fixed some linter issues

src/allencell_ml_segmenter/core/progress_tracker.py

@@ -1,40 +1,41 @@
 from abc import abstractmethod
 
+
 class ProgressTracker():
     """
     Base class for all ProgressTrackers to inherit from. A ProgressTracker
     maintains an integer measure of progress between progress_minimum and
     progress_maximum. The progress value can be used by PyQt progress bars
     for example.
     """
-    
-    def __init__(self, progress_minimum: int=0, progress_maximum: int=0):
+
+    def __init__(self, progress_minimum: int = 0, progress_maximum: int = 0):
         self._progress_minimum: int = progress_minimum
         self._progress_maximum: int = progress_maximum
         self._progress: int = progress_minimum
 
     def get_progress_minimum(self) -> int:
         return self._progress_minimum
-    
+
     def get_progress_maximum(self) -> int:
         return self._progress_maximum
-    
+
     def get_progress(self) -> int:
         return self._progress
-    
+
     def set_progress_minimum(self, progress_minimum: int) -> None:
         self._progress_minimum = progress_minimum
-    
+
     def set_progress_maximum(self, progress_maximum: int) -> None:
         self._progress_maximum = progress_maximum
-    
+
     def set_progress(self, progress: int) -> None:
         self._progress = progress if progress >= self._progress_minimum and progress <= self._progress_maximum else self._progress
-    
+
     @abstractmethod
     def start_tracker(self) -> None:
         pass
 
     @abstractmethod
     def stop_tracker(self) -> None:
-        pass
+        pass

src/allencell_ml_segmenter/core/view.py

@@ -1,11 +1,11 @@
 from abc import abstractmethod
 from qtpy.QtWidgets import QWidget, QProgressDialog
 from PyQt5.QtCore import Qt, QThread, pyqtSignal
-from pathlib import Path
 
 from allencell_ml_segmenter.core.subscriber import Subscriber
 from allencell_ml_segmenter.core.progress_tracker import ProgressTracker
 
+
 class ViewMeta(type(QWidget), type(Subscriber)):
     pass
 
@@ -25,7 +25,8 @@ def run(self):
         # for i in range(1, 101):
         # self.taskProgress.emit(i)
         # self.msleep(100)  # Simulating some work
-
+
+
 class ProgressThread(QThread):
     task_progress: pyqtSignal = pyqtSignal(int)
 
@@ -54,10 +55,10 @@ def startLongTaskWithProgressBar(self, progress_tracker: ProgressTracker):
         self.progressThread = ProgressThread(progress_tracker)
 
         self.progressDialog = QProgressDialog(
-            f"{self.getTypeOfWork()} in Progress", 
-            "Cancel", 
-            progress_tracker.get_progress_minimum(), 
-            progress_tracker.get_progress_maximum(), 
+            f"{self.getTypeOfWork()} in Progress",
+            "Cancel",
+            progress_tracker.get_progress_minimum(),
+            progress_tracker.get_progress_maximum(),
             self
         )
         self.progressDialog.setWindowTitle(f"{self.getTypeOfWork()} Progress")

src/allencell_ml_segmenter/training/metrics_csv_event_handler.py

@@ -2,7 +2,8 @@
 from pathlib import Path
 from csv import DictReader
 
-class  MetricsCSVEventHandler(FileSystemEventHandler):
+
+class MetricsCSVEventHandler(FileSystemEventHandler):
     """
     A MetricsCSVEventHandler calls progress_callback upon any changes to
     the provided target_path CSV file, passing the latest epoch in the modified
@@ -13,19 +14,19 @@ def __init__(self, target_path: Path, progress_callback: callable):
         super().__init__()
         self._target_path: Path = target_path
         self._progress_callback: callable = progress_callback
-    
+
     def _get_latest_epoch(self) -> int:
         if not self._target_path.exists():
             return 0
-        
+
         latest: int = 0
         with self._target_path.open("r", newline="") as fr:
             dict_reader: DictReader = DictReader(fr)
             for row in dict_reader:
-                latest = int(row["epoch"]) if  int(row["epoch"]) > latest else latest
+                latest = int(row["epoch"]) if int(row["epoch"]) > latest else latest
 
         return latest
 
     def on_any_event(self, event: FileSystemEvent) -> None:
         if self._target_path.exists() and self._target_path.samefile(event.src_path):
-            self._progress_callback(self._get_latest_epoch())
+            self._progress_callback(self._get_latest_epoch())

src/allencell_ml_segmenter/training/metrics_csv_progress_tracker.py

@@ -4,14 +4,15 @@
 from allencell_ml_segmenter.core.progress_tracker import ProgressTracker
 from allencell_ml_segmenter.training.metrics_csv_event_handler import MetricsCSVEventHandler
 
+
 class MetricsCSVProgressTracker(ProgressTracker):
     """
     A MetricsCSVProgressTracker measures progress by observing a metrics CSV file
     produced by cyto-dl and taking the greatest epoch listed inside of it as its
     measure of progress. Relies heavily on current cyto-dl file logging procedure.
     """
 
-    def __init__(self, csv_path: Path, progress_minimum: int=0, progress_maximum: int=0):
+    def __init__(self, csv_path: Path, progress_minimum: int = 0, progress_maximum: int = 0):
         super().__init__(progress_minimum, progress_maximum)
 
         self._csv_path: Path = csv_path
@@ -27,9 +28,9 @@ def start_tracker(self) -> None:
         self.stop_tracker()
         self._observer = Observer()
         event_handler: MetricsCSVEventHandler = MetricsCSVEventHandler(self._target_path, self.set_progress)
-        self._observer.schedule(event_handler,  path=self._csv_path,  recursive=True)
+        self._observer.schedule(event_handler, path=self._csv_path, recursive=True)
         self._observer.start()
-    
+
     def stop_tracker(self) -> None:
         if self._observer:
             self._observer.stop()
@@ -49,4 +50,4 @@ def _get_last_csv_version(self) -> int:
                         last_version = int(version_str) if int(version_str) > last_version else last_version
                     except ValueError:
                         continue
-        return last_version
+        return last_version

src/allencell_ml_segmenter/training/view.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-import sys
 from allencell_ml_segmenter.main.i_viewer import IViewer
 from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (
@@ -25,7 +24,7 @@
     ImageSelectionWidget,
 )
 from allencell_ml_segmenter.training.training_model import TrainingModel
-from hydra.core.global_hydra import GlobalHydra
+# from hydra.core.global_hydra import GlobalHydra
 from aicsimageio import AICSImage
 from aicsimageio.readers import TiffReader
 
@@ -34,6 +33,7 @@
 from allencell_ml_segmenter.training.training_model import PatchSize
 from allencell_ml_segmenter.training.metrics_csv_progress_tracker import MetricsCSVProgressTracker
 
+
 class TrainingView(View):
     """
     Holds widgets pertinent to training processes - ImageSelectionWidget & ModelSelectionWidget.
@@ -200,7 +200,7 @@ def __init__(
 
         # apply styling
         self.setStyleSheet(Style.get_stylesheet("training_view.qss"))
-                    
+
     def train_btn_handler(self) -> None:
         """
         Starts training process