Actions away!

.github/workflows/collect_data.yml

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+name: Collect Data
+
+on:
+  workflow_dispatch:
+  workflow_call:
+    inputs:
+      data_directory:
+        type: string
+        required: false
+        default: /tmp/data/petprep_test_data
+      derivatives:
+        type: string
+        required: false
+        default: "petprep freesurfer smriprep"
+    outputs:
+      data_directory:
+        description: 'Path to "cached" data collected with `collect_test_data.py`'
+        value: ${{ inputs.data_directory }}
+env:
+  DATA_DIR: ${{ inputs.data_directory }}
+  DERIVATIVES: ${{ inputs.derivatives }}
+
+jobs:
+  collect-data:
+    outputs:
+      data_directory: ${{ env.DATA_DIR }}
+    runs-on: local
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 200
+          fetch-tags: true
+
+      - name: Check if data directory exists and has data
+        id: check-data
+        run: |
+          if [ -d "$DATA_DIR" ] && [ -n "$(ls -A $DATA_DIR 2>/dev/null)" ]; then
+            echo "Data directory exists and contains data, skipping collection"
+            echo "skip_collection=true" >> $GITHUB_OUTPUT
+          else
+            echo "Data directory is empty or does not exist, re-downloading data"
+            echo "skip_collection=false" >> $GITHUB_OUTPUT
+            # Clean up empty directory if it exists
+            if [ -d "$DATA_DIR" ]; then
+              echo "Removing empty data directory"
+              rm -rf "$DATA_DIR"
+            fi
+          fi
+
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Setup Git for DataLad
+        if: steps.check-data.outputs.skip_collection != 'true'
+        run: |
+          # Configure Git for DataLad
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "[email protected]"
+
+      - name: Collect data
+        if: steps.check-data.outputs.skip_collection != 'true'
+        run: |
+          # Collect the data
+          uv run scripts/collect_test_data.py -o "$DATA_DIR" -d $DERIVATIVES

.github/workflows/run_petprep.yml

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+name: Run PETPREP
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "main" ]
+    tags: "*"
+  pull_request:
+
+env:
+  # for local/self hosted runners one can assume that the 
+  FREESURFER_HOME: /usr/local/freesurfer/7.4.1
+  FSLDIR: /opt/conda/envs/petprep
+  FSL_OUTPUT_TYPE: NIFTI_GZ
+  AFNI_PATH: /opt/afni-latest
+  FSL_PATH: /opt/conda/envs/petprep/share/fsl/bin
+  ANTS_PATH: /opt/ants-2.6.2/bin
+  WORKBENCH_PATH: /opt/workbench/exe_linux64
+
+jobs:
+  collect-data:
+    uses: ./.github/workflows/collect_data.yml
+
+  run-tests:
+    needs: collect-data
+    runs-on: local
+    env:
+      DATA_DIR: ${{ needs.collect-data.outputs.data_directory }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 200
+          fetch-tags: true
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Build and Install PETPREP
+        run: |
+          uv build 
+          pip install dist/*.whl --force-reinstall
+
+      - name: Check petprep is installed
+        run: |
+          which petprep
+          petprep --version
+
+      - name: Verify test data exists
+        run: |
+          if [ ! -d "$DATA_DIR" ] || [ -z "$(ls -A $DATA_DIR 2>/dev/null)" ]; then
+            echo "Error: Test data directory is empty or missing"
+            exit 1
+          fi
+          echo "Test data verified at $DATA_DIR"
+          ls -la "$DATA_DIR"
+
+      - name: Run petprep
+        run: |
+          source "${FREESURFER_HOME}/SetUpFreeSurfer.sh"
+          export PATH="${AFNI_PATH}:${PATH}"
+          export PATH="${FSL_PATH}:${PATH}"
+          export PATH="${ANTS_PATH}:${PATH}"
+          export PATH="${WORKBENCH_PATH}:${PATH}"
+          export FSLDIR="${FSLDIR}"
+          export FSL_OUTPUT_TYPE="${FSL_OUTPUT_TYPE}"
+          petprep "${DATA_DIR}" "${DATA_DIR}/derivatives/petprep" participant --fs-license-file "${FREESURFER_HOME}/license.txt" --sloppy --derivatives anat=${DATA_DIR}/derivatives/smriprep --fs-subjects-dir ${DATA_DIR}/derivatives/freesurfer