Added pyenchant/pylint automated spell checking

Pipfile

@@ -21,6 +21,7 @@ pyinstaller = "==4.2"
 pywin32-ctypes = "==0.2.0" # Eli (3/1/21): this must be explicitly specified when using a Linux dev environment so that it will be included in a Windows build environment
 pefile = "==2019.4.18" # Eli (3/1/21): this must be explicitly specified when using a Linux dev environment so that it will be included in a Windows build environment
 atomicwrites = "==1.4.0" # Eli (3/1/21): this must be explicitly specified when using a Linux dev environment so that it will be included in a Windows build environment
+pyenchant = "==3.2.0"
 
 [packages]
 flask = "==1.1.2"

src/.pylint-spelling-private-dict

@@ -0,0 +1,73 @@
+pragma
+docstring
+mantarray
+backend
+frontend
+hacky
+args
+noqa
+unhandled
+dicts
+xem
+bytearray
+bytearrays
+barcode
+mypy
+kwarg
+centimilliseconds
+spi
+uploader
+zimports
+bool
+barcodes
+timepoint
+dataset
+mcu
+cython
+microcontroller
+subprocess
+subprocesses
+cryptographic
+sawtooth
+init
+nosec
+numpy
+json
+pyinstaller
+Werkzeug
+werkzeug
+untyped
+getter
+unflatten
+subfunction
+csv
+exe
+mixin
+hardcoded
+eval
+pyserial
+dma
+timesteps
+cms
+semver
+CLI
+pytest
+Github
+github
+centimillisecond
+Entrypoint
+entrypoint
+intra
+EP
+STM
+teardown
+freezegun
+fmt
+linux
+Butterworth
+endian
+ADC
+parametrization
+parametrizing
+parametrize
+parametrized

src/entrypoint.py

@@ -10,7 +10,7 @@
 import mantarray_desktop_app
 
 if __name__ == "__main__":
-    multiprocessing.freeze_support()  # This line is not unit tested (Eli 12/24/19 unsure how to test something in this codeblock), but is critical to allow multiprocessing to work in complied PyInstaller bundles https://kite.com/python/docs/multiprocessing.freeze_support
+    multiprocessing.freeze_support()  # This line is not unit tested (Eli 12/24/19 unsure how to test something in this code block), but is critical to allow multiprocessing to work in complied PyInstaller bundles https://kite.com/python/docs/multiprocessing.freeze_support
     multiprocessing.set_start_method(
         "spawn"
     )  # This line is not explicitly unit tested, but an error will be thrown in the main.main script if it is not executed. Windows only allows this start method, so need to make sure that in all development environments it is being tested in this mode.

src/mantarray_desktop_app/constants.py

@@ -229,7 +229,7 @@
 SUBPROCESS_SHUTDOWN_TIMEOUT_SECONDS = 1
 SUBPROCESS_POLL_DELAY_SECONDS = 0.025
 
-SECONDS_TO_WAIT_WHEN_POLLING_QUEUES = 0.02  # Due to the unreliablity of the .empty() .qsize() methods in queues, switched to a .get(timeout=) approach for polling the queues in the subprocesses.  Eli (10/26/20): 0.01 seconds was still causing sporadic failures in Linux CI in Github, so bumped to 0.02 seconds.
+SECONDS_TO_WAIT_WHEN_POLLING_QUEUES = 0.02  # Due to the unreliability of the :method:`.empty()` :method:`.qsize()` methods in queues, switched to a :method:`.get(timeout=)` approach for polling the queues in the subprocesses.  Eli (10/26/20): 0.01 seconds was still causing sporadic failures in Linux CI in Github, so bumped to 0.02 seconds.
 
 # Serial Communication Values
 SERIAL_COMM_BAUD_RATE = 4e6

src/mantarray_desktop_app/data_analyzer.py

@@ -62,7 +62,7 @@ class DataAnalyzerProcess(InfiniteProcess):
     """Process that analyzes data.
 
     Args:
-        board_queues: A tuple (the max number of board connections should be pre-defined, so not a mutable list) of tuples of 2 queues. The first queue is for incoming data for that board that should be analyzed. The second queue is for finalized outgoing data to main process
+        board_queues: A tuple (the max number of board connections should be predefined, so not a mutable list) of tuples of 2 queues. The first queue is for incoming data for that board that should be analyzed. The second queue is for finalized outgoing data to main process
         from_main_queue: a queue of communication from the main process
         to_main_queue: a queue to put general communication back to main
         fatal_error_reporter: a queue to report fatal errors back to the main process

src/mantarray_desktop_app/fifo_read_producer.py

@@ -68,7 +68,7 @@ def produce_data(num_cycles: int, starting_sample_index: int) -> bytearray:
             )
             sample_indices.append(sample_index)
             sawtooth_indices.append(sample_index / FIFO_READ_PRODUCER_SAWTOOTH_PERIOD)
-    # generate sawtooth vals
+    # generate sawtooth values
     sawtooth_vals = signal.sawtooth(sawtooth_indices, width=0.5)
     # generate bytearray data
     data = bytearray(0)

src/mantarray_desktop_app/fifo_simulator.py

@@ -32,7 +32,9 @@ class RunningFIFOSimulator(FrontPanelSimulator, MantarrayFrontPanelMixIn):
     """Simulate a running Mantarray machine with OK board.
 
     Args:
-        simulated_response_queues: dictionary where the ultimate leaves should be multiprocessing_utils.SimpleMultiprocessingQueue objects. These values are popped off the end of the queue and returned as if coming from the XEM. The 'wire_outs' key should contain a sub-dict with keys of integer values representing the ep addresses.
+        simulated_response_queues: dictionary where the ultimate leaves should be multiprocessing_utils.SimpleMultiprocessingQueue objects.
+                                    These values are popped off the end of the queue and returned as if coming from the XEM.
+                                    The 'wire_outs' key should contain a sub-dict with keys of integer values representing the EP addresses.
     """
 
     default_device_id = "M02001900Mantarray Simulator"

src/mantarray_desktop_app/file_writer.py

@@ -164,7 +164,7 @@ class FileWriterProcess(InfiniteProcess):
     """Process that writes data to disk.
 
     Args:
-        board_queues: A tuple (the max number of board connections should be pre-defined, so not a mutable list) of tuples of 2 queues. The first queue is for incoming data for that board that should be saved to disk. The second queue is for outgoing data for that board that has been saved to disk.
+        board_queues: A tuple (the max number of board connections should be predefined, so not a mutable list) of tuples of 2 queues. The first queue is for incoming data for that board that should be saved to disk. The second queue is for outgoing data for that board that has been saved to disk.
         from_main_queue: a queue of communication from the main process
         to_main_queue: a queue to put general communication back to main (including file names of finished files into so the uploader can begin uploading)
         fatal_error_reporter: a queue to report fatal errors back to the main process

src/mantarray_desktop_app/instrument_comm.py

@@ -38,7 +38,7 @@ class InstrumentCommProcess(InfiniteProcess, metaclass=abc.ABCMeta):
     """Process that controls communication with Mantarray instruments.
 
     Args:
-        board_queues: A tuple (the max number of instrument board connections should be pre-defined, so not a mutable list) of tuples of 3 queues. The first queue is for input/communication from the main thread to this sub process, second queue is for communication from this process back to the main thread. Third queue is for streaming communication (largely fo raw data) to the process that controls writing to disk.
+        board_queues: A tuple (the max number of instrument board connections should be predefined, so not a mutable list) of tuples of 3 queues. The first queue is for input/communication from the main thread to this sub process, second queue is for communication from this process back to the main thread. Third queue is for streaming communication (largely of raw data) to the process that controls writing to disk.
         fatal_error_reporter: A queue that reports back any unhandled errors that have caused the process to stop.
         suppress_setup_communication_to_main: if set to true (often during unit testing), messages during the _setup_before_loop will not be put into the queue to communicate back to the main process
     """

src/mantarray_desktop_app/mc_comm.py

@@ -103,7 +103,7 @@ class McCommunicationProcess(InstrumentCommProcess):
     """Process that controls communication with the Mantarray Beta 2 Board(s).
 
     Args:
-        board_queues: A tuple (the max number of MC board connections should be pre-defined, so not a mutable list) of tuples of 3 queues. The first queue is for input/communication from the main thread to this sub process, second queue is for communication from this process back to the main thread. Third queue is for streaming communication (largely fo raw data) to the process that controls writing to disk.
+        board_queues: A tuple (the max number of MC board connections should be predefined, so not a mutable list) of tuples of 3 queues. The first queue is for input/communication from the main thread to this sub process, second queue is for communication from this process back to the main thread. Third queue is for streaming communication (largely of raw data) to the process that controls writing to disk.
         fatal_error_reporter: A queue that reports back any unhandled errors that have caused the process to stop.
         suppress_setup_communication_to_main: if set to true (often during unit tests), messages during the _setup_before_loop will not be put into the queue to communicate back to the main process
     """
@@ -268,7 +268,7 @@ def _commands_for_each_run_iteration(self) -> None:
     def _process_next_communication_from_main(self) -> None:
         """Process the next communication sent from the main process.
 
-        Will just return if no comms from main in queue.
+        Will just return if no communications from main in queue.
         """
         input_queue = self._board_queues[0][0]
         try:
@@ -480,7 +480,7 @@ def _register_magic_word(self, board_idx: int) -> None:
                     break
                 sleep(1)
             else:
-                # if the entire period has passed and no more bytes are available an error has occured with the Mantarray that is considered fatal
+                # if the entire period has passed and no more bytes are available an error has occurred with the Mantarray that is considered fatal
                 raise SerialCommPacketRegistrationTimoutError(magic_word_test_bytes)
         # read more bytes until the magic word is registered, the timeout value is reached, or the maximum number of bytes are read
         num_bytes_checked = 0

src/mantarray_desktop_app/mc_simulator.py

@@ -214,7 +214,7 @@ def _send_data_packet(
             timestamp, module_id, packet_type, data_to_send
         )
         if truncate:
-            trunc_index = random.randint(  # nosec B311 # Tanner (2/4/21): Bandit blacklisted this psuedo-random generator for cryptographic security reasons that do not apply to the desktop app.
+            trunc_index = random.randint(  # nosec B311 # Tanner (2/4/21): Bandit blacklisted this pseudo-random generator for cryptographic security reasons that do not apply to the desktop app.
                 0, len(data_packet) - 1
             )
             data_packet = data_packet[trunc_index:]

src/mantarray_desktop_app/ok_comm.py

@@ -212,7 +212,7 @@ def _create_activate_trigger_in_callable(
 def _comm_delay(
     communication: Dict[str, Any],
 ) -> str:
-    """Pause comms to XEM for given number of milliseconds."""
+    """Pause communications to XEM for given number of milliseconds."""
     num_milliseconds = communication["num_milliseconds"]
     sleep_val = num_milliseconds / 1000
     time.sleep(sleep_val)
@@ -462,7 +462,7 @@ class OkCommunicationProcess(InstrumentCommProcess):
     """Process that controls communication with the OpalKelly Board(s).
 
     Args:
-        board_queues: A tuple (the max number of board connections should be pre-defined, so not a mutable list) of tuples of 3 queues. The first queue is for input/communication from the main thread to this sub process, second queue is for communication from this process back to the main thread. Third queue is for streaming communication (largely fo raw data) to the process that controls writing to disk.
+        board_queues: A tuple (the max number of board connections should be predefined, so not a mutable list) of tuples of 3 queues. The first queue is for input/communication from the main thread to this sub process, second queue is for communication from this process back to the main thread. Third queue is for streaming communication (largely of raw data) to the process that controls writing to disk.
         fatal_error_reporter: A queue that reports back any unhandled errors that have caused the process to stop.
         suppress_setup_communication_to_main: if set to true (often during unit testing), messages during the _setup_before_loop will not be put into the queue to communicate back to the main process
     """

src/mantarray_desktop_app/process_monitor.py

@@ -118,7 +118,7 @@ def _check_and_handle_server_to_main_queue(self) -> None:
 
         msg: str
         if "mantarray_nickname" in communication:
-            # Tanner (1/20/21): items in communication dict are used after this log message is generated, so need to creat a copy of the dict when redacting info
+            # Tanner (1/20/21): items in communication dict are used after this log message is generated, so need to create a copy of the dict when redacting info
             comm_copy = copy.deepcopy(communication)
             comm_copy["mantarray_nickname"] = "*" * len(comm_copy["mantarray_nickname"])
             msg = f"Communication from the Server: {comm_copy}"
@@ -288,7 +288,7 @@ def _check_and_handle_instrument_comm_to_main_queue(self) -> None:
 
         msg: str
         if "mantarray_nickname" in communication:
-            # Tanner (1/20/21): items in communication dict are used after this log message is generated, so need to creat a copy of the dict when redacting info
+            # Tanner (1/20/21): items in communication dict are used after this log message is generated, so need to create a copy of the dict when redacting info
             comm_copy = copy.deepcopy(communication)
             comm_copy["mantarray_nickname"] = "*" * len(comm_copy["mantarray_nickname"])
             msg = f"Communication from the OpalKelly Controller: {comm_copy}"

src/mantarray_desktop_app/request_handler.py

@@ -14,7 +14,7 @@
 class MantarrayRequestHandler(WSGIRequestHandler):
     """Almost identical to WSGIRequestHandler.
 
-    This handler will remove sensitive params from log messages.
+    This handler will remove sensitive parameters from log messages.
     """
 
     # pylint: disable=arguments-differ  # Tanner (1/20/21): The original param was `type` instead of `type_` which overrides the python builtin `type`
@@ -31,7 +31,7 @@ def log(self, type_: str, message: str, *args: Any) -> None:
             args_list = list(args)
             args_list[0] = scrubbed_msg
             args = tuple(args_list)
-        # Eli (3/9/21): Since Flask is running in multi-threaded mode, it might be possible that some log messages get garbled. It's not immediatley clear if Flask itself prevents this, or if the liklihood is prohibitively low to not worry about it, ...or what a robust way to pass the same threading.Lock() to this method as exists in the ServerThread itself. So for now we're not worrying about locking here and we'll see if it causes any issues with garbled logging.
+        # Eli (3/9/21): Since Flask is running in multi-threaded mode, it might be possible that some log messages get garbled. It's not immediately clear if Flask itself prevents this, or if the likelihood is prohibitively low to not worry about it, ...or what a robust way to pass the same threading.Lock() to this method as exists in the ServerThread itself. So for now we're not worrying about locking here and we'll see if it causes any issues with garbled logging.
         _log(
             type_,
             f"{self.address_string()} - - {message}\n",  # type: ignore  # Tanner (1/21/20): mypy is complaining that `address_string` is untyped

src/mantarray_desktop_app/server.py

@@ -129,7 +129,7 @@ def get_server_address_components() -> Tuple[str, str, int]:
     """Get Flask server address components.
 
     Returns:
-        protocol (i.e. http), host (i.e. 127.0.0.1), port (i.e. 4567)
+        protocol (i.e. HTTP), host (i.e. 127.0.0.1), port (i.e. 4567)
     """
     try:
         port_number = get_the_server_thread().get_port_number()
@@ -668,7 +668,7 @@ def queue_activate_trigger_in() -> Response:
 
 @flask_app.route("/insert_xem_command_into_queue/comm_delay", methods=["GET"])
 def queue_comm_delay() -> Response:
-    """Queue up a command delay comms to the XEM for a given period of time.
+    """Queue a command delay communication to the XEM for a period of time.
 
     Mainly to be used in XEM scripting when delays between commands are necessary.
 
@@ -728,7 +728,7 @@ def queue_set_device_id() -> Response:
 
     Do not use this route to set Mantarray Device Nicknames or Serial Numbers.
 
-    This route should be used cautiously as it will overwrite an exisiting Mantarray serial number / ID stored in the XEM.
+    This route should be used cautiously as it will overwrite an existing Mantarray serial number / ID stored in the XEM.
 
     Can be invoked by: curl http://localhost:4567/insert_xem_command_into_queue/set_device_id?new_id=""
     """
@@ -1007,7 +1007,7 @@ def after_request(response: Response) -> Response:
     return response
 
 
-# TODO (Eli 11/3/20): refactor stdlib utils to separate some of the more generic multiprocessing functionality out of the "InfiniteLooping" mixin so that it could be included here without all the other things
+# TODO (Eli 11/3/20): refactor :package:`stdlib-utils` to separate some of the more generic multiprocessing functionality out of the "InfiniteLooping" mixin so that it could be included here without all the other things
 class ServerThread(InfiniteThread):
     """Thread to run the Flask server."""
 

src/mantarray_desktop_app/utils.py

@@ -145,7 +145,7 @@ def get_current_software_version() -> str:
 
 
 def _trim_barcode(barcode: str) -> str:
-    """Trim the trailing 1 or 2 ASCII NUL (0x00) chars off barcode."""
+    """Trim the trailing 1 or 2 ASCII NULL (0x00) characters off barcode."""
     if barcode[11] != chr(0):
         return barcode
     if barcode[10] != chr(0):