codespell: workflow, config + typos fixed

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+# extint - function/variable name
+ignore-words-list = extint

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1

README.rst

@@ -30,7 +30,7 @@ Features
 - 2 TTL output channels (3.3V)
 - 2 amplitude modulation channels
 - Microcontroller can be used standalone (c.f. `Standalone use` section in the docs)
-- Stimulus pulse delivery with  ms or μs accurary
+- Stimulus pulse delivery with  ms or μs accuracy
 - Random selection of a sequence from a sequence library
 - Piping of sequence file to the directory of the latest scan on the MRI computer
 - Error message forwarding to computer

cosplay/dump_mem.py

@@ -12,12 +12,12 @@ def hexlify(buf):
 			return ubinascii.hexlify(buf, ' ')
 	else:
 		def hexlify(buf):
-			# CPython's hexlify doesn't have the notion of a seperator character
+			# CPython's hexlify doesn't have the notion of a separator character
 			# so we just do this the old fashioned way
 			return bytes(' '.join(['{:02x}'.format(b) for b in buf]), 'ascii')
 except AttributeError:
 	def hexlify(buf):
-		# CPython's hexlify doesn't have the notion of a seperator character
+		# CPython's hexlify doesn't have the notion of a separator character
 		# so we just do this the old fashioned way
 		return bytes(' '.join(['{:02x}'.format(b) for b in buf]), 'ascii')
 

cosplay/server.py

@@ -141,7 +141,7 @@ def listdir_nohidden(path):
 	List all entries in `path` excluding hidden ones.
 
 	This function implements the same functionality as `os.listdir`
-	but ignores hidden entires.
+	but ignores hidden entries.
 
 	Parameters
 	----------
@@ -264,7 +264,7 @@ def connect(port_name=None):
 
 	This function tries to connect to `port_name`. If `port_name`
 	is None, tries to connect to the first serial port with a
-	maching VID:PID for the MicroPython Pyboard.
+	matching VID:PID for the MicroPython Pyboard.
 
 	Parameters
 	----------

documentation/COSplay.rst

@@ -16,7 +16,7 @@ Features
 - 2 transistor channels (up to ~3.3V)
 - 2 TTL output channels with variable amplitude
 - Microcontroller can be used standalone (c.f. :ref:`pyboard`)
-- Stimulus pulse delivery with  :math:`ms` or :math:`\mu s` accurary
+- Stimulus pulse delivery with  :math:`ms` or :math:`\mu s` accuracy
 - Random selection of a sequence from a sequence library
 - Piping of sequence file to the directory of the latest scan on the MRI computer
 - Error message forwarding to computer

documentation/pyboard.rst

@@ -90,7 +90,7 @@ Red:
     Warning! Do not unplug or reset the board in this state as files might be corrupted.
 
 Red/Green flashing:
-    An error occured while executing the scripts on the board.
+    An error occurred while executing the scripts on the board.
 
 Standalone use
 ==============
@@ -117,7 +117,7 @@ for every reboot of the pyboard.
 Sequence Errors
 ===============
 
-Before deliverying a sequence, the board checks its consistency.
+Before delivering a sequence, the board checks its consistency.
 If the period is smaller than the pulse width or the values in the out_channel column are not integers between 1 and 6, a SequenceError is raised.
 
 In case the board misses a scheduled onset time or end time of a pulse,
@@ -144,7 +144,7 @@ config.py
 Library path
 ------------
 
-If one copies sequences to the board manually, the path to the directory containing the sequences can be spcified in ``library_path``.
+If one copies sequences to the board manually, the path to the directory containing the sequences can be specified in ``library_path``.
 
 Accuracy
 --------

pyboard/lib/tsv.py

@@ -82,7 +82,7 @@ def dumps(matrix):
 	matrix : 2d array
 	    input matrix
 
-	Retruns
+	Returns
 	-------
 	out : string
 	    tsv formatted string

pyboard/main.py

@@ -30,7 +30,7 @@ def callback_trigger2():
 
 def main():
 
-	#keep the following lines close to the begining of main because laser is switched on until pin_out.value(1)
+	#keep the following lines close to the beginning of main because laser is switched on until pin_out.value(1)
 	pin_out1 = pyb.Pin('Y1',pyb.Pin.OUT_PP,pull=pyb.Pin.PULL_UP)
 	pin_out1.value(not cfg.on_value_out_channel1)
 	pin_out2 = pyb.Pin('Y3',pyb.Pin.OUT_PP,pull=pyb.Pin.PULL_UP)
@@ -175,7 +175,7 @@ def main():
 	eh = ErrorHandler(use_wo_server,pkt,storage_path)
 
 	if cfg.accuracy == 'us':
-		ticks = utime.ticks_us		#Function for utime.measurment
+		ticks = utime.ticks_us		#Function for utime.measurement
 		sleep = utime.sleep_us		#Corresponding sleep function for ticks
 		conversion_factor = 1000000	#converts seconds to the unit specified in cfg.accuracy
 	elif cfg.accuracy == 'ms':

scripts/remove_permissions_for_pyboard

@@ -20,7 +20,7 @@ sudo rm -f /etc/udev/rules.d/$a-pyboard.rules
 echo "/etc/udev/rules.d/$a-pyboard.rules was removed."
 else
 echo $'\n\n'
-echo "md5sum miss match! File was probably altered manually. Make sure there are no rules not related to the pyboard in /etc/udev/rules.d/$a-pyboard.rules and delet it manually."
+echo "md5sum miss match! File was probably altered manually. Make sure there are no rules not related to the pyboard in /etc/udev/rules.d/$a-pyboard.rules and delete it manually."
 echo $'\n\n'
 echo "Lines added by the grant_permissions look as follows:"
 echo "# f055:9800, 9801, 9802 MicroPython pyboard