to run scripts on PRs

Author: joshuacwnewton

.github/workflows/run_batch_script.yml

@@ -0,0 +1,57 @@
+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@v2
+      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@v2
+      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 -d
+
+    - name: Assert 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

.github/workflows/create_release.yml …kflows/run_script_and_create_release.yml.github/workflows/create_release.yml renamed to .github/workflows/run_script_and_create_release.yml .github/workflows/create_release.yml renamed to .github/workflows/run_script_and_create_release.yml

@@ -1,5 +1,7 @@
-name: "Package course data into subsets"
-# The purpose of this workflow is to convert the SCT Course dataset into tutorial-specific datasets.
+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'
@@ -14,14 +16,15 @@ name: "Package course data into subsets"
 #        - 'registration.zip', 'segmentation.zip', etc.: Files required by individual tutorials.
 
 on:
+  pull_request:
   workflow_dispatch:
     inputs:
       release_title:
         description: 'Release title (e.g. rYYYYMMDD)'
         required: true
 
 jobs:
-  create-tutorial-data-release:
+  run-course-script:
     runs-on: ubuntu-latest
     steps:
 
@@ -57,13 +60,17 @@ jobs:
       run: |
         cd ${{ github.event.repository.name }}
         awk -F, '{ print $1,$2 }' tutorial-datasets.csv | xargs -l zip -u
+      # Only package data if workflow is run manually. (This allows the workflow to double as a PR test.)
+      if: github.event_name == 'workflow_dispatch'
 
     - uses: ncipollo/release-action@v1
       name: Create release ('${{ github.event.inputs.release_title }}')
       id: create_release
       with:
         tag: ${{ github.event.inputs.release_title }}
         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
@@ -73,4 +80,6 @@ jobs:
         file: "${{ github.event.repository.name }}/*.zip"
         draft: false
         tag_name: ${{ github.event.inputs.release_title }}
-        release_id: ${{ steps.create_release.outputs.id }}
+        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'