starting ruff manual fixes

miniscope_io/__init__.py

@@ -1,3 +1,7 @@
+"""
+I/O SDK for UCLA Miniscopes
+"""
+
 from pathlib import Path
 
 from miniscope_io.io import SDCard

miniscope_io/data.py

@@ -27,7 +27,8 @@ 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!)
+        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(
@@ -68,8 +69,8 @@ def flatten_headers(
         Return flat list of headers, not grouped by frame
 
         Args:
-            as_dict (bool): If `True`, return a list of dictionaries, if `False` (default),
-                return a list of :class:`.SDBufferHeader` s.
+            as_dict (bool): If `True`, return a list of dictionaries, if `False`
+                (default), return a list of :class:`.SDBufferHeader` s.
         """
         h = []
         for frame in self.frames:

miniscope_io/device_update.py

@@ -1,3 +1,12 @@
+"""
+Update miniscope device configuration.
+
+.. todo::
+
+    What kind of devices does this apply to?
+
+"""
+
 import argparse
 import sys
 import time
@@ -15,11 +24,15 @@
 updateDeviceParser.add_argument("value", help="LED value")
 
 
-def updateDevice():
+def updateDevice() -> None:
     """
     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.
+    This script currently supports updating the excitation LED brightness and
+    electrical wetting lens driver gain.
+
+    .. note::
+
+        Not tested after separating from stream_daq.py.
 
     Examples
     --------
@@ -122,7 +135,7 @@ def updateDevice():
     logger.info("Open serial port")
 
     for uartCommand in command:
-        for repeat in range(uartRepeat):
+        for _ in range(uartRepeat):
             # read UART data until preamble and put into queue
             serial_port.write(uartCommand)
             time.sleep(uartTimeGap)

miniscope_io/devices/__init__.py

@@ -0,0 +1,3 @@
+"""
+Control interfaces for external hardware devices
+"""

miniscope_io/devices/opalkelly.py

@@ -1,4 +1,6 @@
-
+"""
+Interfaces for OpalKelly (model number?) FPGAs
+"""
 
 from miniscope_io.vendor import opalkelly as ok
 
@@ -24,7 +26,13 @@ def __init__(self, serial_id: str = ""):
         if ret == self.NoError:
             print(f"Connected to {self.info.productName}")
 
-    def uploadBit(self, bit_file: str):
+    def uploadBit(self, bit_file: str) -> None:
+        """
+        Upload a configuration bitfile to the FPGA
+
+        Args:
+            bit_file (str): Path to the bitfile
+        """
 
         ret = self.ConfigureFPGA(bit_file)
         if ret == self.NoError:
@@ -38,7 +46,18 @@ def uploadBit(self, bit_file: str):
         )
         ret = self.ResetFPGA()
 
-    def readData(self, length: int, addr: int = 0xA0, blockSize: int = 16):
+    def readData(self, length: int, addr: int = 0xA0, blockSize: int = 16) -> bytearray:
+        """
+        Read a buffer's worth of data
+
+        Args:
+            length (int): Amount of data to read
+            addr (int): FPGA address to read from
+            blockSize (int): Size of individual blocks (in what unit?)
+
+        Returns:
+            :class:`bytearray`
+        """
         buf = bytearray(length)
         ret = self.ReadFromBlockPipeOut(addr, data=buf, blockSize=blockSize)
         if ret < 0:
@@ -47,7 +66,16 @@ def readData(self, length: int, addr: int = 0xA0, blockSize: int = 16):
             print(f"Only {ret} bytes read")
         return buf
 
-    def setWire(self, addr: int, val: int):
+    def setWire(self, addr: int, val: int) -> None:
+        """
+        .. todo::
+
+            Phil! what does this do?
+
+        Args:
+            addr: ?
+            val: ?
+        """
         ret = self.SetWireInValue(addr, val)
         ret = self.UpdateWireIns()
         if ret != self.NoError:

miniscope_io/exceptions.py

@@ -1,6 +1,11 @@
+"""
+Custom exceptions!
+"""
+
 class InvalidSDException(Exception):
     """
-    Raised when :class:`.io.SDCard` is used with a drive that doesn't have the appropriate WRITE KEYS in its header
+    Raised when :class:`.io.SDCard` is used with a drive that doesn't have the
+    appropriate WRITE KEYS in its header
     """