Harden Sphinx autodoc imports to include full API

docs/source/conf.py

@@ -61,10 +61,12 @@ def __call__(self, *args, **kwargs):
     "matplotlib.pyplot",
     "matplotlib.dates",
     "matplotlib.figure",
-    "picamera2",
-    "picamera2",
     "jinja2",
     "seaborn",
+    "PyQt6",
+    "gpiod",
+    "picamera2",
+    "libcamera",
 ]
 
 # Add the module path to sys.path here.
@@ -247,6 +249,4 @@ def __call__(self, *args, **kwargs):
 
 autosectionlabel_prefix_document = True
 
-autodoc_mock_imports = ["PyQt5", "PyQt6", "gpiod", "picamera2", "libcamera"]
-
 suppress_warnings = ["docutils"]

village/calibration/sound_calibration.py

@@ -60,4 +60,3 @@ def run_in_thread(self, daemon: bool = True) -> None:
     def close(self) -> None:
         """Closes the calibration instance and releases resources."""
         return
-

village/classes/abstract_classes.py

@@ -17,6 +17,7 @@ class PyBpodBase:
         session (Session | Any): Bpod session object.
         connected (bool): Connection status.
     """
+
     error: str = "Error connecting to the bpod "
     session: Session | Any = None
     connected: bool = False
@@ -182,6 +183,7 @@ class TelegramBotBase:
     Attributes:
         error (str): Error message.
     """
+
     error: str = "Error connecting to the telegram_bot "
 
     def alarm(self, message: str) -> None:
@@ -199,6 +201,7 @@ class ScaleBase:
     Attributes:
         error (str): Error message.
     """
+
     error: str = "Error connecting to the scale "
 
     def tare(self) -> None:
@@ -228,6 +231,7 @@ class TempSensorBase:
     Attributes:
         error (str): Error message.
     """
+
     error: str = "Error connecting to the temp_sensor "
 
     def start(self) -> None:
@@ -251,6 +255,7 @@ class MotorBase:
         open_angle (int): Angle for open position.
         close_angle (int): Angle for close position.
     """
+
     error: str = "Error connecting to the motor "
     open_angle: int = 0
     close_angle: int = 0
@@ -271,6 +276,7 @@ class SoundDeviceBase:
         samplerate (int): Audio sample rate.
         error (str): Error message.
     """
+
     samplerate: int = 44100
     error: str = (
         ""
@@ -353,6 +359,7 @@ class CameraBase:
         y_position (int): Y coordinate of tracked object.
         chrono (time_utils.Chrono): Timer utility.
     """
+
     area1: list[int] = []
     area2: list[int] = []
     area3: list[int] = []
@@ -477,6 +484,7 @@ class BehaviorWindowBase(QWidget):
     Attributes:
         background_color: The background color.
     """
+
     background_color = None
 
     def start_drawing(self) -> None:
@@ -525,4 +533,3 @@ def get_video_frame(self) -> Optional[QImage]:
             Optional[QImage]: The current frame as a QImage.
         """
         return None
-

village/classes/collection.py

@@ -381,4 +381,3 @@ def convert_active(value) -> str:
             )
 
         return new_df
-

village/classes/enums.py

@@ -91,6 +91,7 @@ class AreaActive(SuperEnum):
 
 class State(SuperEnum):
     """Enum representing the state of the village system."""
+
     WAIT = "All subjects are at home, waiting for RFID detection"
     DETECTION = "Gathering subject data, checking requirements to enter"
     ACCESS = "Closing door1, opening door2"
@@ -226,4 +227,3 @@ class Save(SuperEnum):
     NO = "NO"
     ZERO = "ZERO"
     ERROR = "ERROR"
-

village/classes/settings_class.py

@@ -193,12 +193,12 @@ def get(self, key: str) -> Any:
         val = self.saved_settings.value(key)
         if val is None:
             return setting.value
-        
+
         # If QSettings returns a QVariant/PyQt object/string that is not the value we expect
         # but contains "QSettings", it's likely a Sphinx build artifact or mock issue.
         val_str = str(val)
         if "QSettings" in val_str or "PyQt5" in val_str:
-             return setting.value
+            return setting.value
 
         str_value = str(val)
         try:

village/classes/subject.py

@@ -82,4 +82,3 @@ def minimum_time_ok(self) -> bool:
                 subject=self.name,
             )
             return False
-

village/custom_classes/after_session_base.py

@@ -16,7 +16,7 @@
 
 class AfterSessionBase:
     """Base class for operations performed after a session ends.
-    
+
     This class handles data synchronization (backup) to either a hard drive
     or a remote server based on current settings.
     """
@@ -62,4 +62,3 @@ def run(self) -> None:
 if __name__ == "__main__":
     after_session = AfterSessionBase()
     after_session.run()
-

village/custom_classes/camera_trigger_base.py

@@ -3,21 +3,21 @@
 
 class CameraTriggerBase:
     """Base class for defining custom camera trigger behavior.
-    
+
     This class can be overridden to implement specific actions when detection areas
     are triggered or to monitor subject position.
     """
-    
+
     def __init__(self) -> None:
         """Initializes the CameraTriggerBase instance."""
         self.name = "Camera Trigger"
 
     def trigger(self, cam: CameraBase) -> None:
         """Evaluates camera triggers and performs corresponding actions.
-        
+
         This method is called to check if any defined areas in the camera view
         have been triggered (e.g., by the subject entering them).
-        
+
         Args:
             cam (CameraBase): The camera instance providing the trigger status.
         """
@@ -37,4 +37,3 @@ def trigger(self, cam: CameraBase) -> None:
             cam.write_text("Area 4 triggered")
 
         # or you can check the position of the animal manually
-

village/custom_classes/change_cycle_base.py

@@ -15,7 +15,7 @@
 
 class ChangeCycleBase:
     """Base class for operations performed during the day/night cycle change.
-    
+
     This class handles cleanup tasks such as deleting old video files and ensuring
     disk space is managed, potentially backing up data before deletion.
     """
@@ -64,4 +64,3 @@ def run(self) -> None:
 if __name__ == "__main__":
     change_cycle = ChangeCycleBase()
     change_cycle.run()
-

village/custom_classes/online_plot_base.py

@@ -78,4 +78,3 @@ def update_plot(self, df: pd.DataFrame) -> None:
             return
 
         df.plot(kind="scatter", x="TRIAL_START", y="trial", ax=self.ax)
-

village/custom_classes/session_plot_base.py

@@ -35,4 +35,3 @@ def create_plot(
         df.plot(kind="line", x="TRIAL_START", y="trial", ax=ax)
         ax.scatter(df["TRIAL_START"], df["trial"], color="red")
         return fig
-

village/custom_classes/subject_plot_base.py

@@ -36,4 +36,3 @@ def create_plot(
         ax.set_title("Subject Plot")
         ax.set_ylabel("Number of trials")
         return fig
-

village/custom_classes/task.py

@@ -29,11 +29,13 @@ def __init__(self, message) -> None:
 
 class Event(EventName):
     """Enumeration of Bpod event names."""
+
     pass
 
 
 class Output(OutputChannel):
     """Enumeration of Bpod output channels."""
+
     pass
 
 
@@ -117,6 +119,7 @@ def run_in_thread(self, daemon: bool = True) -> None:
         Args:
             daemon (bool, optional): Whether to run as a daemon thread. Defaults to True.
         """
+
         def test_run():
             self.create_paths()
             self.start()
@@ -562,4 +565,3 @@ def create_paths(self) -> None:
         self.video_path = str(Path(self.video_directory, self.filename + ".mp4"))
         self.video_data_path = str(Path(self.video_directory, self.filename + ".csv"))
         self.subject_path = str(Path(self.sessions_directory, self.subject + ".csv"))
-

village/custom_classes/training_protocol_base.py

@@ -248,4 +248,3 @@ def get_string(self) -> str:
         dict = self.get_dict()
         _, new_dict = self.correct_types_in_dict(dict)
         return json.dumps(new_dict)
-

village/devices/bpod.py

@@ -394,4 +394,3 @@ def get_bpod() -> PyBpodBase:
 
 
 bpod = get_bpod()
-

village/devices/motor.py

@@ -157,7 +157,6 @@ def get_motor(pin: int, angles: list[int]) -> MotorBase:
         return MotorBase()
 
 
-
 import sys
 
 if "sphinx" in sys.modules:
@@ -166,4 +165,3 @@ def get_motor(pin: int, angles: list[int]) -> MotorBase:
 else:
     motor1 = get_motor(settings.get("MOTOR1_PIN"), settings.get("MOTOR1_VALUES"))
     motor2 = get_motor(settings.get("MOTOR2_PIN"), settings.get("MOTOR2_VALUES"))
-

village/devices/rfid.py

@@ -104,4 +104,3 @@ def get_id(self) -> tuple[str, bool]:
 
 
 rfid = Rfid()
-

village/devices/scale.py

@@ -92,7 +92,7 @@ def get_value(self, samples: int = 1, interval_s: float = 0.005) -> int:
             if interval_s > 0 and i < samples - 1:
                 time.sleep(interval_s)
         if not values:
-             return 0
+            return 0
         median = int(np.median(values))
         if median == 0 and self.alarm_timer.has_elapsed():
             log.alarm("Scale not responding, please check the connection.")
@@ -158,4 +158,3 @@ def real_weight_inference(weight_array, threshold) -> tuple[bool, float]:
         return (True, median_weight)
     else:
         return (False, 0.0)
-

village/devices/sound_device.py

@@ -232,4 +232,3 @@ def get_sound_device() -> SoundDeviceBase:
 
 
 sound_device = get_sound_device()
-

village/devices/telegram_bot.py

@@ -196,4 +196,3 @@ def get_telegram_bot() -> TelegramBotBase:
 
 
 telegram_bot = get_telegram_bot()
-

village/devices/temp_sensor.py

@@ -78,4 +78,3 @@ def get_temp_sensor(address: str) -> TempSensorBase:
 
 
 temp_sensor = get_temp_sensor(address=settings.get("TEMP_SENSOR_ADDRESS"))
-

village/gui/data_layout.py

@@ -8,7 +8,6 @@
 import cv2
 import numpy as np
 import pandas as pd
-from village.classes.enums import State
 from pandas import DataFrame
 from PyQt5.QtCore import (
     QAbstractTableModel,
@@ -40,7 +39,7 @@
     QWidget,
 )
 
-from village.classes.enums import DataTable
+from village.classes.enums import DataTable, State
 from village.gui.layout import Layout
 from village.manager import manager
 from village.plots.sound_calibration_plot import sound_calibration_plot

village/gui/gui.py

@@ -78,4 +78,3 @@ def reload_app(self) -> None:
         self.q_app.quit()
         python = sys.executable
         os.execv(python, [python] + sys.argv)
-

village/gui/gui_window.py

@@ -139,4 +139,3 @@ def check_update_chrono(self) -> None:
         """
         if self.update_chrono.get_seconds() > self.screensave_time:
             self.layout.main_button_clicked(auto=True)
-

village/gui/layout.py

@@ -5,7 +5,6 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, Callable
 
-from village.classes.enums import State
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from PyQt5.QtCore import Qt, QTime
 from PyQt5.QtGui import QCloseEvent, QPixmap, QWheelEvent
@@ -21,7 +20,7 @@
     QVBoxLayout,
 )
 
-from village.classes.enums import DataTable
+from village.classes.enums import DataTable, State
 from village.manager import manager
 from village.scripts.log import log
 from village.settings import settings
@@ -32,6 +31,7 @@
 
 class Label(QLabel):
     """Custom styled QLabel."""
+
     def __init__(
         self,
         text: str,
@@ -60,6 +60,7 @@ def __init__(
 
 class LabelImage(QLabel):
     """QLabel for displaying an image from the resources directory."""
+
     def __init__(self, file) -> None:
         """Initializes a LabelImage."""
         super().__init__()
@@ -71,6 +72,7 @@ def __init__(self, file) -> None:
 
 class LineEdit(QLineEdit):
     """Custom QLineEdit that triggers an action on text change."""
+
     def __init__(self, text: str, action: Callable) -> None:
         """Initializes a LineEdit."""
         super().__init__()
@@ -80,6 +82,7 @@ def __init__(self, text: str, action: Callable) -> None:
 
 class TimeEdit(QTimeEdit):
     """Custom QTimeEdit with HH:mm format."""
+
     def __init__(self, text: str, action: Callable) -> None:
         """Initializes a TimeEdit."""
         super().__init__()
@@ -90,6 +93,7 @@ def __init__(self, text: str, action: Callable) -> None:
 
 class PushButton(QPushButton):
     """Custom styled QPushButton."""
+
     def __init__(
         self, text: str, color: str, action: Callable, description: str
     ) -> None:
@@ -105,6 +109,7 @@ def __init__(
 
 class ToggleButton(QPushButton):
     """Button that cycles through a list of values when pressed."""
+
     def __init__(
         self,
         key: str,
@@ -151,6 +156,7 @@ def on_pressed(self) -> None:
 
 class ComboBox(QComboBox):
     """Custom QComboBox linked to a setting or variable."""
+
     def __init__(
         self, key: str, possible_values: list[str], index: int, action: Callable
     ) -> None:
@@ -188,7 +194,6 @@ def wheelEvent(self, event: QWheelEvent) -> None:
         event.ignore()
 
 
-
 class Layout(QGridLayout):
     """Base class for all GUI layouts in the application.