lint!!!

miniscope_io/data.py

@@ -23,20 +23,14 @@ class Frame(BaseModel, arbitrary_types_allowed=True):
 
     @field_validator("headers")
     @classmethod
-    def frame_nums_must_be_equal(
-        cls, v: List[SDBufferHeader]
-    ) -> Optional[List[SDBufferHeader]]:
+    def frame_nums_must_be_equal(cls, v: List[SDBufferHeader]) -> Optional[List[SDBufferHeader]]:
         """
         Each frame_number field in each header must be the same
         (they come from the same frame!)
         """
 
-        if v is not None and not all(
-            [header.frame_num != v[0].frame_num for header in v]
-        ):
-            raise ValueError(
-                f"All frame numbers should be equal! Got f{[h.frame_num for h in v]}"
-            )
+        if v is not None and not all([header.frame_num != v[0].frame_num for header in v]):
+            raise ValueError(f"All frame numbers should be equal! Got f{[h.frame_num for h in v]}")
         return v
 
     @property
@@ -55,16 +49,12 @@ class Frames(BaseModel):
     frames: List[Frame]
 
     @overload
-    def flatten_headers(
-        self, as_dict: Literal[False] = False
-    ) -> List[SDBufferHeader]: ...
+    def flatten_headers(self, as_dict: Literal[False] = False) -> List[SDBufferHeader]: ...
 
     @overload
     def flatten_headers(self, as_dict: Literal[True] = True) -> List[dict]: ...
 
-    def flatten_headers(
-        self, as_dict: bool = False
-    ) -> Union[List[dict], List[SDBufferHeader]]:
+    def flatten_headers(self, as_dict: bool = False) -> Union[List[dict], List[SDBufferHeader]]:
         """
         Return flat list of headers, not grouped by frame
 

miniscope_io/device_update.py

@@ -126,9 +126,7 @@ def updateDevice() -> None:
 
     # set up serial port
     try:
-        serial_port = serial.Serial(
-            port=comport, baudrate=baudrate, timeout=5, stopbits=1
-        )
+        serial_port = serial.Serial(port=comport, baudrate=baudrate, timeout=5, stopbits=1)
     except Exception as e:
         logger.exception(e)
         raise e

miniscope_io/devices/opalkelly.py

@@ -45,13 +45,9 @@ def uploadBit(self, bit_file: str) -> None:
         if ret == self.NoError:
             self.logger.debug(f"Succesfully uploaded {bit_file}")
         else:
-            raise DeviceConfigurationError(
-                f"Configuration of {self.info.productName} failed"
-            )
+            raise DeviceConfigurationError(f"Configuration of {self.info.productName} failed")
         self.logger.debug(
-            "FrontPanel {} supported".format(
-                "is" if self.IsFrontPanelEnabled() else "not"
-            )
+            "FrontPanel {} supported".format("is" if self.IsFrontPanelEnabled() else "not")
         )
         ret = self.ResetFPGA()
 

miniscope_io/io.py

@@ -65,9 +65,7 @@ def config(self) -> SDConfig:
         if self._config is None:
             with open(self.drive, "rb") as sd:
                 sd.seek(self.layout.sectors.config_pos, 0)
-                configSectorData = np.frombuffer(
-                    sd.read(self.layout.sectors.size), dtype=np.uint32
-                )
+                configSectorData = np.frombuffer(sd.read(self.layout.sectors.size), dtype=np.uint32)
 
             self._config = SDConfig(
                 **{
@@ -159,8 +157,7 @@ def frame_count(self) -> int:
 
             self._frame_count = int(
                 np.ceil(
-                    (self.config.n_buffers_recorded + self.config.n_buffers_dropped)
-                    / len(headers)
+                    (self.config.n_buffers_recorded + self.config.n_buffers_dropped) / len(headers)
                 )
             )
 
@@ -187,9 +184,7 @@ def __enter__(self) -> "SDCard":
 
         # init private attrs
         # create an empty frame to hold our data!
-        self._array = np.zeros(
-            (self.config.width * self.config.height, 1), dtype=np.uint8
-        )
+        self._array = np.zeros((self.config.width * self.config.height, 1), dtype=np.uint8)
         self._pixel_count = 0
         self._last_buffer_n = 0
         self._frame = 0
@@ -202,7 +197,7 @@ def __enter__(self) -> "SDCard":
 
         return self
 
-    def __exit__(self, exc_type, exc_value, traceback):
+    def __exit__(self, exc_type, exc_val, exc_tb):  # noqa: ANN001
         self._f.close()
         self._f = None
         self._frame = 0
@@ -224,9 +219,7 @@ def _read_data_header(self, sd: BinaryIO) -> SDBufferHeader:
         dataHeader = np.append(
             dataHeader,
             np.frombuffer(
-                sd.read(
-                    (dataHeader[self.layout.buffer.length] - 1) * self.layout.word_size
-                ),
+                sd.read((dataHeader[self.layout.buffer.length] - 1) * self.layout.word_size),
                 dtype=np.uint32,
             ),
         )
@@ -265,9 +258,7 @@ def _read_size(self, header: SDBufferHeader) -> int:
         them separate in case they are separable actions for now
         """
         n_blocks = self._n_frame_blocks(header)
-        read_size = (n_blocks * self.layout.sectors.size) - (
-            header.length * self.layout.word_size
-        )
+        read_size = (n_blocks * self.layout.sectors.size) - (header.length * self.layout.word_size)
         return read_size
 
     def _read_buffer(self, sd: BinaryIO, header: SDBufferHeader) -> np.ndarray:
@@ -340,18 +331,14 @@ def read(self, return_header: bool = False) -> Union[np.ndarray, Frame]:
                     # blank,  and thus have a value of 0 for the header size, and we
                     # can't read 0 from the card.
                     self._f.seek(last_position, 0)
-                    raise EndOfRecordingException(
-                        "Reached the end of the video!"
-                    ) from None
+                    raise EndOfRecordingException("Reached the end of the video!") from None
                 else:
                     raise e
             except IndexError as e:
                 if "index 0 is out of bounds for axis 0 with size 0" in str(e):
                     # end of file if we are reading from a disk image without any
                     # additional space on disk
-                    raise EndOfRecordingException(
-                        "Reached the end of the video!"
-                    ) from None
+                    raise EndOfRecordingException("Reached the end of the video!") from None
                 else:
                     raise e
 
@@ -387,7 +374,7 @@ def to_video(
         isColor: bool = False,
         force: bool = False,
         progress: bool = True,
-    ):
+    ) -> None:
         """
         Save contents of SD card to video with opencv
 
@@ -411,8 +398,7 @@ def to_video(
         path = Path(path)
         if path.exists() and not force:
             raise FileExistsError(
-                f"{str(path)} already exists, not overwriting. "
-                "Use force=True to overwrite."
+                f"{str(path)} already exists, not overwriting. " "Use force=True to overwrite."
             )
 
         if progress:
@@ -454,7 +440,7 @@ def to_video(
     # General Methods
     # --------------------------------------------------
 
-    def skip(self):
+    def skip(self) -> None:
         """
         Skip a frame
 
@@ -502,9 +488,7 @@ def check_valid(self) -> bool:
         """
         with open(self.drive, "rb") as sd:
             sd.seek(self.layout.sectors.header_pos, 0)
-            headerSectorData = np.frombuffer(
-                sd.read(self.layout.sectors.size), dtype=np.uint32
-            )
+            headerSectorData = np.frombuffer(sd.read(self.layout.sectors.size), dtype=np.uint32)
 
             valid = False
             if (

miniscope_io/logging.py

@@ -1,3 +1,7 @@
+"""
+Logging factory and handlers
+"""
+
 import logging
 from logging.handlers import RotatingFileHandler
 from pathlib import Path
@@ -15,7 +19,7 @@ def init_logger(
     file_level: Optional[LOG_LEVELS] = None,
     log_file_n: Optional[int] = None,
     log_file_size: Optional[int] = None,
-):
+) -> logging.Logger:
     """
     Make a logger.
 
@@ -60,9 +64,7 @@ def init_logger(
 
     # Add handlers for stdout and file
     if log_dir is not False:
-        logger.addHandler(
-            _file_handler(name, file_level, log_dir, log_file_n, log_file_size)
-        )
+        logger.addHandler(_file_handler(name, file_level, log_dir, log_file_n, log_file_size))
 
     logger.addHandler(_rich_handler())
 
@@ -82,9 +84,7 @@ def _file_handler(
     file_handler = RotatingFileHandler(
         str(filename), mode="a", maxBytes=log_file_size, backupCount=log_file_n
     )
-    file_formatter = logging.Formatter(
-        "[%(asctime)s] %(levelname)s [%(name)s]: %(message)s"
-    )
+    file_formatter = logging.Formatter("[%(asctime)s] %(levelname)s [%(name)s]: %(message)s")
     file_handler.setLevel(file_level)
     file_handler.setFormatter(file_formatter)
     return file_handler

miniscope_io/models/__init__.py

@@ -1,3 +1,7 @@
+"""
+Data models :)
+"""
+
 from miniscope_io.models.models import Container, MiniscopeConfig, MiniscopeIOModel
 
 __all__ = [

miniscope_io/models/config.py

@@ -1,3 +1,7 @@
+"""
+Module-global configuration models
+"""
+
 from pathlib import Path
 from typing import Literal, Optional
 
@@ -38,7 +42,10 @@ class LogConfig(MiniscopeIOModel):
 
     @field_validator("level", "level_file", "level_stdout", mode="before")
     @classmethod
-    def uppercase_levels(cls, value: Optional[str] = None):
+    def uppercase_levels(cls, value: Optional[str] = None) -> Optional[str]:
+        """
+        Ensure log level strings are uppercased
+        """
         if value is not None:
             value = value.upper()
         return value
@@ -74,14 +81,16 @@ class Config(BaseSettings):
 
     base_dir: Path = Field(
         _default_basedir,
-        description="Base directory to store configuration and other temporary files, other paths are relative to this by default",
+        description="Base directory to store configuration and other temporary files, "
+        "other paths are relative to this by default",
     )
     log_dir: Path = Field(Path("logs"), description="Location to store logs")
     logs: LogConfig = Field(LogConfig(), description="Additional settings for logs")
 
     @field_validator("base_dir", mode="before")
     @classmethod
     def folder_exists(cls, v: Path) -> Path:
+        """Ensure base_dir exists, make it otherwise"""
         v = Path(v)
         v.mkdir(exist_ok=True, parents=True)
 
@@ -90,6 +99,7 @@ def folder_exists(cls, v: Path) -> Path:
 
     @model_validator(mode="after")
     def paths_relative_to_basedir(self) -> "Config":
+        """If relative paths are given, make them absolute relative to ``base_dir``"""
         paths = ("log_dir",)
         for path_name in paths:
             path = getattr(self, path_name)  # type: Path

miniscope_io/models/mixins.py

@@ -19,6 +19,7 @@ class YAMLMixin:
 
     @classmethod
     def from_yaml(cls: Type[T], file_path: Union[str, Path]) -> T:
+        """Instantiate this class by passing the contents of a yaml file as kwargs"""
         with open(file_path) as file:
             config_data = yaml.safe_load(file)
         return cls(**config_data)

miniscope_io/models/sdcard.py

@@ -117,12 +117,14 @@ class SDLayout(MiniscopeConfig):
     write_key2: int = 0x0D7CBA17
     write_key3: int = 0x0D7CBA17
     """
-    These don't seem to actually be used in the existing reading/writing code, but we will leave them here for continuity's sake :)
+    These don't seem to actually be used in the existing reading/writing code, 
+    but we will leave them here for continuity's sake :)
     """
     word_size: int = 4
     """
-    I'm actually not sure what this is, but 4 is hardcoded a few times in the existing notebook and it
-    appears to be used as a word size when reading from the SD card.
+    I'm actually not sure what this is, but 4 is hardcoded a few times in the 
+    existing notebook and it appears to be used as a word size when
+    reading from the SD card.
     """
 
     header: SDHeaderPositions = SDHeaderPositions()
@@ -140,7 +142,8 @@ class SDConfig(MiniscopeConfig):
     """
     The configuration of a recording taken on this SD card.
 
-    Read from the locations given in :class:`.ConfigPositions` for an SD card with a given :class:`.SDLayout`
+    Read from the locations given in :class:`.ConfigPositions`
+    for an SD card with a given :class:`.SDLayout`
     """
 
     width: int