refactor: standardize codebase formatting, optimize import orders, and update GUI resolution to 1080p

Makefile

@@ -0,0 +1,23 @@
+.PHONY: install test lint fix typecheck run clean
+
+install:
+	uv sync
+
+test:
+	uv run pytest tests/
+
+lint:
+	uv run ruff check src/
+
+fix:
+	uv run ruff check src/ --fix
+
+typecheck:
+	uv run mypy src/
+
+run:
+	uv run python -m pygui
+
+clean:
+	rm -rf .pytest_cache .ruff_cache .mypy_cache
+	find . -type d -name "__pycache__" -exec rm -rf {} +

pyproject.toml

@@ -17,6 +17,7 @@ dependencies = [
     "matplotlib>=3.7.0",
     "scipy>=1.17.1",
     "pyyaml>=6.0.3",
+    "dtw-python",
 ]
 
 [project.optional-dependencies]
@@ -88,6 +89,8 @@ files = [
 [dependency-groups]
 dev = [
     "pytest>=9.0.3",
+    "ruff",
+    "mypy",
 ]
 
 [tool.uv]
@@ -96,3 +99,27 @@ environments = [
     "sys_platform == 'win32'",
     "sys_platform == 'linux'",
 ]
+
+# ===== Ruff Linter and Formatter =====
+[tool.ruff]
+target-version = "py311"
+line-length = 100
+
+[tool.ruff.lint]
+select = [
+    "E",   # pycodestyle errors
+    "W",   # pycodestyle warnings
+    "F",   # pyflakes
+    "I",   # isort (import sorting)
+    "N",   # pep8-naming
+]
+ignore = []
+
+# ===== Mypy Static Type Checker =====
+[tool.mypy]
+python_version = "3.11"
+check_untyped_defs = true
+warn_return_any = true
+warn_unused_configs = true
+ignore_missing_imports = true
+

src/pygui/ISC/Main.qml

@@ -4,8 +4,8 @@ import ISC
 // ===== App Window Shell =====
 Window {
     // ===== Window Dimensions =====
-    width: 1400
-    height: 820
+    width: 1920
+    height: 1080
     minimumWidth: 1100
     minimumHeight: 700
     visible: true

src/pygui/__main__.py

@@ -1,18 +1,19 @@
+import logging
 import sys
 from pathlib import Path
-import logging
 
 from PySide6.QtQml import QQmlApplicationEngine
 from PySide6.QtQuickControls2 import QQuickStyle
 from PySide6.QtWidgets import QApplication
 
 from pygui.backend.controllers.device_controller import DeviceController
+from pygui.backend.controllers.session_controller import SessionController
+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
-from pygui.backend.data.file_browser import FileBrowser
-from pygui.backend.controllers.session_controller import SessionController
+
 # Importing wafer_map_item registers the @QmlElement WaferMapItem (QML: import ISC.Wafer).
-from pygui.backend.visualization.wafer_map_item import WaferMapItem
+
 
 # ===== Application Entry Point =====
 def main() -> int:

src/pygui/backend/__init__.py

@@ -4,29 +4,25 @@
 
 from pygui.backend.controllers.device_controller import DeviceController  # noqa: F401
 from pygui.backend.controllers.session_controller import SessionController  # 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.session_model import SessionModel  # noqa: F401
-from pygui.backend.models.data_model import TemperatureTableModel  # noqa: F401
-from pygui.backend.models.sensor_editor import SensorEditor  # noqa: F401
-from pygui.backend.models.threshold_classifier import ThresholdConfig  # noqa: F401
-from pygui.backend.models.stability_detector import StabilityDetector  # noqa: F401
-
-from pygui.backend.data.csv_recorder import CsvRecorder  # 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.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
-
-from pygui.backend.visualization.wafer_map_item import WaferMapItem  # 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.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.contour_models import ContourLine, ContourSegment  # noqa: F401
-
-from pygui.backend.wafer.zwafer_models import ZWaferData, Sensor, DataRecord  # 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
-from pygui.backend.wafer.wafer_layouts import load_layout, available_families  # noqa: F401

src/pygui/backend/cluster_average.py

@@ -2,7 +2,9 @@
 
 
 from __future__ import annotations
+
 import math
+
 from pygui.backend.wafer.zwafer_models import Sensor
 
 

src/pygui/backend/controllers/__init__.py

@@ -3,4 +3,3 @@ from pygui.backend.controllers.device_controller import DeviceController
 from pygui.backend.controllers.session_controller import SessionController
 
 __all__ = ["DeviceController", "SessionController"]
-    

src/pygui/backend/controllers/device_controller.py

@@ -7,11 +7,12 @@ import threading
 from datetime import datetime
 from typing import Any, Optional
 
-from PySide6.QtCore import QObject, Property, Qt, Signal, Slot
+from PySide6.QtCore import Property, QObject, Qt, Signal, Slot
 
+from pygui.backend.controllers.session_controller import SessionController
+from pygui.backend.data.local_settings import LocalSettings
 from pygui.backend.models.data_model import TemperatureTableModel
 from pygui.backend.visualization.graph_view import GraphView
-from pygui.backend.data.local_settings import LocalSettings
 from pygui.serialcomm.data_parser import (
     convert_to_temperatures,
     parse_binary_data,
@@ -20,7 +21,7 @@ from pygui.serialcomm.data_parser import (
 )
 from pygui.serialcomm.device_service import DeviceService
 from pygui.serialcomm.serial_port import WaferInfo
-from pygui.backend.controllers.session_controller import SessionController
+
 # import pygui.backend.wafer_map_item
 
 stream_controller = SessionController()

src/pygui/backend/controllers/session_controller.py

@@ -1,21 +1,23 @@
 """QML-facing controller for the live/review wafer dashboard."""
 from __future__ import annotations
+
 import logging
 import time
-from typing import Any, Optional
+from typing import Optional
 
-from PySide6.QtCore import QObject, Property, QTimer, Qt, Signal, Slot
+from PySide6.QtCore import Property, QObject, Qt, QTimer, Signal, Slot
 
+from pygui.backend.cluster_average import average_clusters, group_sensors_by_radius
 from pygui.backend.data.csv_recorder import CsvRecorder
 from pygui.backend.models.frame import Frame
 from pygui.backend.models.frame_player import FramePlayer, frames_from_wafer_data
+from pygui.backend.models.sensor_editor import SensorEditor
 from pygui.backend.models.session_model import SessionModel
 from pygui.backend.models.threshold_classifier import ThresholdConfig
 from pygui.backend.wafer.zwafer_models import Sensor
 from pygui.backend.wafer.zwafer_parser import ZWaferParser
 from pygui.serialcomm.stream_reader import StreamReader
-from pygui.backend.models.sensor_editor import SensorEditor
-from pygui.backend.cluster_average import average_clusters, group_sensors_by_radius
+
 log = logging.getLogger(__name__)
 
 MODE_LIVE = "live"
@@ -198,7 +200,12 @@ class SessionController(QObject):
     @Slot(str)
     def loadFile(self, file_path: str) -> None:
         from pathlib import Path
-        from pygui.backend.data.data_records import is_official_csv, read_data_records, read_official_csv
+
+        from pygui.backend.data.data_records import (
+            is_official_csv,
+            read_data_records,
+            read_official_csv,
+        )
         from pygui.backend.wafer.wafer_layouts import WaferLayout, resolve_shape_and_size
 
         frames = []
@@ -319,10 +326,9 @@ class SessionController(QObject):
     # ---- live: stream start/stop ----
     @Slot(str, str)
     def startStream(self, port: str, family_code: str = "") -> None:
-        from pygui.serialcomm.serial_port import SerialPort  # transport open
-        import serial as pyserial
+
         from pygui.backend.wafer.wafer_layouts import load_layout_for_wafer_id
-        import time
+        from pygui.serialcomm.serial_port import SerialPort  # transport open
 
         if family_code:
             try:
@@ -457,4 +463,3 @@ class SessionController(QObject):
         self._reprocess_current()
 
 
-    

src/pygui/backend/crypto/crypto_helper.py

@@ -2,8 +2,8 @@ import secrets
 from pathlib import Path
 from typing import Union
 
-from cryptography.hazmat.primitives.ciphers import Cipher, algorithms, modes
 from cryptography.hazmat.backends import default_backend
+from cryptography.hazmat.primitives.ciphers import Cipher, algorithms, modes
 
 
 # ===== Crypto Utilities =====

src/pygui/backend/data/__init__.py

@@ -1,7 +1,7 @@
 # ===== Data Sub-package =====
-from pygui.backend.data.csv_recorder import CsvRecorder
 from pygui.backend.data.csv_file_metadata import CSVFileMetadata
-from pygui.backend.data.data_records import read_data_records, is_official_csv, read_official_csv
+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

src/pygui/backend/data/csv_recorder.py

@@ -1,13 +1,14 @@
 """Append live frames"""
 from __future__ import annotations
+
 from datetime import datetime
 from pathlib import Path
 from typing import Optional, TextIO
 
-
 from pygui.backend.models.frame import Frame
 from pygui.backend.wafer.zwafer_models import Sensor
 
+
 class CsvRecorder:
     def __init__(self) -> None:
         self._file_handle: Optional[TextIO] = None

src/pygui/backend/data/data_records.py

@@ -1,9 +1,11 @@
 """Read the data section of a Z-wafer CSV into DataRecords, or the official headerless CSV."""
 from __future__ import annotations
+
 from pathlib import Path
 
 from pygui.backend.wafer.zwafer_models import DataRecord, Sensor
 
+
 def read_data_records(file_path: str) -> list[DataRecord]:
     records: list[DataRecord] = []
     in_data = False

src/pygui/backend/data/file_browser.py

@@ -5,12 +5,12 @@ import re
 from datetime import datetime
 from pathlib import Path
 
-from PySide6.QtCore import QObject, Property, QStandardPaths, Signal, Slot
+from PySide6.QtCore import Property, QObject, QStandardPaths, Signal, Slot
 from PySide6.QtWidgets import QFileDialog, QMessageBox
 
+from pygui.backend.data.constants import DEFAULT_DATA_DIR_NAME
 from pygui.backend.data.csv_file_metadata import CSVFileMetadata
 from pygui.backend.wafer.zwafer_parser import ZWaferParser
-from pygui.backend.data.constants import DEFAULT_DATA_DIR_NAME
 
 
 # ===== File Browser Model =====

src/pygui/backend/data/local_settings_model.py

@@ -4,11 +4,10 @@ from copy import deepcopy
 from pathlib import Path
 from typing import Any
 
-from PySide6.QtCore import QObject, Property, QDateTime, QStandardPaths, Signal, Slot
+from PySide6.QtCore import Property, QDateTime, QObject, QStandardPaths, Signal, Slot
 
-from pygui.backend.data.local_settings import LocalSettings
 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")
 

src/pygui/backend/models/__init__.py

@@ -1,12 +1,12 @@
 # ===== 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.session_model import SessionModel, SessionUpdate
-from pygui.backend.models.data_model import TemperatureTableModel
 from pygui.backend.models.sensor_editor import SensorEditor
-from pygui.backend.models.threshold_classifier import ThresholdConfig, classify, resolve_bounds
+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",

src/pygui/backend/models/frame.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+
 from dataclasses import dataclass
 
 

src/pygui/backend/models/frame_player.py

@@ -1,7 +1,9 @@
 from __future__ import annotations
+
 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]:
     """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/models/frame_stats.py

@@ -1,6 +1,7 @@
 """Per-frame descriptive statistics"""
 
 from __future__ import annotations
+
 import math
 from dataclasses import dataclass
 

src/pygui/backend/models/session_model.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+
 from dataclasses import dataclass
 
 from pygui.backend.models.frame import Frame
@@ -6,6 +7,7 @@ from pygui.backend.models.frame_stats import Stats, compute_stats
 from pygui.backend.models.stability_detector import StabilityDetector
 from pygui.backend.models.threshold_classifier import ThresholdConfig, classify, resolve_bounds
 
+
 @dataclass(frozen=True)
 class SessionUpdate:
     seq: int

src/pygui/backend/models/stability_detector.py

@@ -1,5 +1,6 @@
 """Detect process state (Idle, Ramp, Set) from the running average temp"""
 from __future__ import annotations
+
 from typing import Optional
 
 STATE_IDLE = "idle"
@@ -31,4 +32,3 @@ class StabilityDetector:
             return STATE_RAMP
         self._near_since = None
         return STATE_RAMP
-        

src/pygui/backend/models/threshold_classifier.py

@@ -4,6 +4,7 @@ Auto mode derives target=mean, margin=1
 """
 
 from __future__ import annotations
+
 import math
 from dataclasses import dataclass
 

src/pygui/backend/visualization/__init__.py

@@ -1,8 +1,8 @@
 # ===== Visualization Sub-package =====
-from pygui.backend.visualization.wafer_map_item import WaferMapItem
+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.contour_models import ContourLine, ContourSegment
+from pygui.backend.visualization.wafer_map_item import WaferMapItem
 
 __all__ = [
     "WaferMapItem", "GraphView",

src/pygui/backend/visualization/graph_view.py

@@ -9,7 +9,7 @@ from __future__ import annotations
 import logging
 from typing import Any, Optional
 
-from PySide6.QtCore import QObject, Property, Signal, Slot
+from PySide6.QtCore import Property, QObject, Signal, Slot
 from PySide6.QtWidgets import QWidget
 
 log = logging.getLogger(__name__)

src/pygui/backend/visualization/marching_squares.py

@@ -1,4 +1,4 @@
-from typing import List, Tuple, Optional
+from typing import List, Optional, Tuple
 
 import numpy as np
 

src/pygui/backend/visualization/wafer_map_item.py

@@ -13,9 +13,15 @@ from __future__ import annotations
 import math
 
 import numpy as np
-from PySide6.QtCore import Property, QPoint, Signal, Slot, Qt
+from PySide6.QtCore import Property, QPoint, Qt, Signal, Slot
 from PySide6.QtGui import (
-    QBrush, QColor, QFont, QImage, QPainter, QPen, QPolygon,
+    QBrush,
+    QColor,
+    QFont,
+    QImage,
+    QPainter,
+    QPen,
+    QPolygon,
 )
 from PySide6.QtQml import QmlElement
 from PySide6.QtQuick import QQuickPaintedItem

src/pygui/backend/wafer/__init__.py

@@ -1,7 +1,7 @@
 # ===== Wafer Sub-package =====
-from pygui.backend.wafer.zwafer_models import ZWaferData, Sensor, DataRecord
+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
-from pygui.backend.wafer.wafer_layouts import load_layout, available_families
 
 __all__ = [
     "ZWaferData", "Sensor", "DataRecord",

src/pygui/backend/wafer/zwafer_parser.py

@@ -1,8 +1,8 @@
+from datetime import datetime
 from pathlib import Path
-from typing import Tuple, Optional
-from datetime import datetime, timedelta
+from typing import Optional, Tuple
 
-from pygui.backend.wafer.zwafer_models import ZWaferData, Sensor
+from pygui.backend.wafer.zwafer_models import Sensor, ZWaferData
 
 
 # ===== Z-Wafer CSV Parser =====

src/pygui/serialcomm/device_service.py

@@ -6,7 +6,6 @@ QML via @Slot methods on a QObject controller.
 """
 
 import logging
-from pathlib import Path
 from typing import Optional
 
 import serial.tools.list_ports
@@ -42,8 +41,8 @@ class DeviceService:
 
         # On macOS/Linux, also detect virtual loopback serial ports (PTYs) opened by socat
         import platform
-        import subprocess
         import re
+        import subprocess
 
         if platform.system() in ("Darwin", "Linux"):
             try:

src/pygui/serialcomm/stream_reader.py

@@ -1,5 +1,6 @@
 """Continuous serial frame reader (Live-mode source)"""
 from __future__ import annotations
+
 import logging
 import threading
 import time

uv.lock

@@ -2,11 +2,14 @@ version = 1
 revision = 3
 requires-python = ">=3.11"
 resolution-markers = [
-    "python_full_version >= '3.14' and sys_platform == 'darwin'",
+    "python_full_version >= '3.15' and sys_platform == 'darwin'",
+    "python_full_version == '3.14.*' and sys_platform == 'darwin'",
     "python_full_version < '3.14' and sys_platform == 'darwin'",
-    "python_full_version >= '3.14' and sys_platform == 'win32'",
+    "python_full_version >= '3.15' and sys_platform == 'win32'",
+    "python_full_version == '3.14.*' and sys_platform == 'win32'",
     "python_full_version < '3.14' and sys_platform == 'win32'",
-    "python_full_version >= '3.14' and sys_platform == 'linux'",
+    "python_full_version >= '3.15' and sys_platform == 'linux'",
+    "python_full_version == '3.14.*' and sys_platform == 'linux'",
     "python_full_version < '3.14' and sys_platform == 'linux'",
 ]
 supported-markers = [
@@ -15,6 +18,46 @@ supported-markers = [
     "sys_platform == 'linux'",
 ]
 
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 version = "0.1.0"
 source = { editable = "." }
 dependencies = [
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@@ -618,11 +841,14 @@ dev = [
 
 [package.dev-dependencies]
 dev = [
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 [package.metadata.requires-dev]
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