Merge pull request #37 from richardkoehler/feat/update-tests

- Update tests
- Add test coverage
- Add tests to cover at least 50 % lines of code
- Add testing in CI

Author: richardkoehler

.github/workflows/ci.yml

@@ -29,17 +29,11 @@ jobs:
 
       - name: Lint
         run: |
-          uv run ruff check --exclude tests .
+          uv run ruff check .
 
       - name: Format
         run: |
-          uv run ruff format --check --exclude tests .
-
-      # Tests are temporarily disabled in CI until they are ready.
-      # To re-enable, uncomment the step below once tests are stable.
-      # - name: Run pytest
-      #   run: |
-      #     uv run pytest
+          uv run ruff format --check .
 
   type-check:
     name: Type Check
@@ -61,5 +55,47 @@ jobs:
 
       - name: Type check
         run: |
-          uv run ty check src
+          uv run ty check .
+
+  test:
+    name: Tests (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+          - os: windows-latest
+          # Apple Silicon (arm64); see https://github.com/actions/runner-images
+          - os: macos-14
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
 
+      - name: Set up uv
+        uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57
+        with:
+          python-version: "3.14"
+          enable-cache: true
+
+      - name: Sync dependencies
+        run: |
+          uv sync --locked --dev
+
+      # PySide6 links libEGL even for offscreen; ubuntu-latest images omit it by default.
+      - name: Install Qt EGL/XCB dependencies (Ubuntu only)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends \
+            libegl1 \
+            libgl1 \
+            libxkbcommon0 \
+            libdbus-1-3
+
+      - name: Run pytest
+        env:
+          QT_QPA_PLATFORM: offscreen
+        run: |
+          uv run pytest --cov-fail-under=48

.pre-commit-config.yaml

@@ -9,12 +9,12 @@ repos:
     hooks:
       - id: ruff-format
       - id: ruff-check
-        args: ["--fix", "--exclude", "tests"]
+        args: ["--fix"]
 
   - repo: local
     hooks:
       - id: ty-check
-        name: ty check (src)
-        entry: uv run ty check src
+        name: ty check
+        entry: uv run ty check .
         language: system
         pass_filenames: false

pyproject.toml

@@ -33,9 +33,9 @@ dependencies = [
 dev = [
     "pytest>=8.0.0",
     "pytest-qt>=4.4.0",
+    "pytest-timeout>=2.3.0",
     "pytest-cov>=4.1.0",
     "ruff>=0.1.0",
-    # "mypy>=1.8.0",
     "pre-commit>=3.6",
     "ty>=0.0.30",
     "pandas-stubs>=3.0.0.260204",
@@ -76,10 +76,26 @@ python_classes = ["Test*"]
 python_functions = ["test_*"]
 addopts = [
     "--verbose",
+    "--timeout=3",
     "--cov=dbs_annotator",
     "--cov-report=html",
     "--cov-report=term-missing",
 ]
+filterwarnings = [
+    "ignore::DeprecationWarning",
+]
+markers = [
+    "gui: Qt GUI / widget tests",
+    "integration: cross-module behavior",
+    "slow: longer GUI or lazy-loaded wizard flows; skip locally with pytest -m \"not slow\"",
+]
+
+[tool.coverage.run]
+source = ["src"]
+omit = ["*/tests/*"]
+
+[tool.coverage.report]
+omit = ["*/tests/*"]
 
 [tool.ruff]
 line-length = 88
@@ -107,21 +123,3 @@ select = [
 ignore = [
     "E501",  # line too long (handled by formatter/line-length)
 ]
-
-[tool.mypy]
-python_version = "3.11"
-warn_return_any = true
-warn_unused_configs = true
-disallow_untyped_defs = false
-disallow_incomplete_defs = false
-check_untyped_defs = true
-no_implicit_optional = true
-warn_redundant_casts = true
-warn_unused_ignores = true
-warn_no_return = true
-strict_optional = true
-
-[[tool.mypy.overrides]]
-module = "PySide6.*"
-ignore_missing_imports = true
-

src/dbs_annotator/utils/report_chart_utils.py

@@ -54,9 +54,10 @@ def parse_scale_targets(
             targets[name] = {"type": "max", "value": float(smax) if smax else 0.0}
         elif mode == "custom":
             try:
-                targets[name] = {"type": "custom", "value": float(custom_val)}
+                custom_num = float(custom_val)
             except ValueError, TypeError:
-                targets[name] = {"type": "custom", "value": 0.0}
+                custom_num = 0.0
+            targets[name] = {"type": "custom", "value": custom_num}
     return targets
 
 

tests/conftest.py

@@ -0,0 +1,29 @@
+"""Shared pytest fixtures for Qt and the main wizard."""
+
+from __future__ import annotations
+
+import os
+
+# Headless-friendly Qt before any QWidget is constructed (pytest loads conftest early).
+os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
+
+import pytest
+
+from dbs_annotator.views.wizard_window import WizardWindow
+
+
+@pytest.fixture
+def wizard(qtbot, qapp):
+    """Main wizard window bound to the session QApplication."""
+    w = WizardWindow(qapp)
+    qtbot.addWidget(w)
+    w.show()
+    return w
+
+
+@pytest.fixture
+def bids_like_tsv(tmp_path):
+    """Minimal TSV path suitable for SessionData.open_file (new file)."""
+    path = tmp_path / "sub-01_ses-20250101_task-prog_run-01_events.tsv"
+    path.write_text("", encoding="utf-8")
+    return path