add linting, reformat with black

.github/workflows/lint.yml

@@ -0,0 +1,13 @@
+name: Lint
+
+on:
+  push:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
+      - uses: psf/black@stable

miniscope_io/__init__.py

@@ -5,15 +5,15 @@
 from miniscope_io.io import SDCard
 
 BASE_DIR = Path(__file__).parent.resolve()
-DATA_DIR = BASE_DIR / 'data'
-CONFIG_DIR = DATA_DIR / 'config'
-DEVICE_DIR = BASE_DIR / 'devices'
+DATA_DIR = BASE_DIR / "data"
+CONFIG_DIR = DATA_DIR / "config"
+DEVICE_DIR = BASE_DIR / "devices"
 
 __all__ = [
-    'BASE_DIR',
-    'DATA_DIR',
-    'CONFIG_DIR',
-    'Config',
-    'SDCard',
-    'init_logger',
-]
+    "BASE_DIR",
+    "DATA_DIR",
+    "CONFIG_DIR",
+    "Config",
+    "SDCard",
+    "init_logger",
+]

miniscope_io/data.py

@@ -1,31 +1,40 @@
 """
 Classes for using in-memory data from a miniscope
 """
+
 import numpy as np
 from typing import List, Optional, overload, Literal, Union
 from miniscope_io.models.sdcard import SDBufferHeader
 from pydantic import BaseModel, field_validator
 
 import pandas as pd
 
+
 class Frame(BaseModel, arbitrary_types_allowed=True):
     """
     An individual frame from a miniscope recording
 
     Typically returned from :meth:`.SDCard.read`
     """
+
     data: Optional[np.ndarray] = None
     headers: Optional[List[SDBufferHeader]] = None
 
-    @field_validator('headers')
+    @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
@@ -40,15 +49,20 @@ class Frames(BaseModel):
     """
     A collection of frames from a miniscope recording
     """
+
     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: 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
 
@@ -65,7 +79,7 @@ def flatten_headers(self, as_dict:bool = False) -> Union[List[dict],List[SDBuffe
             h.extend(headers)
         return h
 
-    def to_df(self, what:Literal['headers']='headers') -> pd.DataFrame:
+    def to_df(self, what: Literal["headers"] = "headers") -> pd.DataFrame:
         """
         Convert frames to pandas dataframe
 
@@ -77,5 +91,4 @@ def to_df(self, what:Literal['headers']='headers') -> pd.DataFrame:
         if what == "headers":
             return pd.DataFrame(self.flatten_headers(as_dict=True))
         else:
-            raise ValueError('Return mode not implemented!')
-
+            raise ValueError("Return mode not implemented!")

miniscope_io/device_update.py

@@ -13,8 +13,9 @@
 updateDeviceParser.add_argument("module", help="module to update")
 updateDeviceParser.add_argument("value", help="LED value")
 
+
 def updateDevice():
-    '''
+    """
     Script to update hardware settings over a generic UART-USB converter.
     This script currently supports updating the excitation LED brightness and electrical wetting lens driver gain.
     Not tested after separating from stream_daq.py.
@@ -25,8 +26,8 @@ def updateDevice():
 
     ..todo::
         Test to see if changing package structure broke anything.
-    '''
-    logger = init_logger('streamDaq')
+    """
+    logger = init_logger("streamDaq")
 
     args = updateDeviceParser.parse_args()
     moduleList = ["LED", "EWL"]
@@ -73,7 +74,7 @@ def updateDevice():
     except AssertionError as msg:
         err_str = "Available modules:\n"
         for module in moduleList:
-            err_str += "\t" + module + '\n'
+            err_str += "\t" + module + "\n"
         logger.exception(err_str)
         raise msg
 
@@ -103,9 +104,7 @@ def updateDevice():
     command = [0, 0]
 
     command[0] = int(
-        Preamble[0] * 2**preamblePos
-        + deviceTag
-        + np.floor(value / (2**uartPayload))
+        Preamble[0] * 2**preamblePos + deviceTag + np.floor(value / (2**uartPayload))
     ).to_bytes(1, "big")
     command[1] = int(
         Preamble[1] * 2**preamblePos + deviceTag + value % (2**uartPayload)
@@ -131,4 +130,3 @@ def updateDevice():
     logger.info("\t" + module + ": " + str(value))
     logger.info("Close serial port")
     sys.exit(1)
-

miniscope_io/devices/opalkelly.py

@@ -15,6 +15,7 @@ class okDev(ok.okCFrontPanel):
         and how they're generated/where they're located.
 
     """
+
     def __init__(self, serial_id: str = ""):
         super().__init__()
         ret = self.OpenBySerial("")

miniscope_io/exceptions.py

@@ -1,10 +1,10 @@
-
 class InvalidSDException(Exception):
     """
     Raised when :class:`.io.SDCard` is used with a drive that doesn't have the appropriate WRITE KEYS in its header
     """
 
+
 class EndOfRecordingException(StopIteration):
     """
     Raised when :class:`.io.SDCard` is at the end of the available recording!
-    """
+    """

miniscope_io/formats/__init__.py

@@ -6,6 +6,4 @@
 
 from miniscope_io.formats.sdcard import WireFreeSDLayout
 
-__all__ = [
-    "WireFreeSDLayout"
-]
+__all__ = ["WireFreeSDLayout"]

miniscope_io/formats/sdcard.py

@@ -2,49 +2,43 @@
 SD Card data layout formats for different miniscopes!
 """
 
-from miniscope_io.models.sdcard import SectorConfig, ConfigPositions, SDHeaderPositions, \
-    BufferHeaderPositions, SDLayout
+from miniscope_io.models.sdcard import (
+    SectorConfig,
+    ConfigPositions,
+    SDHeaderPositions,
+    BufferHeaderPositions,
+    SDLayout,
+)
 
 WireFreeSDLayout = SDLayout(
     version="0.1.1",
-    sectors=SectorConfig(
-        header = 1022,
-        config = 1023,
-        data   = 1024,
-        size   = 512
+    sectors=SectorConfig(header=1022, config=1023, data=1024, size=512),
+    write_key0=0x0D7CBA17,
+    write_key1=0x0D7CBA17,
+    write_key2=0x0D7CBA17,
+    write_key3=0x0D7CBA17,
+    header=SDHeaderPositions(
+        gain=4, led=5, ewl=6, record_length=7, fs=8, delay_start=9, battery_cutoff=10
     ),
-    write_key0 = 0x0D7CBA17,
-    write_key1 = 0x0D7CBA17,
-    write_key2 = 0x0D7CBA17,
-    write_key3 = 0x0D7CBA17,
-    header = SDHeaderPositions(
-        gain           = 4,
-        led            = 5,
-        ewl            = 6,
-        record_length  = 7,
-        fs             = 8,
-        delay_start    = 9,
-        battery_cutoff = 10
+    config=ConfigPositions(
+        width=0,
+        height=1,
+        fs=2,
+        buffer_size=3,
+        n_buffers_recorded=4,
+        n_buffers_dropped=5,
     ),
-    config = ConfigPositions(
-        width              = 0,
-        height             = 1,
-        fs                 = 2,
-        buffer_size        = 3,
-        n_buffers_recorded = 4,
-        n_buffers_dropped  = 5
+    buffer=BufferHeaderPositions(
+        length=0,
+        linked_list=1,
+        frame_num=2,
+        buffer_count=3,
+        frame_buffer_count=4,
+        write_buffer_count=5,
+        dropped_buffer_count=6,
+        timestamp=7,
+        data_length=8,
     ),
-    buffer = BufferHeaderPositions(
-        length               = 0,
-        linked_list          = 1,
-        frame_num            = 2,
-        buffer_count         = 3,
-        frame_buffer_count   = 4,
-        write_buffer_count   = 5,
-        dropped_buffer_count = 6,
-        timestamp            = 7,
-        data_length          = 8
-    )
 )
 
 WireFreeSDLayout_Battery = SDLayout(**WireFreeSDLayout.model_dump())
@@ -57,42 +51,30 @@
 WireFreeSDLayout_Battery.buffer.battery_voltage = 10
 
 
-
 WireFreeSDLayout_Old = SDLayout(
-    sectors=SectorConfig(
-        header = 1023,
-        config = 1024,
-        data   = 1025,
-        size   = 512
+    sectors=SectorConfig(header=1023, config=1024, data=1025, size=512),
+    write_key0=0x0D7CBA17,
+    write_key1=0x0D7CBA17,
+    write_key2=0x0D7CBA17,
+    write_key3=0x0D7CBA17,
+    header=SDHeaderPositions(gain=4, led=5, ewl=6, record_length=7, fs=8),
+    config=ConfigPositions(
+        width=0,
+        height=1,
+        fs=2,
+        buffer_size=3,
+        n_buffers_recorded=4,
+        n_buffers_dropped=5,
     ),
-    write_key0 = 0x0D7CBA17,
-    write_key1 = 0x0D7CBA17,
-    write_key2 = 0x0D7CBA17,
-    write_key3 = 0x0D7CBA17,
-    header = SDHeaderPositions(
-        gain          = 4,
-        led           = 5,
-        ewl           = 6,
-        record_length = 7,
-        fs            = 8
+    buffer=BufferHeaderPositions(
+        length=0,
+        linked_list=1,
+        frame_num=2,
+        buffer_count=3,
+        frame_buffer_count=4,
+        write_buffer_count=5,
+        dropped_buffer_count=6,
+        timestamp=7,
+        data_length=8,
     ),
-    config = ConfigPositions(
-        width              = 0,
-        height             = 1,
-        fs                 = 2,
-        buffer_size        = 3,
-        n_buffers_recorded = 4,
-        n_buffers_dropped  = 5
-    ),
-    buffer = BufferHeaderPositions(
-        length               = 0,
-        linked_list          = 1,
-        frame_num            = 2,
-        buffer_count         = 3,
-        frame_buffer_count   = 4,
-        write_buffer_count   = 5,
-        dropped_buffer_count = 6,
-        timestamp            = 7,
-        data_length          = 8
-    )
-)
+)

miniscope_io/formats/stream.py

@@ -5,10 +5,10 @@
 from miniscope_io.models.stream import StreamBufferHeaderFormat
 
 StreamBufferHeader = StreamBufferHeaderFormat(
-    linked_list = (0, 32),
-    frame_num = (32, 64),
-    buffer_count = (64, 96),
-    frame_buffer_count = (96, 128),
-    timestamp = (192, 224),
-    pixel_count = (224, 256)
+    linked_list=(0, 32),
+    frame_num=(32, 64),
+    buffer_count=(64, 96),
+    frame_buffer_count=(96, 128),
+    timestamp=(192, 224),
+    pixel_count=(224, 256),
 )