Edit .bashrc to be able to call SCT

#123 (comment)

.github/workflows/run_notebooks.yml

@@ -68,13 +68,17 @@ jobs:
         run: |
           git clone --depth 1 https://github.com/spinalcordtoolbox/spinalcordtoolbox.git
           yes | spinalcordtoolbox/install_sct
-          # Make SCT callable from within the environment
-          source /home/runner/.bashrc
+          # NB: 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
+          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
+          # Make sure SCT can be called from withing the environment
+          sct_check_dependencies
 
       - name: Run Jupyter Notebooks
         continue-on-error: true  # Allow workflow to continue even if notebook execution fails
-        env:
-          PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:${{ env.PATH }}
         run: |
           echo $PATH
           mkdir -p executed_notebooks