From 7429b15f0279e1b9dd6fe3be06c8ee6016f2e6cf Mon Sep 17 00:00:00 2001
From: AndrewVFranco <129307231+AndrewVFranco@users.noreply.github.com>
Date: Fri, 27 Mar 2026 00:58:22 -0700
Subject: [PATCH 1/2] Add GitHub Actions CI pipeline with linting and tests

---
 .github/workflows/ci.yml | 26 ++++++++++++++++++++++++++
 tests/test_dataset.py    |  1 +
 2 files changed, 27 insertions(+)
 create mode 100644 .github/workflows/ci.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..6679ba2
--- /dev/null
+++ b/.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
+
diff --git a/tests/test_dataset.py b/tests/test_dataset.py
index eed179b..94e07ef 100644
--- a/tests/test_dataset.py
+++ b/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"

From a28d48b065d1f72931257d56c8cfcf3ecc6cc6ab Mon Sep 17 00:00:00 2001
From: AndrewVFranco <129307231+AndrewVFranco@users.noreply.github.com>
Date: Fri, 27 Mar 2026 01:03:33 -0700
Subject: [PATCH 2/2] Fix linting errors

---
 src/preprocessing/create_splits.py | 2 +-
 src/training/train.py              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/preprocessing/create_splits.py b/src/preprocessing/create_splits.py
index 685979f..96d1b2d 100644
--- a/src/preprocessing/create_splits.py
+++ b/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)
diff --git a/src/training/train.py b/src/training/train.py
index 75bb2e4..e918d2a 100644
--- a/src/training/train.py
+++ b/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