accusleepy 0.10.0__tar.gz → 0.11.0__tar.gz

{accusleepy-0.10.0 → accusleepy-0.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: accusleepy
-Version: 0.10.0
+Version: 0.11.0
 Summary: Python implementation of AccuSleep
 License: GPL-3.0-only
 Author: Zeke Barger
@@ -11,14 +11,13 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: fastparquet (>=2024.11.0,<2025.0.0)
-Requires-Dist: joblib (>=1.4.2,<2.0.0)
 Requires-Dist: matplotlib (>=3.10.1,<4.0.0)
 Requires-Dist: numpy (>=2.2.4,<3.0.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: pillow (>=11.1.0,<12.0.0)
-Requires-Dist: pre-commit (>=4.2.0,<5.0.0)
-Requires-Dist: pyside6 (>=6.9.0,<6.9.3)
+Requires-Dist: platformdirs (>=4.0.0,<5.0.0)
+Requires-Dist: pyarrow (>=23.0.0,<24.0.0)
+Requires-Dist: pyside6 (>=6.10.1,<7.0.0)
 Requires-Dist: scipy (>=1.15.2,<2.0.0)
 Requires-Dist: torch (>=2.8.0,<3.0.0)
 Requires-Dist: torchvision (>=0.23.0,<1.0.0)
@@ -62,13 +61,14 @@ etc.) with python >=3.11,<3.14
 - `pip install accusleepy`
 - (optional) download a classification model from https://osf.io/py5eb/ under /python_format/models/
 
-Note that upgrading or reinstalling the package will overwrite any changes
-to the [config file](accusleepy/config.json).
 
 ## Usage
 
 `python -m accusleepy` will open the primary interface.
 
+Your settings are saved to a platform-specific location
+(e.g., `~/Library/Application Support/accusleepy/config.json` on macOS)
+
 [Guide to the primary interface](accusleepy/gui/text/main_guide.md)
 
 [Guide to the manual scoring interface](accusleepy/gui/text/manual_scoring_guide.md)
@@ -79,10 +79,9 @@ please consult the [developer guide](accusleepy/gui/text/dev_guide.md).
 
 ## Changelog
 
-- 0.10.0: Improved zoom behavior
-- 0.8.1-0.9.3: Improved error handling and code quality
-- 0.8.0: More configurable settings, visual improvements
-- 0.7.1-0.7.3: Bugfixes, code cleanup
+- 0.11.0: Store config file in a user directory
+- 0.10.0-0.10.1: Improved zoom behavior, updated dependencies
+- 0.7.1-0.9.3: Bugfixes, code cleanup, additional config settings
 - 0.7.0: More settings can be configured in the UI
 - 0.6.0: Confidence scores can now be displayed and saved. Retraining your models is recommended
     since the new calibration feature will make the confidence scores more accurate.

{accusleepy-0.10.0 → accusleepy-0.11.0}/README.md

@@ -35,13 +35,14 @@ etc.) with python >=3.11,<3.14
 - `pip install accusleepy`
 - (optional) download a classification model from https://osf.io/py5eb/ under /python_format/models/
 
-Note that upgrading or reinstalling the package will overwrite any changes
-to the [config file](accusleepy/config.json).
 
 ## Usage
 
 `python -m accusleepy` will open the primary interface.
 
+Your settings are saved to a platform-specific location
+(e.g., `~/Library/Application Support/accusleepy/config.json` on macOS)
+
 [Guide to the primary interface](accusleepy/gui/text/main_guide.md)
 
 [Guide to the manual scoring interface](accusleepy/gui/text/manual_scoring_guide.md)
@@ -52,10 +53,9 @@ please consult the [developer guide](accusleepy/gui/text/dev_guide.md).
 
 ## Changelog
 
-- 0.10.0: Improved zoom behavior
-- 0.8.1-0.9.3: Improved error handling and code quality
-- 0.8.0: More configurable settings, visual improvements
-- 0.7.1-0.7.3: Bugfixes, code cleanup
+- 0.11.0: Store config file in a user directory
+- 0.10.0-0.10.1: Improved zoom behavior, updated dependencies
+- 0.7.1-0.9.3: Bugfixes, code cleanup, additional config settings
 - 0.7.0: More settings can be configured in the UI
 - 0.6.0: Confidence scores can now be displayed and saved. Retraining your models is recommended
     since the new calibration feature will make the confidence scores more accurate.

accusleepy-0.11.0/accusleepy/__init__.py

@@ -0,0 +1 @@
+"""AccuSleePy: Python implementation of AccuSleep for automated sleep scoring."""

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/__main__.py

@@ -1,3 +1,5 @@
+"""Entry point for running AccuSleePy as a module (python -m accusleepy)."""
+
 from accusleepy.gui.main import run_primary_window
 
 if __name__ == "__main__":

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/bouts.py

@@ -1,3 +1,5 @@
+"""Brain state bout length enforcement."""
+
 import re
 from dataclasses import dataclass
 from operator import attrgetter

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/brain_state_set.py

@@ -1,3 +1,5 @@
+"""Define and organize brain states."""
+
 from dataclasses import dataclass
 
 import numpy as np

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/classification.py

@@ -1,3 +1,5 @@
+"""Model training and brain state classification."""
+
 import os
 
 import numpy as np

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/constants.py

@@ -1,3 +1,5 @@
+"""Application-wide constants and default settings."""
+
 import numpy as np
 
 # probably don't change these unless you really need to
@@ -24,8 +26,9 @@ MIN_EPOCHS_PER_STATE = 3
 
 
 # very unlikely you will want to change values from here onwards
-# config file location
-CONFIG_FILE = "config.json"
+# config file names
+DEFAULT_CONFIG_FILE = "default_config.json"
+USER_CONFIG_FILE = "config.json"
 # number of times to include the EMG power in a training image
 EMG_COPIES = 9
 # minimum spectrogram window length, in seconds

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/fileio.py

@@ -1,14 +1,18 @@
+"""File I/O for recordings, labels, calibration data, and configuration."""
+
 import json
 import os
+import shutil
 from dataclasses import dataclass
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import PackageNotFoundError, version
+from importlib.resources import files
 
 import numpy as np
 import pandas as pd
-from PySide6.QtWidgets import QListWidgetItem
+from platformdirs import user_config_dir
 
-from accusleepy.brain_state_set import BRAIN_STATES_KEY, BrainState, BrainStateSet
 import accusleepy.constants as c
+from accusleepy.brain_state_set import BRAIN_STATES_KEY, BrainState, BrainStateSet
 
 
 @dataclass
@@ -55,7 +59,6 @@ class Recording:
     label_file: str = ""  # path to label file
     calibration_file: str = ""  # path to calibration file
     sampling_rate: int | float = 0.0  # sampling rate, in Hz
-    widget: QListWidgetItem = None  # list item widget shown in the GUI
 
 
 def load_calibration_file(filename: str) -> tuple[np.ndarray, np.ndarray]:
@@ -128,6 +131,16 @@ def save_labels(
         pd.DataFrame({c.BRAIN_STATE_COL: labels}).to_csv(filename, index=False)
 
 
+def _get_user_config_path() -> str:
+    """Return the path to the user's config file in the platform config directory."""
+    return os.path.join(user_config_dir("accusleepy"), c.USER_CONFIG_FILE)
+
+
+def _get_default_config_path() -> str:
+    """Return the path to the bundled default config file."""
+    return str(files("accusleepy").joinpath(c.DEFAULT_CONFIG_FILE))
+
+
 def load_config() -> AccuSleePyConfig:
     """Load configuration file with brain state options
 
@@ -143,9 +156,11 @@ def load_config() -> AccuSleePyConfig:
         default autoscroll state for manual scoring,
         setting to delete training images automatically
     """
-    with open(
-        os.path.join(os.path.dirname(os.path.abspath(__file__)), c.CONFIG_FILE), "r"
-    ) as f:
+    user_config = _get_user_config_path()
+    if not os.path.exists(user_config):
+        os.makedirs(os.path.dirname(user_config), exist_ok=True)
+        shutil.copy2(_get_default_config_path(), user_config)
+    with open(user_config) as f:
         data = json.load(f)
 
     return AccuSleePyConfig(
@@ -229,9 +244,9 @@ def save_config(
     output_dict.update({c.EPOCHS_TO_SHOW_KEY: epochs_to_show})
     output_dict.update({c.AUTOSCROLL_KEY: autoscroll_state})
     output_dict.update({c.DELETE_TRAINING_IMAGES_KEY: delete_training_images})
-    with open(
-        os.path.join(os.path.dirname(os.path.abspath(__file__)), c.CONFIG_FILE), "w"
-    ) as f:
+    user_config = _get_user_config_path()
+    os.makedirs(os.path.dirname(user_config), exist_ok=True)
+    with open(user_config, "w") as f:
         json.dump(output_dict, f, indent=4)
         f.write("\n")
 
@@ -242,7 +257,7 @@ def load_recording_list(filename: str) -> list[Recording]:
     :param filename: filename of list of recordings
     :return: list of recordings
     """
-    with open(filename, "r") as f:
+    with open(filename) as f:
         data = json.load(f)
     recording_list = [Recording(**r) for r in data[c.RECORDING_LIST_NAME]]
     for i, r in enumerate(recording_list):

accusleepy-0.11.0/accusleepy/gui/__init__.py

@@ -0,0 +1 @@
+"""Graphical user interface components for AccuSleePy."""

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/gui/main.py

@@ -1,5 +1,7 @@
-# AccuSleePy main window
-# Icon source: Arkinasi, https://www.flaticon.com/authors/arkinasi
+"""AccuSleePy main window.
+
+Icon source: Arkinasi, https://www.flaticon.com/authors/arkinasi
+"""
 
 import logging
 import os
@@ -39,10 +41,10 @@ from accusleepy.constants import (
     UNDEFINED_LABEL,
 )
 from accusleepy.fileio import (
+    get_version,
     load_config,
     load_labels,
     load_recording,
-    get_version,
 )
 from accusleepy.gui.dialogs import select_existing_file, select_save_location
 from accusleepy.gui.manual_scoring import ManualScoringWindow
@@ -56,9 +58,8 @@ from accusleepy.services import (
     create_calibration,
     score_recording_list,
 )
-from accusleepy.validation import validate_and_correct_labels
 from accusleepy.signal_processing import resample_and_standardize
-from accusleepy.validation import check_config_consistency
+from accusleepy.validation import check_config_consistency, validate_and_correct_labels
 
 logger = logging.getLogger(__name__)
 
@@ -93,7 +94,7 @@ class AccuSleepWindow(QMainWindow):
     """AccuSleePy primary window"""
 
     def __init__(self):
-        super(AccuSleepWindow, self).__init__()
+        super().__init__()
 
         # initialize the UI
         self.ui = Ui_PrimaryWindow()
@@ -361,22 +362,18 @@ class AccuSleepWindow(QMainWindow):
         except Exception:
             logger.exception("Failed to load %s", filename)
             self.show_message(
-                (
-                    "ERROR: could not load classification model. Check "
-                    "user manual for instructions on creating this file."
-                )
+                "ERROR: could not load classification model. Check "
+                "user manual for instructions on creating this file."
             )
             return
 
         # make sure only "default" model type is loaded
         if model_type != DEFAULT_MODEL_TYPE:
             self.show_message(
-                (
-                    "ERROR: only 'default'-style models can be used. "
-                    "'Real-time' models are not supported. "
-                    "See classification.example_real_time_scoring_function.py "
-                    "for an example of how to classify brain states in real time."
-                )
+                "ERROR: only 'default'-style models can be used. "
+                "'Real-time' models are not supported. "
+                "See classification.example_real_time_scoring_function.py "
+                "for an example of how to classify brain states in real time."
             )
             return
 
@@ -431,10 +428,8 @@ class AccuSleepWindow(QMainWindow):
             )
             status_widget.setText("could not load recording")
             self.show_message(
-                (
-                    "ERROR: could not load recording. "
-                    "Check user manual for formatting instructions."
-                )
+                "ERROR: could not load recording. "
+                "Check user manual for formatting instructions."
             )
             return None, None, None, False
 
@@ -504,10 +499,8 @@ class AccuSleepWindow(QMainWindow):
                 logger.exception("Failed to load %s", label_file)
                 self.ui.manual_scoring_status.setText("could not load labels")
                 self.show_message(
-                    (
-                        "ERROR: could not load labels. "
-                        "Check user manual for formatting instructions."
-                    )
+                    "ERROR: could not load labels. "
+                    "Check user manual for formatting instructions."
                 )
                 return
         else:

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/gui/manual_scoring.py

@@ -1,8 +1,9 @@
-# AccuSleePy manual scoring GUI
-# Icon sources:
-#   Arkinasi, https://www.flaticon.com/authors/arkinasi
-#   kendis lasman, https://www.flaticon.com/packs/ui-79
+"""AccuSleePy manual scoring GUI.
 
+Icon sources:
+    Arkinasi, https://www.flaticon.com/authors/arkinasi
+    kendis lasman, https://www.flaticon.com/packs/ui-79
+"""
 
 import copy
 import os
@@ -33,7 +34,7 @@ from PySide6.QtWidgets import (
 )
 
 from accusleepy.constants import UNDEFINED_LABEL
-from accusleepy.fileio import load_config, save_labels, EMGFilter
+from accusleepy.fileio import EMGFilter, load_config, save_labels
 from accusleepy.gui.mplwidget import resample_x_ticks
 from accusleepy.gui.viewer_window import Ui_ViewerWindow
 from accusleepy.signal_processing import create_spectrogram, get_emg_power
@@ -85,8 +86,8 @@ BRIGHTER_SCALE_FACTOR = 0.96
 DIMMER_SCALE_FACTOR = 1.07
 # zoom factor for upper plots - larger values = bigger changes
 ZOOM_FACTOR = 0.1
-# interval in seconds between zoom events triggered by scrolling
-ZOOM_DELAY = 0.05
+# rate limit for zoom events triggered by scrolling
+MAX_SCROLL_EVENTS_PER_SEC = 24
 
 
 @dataclass
@@ -123,7 +124,7 @@ class ManualScoringWindow(QDialog):
         :param epoch_length: epoch length, in seconds
         :param emg_filter: EMG filter parameters
         """
-        super(ManualScoringWindow, self).__init__()
+        super().__init__()
 
         self.label_file = label_file
         self.eeg = eeg
@@ -914,9 +915,7 @@ class ManualScoringWindow(QDialog):
         )
         self.ui.lowerfigure.canvas.axes[1].set_xticklabels(
             [
-                "{:02d}:{:02d}:{:05.2f}".format(
-                    int(x // 3600), int(x // 60) % 60, (x % 60)
-                )
+                f"{int(x // 3600):02d}:{int(x // 60) % 60:02d}:{x % 60:05.2f}"
                 for x in x_ticks * self.epoch_length
             ]
         )
@@ -983,11 +982,15 @@ class ManualScoringWindow(QDialog):
             return
 
         self.now_zooming = True
+        start_time = time.time()
         if event.button == "up":
             self.zoom_x(direction=ZOOM_IN)
         else:
             self.zoom_x(direction=ZOOM_OUT)
-        time.sleep(ZOOM_DELAY)
+        end_time = time.time()
+        time_elapsed = end_time - start_time
+        if time_elapsed < 1 / MAX_SCROLL_EVENTS_PER_SEC:
+            time.sleep(1 / MAX_SCROLL_EVENTS_PER_SEC - time_elapsed)
         self.now_zooming = False
 
 

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/gui/mplwidget.py

@@ -1,4 +1,5 @@
-# Widget with a matplotlib FigureCanvas for manual scoring
+"""Matplotlib FigureCanvas widget for manual scoring."""
+
 from collections.abc import Callable
 
 import matplotlib.ticker as mticker
@@ -293,7 +294,7 @@ class MplWidget(QtWidgets.QWidget):
                 [1 - marker_dy, 1],
             ]
         )
-        for x, y in zip(marker_x, marker_y):
+        for x, y in zip(marker_x, marker_y, strict=True):
             self.top_marker.append(axes[0].plot(x, y - marker_y_offset_top, "r")[0])
 
         # EMG subplot
@@ -317,7 +318,7 @@ class MplWidget(QtWidgets.QWidget):
             linewidth=0.5,
         )[0]
 
-        for x, y in zip(marker_x, marker_y):
+        for x, y in zip(marker_x, marker_y, strict=True):
             self.bottom_marker.append(
                 axes[1].plot(x, -1 * (y - marker_y_offset_bottom), "r")[0]
             )
@@ -355,9 +356,7 @@ class MplWidget(QtWidgets.QWidget):
 
     def time_formatter(self, x, pos):
         x = x * self.epoch_length
-        return "{:02d}:{:02d}:{:05.2f}".format(
-            int(x // 3600), int(x // 60) % 60, (x % 60)
-        )
+        return f"{int(x // 3600):02d}:{int(x // 60) % 60:02d}:{x % 60:05.2f}"
 
 
 def resample_x_ticks(x_ticks: np.array) -> np.array:

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/gui/primary_window.py

@@ -1,9 +1,7 @@
-# -*- coding: utf-8 -*-
-
 ################################################################################
 ## Form generated from reading UI file 'primary_window.ui'
 ##
-## Created by: Qt User Interface Compiler version 6.9.2
+## Created by: Qt User Interface Compiler version 6.10.2
 ##
 ## WARNING! All changes made in this file will be lost when recompiling UI file!
 ################################################################################
@@ -32,10 +30,11 @@ from PySide6.QtWidgets import (
     QVBoxLayout,
     QWidget,
 )
+
 import accusleepy.gui.resources_rc  # noqa F401
 
 
-class Ui_PrimaryWindow(object):
+class Ui_PrimaryWindow:
     def setupUi(self, PrimaryWindow):
         if not PrimaryWindow.objectName():
             PrimaryWindow.setObjectName("PrimaryWindow")
@@ -3148,7 +3147,6 @@ class Ui_PrimaryWindow(object):
                 "This is the current set of brain states. Important notes:\n"
                 "- You must click 'Save settings' for changes to take effect.\n"
                 "- Changing these settings can prevent existing label files, calibration files, and trained models from working properly.\n"
-                "- Reinstalling AccuSleePy will overwrite this configuration.\n"
                 "\n"
                 "Each brain state has several attributes:\n"
                 "- Digit: the indicator for this state in label files, and the keyboard shortcut for this state in manual scoring.\n"

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/gui/primary_window.ui

@@ -3701,7 +3701,6 @@ color: rgb(244, 195, 68);</string>
                      <string>This is the current set of brain states. Important notes:
 - You must click 'Save settings' for changes to take effect.
 - Changing these settings can prevent existing label files, calibration files, and trained models from working properly.
-- Reinstalling AccuSleePy will overwrite this configuration.
 
 Each brain state has several attributes:
 - Digit: the indicator for this state in label files, and the keyboard shortcut for this state in manual scoring.

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/gui/recording_manager.py

@@ -1,11 +1,20 @@
 """Recording list manager"""
 
+from dataclasses import dataclass
+
 from PySide6.QtCore import QObject
 from PySide6.QtWidgets import QListWidget, QListWidgetItem
 
 from accusleepy.fileio import Recording, load_recording_list, save_recording_list
 
 
+@dataclass
+class RecordingListItem(Recording):
+    """A Recording with an associated QListWidget item for the GUI"""
+
+    widget: QListWidgetItem = None
+
+
 class RecordingListManager(QObject):
     """Manages the list of recordings and the associated QListWidget"""
 
@@ -14,19 +23,19 @@ class RecordingListManager(QObject):
         self._widget = list_widget
 
         # Create initial empty recording (there is always at least one)
-        first_recording = Recording(
+        first_recording = RecordingListItem(
             widget=QListWidgetItem("Recording 1", self._widget),
         )
-        self._recordings: list[Recording] = [first_recording]
+        self._recordings: list[RecordingListItem] = [first_recording]
         self._widget.addItem(first_recording.widget)
         self._widget.setCurrentRow(0)
 
     @property
-    def current(self) -> Recording:
+    def current(self) -> RecordingListItem:
         """The currently selected recording"""
         return self._recordings[self._widget.currentRow()]
 
-    def add(self, sampling_rate: int | float) -> Recording:
+    def add(self, sampling_rate: int | float) -> RecordingListItem:
         """Add a new recording to the list
 
         :param sampling_rate: sampling rate for the new recording
@@ -35,7 +44,7 @@ class RecordingListManager(QObject):
         new_name = max(r.name for r in self._recordings) + 1
 
         # Create recording with widget
-        recording = Recording(
+        recording = RecordingListItem(
             name=new_name,
             sampling_rate=sampling_rate,
             widget=QListWidgetItem(f"Recording {new_name}", self._widget),
@@ -63,7 +72,7 @@ class RecordingListManager(QObject):
         else:
             # Reset the single recording to defaults
             recording_name = self._recordings[0].name
-            self._recordings[0] = Recording(widget=self._recordings[0].widget)
+            self._recordings[0] = RecordingListItem(widget=self._recordings[0].widget)
             self._recordings[0].widget.setText(f"Recording {self._recordings[0].name}")
             return f"cleared Recording {recording_name}"
 
@@ -85,14 +94,15 @@ class RecordingListManager(QObject):
         try:
             self._widget.clear()
 
-            # Load recordings
-            self._recordings = load_recording_list(filename)
-
-            # Create widgets for each recording
-            for recording in self._recordings:
-                recording.widget = QListWidgetItem(
-                    f"Recording {recording.name}", self._widget
+            # Load recordings and create widgets
+            self._recordings = [
+                RecordingListItem(
+                    **r.__dict__,
+                    widget=QListWidgetItem(f"Recording {r.name}", self._widget),
                 )
+                for r in load_recording_list(filename)
+            ]
+            for recording in self._recordings:
                 self._widget.addItem(recording.widget)
         finally:
             self._widget.blockSignals(False)
@@ -106,5 +116,5 @@ class RecordingListManager(QObject):
     def __len__(self):
         return len(self._recordings)
 
-    def __getitem__(self, index: int) -> Recording:
+    def __getitem__(self, index: int) -> RecordingListItem:
         return self._recordings[index]

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/gui/settings_widget.py

@@ -197,7 +197,7 @@ class SettingsWidget(QObject):
         # Brain states
         states = {b.digit: b for b in self._brain_state_set.brain_states}
         for digit in range(10):
-            if digit in states.keys():
+            if digit in states:
                 self._settings_widgets[digit].enabled_widget.setChecked(True)
                 self._settings_widgets[digit].name_widget.setText(states[digit].name)
                 self._settings_widgets[digit].is_scored_widget.setChecked(

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/gui/viewer_window.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 ################################################################################
 ## Form generated from reading UI file 'viewer_window.ui'
 ##
@@ -23,11 +21,11 @@ from PySide6.QtWidgets import (
     QVBoxLayout,
 )
 
-from accusleepy.gui.mplwidget import MplWidget
 import accusleepy.gui.resources_rc  # noqa F401
+from accusleepy.gui.mplwidget import MplWidget
 
 
-class Ui_ViewerWindow(object):
+class Ui_ViewerWindow:
     def setupUi(self, ViewerWindow):
         if not ViewerWindow.objectName():
             ViewerWindow.setObjectName("ViewerWindow")

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/models.py

@@ -1,3 +1,5 @@
+"""Neural network model definitions for sleep stage classification."""
+
 from torch import device, flatten, nn
 from torch import load as torch_load
 from torch import save as torch_save

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/multitaper.py

@@ -14,10 +14,6 @@ import timeit
 import warnings
 
 import numpy as np
-from joblib import Parallel, cpu_count, delayed
-
-# from scipy.signal import detrend # unused by AccuSleePy
-# from scipy.signal.windows import dpss # lazily loaded later
 
 
 # MULTITAPER SPECTROGRAM #
@@ -206,19 +202,9 @@ def spectrogram(
         wt,
     )
 
-    if multiprocess:  # use multiprocessing
-        n_jobs = max(cpu_count() - 1, 1) if n_jobs is None else n_jobs
-        mt_spectrogram = np.vstack(
-            Parallel(n_jobs=n_jobs)(
-                delayed(calc_mts_segment)(data_segments[num_window, :], *mts_params)
-                for num_window in range(num_windows)
-            )
-        )
-
-    else:  # if no multiprocessing, compute normally
-        mt_spectrogram = np.apply_along_axis(
-            calc_mts_segment, 1, data_segments, *mts_params
-        )
+    mt_spectrogram = np.apply_along_axis(
+        calc_mts_segment, 1, data_segments, *mts_params
+    )
 
     # Compute one-sided PSD spectrum
     mt_spectrogram = mt_spectrogram.T
@@ -251,37 +237,6 @@ def spectrogram(
     if np.all(mt_spectrogram.flatten() == 0):
         print("\n Data was all zeros, no output")
 
-    # # Plot multitaper spectrogram
-    # if plot_on:
-    #     # convert from power to dB
-    #     spect_data = nanpow2db(mt_spectrogram)
-    #
-    #     # Set x and y axes
-    #     dx = stimes[1] - stimes[0]
-    #     dy = sfreqs[1] - sfreqs[0]
-    #     extent = [stimes[0] - dx, stimes[-1] + dx, sfreqs[-1] + dy, sfreqs[0] - dy]
-    #
-    #     # Plot spectrogram
-    #     if ax is None:
-    #         fig, ax = plt.subplots()
-    #     else:
-    #         fig = ax.get_figure()
-    #     im = ax.imshow(spect_data, extent=extent, aspect="auto")
-    #     fig.colorbar(im, ax=ax, label="PSD (dB)", shrink=0.8)
-    #     ax.set_xlabel("Time (HH:MM:SS)")
-    #     ax.set_ylabel("Frequency (Hz)")
-    #     im.set_cmap(plt.cm.get_cmap("cet_rainbow4"))
-    #     ax.invert_yaxis()
-    #
-    #     # Scale colormap
-    #     if clim_scale:
-    #         clim = np.percentile(spect_data, [5, 98])  # from 5th percentile to 98th
-    #         im.set_clim(clim)  # actually change colorbar scale
-    #
-    #     fig.show()
-    #     if return_fig:
-    #         return mt_spectrogram, stimes, sfreqs, (fig, ax)
-
     return mt_spectrogram, stimes, sfreqs
 
 
@@ -376,7 +331,8 @@ def process_input(
             + str(frequency_range[0])
             + ", "
             + str(frequency_range[1])
-            + "]"
+            + "]",
+            stacklevel=2,
         )
 
     # Set number of tapers if none provided
@@ -387,7 +343,8 @@ def process_input(
     if num_tapers != math.floor(2 * time_bandwidth) - 1:
         warnings.warn(
             "Number of tapers is optimal at floor(2*TW) - 1. consider using "
-            + str(math.floor(2 * time_bandwidth) - 1)
+            + str(math.floor(2 * time_bandwidth) - 1),
+            stacklevel=2,
         )
 
     # If no window params provided, set to defaults
@@ -400,7 +357,8 @@ def process_input(
         warnings.warn(
             "Window size is not divisible by sampling frequency. Adjusting window size to "
             + str(winsize_samples / fs)
-            + " seconds"
+            + " seconds",
+            stacklevel=2,
         )
     else:
         winsize_samples = window_params[0] * fs
@@ -411,7 +369,8 @@ def process_input(
         warnings.warn(
             "Window step size is not divisible by sampling frequency. Adjusting window step size to "
             + str(winstep_samples / fs)
-            + " seconds"
+            + " seconds",
+            stacklevel=2,
         )
     else:
         winstep_samples = window_params[1] * fs
@@ -553,7 +512,7 @@ def nanpow2db(y):
         ydB (float or np array): inputs converted to dB with 0s and negatives resulting in nans
     """
 
-    if isinstance(y, int) or isinstance(y, float):
+    if isinstance(y, int | float):
         if y == 0:
             return np.nan
         else:
@@ -568,18 +527,6 @@ def nanpow2db(y):
     return ydB
 
 
-# Helper #
-def is_outlier(data):
-    smad = 1.4826 * np.median(
-        abs(data - np.median(data))
-    )  # scaled median absolute deviation
-    outlier_mask = (
-        abs(data - np.median(data)) > 3 * smad
-    )  # outliers are more than 3 smads away from median
-    outlier_mask = outlier_mask | np.isnan(data) | np.isinf(data)
-    return outlier_mask
-
-
 # CALCULATE MULTITAPER SPECTRUM ON SINGLE SEGMENT
 def calc_mts_segment(
     data_segment,
@@ -638,7 +585,7 @@ def calc_mts_segment(
         spower_iter = np.mean(spower[:, 0:2], 1)
         spower_iter = spower_iter[:, np.newaxis]
         a = (1 - dpss_eigen) * tpower
-        for i in range(3):  # 3 iterations only
+        for _i in range(3):  # 3 iterations only
             # Calc the MSE weights
             b = np.dot(spower_iter, np.ones((1, num_tapers))) / (
                 (np.dot(spower_iter, np.transpose(dpss_eigen)))

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/services.py

@@ -8,8 +8,8 @@ import datetime
 import logging
 import os
 import shutil
+from collections.abc import Callable
 from dataclasses import dataclass, field
-from typing import Callable
 
 import numpy as np
 import pandas as pd
@@ -21,9 +21,9 @@ from accusleepy.constants import (
     CALIBRATION_ANNOTATION_FILENAME,
     DEFAULT_MODEL_TYPE,
     MIN_EPOCHS_PER_STATE,
-    UNDEFINED_LABEL,
     MIXTURE_MEAN_COL,
     MIXTURE_SD_COL,
+    UNDEFINED_LABEL,
 )
 from accusleepy.fileio import (
     EMGFilter,
@@ -36,10 +36,10 @@ from accusleepy.fileio import (
 )
 from accusleepy.models import SSANN
 from accusleepy.signal_processing import (
-    create_training_images,
-    resample_and_standardize,
     create_eeg_emg_image,
+    create_training_images,
     get_mixture_values,
+    resample_and_standardize,
 )
 from accusleepy.validation import check_label_validity
 

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/signal_processing.py

@@ -1,3 +1,5 @@
+"""EEG/EMG signal processing, mixture z-scoring, and training image generation."""
+
 import logging
 import os
 import warnings
@@ -19,10 +21,10 @@ from accusleepy.constants import (
     LABEL_COL,
     MIN_EPOCHS_PER_STATE,
     MIN_WINDOW_LEN,
-    UPPER_FREQ,
     SPECTROGRAM_UPPER_FREQ,
+    UPPER_FREQ,
 )
-from accusleepy.fileio import Recording, load_labels, load_recording, EMGFilter
+from accusleepy.fileio import EMGFilter, Recording, load_labels, load_recording
 from accusleepy.multitaper import spectrogram
 
 # note: scipy is lazily imported
@@ -149,7 +151,7 @@ def create_spectrogram(
     # pad the EEG signal so that the first spectrogram window is centered
     # on the first epoch
     # it's possible there's some jank here, if this isn't close to an integer
-    pad_length = round((sampling_rate * (window_length_sec - epoch_length) / 2))
+    pad_length = round(sampling_rate * (window_length_sec - epoch_length) / 2)
     padded_eeg = np.concatenate(
         [eeg[:pad_length][::-1], eeg, eeg[(len(eeg) - pad_length) :][::-1]]
     )
@@ -326,7 +328,10 @@ def mixture_z_score_img(
     if labels is None and (mixture_means is None or mixture_sds is None):
         raise ValueError("must provide either labels or mixture means+SDs")
     if labels is not None and ((mixture_means is not None) ^ (mixture_sds is not None)):
-        warnings.warn("labels were given, mixture means / SDs will be ignored")
+        warnings.warn(
+            "labels were given, mixture means / SDs will be ignored",
+            stacklevel=2,
+        )
 
     if labels is not None:
         mixture_means, mixture_sds = get_mixture_values(

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/temperature_scaling.py

@@ -1,3 +1,5 @@
+"""Temperature scaling for model confidence calibration."""
+
 import logging
 
 import numpy as np
@@ -18,7 +20,7 @@ class ModelWithTemperature(nn.Module):
     """
 
     def __init__(self, model):
-        super(ModelWithTemperature, self).__init__()
+        super().__init__()
         self.model = model
         # https://github.com/gpleiss/temperature_scaling/issues/20
         # for another approach, see https://github.com/gpleiss/temperature_scaling/issues/36
@@ -140,7 +142,7 @@ class _ECELoss(nn.Module):
         """
         n_bins (int): number of confidence interval bins
         """
-        super(_ECELoss, self).__init__()
+        super().__init__()
         bin_boundaries = torch.linspace(0, 1, n_bins + 1)
         self.bin_lowers = bin_boundaries[:-1]
         self.bin_uppers = bin_boundaries[1:]
@@ -151,7 +153,7 @@ class _ECELoss(nn.Module):
         accuracies = predictions.eq(labels)
 
         ece = torch.zeros(1, device=logits.device)
-        for bin_lower, bin_upper in zip(self.bin_lowers, self.bin_uppers):
+        for bin_lower, bin_upper in zip(self.bin_lowers, self.bin_uppers, strict=True):
             # Calculated |confidence - accuracy| in each bin
             in_bin = confidences.gt(bin_lower.item()) * confidences.le(bin_upper.item())
             prop_in_bin = in_bin.float().mean()

{accusleepy-0.10.0 → accusleepy-0.11.0}/accusleepy/validation.py

@@ -1,3 +1,5 @@
+"""Validation utilities for brain state labels and recordings."""
+
 import numpy as np
 
 from accusleepy.brain_state_set import BrainStateSet
@@ -39,9 +41,10 @@ def check_label_validity(
     ):
         return "label file contains invalid entries"
 
-    if confidence_scores is not None:
-        if np.min(confidence_scores) < 0 or np.max(confidence_scores) > 1:
-            return "label file contains invalid confidence scores"
+    if confidence_scores is not None and (
+        np.min(confidence_scores) < 0 or np.max(confidence_scores) > 1
+    ):
+        return "label file contains invalid confidence scores"
 
     return None
 
@@ -141,7 +144,9 @@ def check_config_consistency(
     # generate message comparing the brain state configs
     config_comparisons = list()
     for config, config_name in zip(
-        [current_scored_states, model_scored_states], ["current", "model's"]
+        [current_scored_states, model_scored_states],
+        ["current", "model's"],
+        strict=True,
     ):
         config_comparisons.append(
             f"Scored brain states in {config_name} configuration: "
@@ -152,6 +157,7 @@ def check_config_consistency(
                         for x, y in zip(
                             config["digit"],
                             config["name"],
+                            strict=True,
                         )
                     ]
                 )
@@ -162,32 +168,26 @@ def check_config_consistency(
     len_diff = len(current_scored_states["name"]) - len(model_scored_states["name"])
     if len_diff != 0:
         output.append(
-            (
-                "WARNING: current brain state configuration has "
-                f"{'fewer' if len_diff < 0 else 'more'} "
-                "scored brain states than the model's configuration."
-            )
+            "WARNING: current brain state configuration has "
+            f"{'fewer' if len_diff < 0 else 'more'} "
+            "scored brain states than the model's configuration."
         )
         output = output + config_comparisons
     else:
         # the length is the same, but names might be different
         if current_scored_states["name"] != model_scored_states["name"]:
             output.append(
-                (
-                    "WARNING: current brain state configuration appears "
-                    "to contain different brain states than "
-                    "the model's configuration."
-                )
+                "WARNING: current brain state configuration appears "
+                "to contain different brain states than "
+                "the model's configuration."
             )
             output = output + config_comparisons
 
     if current_epoch_length != model_epoch_length:
         output.append(
-            (
-                "Warning: the epoch length used when training this model "
-                f"({model_epoch_length} seconds) "
-                "does not match the current epoch length setting."
-            )
+            "Warning: the epoch length used when training this model "
+            f"({model_epoch_length} seconds) "
+            "does not match the current epoch length setting."
         )
 
     return output

{accusleepy-0.10.0 → accusleepy-0.11.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "accusleepy"
-version = "0.10.0"
+version = "0.11.0"
 description = "Python implementation of AccuSleep"
 authors = [
     {name = "Zeke Barger",email = "zekebarger@gmail.com"}
@@ -15,15 +15,15 @@ dependencies = [
     "torchvision (>=0.23.0,<1.0.0)",
     "scipy (>=1.15.2,<2.0.0)",
     "matplotlib (>=3.10.1,<4.0.0)",
-    "joblib (>=1.4.2,<2.0.0)",
     "pillow (>=11.1.0,<12.0.0)",
-    "fastparquet (>=2024.11.0,<2025.0.0)",
-    "pre-commit (>=4.2.0,<5.0.0)",
     "tqdm (>=4.67.1,<5.0.0)",
-    "pyside6 (>=6.9.0, <6.9.3)",
+    "pyside6 (>=6.10.1,<7.0.0)",
+    "pyarrow (>=23.0.0,<24.0.0)",
+    "platformdirs (>=4.0.0,<5.0.0)",
 ]
 
 [tool.poetry.group.dev.dependencies]
+pre-commit = ">=4.2.0,<5.0.0"
 pytest = ">=8.3.5,<9.0.0"
 pytest-qt = ">=4.4.0,<5.0.0"
 ruff = ">=0.11.2,<0.12.0"
@@ -35,6 +35,9 @@ build-backend = "poetry.core.masonry.api"
 [tool.ruff]
 extend-exclude = ["*.ipynb"]
 
+[tool.ruff.lint]
+select = ["E4", "E7", "E9", "F", "I", "UP", "B", "SIM", "RUF"]
+
 [tool.pytest.ini_options]
 markers = [
     "gui: marks tests as GUI tests (may require display or xvfb)",