Add GitHub Actions CI pipeline with linting and tests

.github/workflows/ci.yml

@@ -0,0 +1,26 @@
+name: "brats-tumor-segmentation-pipeline"
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: "Checkout code"
+        uses: actions/checkout@v4
+      - name: "Setup python 3.11 environment"
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: "Install python libraries"
+        run: |
+          pip install -r requirements.txt
+          pip install -e .
+      - name: "Run ruff linting"
+        run: ruff check src/
+      - name: "Run pytest"
+        run: pytest tests/ -v
+

src/preprocessing/create_splits.py

@@ -26,7 +26,7 @@ def create_splits(data_dir: Path, output_dir: Path):
     for case in case_names:
         seg = nib.load(data_dir / case / f"{case}-seg.nii.gz").get_fdata()
         labels = np.unique(seg)
-        tumor_labels = [str(l) for l in [1, 2, 3] if l in labels]
+        tumor_labels = [str(label_id) for label_id in [1, 2, 3] if label_id in labels]
         strat_labels.append("_".join(tumor_labels))
 
     label_counts = Counter(strat_labels)

src/training/train.py

@@ -212,7 +212,7 @@ def main():
                     "epoch": epoch + 1,
                     "best_val_loss": best_val_loss,
                     "scheduler": scheduler.state_dict()
-                }, CHECKPOINT_DIR / f"best_model.pth")
+                }, CHECKPOINT_DIR / "best_model.pth")
             else:
                 epochs_no_improvement += 1
 

tests/test_dataset.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 from src.training.dataset import BraTSDataset
 
+@pytest.mark.skipif(not Path("data/processed").exists(), reason="No data available")
 def test_dataset_output():
     PROJECT_ROOT = Path(__file__).resolve().parents[1]
     DATA_DIR = PROJECT_ROOT / "data" / "processed"