add pre-commit checks

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.10
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black

miniscope_io/data.py

@@ -18,8 +18,8 @@ class Frame(BaseModel, arbitrary_types_allowed=True):
     Typically returned from :meth:`.SDCard.read`
     """
 
-    data: Optional[np.ndarray] = None
-    headers: Optional[List[SDBufferHeader]] = None
+    data: np.ndarray
+    headers: List[SDBufferHeader]
 
     @field_validator("headers")
     @classmethod
@@ -34,9 +34,9 @@ def frame_nums_must_be_equal(cls, v: List[SDBufferHeader]) -> Optional[List[SDBu
         return v
 
     @property
-    def frame_num(self) -> int:
+    def frame_num(self) -> Optional[int]:
         """
-        Frame number for this set of headers
+        Frame number for this set of headers, if headers are present
         """
         return self.headers[0].frame_num
 
@@ -49,10 +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]) -> List[SDBufferHeader]:
+        ...
 
     @overload
-    def flatten_headers(self, as_dict: Literal[True] = True) -> List[dict]: ...
+    def flatten_headers(self, as_dict: Literal[True]) -> List[dict]:
+        ...
 
     def flatten_headers(self, as_dict: bool = False) -> Union[List[dict], List[SDBufferHeader]]:
         """
@@ -62,8 +64,9 @@ def flatten_headers(self, as_dict: bool = False) -> Union[List[dict], List[SDBuf
             as_dict (bool): If `True`, return a list of dictionaries, if `False`
                 (default), return a list of :class:`.SDBufferHeader` s.
         """
-        h = []
+        h: Union[List[dict], List[SDBufferHeader]] = []
         for frame in self.frames:
+            headers: Union[List[dict], List[SDBufferHeader]]
             if as_dict:
                 headers = [header.model_dump() for header in frame.headers]
             else:

miniscope_io/devices/mocks.py

@@ -11,7 +11,7 @@
 
 import os
 from pathlib import Path
-from typing import Dict
+from typing import Dict, Optional
 
 from miniscope_io.exceptions import EndOfRecordingException
 
@@ -21,7 +21,7 @@ class okDevMock:
     Mock class for :class:`~miniscope_io.devices.opalkelly.okDev`
     """
 
-    DATA_FILE = None
+    DATA_FILE: Optional[Path] = None
     """
     Recorded data file to use for simulating read.
     
@@ -34,19 +34,22 @@ class okDevMock:
 
     def __init__(self, serial_id: str = ""):
         self.serial_id = serial_id
-        self.bit_file = None
+        self.bit_file: Optional[Path] = None
 
         self._wires: Dict[int, int] = {}
         self._buffer_position = 0
 
         # preload the data file to a byte array
         if self.DATA_FILE is None:
-            if os.environ.get("PYTEST_OKDEV_DATA_FILE", False):
+            if os.environ.get("PYTEST_OKDEV_DATA_FILE") is not None:
                 # need to get file from env variables here because on some platforms
                 # the default method for creating a new process is "spawn" which creates
                 # an entirely new python session instead of "fork" which would preserve
                 # the classvar
-                okDevMock.DATA_FILE = Path(os.environ.get("PYTEST_OKDEV_DATA_FILE"))
+                data_file: str = os.environ.get("PYTEST_OKDEV_DATA_FILE")  # type: ignore
+
+                self.DATA_FILE = Path(data_file)
+                okDevMock.DATA_FILE = Path(data_file)
             else:
                 raise RuntimeError("DATA_FILE class attr must be set before using the mock")
 
@@ -55,7 +58,7 @@ def __init__(self, serial_id: str = ""):
 
     def uploadBit(self, bit_file: str) -> None:
         assert Path(bit_file).exists()
-        self.bit_file = bit_file
+        self.bit_file = Path(bit_file)
 
     def readData(self, length: int, addr: int = 0xA0, blockSize: int = 16) -> bytearray:
         if self._buffer_position >= len(self._buffer):

miniscope_io/utils.py

@@ -38,7 +38,7 @@ def hash_file(path: Union[Path, str]) -> str:
 
 def hash_video(
     path: Union[Path, str],
-    method: hashlib.algorithms_available = "blake2s",
+    method: str = "blake2s",
 ) -> str:
     """
     Create a hash of a video by digesting the byte string each of its decoded frames.
@@ -60,6 +60,6 @@ def hash_video(
         ret, frame = vid.read()
         if not ret:
             break
-        h.update(frame)
+        h.update(frame)  # type: ignore
 
     return h.hexdigest()