refactor: prune orphaned attic modules and standardize project configurations

- Move orphaned modules (data_segment.py, contour_models.py, marching_squares.py) to attic/.
- Standardize local settings logic, serial port parameters, and graph view plots.
- Update pyproject.toml pyside6-project dependencies and configure gitignore.

.gitignore

@@ -41,3 +41,6 @@ dist/
 *.ico
 # Superpowers brainstorming visual companion
 .superpowers/
+.llm-wiki/
+.agents/
+.pi/

pyproject.toml

@@ -49,7 +49,7 @@ files = [
     "src/pygui/ISC/Tabs/qmldir",
     "src/pygui/__main__.py",
     "src/pygui/backend/contour_models.py",
-    "src/pygui/backend/crypto_helper.py",
+    "src/pygui/backend/crypto/crypto_helper.py",
     "src/pygui/backend/csv_file_metadata.py",
     "src/pygui/backend/data_model.py",
     "src/pygui/backend/data_segment.py",
@@ -103,7 +103,7 @@ environments = [
 # ===== Ruff Linter and Formatter =====
 [tool.ruff]
 target-version = "py311"
-line-length = 100
+line-length = 125
 
 [tool.ruff.lint]
 select = [
@@ -113,7 +113,11 @@ select = [
     "I",   # isort (import sorting)
     "N",   # pep8-naming
 ]
-ignore = []
+ignore = [
+    "N802",  # Function name should be lowercase (standard for Qt Slots and Properties)
+    "N815",  # Class attribute should not be mixedCase (standard for Qt Properties and Signals)
+    "E702",  # Multiple statements on one line (semicolon, standard for inline Qt property setters with self.update())
+]
 
 # ===== Mypy Static Type Checker =====
 [tool.mypy]

src/pygui/ISC/Tabs/SettingsTab.qml

@@ -225,7 +225,7 @@ Item {
                             Layout.preferredWidth: 90
                             Layout.preferredHeight: Theme.settingsButtonHeight
                             onClicked: {
-                                settingsModel.setChamberId(chamberField.text);
+                                settingsModel.ChamberId = chamberField.text;
                                 settingsModel.saveSettings();
                             }
                         }
@@ -296,7 +296,7 @@ Item {
                         SettingsToggle {
                             text: "Reverse Z Wafer"
                             checked: settingsModel.reverseZWafer
-                            onToggled: settingsModel.setReverseZWafer(checked)
+                            onToggled: settingsModel.reverseZWafer = checked
                         }
                     }
                 }

src/pygui/backend/__init__.py

@@ -7,7 +7,6 @@ from pygui.backend.controllers.session_controller import SessionController  # no
 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.data_segment import DataSegment  # 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
@@ -19,7 +18,6 @@ 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.contour_models import ContourLine, ContourSegment  # 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

src/pygui/backend/attic/marching_squares.py

@@ -2,7 +2,7 @@ from typing import List, Optional, Tuple
 
 import numpy as np
 
-from pygui.backend.visualization.contour_models import ContourLine, ContourSegment
+from pygui.backend.attic.contour_models import ContourLine, ContourSegment
 
 
 # ===== Contour Generation =====

src/pygui/backend/data/__init__.py

@@ -2,7 +2,6 @@
 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.data_segment import DataSegment
 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
@@ -10,7 +9,6 @@ from pygui.backend.data.local_settings_model import LocalSettingsModel
 __all__ = [
     "CsvRecorder", "CSVFileMetadata",
     "read_data_records", "is_official_csv", "read_official_csv",
-    "DataSegment",
     "FileBrowser",
     "LocalSettings", "LocalSettingsModel",
 ]

src/pygui/backend/data/local_settings.py

@@ -1,7 +1,10 @@
 import json
+import logging
 import os
 from pathlib import Path
 
+log = logging.getLogger(__name__)
+
 
 # ===== Settings Persistence Model =====
 class LocalSettings:
@@ -51,7 +54,8 @@ class LocalSettings:
                 if hasattr(settings, key):
                     setattr(settings, key, value)
         except Exception as e:
-            print(f"Error reading setting file: {e}")
+            log = logging.getLogger(__name__)
+            log.warning("Error reading setting file: %s",e)
 
         return settings
 
@@ -66,7 +70,7 @@ class LocalSettings:
             with open(path, "w", encoding="utf-8") as f:
                 json.dump(data, f, indent=4)
         except Exception as e:
-            print(f"Error saving settings: {e}")
+            log.exception("Error saving settings: %s",e)
 
     # ===== Master File Helpers =====
     @classmethod

src/pygui/backend/data/local_settings_model.py

@@ -334,27 +334,3 @@ class LocalSettingsModel(QObject):
     @Slot(str)
     def clearMaster(self, family: str) -> None:
         self.setMaster(family, "")
-
-    @Slot(str)
-    def setChamberId(self, value: str) -> None:
-        self.chamberId = value
-
-    @Slot(bool)
-    def setReverseZWafer(self, value: bool) -> None:
-        self.reverseZWafer = value
-
-    @Slot(bool)
-    def setDebugMode(self, value: bool) -> None:
-        self.debugMode = value
-
-    @Slot(int)
-    def setWaferReadTimeout(self, value: int) -> None:
-        self.waferReadTimeout = value
-
-    @Slot(int)
-    def setWaferDetectTimeout(self, value: int) -> None:
-        self.waferDetectTimeout = value
-
-    @Slot(int)
-    def setWaferRetries(self, value: int) -> None:
-        self.waferRetries = value

src/pygui/backend/visualization/__init__.py

@@ -1,5 +1,4 @@
 # ===== Visualization Sub-package =====
-from pygui.backend.visualization.contour_models import ContourLine, ContourSegment
 from pygui.backend.visualization.graph_view import GraphView
 from pygui.backend.visualization.rbf_heatmap import interpolate_field
 from pygui.backend.visualization.wafer_map_item import WaferMapItem
@@ -7,5 +6,4 @@ from pygui.backend.visualization.wafer_map_item import WaferMapItem
 __all__ = [
     "WaferMapItem", "GraphView",
     "interpolate_field",
-    "ContourLine", "ContourSegment",
 ]

src/pygui/backend/visualization/graph_view.py

@@ -9,16 +9,13 @@ from __future__ import annotations
 import logging
 from typing import Any, Optional
 
+import pyqtgraph as pg
+from pyqtgraph import PlotWidget
 from PySide6.QtCore import Property, QObject, Signal, Slot
 from PySide6.QtWidgets import QWidget
 
 log = logging.getLogger(__name__)
 
-# Import pyqtgraph after Qt is initialized
-import pyqtgraph as pg
-from pyqtgraph import PlotWidget
-
-
 class GraphView(QObject):
     """QML-exposed controller for a pyqtgraph line chart.
 

src/pygui/backend/wafer/zwafer_parser.py

@@ -33,10 +33,9 @@ class ZWaferParser:
     # ===== Header Parsing =====
     def _process_header(self, file_obj) -> ZWaferData:
         """Parse header and sensor layout from open file object.
-        
         Handles two CSV row orderings:
-          1. Label/X/Y rows BEFORE 'data' (fixture test format)
-          2. 'data' row BEFORE Label/X/Y (some real CSV files)
+        1. Label/X/Y rows BEFORE 'data' (fixture test format)
+        2. 'data' row BEFORE Label/X/Y (some real CSV files)
         The C# parser handles both by collecting sensor layout rows
         regardless of whether 'data' has been seen.
         """

src/pygui/serialcomm/serial_port.py

@@ -196,7 +196,6 @@ class SerialPort:
           bytes 1016-1019 : Runtime   (2 bytes hex → decimal seconds)
           bytes 1020-1023 : Cycle time (2 bytes hex → decimal cycles)
         """
-        raw = bytes.fromhex(hex_response)
 
         family_code = self._hex_to_ascii(hex_response[0:2])
         serial_num = f"{family_code}{int(hex_response[2:6], 16):05d}"