chore: apply linting fixes and expand ruff coverage to test suite

Makefile

@@ -3,14 +3,14 @@
 install:
 	uv sync
 
-test:
+test: lint
 	uv run pytest tests/
 
 lint:
-	uv run ruff check src/
+	uv run ruff check src/ tests/
 
 fix:
-	uv run ruff check src/ --fix
+	uv run ruff check src/ tests/ --fix
 
 typecheck:
 	uv run mypy src/

src/pygui/ISC/AboutDialog.qml

@@ -3,6 +3,14 @@ import QtQuick.Controls
 import QtQuick.Layouts
 import ISC
 
+// TODO P3.1 + P3.2: license grid, "Load License" picker, version binding
+//   THINKING: C# parity requires the dgvLicense grid (Wafer SN, Mfg Date,
+//   License Level, License Date) fed from AES-128-CBC .bin files under
+//   <app_data>/licenses/ — CryptoHelper (backend/crypto/crypto_helper.py)
+//   already has the primitives; the missing piece is the license file model
+//   (P3.1 backend). "Version 0.1.0" below is hardcoded and will drift from
+//   pyproject.toml — expose importlib.metadata.version("pygui") via a context
+//   property instead (P3.2). See docs/pending/alpha-release-polish-plan.md §3.
 Popup {
     id: root
     modal: true

src/pygui/backend/controllers/session_controller.py

@@ -603,6 +603,14 @@ class SessionController(QObject):
             return average_clusters(edited, getattr(self, "_active_clusters", []))
         return edited
 
+    # TODO P2.4: throttle live-frame UI updates to ~30Hz
+    #   THINKING: every decoded serial frame triggers frameUpdated/stateChanged,
+    #   which repaints WaferMapItem + trend chart; at high stream rates the GUI
+    #   thread saturates on paint, not decode. Buffer the latest frame and flush
+    #   via a 33ms QTimer (latest-wins, no queue growth). Recording must keep
+    #   writing every frame — only the UI emit is throttled, so place the timer
+    #   here rather than in StreamReader. Depends on nothing; verify with P4.3.
+    #   See docs/pending/alpha-release-polish-plan.md §2.4.
     def _emit_current(self) -> None:
         frame = self._player.current()
         if frame is None:

src/pygui/backend/visualization/rbf_heatmap.py

@@ -18,6 +18,13 @@ _KERNEL = "thin_plate_spline"
 _SMOOTHING = 0.0
 
 
+# TODO P2.2: decouple grid resolution from output size
+#   THINKING: callers pass widget pixel size as width/height, so RBF evaluation
+#   count scales quadratically with viewport size (600px → 360k evaluations).
+#   Interpolate on a fixed ~100×100 grid and let the caller scale the QImage;
+#   sensor density (≤244 points) carries no more spatial information than that.
+#   Called from WaferMapItem._rebuild_heatmap (see its P2.2/P2.3 TODO).
+#   See docs/pending/alpha-release-polish-plan.md §2.2.
 def interpolate_field(
     xs: np.ndarray,
     ys: np.ndarray,

src/pygui/backend/visualization/wafer_map_item.py

@@ -290,6 +290,12 @@ class WaferMapItem(QQuickPaintedItem):
                 return idx
         return -1
 
+    # TODO P6.1: build batch export on top of this single-frame export
+    #   THINKING: export_image() already does the hard part (grabToImage → PNG);
+    #   batch export is just a loop over file_browser.files that loads each CSV
+    #   through the existing wafer-map pipeline and calls this per file into a
+    #   chosen output dir, plus an optional summary CSV of (file, min/max/mean).
+    #   No new rendering code needed — see docs/pending/alpha-release-polish-plan.md §6.1.
     @Slot(str, result=bool)
     def export_image(self, file_path: str) -> bool:
         """Export the current wafer map rendering to a PNG file
@@ -377,6 +383,13 @@ class WaferMapItem(QQuickPaintedItem):
         r = max(math.hypot(s.x, s.y) for s in self._sensors)
         return r * 1.05
 
+    # TODO P6.2: reuse this for the edge-to-center delta metric
+    #   THINKING: radial_metrics.py (new) needs the same "which sensors are near
+    #   the edge vs. near the center" bucketing this function already computes
+    #   for ring-line drawing — do NOT re-derive ring boundaries separately, this
+    #   already handles round vs. square wafer shapes correctly (see family_spec.py
+    #   square-wafer work). Outermost group ≈ edge sensors, innermost ≈ center.
+    #   See docs/pending/alpha-release-polish-plan.md §6.2.
     def _sensor_ring_radii_mm(self) -> list[float]:
         """Distinct radial distances of sensor groups, sorted ascending, plus the outer boundary."""
         if not self._sensors:
@@ -413,6 +426,15 @@ class WaferMapItem(QQuickPaintedItem):
         self._markers = {i: self._to_px(s.x, s.y, cx, cy, sc)
                          for i, s in enumerate(self._sensors)}
 
+    # TODO P2.2 + P2.3: fixed-resolution RBF grid, then offload to QThreadPool
+    #   THINKING: width=height=ds couples RBF cost to widget pixel size — a 600px
+    #   viewport solves a 360k-point system per frame where a fixed 100×100 grid
+    #   (10k points, GPU bilinear-scales the QImage up) is visually identical
+    #   through the 0.4-opacity blend. Do P2.2 first: it may make P2.3 (QRunnable
+    #   worker emitting heatmapReady(QImage), guarding against stale results when
+    #   sensors change mid-flight) unnecessary for alpha. Grid width param lands
+    #   in interpolate_field (see matching TODO in rbf_heatmap.py).
+    #   See docs/pending/alpha-release-polish-plan.md §2.2/§2.3.
     def _rebuild_heatmap(self) -> None:
         if not self._sensors or not self._values or self._blend == 0.0:
             self._heatmap = None
@@ -612,6 +634,13 @@ class WaferMapItem(QQuickPaintedItem):
                 ox = getattr(s, "offset_x", 0.0) * r
                 oy = getattr(s, "offset_y", 0.0) * r
 
+                # TODO P2.1: hoist fontMetrics() out of the sensor loop
+                #   THINKING: id_font/temp_font are fixed for the whole paint pass,
+                #   but fontMetrics() is re-queried per sensor — 65+ OS font-engine
+                #   round-trips per frame on a dense wafer, ~30/s in Live mode.
+                #   Compute id_fm/temp_fm once before `for i, s in ...` (they only
+                #   change when r/font_scale change). Verified by P4.3 benchmark.
+                #   See docs/pending/alpha-release-polish-plan.md §2.1.
                 painter.setFont(id_font)
                 id_fm = painter.fontMetrics()
                 id_line_h = id_fm.height()

src/pygui/backend/wafer/wafer_layouts.py

@@ -69,6 +69,12 @@ def _load_yaml(path: Path) -> dict:
         return yaml.safe_load(f)
 
 
+# TODO P6.3: expose this list to a new LayoutSelector.qml (4-button chooser)
+#   THINKING: this already returns everything the UI needs (family names) —
+#   the missing piece is a context-property exposure (SessionController or a
+#   thin new property) and a setLayout(family) slot that calls load_layout()
+#   below. No parsing work needed; this is a wiring-only task.
+#   See docs/pending/alpha-release-polish-plan.md §6.3.
 def available_families() -> list[str]:
     return [_family_name(_load_yaml(p)["name"]) for p in _LAYOUTS_DIR.glob("*.yaml")]
 

tests/test_cluster_average.py

@@ -1,6 +1,6 @@
 """Tests for src/pygui/backend/cluster_average.py."""
 import math
-import pytest
+
 from pygui.backend.cluster_average import average_clusters, group_sensors_by_radius
 from pygui.backend.wafer.zwafer_models import Sensor
 

tests/test_comparison.py

@@ -1,6 +1,5 @@
 """Tests for src/pygui/backend/comparison.py."""
 
-import numpy as np
 from pygui.backend.comparison import compare_runs
 
 

tests/test_data_parser.py

@@ -1,13 +1,14 @@
 """Tests for serialcomm/data_parser.py binary parsing pipeline."""
 
 import pytest
+
 from pygui.serialcomm.data_parser import (
+    _convert_hex_to_temp,
+    convert_to_temperatures,
     csv_column_count,
     parse_binary_data,
-    convert_to_temperatures,
     remove_trailing_zeros,
     save_to_csv,
-    _convert_hex_to_temp,
 )
 
 # ── csv_column_count ──────────────────────────────────────────────────────────
@@ -271,7 +272,7 @@ class TestSaveToCsv:
         result = save_to_csv(data, "P", "P00001", str(tmp_path))
         assert result is not None
         headers = open(result).readline().strip().split(",")
-        assert len(headers) == 60, f"data width 60 should win over display 48"
+        assert len(headers) == 60, "data width 60 should win over display 48"
         assert headers[0] == "Sensor1"
         assert headers[-1] == "Sensor60"
 

tests/test_device_controller.py

@@ -1,10 +1,13 @@
-import pytest
 import logging
 from unittest.mock import MagicMock, patch
+
+import pytest
+
 from pygui.backend.controllers.device_controller import DeviceController
 from pygui.backend.data.local_settings import LocalSettings
 from pygui.serialcomm.serial_port import WaferInfo
 
+
 @pytest.fixture
 def mock_settings():
     s = LocalSettings()
@@ -16,8 +19,8 @@ def mock_settings():
 
 @pytest.fixture
 def controller(mock_settings):
-    import tempfile
     import shutil
+    import tempfile
     temp_dir = tempfile.mkdtemp()
     yield DeviceController(mock_settings, temp_dir)
     shutil.rmtree(temp_dir)
@@ -159,8 +162,8 @@ def test_logging_handler(controller):
     assert any("Hello QML Activity Log" in line for line in controller._activity_log)
 
 def test_fresh_session_on_startup(mock_settings):
-    import tempfile
     import shutil
+    import tempfile
 
     # Configure mock settings with some data to simulate previous session
     mock_settings.activity_log = ["[12:00:00] Old message"]
@@ -191,7 +194,7 @@ def test_detect_wafer_clears_old_session(controller):
     # We mock detect_all_ports to not run long or fail
     controller._service.detect_all_ports = MagicMock(return_value=(None, None))
 
-    with patch("threading.Thread") as mock_thread:
+    with patch("threading.Thread"):
         controller.detectWafer()
 
         # Verify it cleared all session variables and logs immediately at start of detect
@@ -227,6 +230,6 @@ def test_device_service_port_caching(controller):
 
         # Clear cache and scan again should invoke subprocess
         service.clear_port_scan_cache()
-        ports3 = service.enumerate_ports()
+        service.enumerate_ports()
         assert mock_run.call_count == 2
 

tests/test_frame_player.py

@@ -1,6 +1,7 @@
 from pygui.backend.models.frame import Frame
 from pygui.backend.models.frame_player import FramePlayer
 
+
 def frames(n):
     return [Frame(seq=i, time=float(i), values=[149.0 + i])for i in range(n)]
 

tests/test_frame_stats.py

@@ -1,6 +1,8 @@
 import math
+
 import pytest
-from pygui.backend.models.frame_stats import compute_stats, Stats
+
+from pygui.backend.models.frame_stats import Stats, compute_stats
 
 
 def test_basic_stat():
@@ -20,3 +22,9 @@ def test_empty_values_returns_zeros():
 
 def test_ignores_nan():
     s = compute_stats([149.0, float("nan"), 151.0])
+    assert s.min == 149.0 and s.min_index == 0
+    assert s.max == 151.0 and s.max_index == 2
+    assert s.diff == pytest.approx(2.0)
+    assert s.avg == pytest.approx(150.0)
+    assert s.sigma == pytest.approx(1.0)
+    assert s.three_sigma == pytest.approx(3.0)

tests/test_graph_view.py

@@ -1,8 +1,6 @@
 """Tests for src/pygui/backend/visualization/graph_view.py."""
 import json
-from unittest.mock import MagicMock, PropertyMock, patch
+from unittest.mock import MagicMock
-
-import pytest
 
 
 def _make_plot_widget():

tests/test_rbf_heatmap.py

@@ -1,6 +1,7 @@
 """Tests for src/pygui/backend/rbf_heatmap.py."""
 import numpy as np
-from pygui.backend.visualization.rbf_heatmap import interpolate_field, BACKEND
+
+from pygui.backend.visualization.rbf_heatmap import BACKEND, interpolate_field
 
 
 def test_field_shape_and_interpolates_at_sites():

tests/test_sensor_editor.py

@@ -1,5 +1,4 @@
 """Tests for src/pygui/backend/sensor_editor.py."""
-import pytest
 from pygui.backend.models.sensor_editor import SensorEditor
 
 

tests/test_session_controller.py

@@ -1,7 +1,10 @@
+from unittest.mock import MagicMock
+
 import pytest
-from unittest.mock import MagicMock, patch
+
 from pygui.backend.controllers.session_controller import SessionController
 
+
 @pytest.fixture
 def controller():
     return SessionController()
@@ -9,7 +12,7 @@ def controller():
 def test_initial_default(controller):
     assert controller.mode == "review"
     assert controller.state == "idle"
-    assert controller.recording == False
+    assert not controller.recording
 
 def test_playback_flow(controller):
     controller.loadFile("tests/fixtures/sample_stream.csv")
@@ -223,10 +226,10 @@ Item {
 def test_recording_toggle(controller, tmp_path):
     csv_path = str(tmp_path / "rec" / "live_test.csv")
     controller.startRecording(csv_path, "SN123")
-    assert controller.recording == True
+    assert controller.recording
 
     controller.stopRecording()
-    assert controller.recording == False
+    assert not controller.recording
 
     # Header written with wafer serial
     content = open(csv_path).read()

tests/test_session_model.py

@@ -1,7 +1,6 @@
 from pygui.backend.models.frame import Frame
-from pygui.backend.models.threshold_classifier import ThresholdConfig, BAND_HIGH, BAND_IN, BAND_LOW
+from pygui.backend.models.session_model import SessionModel
-from pygui.backend.models.session_model import SessionModel, SessionUpdate
+from pygui.backend.models.threshold_classifier import BAND_HIGH, BAND_IN, BAND_LOW, ThresholdConfig
-
 
 
 def test_manual_banding_and_stats():
@@ -25,4 +24,3 @@ def test_set_thresholds_reband_on_next_frame():
     m.set_thresholds(ThresholdConfig(set_point=149.0, margin=5.0, auto=False))
     upd = m.process(Frame(seq=0, time=0.0, values=[151.0]))
     assert upd.bands == [BAND_IN]
-    

tests/test_stability_detector.py

@@ -1,8 +1,10 @@
 from pygui.backend.models.stability_detector import (
-    StabilityDetector, STATE_IDLE, STATE_RAMP, STATE_SET,
+    STATE_IDLE,
+    STATE_RAMP,
+    STATE_SET,
+    StabilityDetector,
 )
 
-
 SET_POINT = 149.0
 
 def make():

tests/test_stream_reader.py

@@ -1,7 +1,9 @@
 import time
+
 from pygui.backend.models.frame import Frame
 from pygui.serialcomm.stream_reader import StreamReader
 
+
 class FakeTransport:
     """Yield canned data then blocks (returns b'')."""
     def __init__(self, lines):

tests/test_threshold_classifier.py

@@ -1,8 +1,13 @@
 import math
 
 from pygui.backend.models.threshold_classifier import (
-    ThresholdConfig, classify, classify_all, resolve_bounds,
+    BAND_HIGH,
-    BAND_IN, BAND_HIGH, BAND_LOW
+    BAND_IN,
+    BAND_LOW,
+    ThresholdConfig,
+    classify,
+    classify_all,
+    resolve_bounds,
 )
 
 
@@ -26,4 +31,3 @@ def test_auto_bounds_use_mean_and_sigma():
 def test_classify_all_manual():
     cfg = ThresholdConfig(set_point=149.0, margin=1.0, auto=False)
     assert classify_all([149.0, 151.0, 147.0], cfg) == [BAND_IN, BAND_HIGH, BAND_LOW]
-    

tests/test_wafer_layouts.py

@@ -1,6 +1,7 @@
 """Tests for src/pygui/backend/wafer_layouts.py."""
 import pytest
-from pygui.backend.wafer.wafer_layouts import load_layout, available_families
+
+from pygui.backend.wafer.wafer_layouts import available_families, load_layout
 from pygui.backend.wafer.zwafer_models import Sensor
 
 

tests/test_wafer_map_item.py

@@ -1,9 +1,8 @@
 """Tests for src/pygui/backend/visualization/wafer_map_item.py."""
-from unittest.mock import MagicMock, patch
+from unittest.mock import MagicMock
 
 import pytest
 
-
 # Use the session-scoped qapp fixture from conftest.py so Qt Property/Signal
 # descriptors work properly.
 pytestmark = pytest.mark.usefixtures("qapp")