refactor(backend): clean up package re-exports, settings model properties, and unused signals

.gitignore

@@ -40,3 +40,21 @@ dist/
 *.spec
 *.icns
 *.ico
+
+# Runtime scratch data
+tmp/
+
+# Superpowers brainstorming visual companion
+.superpowers/
+.llm-wiki/
+.agents/
+.pi/
+
+# Planning / personal docs (root level)
+CLAUDE.md
+LEARNINGS.md
+MIGRATION.md
+AGENTS.md
+CONVENTIONS.md
+specs/
+graphify-out/

README.md

@@ -14,11 +14,13 @@ The `ISenseCloud` application provides a real-time monitor and analysis dashboar
 - **Custom Safety Limits & Thresholds**: Configurable alarm thresholds and set-points with automatic alerts when temperatures diverge from normal boundaries.
 
 ### App Showcase
+
 ![ISenseCloud UI displaying successful connection on COM6](image-1.png)
 *Figure 1: Main Status Dashboard displaying successful connection, active serial communications, and automated logging terminal.*
 
 > [!NOTE]
 > **Take Screenshots for Visual Placeholders:**
+>
 > - **Wafer Heatmap Tab**: Take a screenshot of the Wafer Map tab showing the radial heatmap interpolation, save it to `docs/design/wafer_heatmap_tab.png` and add it here.
 > - **Temperature Trend Graph**: Take a screenshot of the Graph tab plotting multi-sensor trend lines, save it to `docs/design/temp_trend_tab.png` and add it here.
 
@@ -42,12 +44,15 @@ During the refactoring from the flat-layout prototype (`SettingTab` branch) to t
 From the project root:
 
 ### Option A: Using `uv` (Recommended)
+
 If you have [uv](https://docs.astral.sh/uv/) installed:
+
 ```bash
 uv sync
 ```
 
 ### Option B: Using `pip`
+
 ```bash
 python3 -m venv .venv
 source .venv/bin/activate   # or .venv\Scripts\activate on Windows
@@ -59,9 +64,11 @@ pip install -e .            # install the `pygui` package (src/ layout) in edita
 ## Run
 
 ### Launch PySide6 QML App
+
 ```bash
 make run
 ```
+
 This launches the Qt window and loads the `ISC` QML module from `src/pygui/ISC/Main.qml`.
 
 ## Development
@@ -71,7 +78,7 @@ The project uses `uv` for dependency management and tooling, `Ruff` for linting
 A `Makefile` is provided to simplify common development and verification tasks:
 
 | Command | Description |
-|---------|-------------|
+| --------- | ------------- |
 | `make install` | Sync dependencies and set up the local `.venv` using `uv` |
 | `make run` | Launch the ISenseCloud application |
 | `make test` | Run the `pytest` test suite |
@@ -83,6 +90,7 @@ A `Makefile` is provided to simplify common development and verification tasks:
 ### Ruff Configuration
 
 Ruff is configured in `pyproject.toml` to enforce:
+
 - **E/W**: Pycodestyle errors and warnings
 - **F**: Pyflakes linter rules
 - **I**: Import sorting (isort parity)
@@ -174,11 +182,13 @@ Window {
 - If the app does not start, verify the virtual environment is active and dependencies are installed:
 
   *Using `uv`:*
+
   ```bash
   uv sync
   ```
 
   *Using `pip`:*
+
   ```bash
   source .venv/bin/activate   # or .venv\Scripts\activate on Windows
   pip install -r requirements.txt
@@ -187,17 +197,20 @@ Window {
 - If no window appears, ensure you are running in a desktop session with GUI access.
 
 - **Windows COM Port Connection Issues:**
-  * Standard Windows serial drivers don't support custom baud rates (e.g. `888888`), throwing an expected `OSError(22)` warning before falling back to `115200` baud.
+  - Standard Windows serial drivers don't support custom baud rates (e.g. `888888`), throwing an expected `OSError(22)` warning before falling back to `115200` baud.
 
 ### Step-by-Step Windows Simulator Connection Guide
 
 #### Step 1: Create the Virtual Serial Port Bridge
+
 Open **HHD Virtual Serial Port Tools**. Under the **Local Bridges** panel on the left, click the green **`+`** (Add) button to create a new port pair. Configure it to bridge **`COM5 ↔ COM6`**.
 
 ![HHD Virtual Serial Port Tools showing COM5 ↔ COM6 Local Bridge](image.png)
 
 #### Step 2: Configure and Start the Wafer Simulator
+
 Launch the **Wafer Simulator Control Panel** (`wafer_sim_gui.py`):
+
 1. Set the **Serial Port** to **`COM5`**.
 2. **Uncheck** the `Auto-create Virtual Port (com0com)` checkbox.
 3. Choose your desired **Wafer Type** (e.g., `aepwafer`) and **Family Code** (e.g., `A`).
@@ -206,6 +219,7 @@ Launch the **Wafer Simulator Control Panel** (`wafer_sim_gui.py`):
 ![Wafer Simulator Control Panel configured on COM5 and streaming](image-2.png)
 
 #### Step 3: Run the UI and Connect
+
 Launch the `pygui` client application. On the left navigation rail, click **DETECT WAFER**. The application will scan all active COM ports, automatically detect the virtual wafer simulator on **`COM6`**, and update the status indicator to **Connected** (green).
 
 ![ISenseCloud UI displaying successful connection on COM6](image-1.png)

src/pygui/backend/__init__.py

@@ -1,26 +0,0 @@
-# ===== Backend Package =====
-# Backward-compatible re-exports so existing callers keep working
-# while imports are migrated to the new sub-package paths.
-
-from pygui.backend.controllers.device_controller import DeviceController  # noqa: F401
-from pygui.backend.controllers.session_controller import SessionController  # noqa: F401
-from pygui.backend.data.csv_file_metadata import CSVFileMetadata  # noqa: F401
-from pygui.backend.data.csv_recorder import CsvRecorder  # noqa: F401
-from pygui.backend.data.data_records import read_data_records  # noqa: F401
-from pygui.backend.data.file_browser import FileBrowser  # noqa: F401
-from pygui.backend.data.local_settings import LocalSettings  # noqa: F401
-from pygui.backend.data.local_settings_model import LocalSettingsModel  # noqa: F401
-from pygui.backend.models.data_model import TemperatureTableModel  # noqa: F401
-from pygui.backend.models.frame import Frame  # noqa: F401
-from pygui.backend.models.frame_player import FramePlayer, frames_from_wafer_data  # noqa: F401
-from pygui.backend.models.frame_stats import Stats, compute_stats  # noqa: F401
-from pygui.backend.models.sensor_editor import SensorEditor  # noqa: F401
-from pygui.backend.models.session_model import SessionModel  # noqa: F401
-from pygui.backend.models.stability_detector import StabilityDetector  # noqa: F401
-from pygui.backend.models.threshold_classifier import ThresholdConfig  # noqa: F401
-from pygui.backend.visualization.graph_view import GraphView  # noqa: F401
-from pygui.backend.visualization.rbf_heatmap import interpolate_field  # noqa: F401
-from pygui.backend.visualization.wafer_map_item import WaferMapItem  # noqa: F401
-from pygui.backend.wafer.wafer_layouts import available_families, load_layout  # noqa: F401
-from pygui.backend.wafer.zwafer_models import DataRecord, Sensor, ZWaferData  # noqa: F401
-from pygui.backend.wafer.zwafer_parser import ZWaferParser  # noqa: F401

src/pygui/backend/controllers/__init__.py

@@ -1,5 +0,0 @@
-# ===== Controllers Sub-package =====
-from pygui.backend.controllers.device_controller import DeviceController
-from pygui.backend.controllers.session_controller import SessionController
-
-__all__ = ["DeviceController", "SessionController"]

src/pygui/backend/controllers/session_controller.py

@@ -14,7 +14,7 @@ from pygui.backend.models.frame import Frame
 from pygui.backend.models.frame_player import FramePlayer, frames_from_wafer_data
 from pygui.backend.models.replay_stats import ReplayStatsTracker
 from pygui.backend.models.sensor_editor import SensorEditor
-from pygui.backend.models.session_model import SessionModel
+from pygui.backend.models.session_model import SessionModel, SessionUpdate
 from pygui.backend.models.threshold_classifier import ThresholdConfig
 from pygui.backend.utils import slot_error_boundary
 from pygui.backend.wafer.zwafer_models import Sensor
@@ -37,7 +37,6 @@ class SessionController(QObject):
     loadedFileChanged = Signal()
     loadFileError = Signal(str)
     clusterAveragingEnabledChanged = Signal()
-    settingsChanged = Signal()  # emitted when session state changes that should be persisted
     liveStatsChanged = Signal()  # emitted when receivedCount or errorCount change
     # trend: per-frame avg for live graph
     trendData = Signal(str)  # JSON array of floats
@@ -50,8 +49,7 @@ class SessionController(QObject):
     _liveFrame = Signal(object)    # Frame
     _liveError = Signal()          # worker-thread error ping
 
-    def __init__(self, parent: QObject | None = None,
-                 settings: dict | None = None) -> None:
+    def __init__(self, parent: QObject | None = None) -> None:
         super().__init__(parent)
         self._mode = MODE_REVIEW
         self._model = SessionModel()
@@ -59,7 +57,7 @@ class SessionController(QObject):
         self._reader: Optional[StreamReader] = None
         self._recorder = CsvRecorder()
         self._sensors: list[Sensor] = []
-        self._last = None              # last SessionUpdate
+        self._last: Optional[SessionUpdate] = None
         self._elapsed = 0.0
         self._trend_buffer: list[float] = [] # rolling window
         self._trend_timestamps: list[float] = []  # monotonic timestamps
@@ -96,21 +94,6 @@ class SessionController(QObject):
         self._compare_recs_b: list = []
         self._compare_alignment_map: dict[int, int] = {}
 
-        # Restore persisted state if available
-        self._load_settings(settings or {})
-
-    # ---- persisted settings ----
-
-    def _load_settings(self, settings: dict) -> None:
-        """Restore session state from persisted settings dict."""
-        # Do NOT auto-restore the last session file — always start fresh.
-
-    def collect_settings(self) -> dict:
-        """Return a dict of session state to persist."""
-        return {
-            "session_last_file": self._loaded_file,
-        }
-
     # ---- properties QML binds to ----
     @Property(str, notify=modeChanged)
     def mode(self) -> str: return self._mode
@@ -150,7 +133,7 @@ class SessionController(QObject):
                         "value": round(v, 2), "band": band, "index": i})
         return out
 
-    @Property("QVariantList", notify=sensorsChanged)
+    @Property("QVariantList", notify=sensorsChanged)  # type: ignore[arg-type]
     def sensorLayout(self) -> list:
         """[{label, x, y, side, offset_x, offset_y}] for WaferMapItem.sensors."""
         return [
@@ -175,14 +158,14 @@ class SessionController(QObject):
         """Wafer size in mm."""
         return getattr(self._sensors, "size", 300.0)
 
-    @Property("QVariantList", notify=frameUpdated)
+    @Property("QVariantList", notify=frameUpdated)  # type: ignore[arg-type]
     def sensorValues(self) -> list:
         """[float] in sensor order."""
         if not self._last:
             return []
         return [round(v, 3) for v in self._last.values]
 
-    @Property("QVariantList", notify=frameUpdated)
+    @Property("QVariantList", notify=frameUpdated)  # type: ignore[arg-type]
     def sensorBands(self) -> list:
         """['in_range'|'high'|'low'] in sensor order."""
         if not self._last:
@@ -212,7 +195,7 @@ class SessionController(QObject):
     @Property(str, notify=loadedFileChanged)
     def loadedFile(self) -> str: return self._loaded_file
 
-    @Property("QVariantList", notify=frameUpdated)
+    @Property("QVariantList", notify=frameUpdated)  # type: ignore[arg-type]
     def overriddenSensors(self) -> list[int]:
         """Indices of sensors that currently have a replacement or offset."""
         return self._sensor_editor.active_indices()
@@ -221,7 +204,7 @@ class SessionController(QObject):
     def clusterAveragingEnabled(self) -> bool:
         return self._cluster_averaging_enabled
 
-    @clusterAveragingEnabled.setter
+    @clusterAveragingEnabled.setter  # type: ignore[no-redef]
     def clusterAveragingEnabled(self, value: bool) -> None:
         if self._cluster_averaging_enabled == value:
             return
@@ -319,7 +302,6 @@ class SessionController(QObject):
         for frame in self._player._frames:
             self._stats_tracker.track(frame.seq, frame.values)
         self.trendData.emit(json.dumps(self._stats_tracker.get_trend()))
-        self.settingsChanged.emit()
 
     @Slot()
     @slot_error_boundary
@@ -331,7 +313,6 @@ class SessionController(QObject):
         self._loaded_file = ""
         self.loadedFileChanged.emit()
         self.sensorsChanged.emit()
-        self.settingsChanged.emit()
 
     # ---- comparison: DTW between two CSV files ----
     @Slot(str, str)

src/pygui/backend/crypto/__init__.py

@@ -1,2 +0,0 @@
-# ===== Crypto Sub-package =====
-from pygui.backend.crypto.crypto_helper import *  # noqa: F403

src/pygui/backend/data/__init__.py

@@ -1,14 +0,0 @@
-# ===== Data Sub-package =====
-from pygui.backend.data.csv_file_metadata import CSVFileMetadata
-from pygui.backend.data.csv_recorder import CsvRecorder
-from pygui.backend.data.data_records import is_official_csv, read_data_records, read_official_csv
-from pygui.backend.data.file_browser import FileBrowser
-from pygui.backend.data.local_settings import LocalSettings
-from pygui.backend.data.local_settings_model import LocalSettingsModel
-
-__all__ = [
-    "CsvRecorder", "CSVFileMetadata",
-    "read_data_records", "is_official_csv", "read_official_csv",
-    "FileBrowser",
-    "LocalSettings", "LocalSettingsModel",
-]

src/pygui/backend/data/constants.py

@@ -1,3 +1,14 @@
 # ===== Backend Data Constants =====
 
+from pathlib import Path
+
+from PySide6.QtCore import QStandardPaths
+
 DEFAULT_DATA_DIR_NAME = "isc_data"
+
+
+def default_data_dir() -> Path:
+    """Documents-folder isc_data directory used as the default app data location."""
+    documents_dir = QStandardPaths.writableLocation(QStandardPaths.StandardLocation.DocumentsLocation)
+    base_dir = Path(documents_dir) if documents_dir else (Path.home() / "Documents")
+    return base_dir / DEFAULT_DATA_DIR_NAME

src/pygui/backend/data/csv_file_metadata.py

@@ -19,8 +19,8 @@ class CSVFileMetadata:
         """Return the first character of the wafer string, or empty if none"""
         return self.wafer[0] if self.wafer else ""
 
-    def get_date(self) -> datetime:
-        """Parsifes the date string. Returns current time if parsing fails"""
+    def get_date(self) -> datetime | None:
+        """Parsifes the date string. Returns None if parsing fails"""
         date_format = "%Y-%m-%d %H:%M:%S"
         try:
             return datetime.strptime(self.date, date_format)

src/pygui/backend/data/csv_recorder.py

@@ -1,4 +1,5 @@
 """Append live frames"""
+
 from __future__ import annotations
 
 from datetime import datetime
@@ -12,17 +13,15 @@ from pygui.backend.wafer.zwafer_models import Sensor
 class CsvRecorder:
     def __init__(self) -> None:
         self._file_handle: Optional[TextIO] = None
-        self._oath: Optional[str] = None
-
+        self._path: Optional[str] = None
 
     @property
     def is_recording(self) -> bool:
         return self._file_handle is not None
 
-
-    def start(self, path: str, sensors:list[Sensor], serial: str = "") -> None:
+    def start(self, path: str, sensors: list[Sensor], serial: str = "") -> None:
         Path(path).parent.mkdir(parents=True, exist_ok=True)
-        file_handle = open(path, "w", encoding="utf-8", newline ="")
+        file_handle = open(path, "w", encoding="utf-8", newline="")
         file_handle.write(f"Wafer ID={serial}\n")
         file_handle.write(f"Acquisition Date={datetime.now():%m/%d/%Y}\n")
         file_handle.write("Label," + ",".join(s.label for s in sensors) + "\n")
@@ -65,21 +64,11 @@ class CsvRecorder:
         Returns:
             True on success (at least one frame written).
         """
-        from pygui.backend.data.data_records import is_official_csv
+        from pygui.backend.data.data_records import is_data_row, is_official_csv
 
         if start_frame < 0 or end_frame < start_frame:
             return False
 
-        def _is_data_row(stripped: str) -> bool:
-            cols = [c.strip() for c in stripped.split(",") if c.strip()]
-            if not cols:
-                return False
-            try:
-                [float(c) for c in cols]
-            except ValueError:
-                return False
-            return True
-
         with open(source_path, "r", encoding="utf-8") as f:
             lines = f.readlines()
 
@@ -99,7 +88,7 @@ class CsvRecorder:
                 # official format: row 0 is the sensor-name header
                 out.append(line)
                 continue
-            if not stripped or not _is_data_row(stripped):
+            if not stripped or not is_data_row(stripped):
                 continue
             frame_idx += 1
             if start_frame <= frame_idx <= end_frame:
@@ -112,4 +101,3 @@ class CsvRecorder:
         with open(file_path, "w", encoding="utf-8", newline="") as f:
             f.writelines(out)
         return True
-

src/pygui/backend/data/data_records.py

@@ -1,4 +1,5 @@
 """Read the data section of a Z-wafer CSV into DataRecords, or the official headerless CSV."""
+
 from __future__ import annotations
 
 from pathlib import Path
@@ -6,6 +7,20 @@ from pathlib import Path
 from pygui.backend.wafer.zwafer_models import DataRecord, Sensor
 
 
+def is_data_row(line: str) -> bool:
+    """True if *line* is a single CSV row of numeric values (no headers/metadata)."""
+    cols = [c.strip() for c in line.split(",") if c.strip() != ""]
+    return bool(cols) and all(_is_float(c) for c in cols)
+
+
+def _is_float(s: str) -> bool:
+    try:
+        float(s)
+    except ValueError:
+        return False
+    return True
+
+
 def read_data_records(file_path: str) -> list[DataRecord]:
     records: list[DataRecord] = []
     in_data = False
@@ -18,13 +33,10 @@ def read_data_records(file_path: str) -> list[DataRecord]:
                 if line.split(",")[0].lower() == "data":
                     in_data = True
                 continue
+            if not is_data_row(line):
+                continue
             cols = [c.strip() for c in line.split(",") if c.strip() != ""]
-            try:
             nums = [float(c) for c in cols]
-            except ValueError:
-                continue
-            if not nums:
-                continue
             records.append(DataRecord(time=nums[0], values=nums[1:]))
         return records
 

src/pygui/backend/data/file_browser.py

@@ -5,10 +5,10 @@ import re
 from datetime import datetime
 from pathlib import Path
 
-from PySide6.QtCore import Property, QObject, QStandardPaths, Signal, Slot
+from PySide6.QtCore import Property, QObject, Signal, Slot
 from PySide6.QtWidgets import QFileDialog, QMessageBox
 
-from pygui.backend.data.constants import DEFAULT_DATA_DIR_NAME
+from pygui.backend.data.constants import default_data_dir
 from pygui.backend.data.csv_file_metadata import CSVFileMetadata
 from pygui.backend.wafer.zwafer_parser import ZWaferParser
 
@@ -28,7 +28,7 @@ class FileBrowser(QObject):
         self._refresh_files(show_empty_message=False)
 
     # ===== Exposed Properties =====
-    @Property("QVariantList", notify=filesChanged)
+    @Property("QVariantList", notify=filesChanged)  # type: ignore[arg-type]
     def files(self) -> list[dict[str, object]]:
         return [dict(row) for row in self._files]
 
@@ -42,7 +42,7 @@ class FileBrowser(QObject):
         selected_dir = QFileDialog.getExistingDirectory(
             None,
             "Select CSV Folder",
-            self.currentDirectory,
+            str(self._current_directory),
         )
         if not selected_dir:
             return
@@ -235,11 +235,7 @@ class FileBrowser(QObject):
 
     # ===== Internal Helpers =====
     def _resolve_default_directory(self) -> Path:
-        documents_dir = QStandardPaths.writableLocation(
-            QStandardPaths.DocumentsLocation
-        )
-        base_dir = Path(documents_dir) if documents_dir else (Path.home() / "Documents")
-        return base_dir / DEFAULT_DATA_DIR_NAME
+        return default_data_dir()
 
     def _set_current_directory(self, directory: Path) -> None:
         normalized = Path(directory)

src/pygui/backend/data/local_settings.py

@@ -13,8 +13,8 @@ class LocalSettings:
         # Configuration settings
         self.chamber_id = ""
         self.reverse_z_wafer = False
-        self.master = {}  # Dict[str, str]
-        self.wafer_data_size = {}  # Dict[str, int]
+        self.master: dict[str, str] = {}
+        self.wafer_data_size: dict[str, int] = {}
         self.debug = False
         self.wafer_read_retries = 8
         # Timeout in msec for reading from the wafer (default 2 min)
@@ -32,9 +32,6 @@ class LocalSettings:
         self.data_col_count = 0
         self.last_csv_path = ""
 
-        # Session persistence
-        self.session_last_file = ""
-
     # ===== File Path Helpers =====
     @classmethod
     def _settings_path(cls, directory: str) -> Path:

src/pygui/backend/data/local_settings_model.py

@@ -2,17 +2,26 @@ from __future__ import annotations
 
 from copy import deepcopy
 from pathlib import Path
-from typing import Any
+from typing import Any, Callable
 
-from PySide6.QtCore import Property, QDateTime, QObject, QStandardPaths, Signal, Slot
+from PySide6.QtCore import Property, QDateTime, QObject, Signal, Slot
 
-from pygui.backend.data.constants import DEFAULT_DATA_DIR_NAME
 from pygui.backend.data.local_settings import LocalSettings
 
 MASTER_FAMILIES = ("A", "B", "C", "D", "E", "F", "P", "X", "Z")
 
 
 class LocalSettingsModel(QObject):
+    # Draft attrs are seeded via setattr() in __init__ from _new_defaults();
+    # declared here so mypy knows their types.
+    _chamber_id: str
+    _reverse_z_wafer: bool
+    _debug_mode: bool
+    _wafer_read_timeout: int
+    _wafer_detect_timeout: int
+    _wafer_retries: int
+    _masters: dict[str, str]
+
     chamberIdChanged = Signal()
     reverseZWaferChanged = Signal()
     debugModeChanged = Signal()
@@ -26,18 +35,35 @@ class LocalSettingsModel(QObject):
     saveStatusChanged = Signal()
     lastSavedAtChanged = Signal()
 
-    def __init__(self, parent: QObject | None = None) -> None:
+    # Draft attr (this class) <-> LocalSettings attr (the shared, persisted
+    # instance also held by DeviceController) <-> coercer applied on both
+    # load and revert/reset. One table drives load/save/revert/reset instead
+    # of four hand-written field-by-field copies.
+    _FIELD_MAP: tuple[tuple[str, str, Callable[[Any], Any]], ...] = (
+        ("_chamber_id", "chamber_id", str),
+        ("_reverse_z_wafer", "reverse_z_wafer", bool),
+        ("_debug_mode", "debug", bool),
+        ("_wafer_read_timeout", "wafer_read_timeout", int),
+        ("_wafer_detect_timeout", "wafer_detect_timeout", int),
+        ("_wafer_retries", "wafer_read_retries", int),
+    )
+
+    def __init__(
+        self,
+        settings: LocalSettings,
+        data_dir: Path | str,
+        parent: QObject | None = None,
+    ) -> None:
         super().__init__(parent)
-        self._data_dir = self._resolve_data_dir()
+        # Shared with DeviceController — saving here must mutate this same
+        # instance, not a throwaway copy, or the device layer keeps using
+        # stale config until restart.
+        self._settings = settings
+        self._data_dir = Path(data_dir)
         self._defaults = self._new_defaults()
 
-        self._chamber_id = self._defaults["chamberId"]
-        self._reverse_z_wafer = self._defaults["reverseZWafer"]
-        self._debug_mode = self._defaults["debugMode"]
-        self._wafer_read_timeout = self._defaults["waferReadTimeout"]
-        self._wafer_detect_timeout = self._defaults["waferDetectTimeout"]
-        self._wafer_retries = self._defaults["waferRetries"]
-        self._masters = deepcopy(self._defaults["masters"])
+        for draft_attr, default_value in self._defaults.items():
+            setattr(self, draft_attr, deepcopy(default_value))
 
         self._is_dirty = False
         self._is_valid = True
@@ -47,34 +73,21 @@ class LocalSettingsModel(QObject):
         self._saved_snapshot = self._snapshot()
         self._recompute_derived()
 
-    def _resolve_data_dir(self) -> Path:
-        documents_dir = QStandardPaths.writableLocation(
-            QStandardPaths.DocumentsLocation
-        )
-        base_dir = Path(documents_dir) if documents_dir else (Path.home() / "Documents")
-        return base_dir / DEFAULT_DATA_DIR_NAME
-
     def _new_defaults(self) -> dict[str, Any]:
         return {
-            "chamberId": "2",
-            "reverseZWafer": False,
-            "debugMode": False,
-            "waferReadTimeout": 120000,
-            "waferDetectTimeout": 5000,
-            "waferRetries": 8,
-            "masters": {family: "" for family in MASTER_FAMILIES},
+            "_chamber_id": "2",
+            "_reverse_z_wafer": False,
+            "_debug_mode": False,
+            "_wafer_read_timeout": 120000,
+            "_wafer_detect_timeout": 5000,
+            "_wafer_retries": 8,
+            "_masters": {family: "" for family in MASTER_FAMILIES},
         }
 
     def _snapshot(self) -> dict[str, Any]:
-        return {
-            "chamberId": self._chamber_id,
-            "reverseZWafer": self._reverse_z_wafer,
-            "debugMode": self._debug_mode,
-            "waferReadTimeout": self._wafer_read_timeout,
-            "waferDetectTimeout": self._wafer_detect_timeout,
-            "waferRetries": self._wafer_retries,
-            "masters": deepcopy(self._masters),
-        }
+        snap = {attr: getattr(self, attr) for attr, _, _ in self._FIELD_MAP}
+        snap["_masters"] = deepcopy(self._masters)
+        return snap
 
     def _set_is_dirty(self, value: bool) -> None:
         if self._is_dirty != value:
@@ -137,22 +150,19 @@ class LocalSettingsModel(QObject):
         self.waferRetriesChanged.emit()
         self.mastersChanged.emit()
 
-    def _to_local_settings(self) -> LocalSettings:
-        settings = LocalSettings()
-        settings.chamber_id = self._chamber_id
-        settings.reverse_z_wafer = self._reverse_z_wafer
-        settings.debug = self._debug_mode
-        settings.wafer_read_timeout = self._wafer_read_timeout
-        settings.wafer_detect_timeout = self._wafer_detect_timeout
-        settings.wafer_read_retries = self._wafer_retries
-        settings.master = deepcopy(self._masters)
-        return settings
+    def _normalized_masters(self, source: dict[str, str]) -> dict[str, str]:
+        masters = {family: "" for family in MASTER_FAMILIES}
+        for family, value in source.items():
+            normalized = str(family).strip().upper()
+            if normalized in masters:
+                masters[normalized] = str(value).strip()
+        return masters
 
     @Property(str, notify=chamberIdChanged)
     def chamberId(self) -> str:
         return self._chamber_id
 
-    @chamberId.setter
+    @chamberId.setter  # type: ignore[no-redef]
     def chamberId(self, value: str) -> None:
         next_value = str(value).strip()
         if self._chamber_id == next_value:
@@ -165,7 +175,7 @@ class LocalSettingsModel(QObject):
     def reverseZWafer(self) -> bool:
         return self._reverse_z_wafer
 
-    @reverseZWafer.setter
+    @reverseZWafer.setter  # type: ignore[no-redef]
     def reverseZWafer(self, value: bool) -> None:
         if self._reverse_z_wafer == value:
             return
@@ -177,7 +187,7 @@ class LocalSettingsModel(QObject):
     def debugMode(self) -> bool:
         return self._debug_mode
 
-    @debugMode.setter
+    @debugMode.setter  # type: ignore[no-redef]
     def debugMode(self, value: bool) -> None:
         if self._debug_mode == value:
             return
@@ -189,7 +199,7 @@ class LocalSettingsModel(QObject):
     def waferReadTimeout(self) -> int:
         return self._wafer_read_timeout
 
-    @waferReadTimeout.setter
+    @waferReadTimeout.setter  # type: ignore[no-redef]
     def waferReadTimeout(self, value: int) -> None:
         if self._wafer_read_timeout == value:
             return
@@ -201,7 +211,7 @@ class LocalSettingsModel(QObject):
     def waferDetectTimeout(self) -> int:
         return self._wafer_detect_timeout
 
-    @waferDetectTimeout.setter
+    @waferDetectTimeout.setter  # type: ignore[no-redef]
     def waferDetectTimeout(self, value: int) -> None:
         if self._wafer_detect_timeout == value:
             return
@@ -213,7 +223,7 @@ class LocalSettingsModel(QObject):
     def waferRetries(self) -> int:
         return self._wafer_retries
 
-    @waferRetries.setter
+    @waferRetries.setter  # type: ignore[no-redef]
     def waferRetries(self, value: int) -> None:
         if self._wafer_retries == value:
             return
@@ -251,22 +261,11 @@ class LocalSettingsModel(QObject):
 
     @Slot()
     def loadSettings(self) -> None:
-        loaded = LocalSettings.read_settings(str(self._data_dir))
-        self._chamber_id = str(loaded.chamber_id).strip() or str(
-            self._defaults["chamberId"]
-        )
-        self._reverse_z_wafer = bool(loaded.reverse_z_wafer)
-        self._debug_mode = bool(loaded.debug)
-        self._wafer_read_timeout = int(loaded.wafer_read_timeout)
-        self._wafer_detect_timeout = int(loaded.wafer_detect_timeout)
-        self._wafer_retries = int(loaded.wafer_read_retries)
-
-        masters = {family: "" for family in MASTER_FAMILIES}
-        for family, value in loaded.master.items():
-            normalized = str(family).strip().upper()
-            if normalized in masters:
-                masters[normalized] = str(value).strip()
-        self._masters = masters
+        """Seed draft fields from the shared LocalSettings instance."""
+        for draft_attr, settings_attr, coerce in self._FIELD_MAP:
+            setattr(self, draft_attr, coerce(getattr(self._settings, settings_attr)))
+        self._chamber_id = self._chamber_id.strip() or str(self._defaults["_chamber_id"])
+        self._masters = self._normalized_masters(self._settings.master)
 
         self._saved_snapshot = self._snapshot()
         self._emit_all_changed()
@@ -275,13 +274,18 @@ class LocalSettingsModel(QObject):
 
     @Slot()
     def saveSettings(self) -> None:
+        """Write draft fields onto the shared LocalSettings instance and persist it."""
         self._recompute_derived()
         if not self._is_valid:
             self._set_save_status("error: invalid settings")
             return
 
         try:
-            LocalSettings.save_settings(str(self._data_dir), self._to_local_settings())
+            for draft_attr, settings_attr, _coerce in self._FIELD_MAP:
+                setattr(self._settings, settings_attr, getattr(self, draft_attr))
+            self._settings.master = deepcopy(self._masters)
+            LocalSettings.save_settings(str(self._data_dir), self._settings)
+
             self._saved_snapshot = self._snapshot()
             self._recompute_derived()
             self._set_save_status("Saved")
@@ -293,13 +297,9 @@ class LocalSettingsModel(QObject):
     @Slot()
     def revertChanges(self) -> None:
         snap = self._saved_snapshot
-        self._chamber_id = str(snap["chamberId"])
-        self._reverse_z_wafer = bool(snap["reverseZWafer"])
-        self._debug_mode = bool(snap["debugMode"])
-        self._wafer_read_timeout = int(snap["waferReadTimeout"])
-        self._wafer_detect_timeout = int(snap["waferDetectTimeout"])
-        self._wafer_retries = int(snap["waferRetries"])
-        self._masters = deepcopy(snap["masters"])
+        for draft_attr, _settings_attr, coerce in self._FIELD_MAP:
+            setattr(self, draft_attr, coerce(snap[draft_attr]))
+        self._masters = deepcopy(snap["_masters"])
 
         self._emit_all_changed()
         self._recompute_derived()
@@ -307,13 +307,9 @@ class LocalSettingsModel(QObject):
 
     @Slot()
     def resetDefaults(self) -> None:
-        self._chamber_id = str(self._defaults["chamberId"])
-        self._reverse_z_wafer = bool(self._defaults["reverseZWafer"])
-        self._debug_mode = bool(self._defaults["debugMode"])
-        self._wafer_read_timeout = int(self._defaults["waferReadTimeout"])
-        self._wafer_detect_timeout = int(self._defaults["waferDetectTimeout"])
-        self._wafer_retries = int(self._defaults["waferRetries"])
-        self._masters = deepcopy(self._defaults["masters"])
+        for draft_attr, _settings_attr, coerce in self._FIELD_MAP:
+            setattr(self, draft_attr, coerce(self._defaults[draft_attr]))
+        self._masters = deepcopy(self._defaults["_masters"])
 
         self._emit_all_changed()
         self._recompute_derived()

src/pygui/backend/license/__init__.py

@@ -1,15 +0,0 @@
-from pygui.backend.license.license_manager import (
-    LICENSE_FILENAME_RE,
-    License,
-    parse_license_blob,
-    read_license_files,
-)
-from pygui.backend.license.license_model import LicenseModel
-
-__all__ = [
-    "LICENSE_FILENAME_RE",
-    "License",
-    "LicenseModel",
-    "parse_license_blob",
-    "read_license_files",
-]

src/pygui/backend/license/license_model.py

@@ -50,7 +50,7 @@ class LicenseModel(QObject):
         self.refresh()
 
     # ── Grid rows ─────────────────────────────────────────────────────
-    @Property("QVariantList", notify=licensesChanged)
+    @Property("QVariantList", notify=licensesChanged)  # type: ignore[arg-type]
     def licenses(self) -> list:
         """Rows for the About grid: serial, mfg date, level, license date."""
         return [

src/pygui/backend/models/__init__.py

@@ -1,19 +0,0 @@
-# ===== Models Sub-package =====
-from pygui.backend.models.data_model import TemperatureTableModel
-from pygui.backend.models.frame import Frame
-from pygui.backend.models.frame_player import FramePlayer, frames_from_wafer_data
-from pygui.backend.models.frame_stats import Stats, compute_stats
-from pygui.backend.models.sensor_editor import SensorEditor
-from pygui.backend.models.session_model import SessionModel, SessionUpdate
-from pygui.backend.models.stability_detector import StabilityDetector
-from pygui.backend.models.threshold_classifier import ThresholdConfig, classify, resolve_bounds
-
-__all__ = [
-    "Frame", "FramePlayer", "frames_from_wafer_data",
-    "Stats", "compute_stats",
-    "SessionModel", "SessionUpdate",
-    "TemperatureTableModel",
-    "SensorEditor",
-    "ThresholdConfig", "classify", "resolve_bounds",
-    "StabilityDetector",
-]

src/pygui/backend/models/data_model.py

@@ -55,7 +55,7 @@ class TemperatureTableModel(QAbstractTableModel):
         # Column 0 = row index, columns 1..N = sensor values
         return self._col_count + 1
 
-    def data(self, index: Any, role: int = ...) -> Any:
+    def data(self, index: Any, role: int = ...) -> Any:  # type: ignore[assignment]
         if not index.isValid():
             return None
 
@@ -73,7 +73,7 @@ class TemperatureTableModel(QAbstractTableModel):
         return None
 
     def headerData(
-        self, section: int, orientation: int, role: int = ...
+        self, section: int, orientation: Qt.Orientation, role: int = ...  # type: ignore[assignment]
     ) -> Any:
         if role != Qt.ItemDataRole.DisplayRole:
             return None

src/pygui/backend/models/frame_player.py

@@ -4,7 +4,7 @@ from pygui.backend.models.frame import Frame
 from pygui.backend.wafer.zwafer_models import ZWaferData
 
 
-def frames_from_wafer_data(data: ZWaferData, records) -> list[Frame]:
+def frames_from_wafer_data(data: ZWaferData | None, records) -> list[Frame]:
     """Build Frames from parsed DataRecords (records = list[DataRecord].)"""
     return [Frame(seq=i, time=r.time, values=list(r.values)) for i, r in enumerate(records)]
 

src/pygui/backend/visualization/__init__.py

@@ -1,11 +0,0 @@
-# ===== Visualization Sub-package =====
-from pygui.backend.visualization.graph_quick_item import GraphQuickItem
-from pygui.backend.visualization.graph_view import GraphView
-from pygui.backend.visualization.rbf_heatmap import interpolate_field
-from pygui.backend.visualization.trend_chart_item import TrendChartItem
-from pygui.backend.visualization.wafer_map_item import WaferMapItem
-
-__all__ = [
-    "GraphQuickItem", "GraphView", "TrendChartItem", "WaferMapItem",
-    "interpolate_field",
-]

src/pygui/backend/visualization/chart_geometry.py

@@ -0,0 +1,33 @@
+"""Pure coordinate-mapping math shared by the QQuickPaintedItem chart items
+(GraphQuickItem, TrendChartItem). No QPainter or Qt-widget dependency, so
+it's testable without a GUI — unlike the paint() methods that call it.
+"""
+from __future__ import annotations
+
+
+def value_to_pixel(
+    value: float,
+    value_min: float,
+    value_max: float,
+    pixel_start: float,
+    pixel_span: float,
+) -> float:
+    """Map a value onto a pixel range, inverted so larger values sit at
+    smaller pixel coordinates (screen y grows downward).
+
+    Also used for evenly-spaced tick indices: pass the tick index as
+    `value` and `(tick_count - 1)` as `value_max` with `value_min=0`.
+    """
+    value_range = value_max - value_min
+    if value_range < 1e-9:
+        return pixel_start + pixel_span / 2
+    fraction = 1.0 - (value - value_min) / value_range
+    return pixel_start + fraction * pixel_span
+
+
+def index_to_pixel(index: float, count: int, pixel_start: float, pixel_span: float) -> float:
+    """Map a 0-based sample index onto a pixel range, left to right."""
+    if count <= 1:
+        return pixel_start + pixel_span / 2
+    fraction = index / (count - 1)
+    return pixel_start + fraction * pixel_span

src/pygui/backend/visualization/graph_quick_item.py

@@ -26,6 +26,8 @@ from PySide6.QtGui import QColor, QFont, QFontMetrics, QPainter, QPen
 from PySide6.QtQml import QmlElement
 from PySide6.QtQuick import QQuickPaintedItem
 
+from pygui.backend.visualization.chart_geometry import index_to_pixel, value_to_pixel
+
 QML_IMPORT_NAME = "ISC.Wafer"
 QML_IMPORT_MAJOR_VERSION = 1
 
@@ -78,7 +80,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def seriesData(self) -> list:
         return self._series_data
 
-    @seriesData.setter
+    @seriesData.setter  # type: ignore[no-redef]
     def seriesData(self, val: list) -> None:
         self._series_data = [list(s) for s in (val or [])]
         self._auto_range()
@@ -89,7 +91,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def sensorNames(self) -> list:
         return self._sensor_names
 
-    @sensorNames.setter
+    @sensorNames.setter  # type: ignore[no-redef]
     def sensorNames(self, val: list) -> None:
         self._sensor_names = list(val or [])
         self.sensorNamesChanged.emit()
@@ -99,7 +101,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def title(self) -> str:
         return self._title
 
-    @title.setter
+    @title.setter  # type: ignore[no-redef]
     def title(self, val: str) -> None:
         self._title = str(val or "")
         self.titleChanged.emit()
@@ -109,7 +111,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def xLabel(self) -> str:
         return self._x_label
 
-    @xLabel.setter
+    @xLabel.setter  # type: ignore[no-redef]
     def xLabel(self, val: str) -> None:
         self._x_label = str(val or "")
         self.xLabelChanged.emit()
@@ -119,7 +121,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def yLabel(self) -> str:
         return self._y_label
 
-    @yLabel.setter
+    @yLabel.setter  # type: ignore[no-redef]
     def yLabel(self, val: str) -> None:
         self._y_label = str(val or "")
         self.yLabelChanged.emit()
@@ -129,7 +131,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def showLegend(self) -> bool:
         return self._show_legend
 
-    @showLegend.setter
+    @showLegend.setter  # type: ignore[no-redef]
     def showLegend(self, val: bool) -> None:
         self._show_legend = bool(val)
         self.colorsChanged.emit()
@@ -141,7 +143,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def backgroundColor(self) -> QColor:
         return self._bg_color
 
-    @backgroundColor.setter
+    @backgroundColor.setter  # type: ignore[no-redef]
     def backgroundColor(self, c: QColor) -> None:
         self._bg_color = c
         self.update()
@@ -150,7 +152,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def gridColor(self) -> QColor:
         return self._grid_color
 
-    @gridColor.setter
+    @gridColor.setter  # type: ignore[no-redef]
     def gridColor(self, c: QColor) -> None:
         self._grid_color = c
         self.update()
@@ -159,7 +161,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def axisColor(self) -> QColor:
         return self._axis_color
 
-    @axisColor.setter
+    @axisColor.setter  # type: ignore[no-redef]
     def axisColor(self, c: QColor) -> None:
         self._axis_color = c
         self.update()
@@ -168,7 +170,7 @@ class GraphQuickItem(QQuickPaintedItem):
     def textColor(self) -> QColor:
         return self._text_color
 
-    @textColor.setter
+    @textColor.setter  # type: ignore[no-redef]
     def textColor(self, c: QColor) -> None:
         self._text_color = c
         self.update()
@@ -178,7 +180,7 @@ class GraphQuickItem(QQuickPaintedItem):
         """Return hex strings of the current series color palette."""
         return [c.name() for c in self._series_colors]
 
-    @seriesColors.setter
+    @seriesColors.setter  # type: ignore[no-redef]
     def seriesColors(self, hex_list: list) -> None:
         colors = []
         for h in (hex_list or []):
@@ -275,8 +277,7 @@ class GraphQuickItem(QQuickPaintedItem):
 
         for i in range(n_y_ticks):
             y_val = self._min_y + i * y_step
-            y_frac = 1.0 - (i / (n_y_ticks - 1)) if n_y_ticks > 1 else 0.5
-            y_px = plot_top + y_frac * plot_h
+            y_px = value_to_pixel(i, 0, n_y_ticks - 1, plot_top, plot_h)
 
             # Grid line
             painter.setPen(grid_pen)
@@ -325,8 +326,7 @@ class GraphQuickItem(QQuickPaintedItem):
             x_tick_step = (num_points - 1) / max(1, n_x_ticks - 1)
             for i in range(n_x_ticks):
                 idx = int(round(i * x_tick_step))
-                x_frac = idx / (num_points - 1)
-                x_px = plot_left + x_frac * plot_w
+                x_px = index_to_pixel(idx, num_points, plot_left, plot_w)
                 painter.setPen(axis_pen)
                 painter.drawText(
                     int(x_px - 12), int(plot_top + plot_h + 14),
@@ -358,10 +358,8 @@ class GraphQuickItem(QQuickPaintedItem):
                     v = float(val)
                 except (ValueError, TypeError):
                     continue
-                x_frac = i / (max_len - 1) if max_len > 1 else 0.5
-                y_frac = 1.0 - ((v - self._min_y) / y_range) if y_range > 0 else 0.5
-                x_px = plot_left + x_frac * plot_w
-                y_px = plot_top + y_frac * plot_h
+                x_px = index_to_pixel(i, max_len, plot_left, plot_w)
+                y_px = value_to_pixel(v, self._min_y, self._max_y, plot_top, plot_h)
                 pts.append((x_px, y_px))
 
             if len(pts) < 2:

src/pygui/backend/visualization/graph_view.py

@@ -23,6 +23,9 @@ class GraphView(QObject):
     each sensor as a separate line series.
     """
 
+    # Set lazily in updateTrend (guarded by hasattr); declared for mypy.
+    _trend_line: Any
+
     # ---- signals ----
     dataReady = Signal(object)  # {"success": bool, "sensory_names": list, "series": list}
 
@@ -227,7 +230,7 @@ class GraphView(QObject):
             index_a, index_b = path[i]
             if index_a < len(a) and index_b < len(b):
                 line = pg.InfiniteLine(pos=index_a, angle=90, pen=pg.mkPen("#666666", width=1,
-                style=Qt.DashLine))
+                style=Qt.PenStyle.DashLine))
                 self._plot_widget.addItem(line)
 
             self._plot_widget.setTitle("DTW Comparison")

src/pygui/backend/visualization/rbf_heatmap.py

@@ -73,7 +73,8 @@ def interpolate_field(
         dist = ((grid_x - cx) / rx) ** 2 + ((grid_y - cy) / ry) ** 2
         field = np.where(dist <= 1.0, field, np.nan)
 
-    return field.astype(np.float64)
+    result: np.ndarray = field.astype(np.float64)
+    return result
 
 
 def refine_field(field: np.ndarray, factor: int = REFINE_FACTOR) -> np.ndarray:
@@ -84,7 +85,8 @@ def refine_field(field: np.ndarray, factor: int = REFINE_FACTOR) -> np.ndarray:
     resampling across a NaN/zero-filled hole rings at the boundary, and any
     mask derived from the coarse grid keeps its staircase when upscaled.
     """
-    return _ndi_zoom(field, factor, order=3)
+    refined: np.ndarray = _ndi_zoom(field, factor, order=3)
+    return refined
 
 
 def ellipse_alpha(height: int, width: int, feather_px: float = 1.2) -> np.ndarray:

src/pygui/backend/visualization/trend_chart_item.py

@@ -20,6 +20,8 @@ from PySide6.QtGui import QColor, QFont, QPainter, QPen, QPolygon
 from PySide6.QtQml import QmlElement
 from PySide6.QtQuick import QQuickPaintedItem
 
+from pygui.backend.visualization.chart_geometry import index_to_pixel, value_to_pixel
+
 log = logging.getLogger(__name__)
 
 QML_IMPORT_NAME = "ISC.Wafer"
@@ -60,7 +62,7 @@ class TrendChartItem(QQuickPaintedItem):
     def data(self) -> list[float]:
         return self._data
 
-    @data.setter
+    @data.setter  # type: ignore[no-redef]
     def data(self, val) -> None:
         coerced = self._coerce_floats(val)
         if coerced == self._data:
@@ -82,7 +84,7 @@ class TrendChartItem(QQuickPaintedItem):
     def lineColor(self) -> QColor:
         return self._line_color
 
-    @lineColor.setter
+    @lineColor.setter  # type: ignore[no-redef]
     def lineColor(self, c: QColor) -> None:
         if c == self._line_color:
             return
@@ -94,7 +96,7 @@ class TrendChartItem(QQuickPaintedItem):
     def gridColor(self) -> QColor:
         return self._grid_color
 
-    @gridColor.setter
+    @gridColor.setter  # type: ignore[no-redef]
     def gridColor(self, c: QColor) -> None:
         if c == self._grid_color:
             return
@@ -106,7 +108,7 @@ class TrendChartItem(QQuickPaintedItem):
     def textColor(self) -> QColor:
         return self._text_color
 
-    @textColor.setter
+    @textColor.setter  # type: ignore[no-redef]
     def textColor(self, c: QColor) -> None:
         if c == self._text_color:
             return
@@ -118,7 +120,7 @@ class TrendChartItem(QQuickPaintedItem):
     def padding(self) -> int:
         return self._padding
 
-    @padding.setter
+    @padding.setter  # type: ignore[no-redef]
     def padding(self, val: int) -> None:
         v = max(0, int(val))
         if v == self._padding:
@@ -201,15 +203,10 @@ class TrendChartItem(QQuickPaintedItem):
         return math.floor(lo / step) * step, math.ceil(hi / step) * step
 
     def _x_to_px(self, i: int, n: int, plot_rect: QRectF) -> float:
-        if n <= 1:
-            return plot_rect.left()
-        return plot_rect.left() + (i / (n - 1)) * plot_rect.width()
+        return index_to_pixel(i, n, plot_rect.left(), plot_rect.width())
 
     def _y_to_px(self, v: float, y_min: float, y_max: float, plot_rect: QRectF) -> float:
-        if y_max - y_min < 1e-9:
-            return plot_rect.center().y()
-        t = (v - y_min) / (y_max - y_min)
-        return plot_rect.bottom() - t * plot_rect.height()
+        return value_to_pixel(v, y_min, y_max, plot_rect.top(), plot_rect.height())
 
     def _draw_grid(self, painter: QPainter, plot_rect: QRectF) -> None:
         pen = QPen(self._grid_color)

src/pygui/backend/visualization/wafer_map_item.py

@@ -107,7 +107,7 @@ class WaferMapItem(QQuickPaintedItem):
     def sensors(self) -> list:
         return [{"label": s.label, "x": s.x, "y": s.y} for s in self._sensors]
 
-    @sensors.setter
+    @sensors.setter  # type: ignore[no-redef]
     def sensors(self, val: list) -> None:
         self._sensors = [
             Sensor(
@@ -127,7 +127,7 @@ class WaferMapItem(QQuickPaintedItem):
     def values(self) -> list:
         return self._values
 
-    @values.setter
+    @values.setter  # type: ignore[no-redef]
     def values(self, val: list) -> None:
         self._values = list(val or [])
         self._rebuild_heatmap()
@@ -138,7 +138,7 @@ class WaferMapItem(QQuickPaintedItem):
     def bands(self) -> list:
         return self._bands
 
-    @bands.setter
+    @bands.setter  # type: ignore[no-redef]
     def bands(self, val: list) -> None:
         self._bands = list(val or [])
         self.bandsChanged.emit()
@@ -148,7 +148,7 @@ class WaferMapItem(QQuickPaintedItem):
     def target(self) -> float:
         return self._target
 
-    @target.setter
+    @target.setter  # type: ignore[no-redef]
     def target(self, val: float) -> None:
         self._target = float(val)
         self._rebuild_heatmap()
@@ -159,7 +159,7 @@ class WaferMapItem(QQuickPaintedItem):
     def margin(self) -> float:
         return self._margin
 
-    @margin.setter
+    @margin.setter  # type: ignore[no-redef]
     def margin(self, val: float) -> None:
         self._margin = float(val)
         self._rebuild_heatmap()
@@ -170,7 +170,7 @@ class WaferMapItem(QQuickPaintedItem):
     def blend(self) -> float:
         return self._blend
 
-    @blend.setter
+    @blend.setter  # type: ignore[no-redef]
     def blend(self, val: float) -> None:
         self._blend = max(0.0, min(1.0, float(val)))
         if self._blend > 0 and self._heatmap is None:
@@ -182,7 +182,7 @@ class WaferMapItem(QQuickPaintedItem):
     def showLabels(self) -> bool:
         return self._show_labels
 
-    @showLabels.setter
+    @showLabels.setter  # type: ignore[no-redef]
     def showLabels(self, val: bool) -> None:
         self._show_labels = bool(val)
         self.showLabelsChanged.emit()
@@ -192,7 +192,7 @@ class WaferMapItem(QQuickPaintedItem):
     def shape(self) -> str:
         return self._shape
 
-    @shape.setter
+    @shape.setter  # type: ignore[no-redef]
     def shape(self, val: str) -> None:
         self._shape = str(val).lower()
         self._rebuild()
@@ -202,7 +202,7 @@ class WaferMapItem(QQuickPaintedItem):
     def size(self) -> float:
         return self._size
 
-    @size.setter
+    @size.setter  # type: ignore[no-redef]
     def size(self, val: float) -> None:
         self._size = float(val)
         self._rebuild()
@@ -212,7 +212,7 @@ class WaferMapItem(QQuickPaintedItem):
     def thicknessData(self) -> list:
         return self._thickness_data
 
-    @thicknessData.setter
+    @thicknessData.setter  # type: ignore[no-redef]
     def thicknessData(self, val:list) -> None:
         self._thickness_data = list(val or [])
         self._rebuild_thickness()
@@ -223,7 +223,7 @@ class WaferMapItem(QQuickPaintedItem):
     def showThickness(self) -> bool:
         return self._show_thickness
 
-    @showThickness.setter
+    @showThickness.setter  # type: ignore[no-redef]
     def showThickness(self, val: bool) -> None:
         self._show_thickness = bool(val)
         self.showThicknessChanged.emit()
@@ -233,7 +233,7 @@ class WaferMapItem(QQuickPaintedItem):
     def hoveredIndex(self) -> int:
         return self._hovered_index
 
-    @hoveredIndex.setter
+    @hoveredIndex.setter  # type: ignore[no-redef]
     def hoveredIndex(self, val: int) -> None:
         val = int(val)
         if val == self._hovered_index:
@@ -246,7 +246,7 @@ class WaferMapItem(QQuickPaintedItem):
     def hoverScale(self) -> float:
         return self._hover_scale
 
-    @hoverScale.setter
+    @hoverScale.setter  # type: ignore[no-redef]
     def hoverScale(self, val: float) -> None:
         self._hover_scale = float(val)
         self.hoverScaleChanged.emit()
@@ -255,32 +255,32 @@ class WaferMapItem(QQuickPaintedItem):
     # Colour properties — QML can bind these to Theme tokens
     @Property(QColor, notify=colorsChanged)
     def ringColor(self) -> QColor: return self._ring_color
-    @ringColor.setter
+    @ringColor.setter  # type: ignore[no-redef]
     def ringColor(self, c: QColor) -> None: self._ring_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def axisColor(self) -> QColor: return self._axis_color
-    @axisColor.setter
+    @axisColor.setter  # type: ignore[no-redef]
     def axisColor(self, c: QColor) -> None: self._axis_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def lowColor(self) -> QColor: return self._low_color
-    @lowColor.setter
+    @lowColor.setter  # type: ignore[no-redef]
     def lowColor(self, c: QColor) -> None: self._low_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def inRangeColor(self) -> QColor: return self._in_range_color
-    @inRangeColor.setter
+    @inRangeColor.setter  # type: ignore[no-redef]
     def inRangeColor(self, c: QColor) -> None: self._in_range_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def highColor(self) -> QColor: return self._high_color
-    @highColor.setter
+    @highColor.setter  # type: ignore[no-redef]
     def highColor(self, c: QColor) -> None: self._high_color = c; self.update()
 
     @Property(QColor, notify=colorsChanged)
     def textColor(self) -> QColor: return self._text_color
-    @textColor.setter
+    @textColor.setter  # type: ignore[no-redef]
     def textColor(self, c: QColor) -> None: self._text_color = c; self.update()
 
     # ── slots ─────────────────────────────────────────────────────────────
@@ -314,7 +314,7 @@ class WaferMapItem(QQuickPaintedItem):
             return False
         try:
             result = self.grabToImage()
-            img = result.image()
+            img = result.image()  # type: ignore[attr-defined]
             img.save(file_path, "PNG")
             return True
         except Exception as e:
@@ -702,11 +702,11 @@ class WaferMapItem(QQuickPaintedItem):
                 painter.setPen(QPen(self._text_color))
                 y1 = ly + id_ascent
                 if side in ("top", "bottom"):
-                    painter.drawText(lx + (text_w - id_w) // 2, y1, id_text)
+                    painter.drawText(lx + (text_w - id_w) // 2, y1, id_text)  # type: ignore[arg-type]
                 elif side == "left":
-                    painter.drawText(lx + (text_w - id_w), y1, id_text)
+                    painter.drawText(lx + (text_w - id_w), y1, id_text)  # type: ignore[arg-type]
                 else:
-                    painter.drawText(lx, y1, id_text)
+                    painter.drawText(lx, y1, id_text)  # type: ignore[arg-type]
 
                 # Draw Temperature (second line)
                 if has_temp:
@@ -714,8 +714,8 @@ class WaferMapItem(QQuickPaintedItem):
                     painter.setPen(QPen(color))
                     y2 = ly + id_line_h + temp_ascent
                     if side in ("top", "bottom"):
-                        painter.drawText(lx + (text_w - temp_w) // 2, y2, temp_text)
+                        painter.drawText(lx + (text_w - temp_w) // 2, y2, temp_text)  # type: ignore[arg-type]
                     elif side == "left":
-                        painter.drawText(lx + (text_w - temp_w), y2, temp_text)
+                        painter.drawText(lx + (text_w - temp_w), y2, temp_text)  # type: ignore[arg-type]
                     else:
-                        painter.drawText(lx, y2, temp_text)
+                        painter.drawText(lx, y2, temp_text)  # type: ignore[arg-type]

src/pygui/backend/wafer/__init__.py

@@ -1,12 +0,0 @@
-# ===== Wafer Sub-package =====
-from pygui.backend.wafer.family_spec import sensor_count_for
-from pygui.backend.wafer.wafer_layouts import available_families, load_layout
-from pygui.backend.wafer.zwafer_models import DataRecord, Sensor, ZWaferData
-from pygui.backend.wafer.zwafer_parser import ZWaferParser
-
-__all__ = [
-    "ZWaferData", "Sensor", "DataRecord",
-    "ZWaferParser",
-    "load_layout", "available_families",
-    "sensor_count_for",
-]

src/pygui/backend/wafer/wafer_layouts.py

@@ -66,7 +66,8 @@ def _family_name(raw_name: str) -> str:
 
 def _load_yaml(path: Path) -> dict:
     with path.open(encoding="utf-8") as f:
-        return yaml.safe_load(f)
+        loaded: dict = yaml.safe_load(f)
+        return loaded
 
 
 # TODO P6.3: expose this list to a new LayoutSelector.qml (4-button chooser)

src/pygui/backend/wafer/zwafer_parser.py

@@ -115,7 +115,7 @@ class ZWaferParser:
         y_coords: Optional[list],
     ) -> None:
         """Build sensor list from layout arrays."""
-        if not all([labels, x_coords, y_coords]):
+        if not (labels and x_coords and y_coords):
             raise ValueError("Sensor layout section is incomplete or missing.")
 
         if len(labels) != len(x_coords) or len(labels) != len(y_coords):

src/pygui/serialcomm/data_parser.py

@@ -10,6 +10,7 @@ Mirrors the C# Form1.cs binary parsing pipeline:
 
 import logging
 import os
+from datetime import datetime
 from typing import Optional
 
 from pygui.backend.wafer.family_spec import sensor_count_for
@@ -266,7 +267,6 @@ def save_to_csv(
     try:
         os.makedirs(output_dir, exist_ok=True)
         # Build filename: P00001-20260505_133045.csv
-        from datetime import datetime
 
         timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
         filename = f"{serial_number}-{timestamp}.csv"

src/pygui/serialcomm/stream_reader.py

@@ -45,7 +45,7 @@ class StreamReader:
         Reads up to 256 bytes in one shot. If nothing is immediately
         available, yields briefly to avoid a busy spin.
         """
-        chunk = self._transport.read(max(min_bytes, 256))
+        chunk: bytes = self._transport.read(max(min_bytes, 256))
         if not chunk:
             time.sleep(0.005)
         return chunk
@@ -106,7 +106,7 @@ class StreamReader:
             except Exception:
                 pass
 
-    def _run_binary(self, initial_bytes: bytes) -> None:
+    def _run_binary(self, initial_bytes: bytes | bytearray) -> None:
         log.info("StreamReader: starting binary stream parsing")
         buf = bytearray(initial_bytes)
         resync_attempts = 0
@@ -149,7 +149,7 @@ class StreamReader:
                 payload = buf[7:7 + payload_len]
 
                 try:
-                    frame = self._parse(payload, seq)
+                    frame = self._parse(payload, seq)  # type: ignore[arg-type]
                     self._on_frame(frame)
                 except Exception as exc:
                     self.error_count += 1
@@ -238,7 +238,7 @@ class StreamReader:
             for hex_val in valid_hex_words:
                 try:
                     swapped = hex_val[2:4] + hex_val[0:2]
-                    t = _convert_hex_to_temp(swapped, self._family_code)
+                    t = _convert_hex_to_temp(swapped, self._family_code)  # type: ignore[arg-type]
                     values.append(t)
                 except Exception:
                     values.append(0.0)
@@ -262,7 +262,7 @@ class StreamReader:
                 line = line_bytes.decode('utf-8', errors='ignore').strip()
                 if line:
                     try:
-                        frame = self._parse(line, seq)
+                        frame = self._parse(line, seq)  # type: ignore[arg-type]
                         if frame:
                             self._on_frame(frame)
                             seq += 1

tests/test_chart_geometry.py

@@ -0,0 +1,28 @@
+import pytest
+
+from pygui.backend.visualization.chart_geometry import index_to_pixel, value_to_pixel
+
+
+def test_value_to_pixel_min_maps_to_bottom():
+    assert value_to_pixel(0.0, 0.0, 100.0, pixel_start=10.0, pixel_span=200.0) == pytest.approx(210.0)
+
+
+def test_value_to_pixel_max_maps_to_top():
+    assert value_to_pixel(100.0, 0.0, 100.0, pixel_start=10.0, pixel_span=200.0) == pytest.approx(10.0)
+
+
+def test_value_to_pixel_midpoint():
+    assert value_to_pixel(50.0, 0.0, 100.0, pixel_start=0.0, pixel_span=200.0) == pytest.approx(100.0)
+
+
+def test_value_to_pixel_degenerate_range_centers():
+    assert value_to_pixel(5.0, 5.0, 5.0, pixel_start=0.0, pixel_span=200.0) == pytest.approx(100.0)
+
+
+def test_index_to_pixel_first_and_last():
+    assert index_to_pixel(0, 5, pixel_start=0.0, pixel_span=100.0) == pytest.approx(0.0)
+    assert index_to_pixel(4, 5, pixel_start=0.0, pixel_span=100.0) == pytest.approx(100.0)
+
+
+def test_index_to_pixel_single_point_centers():
+    assert index_to_pixel(0, 1, pixel_start=0.0, pixel_span=100.0) == pytest.approx(50.0)

tests/test_local_settings_model.py

@@ -0,0 +1,61 @@
+import pytest
+
+from pygui.backend.data.local_settings import LocalSettings
+from pygui.backend.data.local_settings_model import LocalSettingsModel
+
+
+@pytest.fixture
+def shared_settings():
+    return LocalSettings()
+
+
+@pytest.fixture
+def model(qapp, tmp_path, shared_settings):
+    return LocalSettingsModel(shared_settings, tmp_path)
+
+
+def test_save_mutates_the_shared_instance_in_place(model, shared_settings):
+    # This is the bug candidate 1 fixes: DeviceController holds the same
+    # LocalSettings object, so a save here must be visible to it without
+    # a reload — no throwaway copy, no stale read until restart.
+    model.chamberId = "7"
+    model.waferReadTimeout = 45000
+    model.saveSettings()
+
+    assert shared_settings.chamber_id == "7"
+    assert shared_settings.wafer_read_timeout == 45000
+
+
+def test_save_persists_to_disk_and_reload_round_trips(tmp_path, qapp, shared_settings):
+    model = LocalSettingsModel(shared_settings, tmp_path)
+    model.chamberId = "9"
+    model.waferRetries = 3
+    model.saveSettings()
+
+    reloaded_settings = LocalSettings.read_settings(str(tmp_path))
+    other_model = LocalSettingsModel(reloaded_settings, tmp_path)
+    other_model.loadSettings()
+
+    assert other_model.chamberId == "9"
+    assert other_model.waferRetries == 3
+
+
+def test_revert_restores_last_saved_values(model):
+    model.chamberId = "2"
+    model.saveSettings()
+
+    model.chamberId = "unsaved-edit"
+    assert model.isDirty is True
+
+    model.revertChanges()
+    assert model.chamberId == "2"
+    assert model.isDirty is False
+
+
+def test_invalid_chamber_id_blocks_save(model, shared_settings):
+    shared_settings.chamber_id = "before"
+    model.chamberId = ""
+    model.saveSettings()
+
+    assert model.saveStatus.startswith("error:")
+    assert shared_settings.chamber_id == "before"  # unsaved, shared instance untouched

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")
@@ -119,10 +122,10 @@ 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()