Add CI pipeline and clean up test suite

.github/workflows/ci.yml

@@ -0,0 +1,59 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+# Cancel superseded runs on the same ref (e.g. rapid pushes to a PR).
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint (syntax / undefined names)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install ruff
+        run: pip install ruff
+      # Only fail on real errors: syntax errors and undefined names.
+      # This is a fast safety net, not a style gate.
+      - name: Check for fatal errors
+        run: ruff check --select E9,F63,F7,F82 src tests
+
+  test:
+    name: Tests (py${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.11"]
+    env:
+      # Run Qt without a display.
+      QT_QPA_PLATFORM: offscreen
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      # System libraries needed by PyQt5 / napari / VTK in a headless runner.
+      - name: Install Qt system dependencies
+        uses: tlambert03/setup-qt-libs@v1
+
+      - name: Install package and test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+
+      - name: Run test suite
+        run: pytest tests/ -v

CONTRIBUTING.md

@@ -63,6 +63,22 @@ If you encounter issues, please open an issue or reach out for help.
 - Add tests for new features and bug fixes when possible.
 - If adding new modules, consider including a corresponding test file.
 
+Install the test dependencies and run the suite:
+
+```bash
+pip install -e ".[test]"
+
+# GUI tests need a Qt platform; use the offscreen backend when headless.
+QT_QPA_PLATFORM=offscreen pytest tests/
+```
+
+Markers:
+- `gui` — needs a Qt application (deselect with `-m "not gui"`)
+- `integration` — needs real data paths
+
+The full suite runs automatically on every push and pull request via GitHub
+Actions (`.github/workflows/ci.yml`).
+
 ## Reporting Bugs
 If you find a bug:
 1. Search [existing issues](https://github.com/baradlab/surface-morphometrics-gui/issues) to see if it has already been reported.

pyproject.toml

@@ -32,6 +32,15 @@ dependencies = [
     "libigl<2.5.0",
 ]
 
+[project.optional-dependencies]
+# Test/dev tooling. PyQt5 is included so the suite has a Qt binding outside the
+# conda `morphometrics` env (e.g. in CI / a plain virtualenv).
+test = [
+    "pytest",
+    "pytest-qt",
+    "PyQt5",
+]
+
 [project.scripts]
 surface-morphometrics-gui = "surface_morphometrics_gui.main:main"
 

tests/test_known_bugs.py

@@ -181,12 +181,14 @@ def test_no_clear_during_programmatic_clear(self, qapp):
                 em.data_dir.value = "/user/data"
                 em.cores_input.setValue(8)
 
-                # Simulate programmatic clear (index goes to -1)
+                # Simulate programmatic clear (index goes to -1); this fires
+                # _on_experiment_selected via the currentIndexChanged signal.
                 em.experiment_name.setCurrentIndex(-1)
-                # _on_experiment_selected fires via signal
 
-                # After fix, user values should be preserved during programmatic clears
-                # (The fix should guard against clearing during non-user-initiated changes)
+                # The fix guards on currentIndex() >= 0, so a negative index
+                # (non-user-initiated change) must not wipe the user's values.
+                assert str(em.data_dir.value) == "/user/data"
+                assert em.cores_input.value() == 8
 
 
 class TestBug10_TimeSleep: