diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml index af4036ae..ba4d1d99 100644 --- a/.github/workflows/documentation.yaml +++ b/.github/workflows/documentation.yaml @@ -11,22 +11,37 @@ on: - 'bpod_core/**' permissions: - contents: write + contents: read + pages: write + id-token: write + +concurrency: + group: pages + cancel-in-progress: true jobs: - docs: + build: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v6 + - uses: astral-sh/setup-uv@v7 + with: + python-version: 3.13 - uses: ts-graphviz/setup-graphviz@v2 - name: sync dependencies run: uv sync --no-default-groups --group doc - name: build documentation run: uv run sphinx-build docs/source docs/build - - uses: peaceiris/actions-gh-pages@v4 + - uses: actions/upload-pages-artifact@v3 with: - publish_branch: gh-pages - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: docs/build/ - force_orphan: true + path: docs/build/ + + deploy: + needs: build + runs-on: ubuntu-latest + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - id: deployment + uses: actions/deploy-pages@v4 \ No newline at end of file diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml index b898228f..5a100fa4 100644 --- a/.github/workflows/publish.yaml +++ b/.github/workflows/publish.yaml @@ -3,7 +3,7 @@ on: workflow_dispatch: push: tags: - - '[0-9]+.[0-9]+.[0-9][abrc]?[0-9]*' # Matches semantic version tags + - '[0-9]+\\.[0-9]+\\.[0-9](?:(?:a|b|rc)[0-9]+)?' # Matches semantic version tags jobs: build: diff --git a/.gitignore b/.gitignore index 65de09cc..24aa61a4 100644 --- a/.gitignore +++ b/.gitignore @@ -193,6 +193,9 @@ target/ profile_default/ ipython_config.py +# LLM files +.repotomdrc + # pyenv # For a library or package, you might want to ignore these files since the code is # intended to run in multiple environments; otherwise, check them in: diff --git a/CHANGELOG.md b/CHANGELOG.md index 96b88dba..0769a664 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,23 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [0.1.0a7] + +### Added +- `com.find_ports` for finding serial ports that match given filter criteria. +- `com.verify_serial_discovery` for checking if a serial device sends an expected + discovery message. +- convenience functions for reading and writing integers in `com.ExtendedSerial`. +- `misc.extend_packed` for extending a bytearray by multiple values of the same format. +- `misc.DocstringInheritanceMixin` for inheriting docstrings from base classes. +- more examples. + +### Changed +- more verbose debug logging during state machine runs. +- replace unmaintained `appdirs` dependency with `platformdirs`. +- switch to zero-based indexing for global counters, timers, conditions and soft-codes. +- added file locking to `misc.SettingsDict`. + ## [0.1.0a6] - 2025-10-29 ### Added @@ -19,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `com.to_bytes` - dependency on Pandas + ## [0.1.0a5] - 2025-09-03 ### Added @@ -87,6 +105,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 First alpha release. Nothing works. +[0.1.0a7]: https://github.com/int-brain-lab/bpod-core/releases/tag/0.1.0a7 +[0.1.0a6]: https://github.com/int-brain-lab/bpod-core/releases/tag/0.1.0a6 [0.1.0a5]: https://github.com/int-brain-lab/bpod-core/releases/tag/0.1.0a5 [0.1.0a4]: https://github.com/int-brain-lab/bpod-core/releases/tag/0.1.0a4 [0.1.0a3]: https://github.com/int-brain-lab/bpod-core/releases/tag/0.1.0-alpha.3 diff --git a/README.md b/README.md index 78f82b16..00218d18 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,9 @@ A Python library for communicating with the [*Bpod Finite State Machine*](https://sanworks.io/). +> [!WARNING] +> bpod-core is under development and not yet ready for production use. + This project is maintained by the software development team at the [*International Brain Lab*](https://internationalbrainlab.org/). diff --git a/bpod_core/bpod.py b/bpod_core/bpod.py index 151f062f..abad485d 100644 --- a/bpod_core/bpod.py +++ b/bpod_core/bpod.py @@ -6,7 +6,8 @@ import threading import traceback import weakref -from collections.abc import Callable +from abc import ABC, abstractmethod +from collections.abc import Callable, Iterator from dataclasses import dataclass, field from types import TracebackType from typing import Any, NamedTuple, cast @@ -14,23 +15,42 @@ import msgspec import numpy as np from numpy.typing import NDArray +from platformdirs import user_config_path from pydantic import validate_call from serial import SerialException -from serial.tools.list_ports import comports -from typing_extensions import Self from bpod_core import __version__ as bpod_core_version -from bpod_core.com import ExtendedSerial +from bpod_core.com import ( + ExtendedSerial, + USBSerialDevice, + find_ports, + verify_serial_discovery, +) +from bpod_core.constants import STRUCT_UINT32, VID_TEENSY, PIDsTeensy from bpod_core.fsm import StateMachine from bpod_core.ipc import DualChannelClient, DualChannelHost -from bpod_core.misc import SettingsDict, suggest_similar - -PROJECT_NAME = 'bpod-core' -AUTHOR_NAME = 'International Brain Laboratory' -VENDOR_IDS_BPOD = [0x16C0] # vendor IDs of supported Bpod devices -MIN_BPOD_FW_VERSION = (23, 0) # minimum supported firmware version (major, minor) -MIN_BPOD_HW_VERSION = 3 # minimum supported hardware version -MAX_BPOD_HW_VERSION = 4 # maximum supported hardware version +from bpod_core.misc import ( + DocstringInheritanceMixin, + SettingsDict, + extend_packed, + suggest_similar, +) + +VIDS_BPOD = [VID_TEENSY] +"""Vendor IDs of supported Bpod devices""" + +PIDS_BPOD = [PIDsTeensy.SERIAL, PIDsTeensy.DUAL_SERIAL, PIDsTeensy.TRIPLE_SERIAL] +"""List of Product IDs of supported Bpod devices""" + +MIN_BPOD_FW_VERSION = (23, 0) +"""minimum supported firmware version (major, minor)""" + +MIN_BPOD_HW_VERSION = 3 +"""minimum supported hardware version""" + +MAX_BPOD_HW_VERSION = 4 +"""maximum supported hardware version""" + CHANNEL_TYPES_INPUT = { b'U': 'Serial', b'X': 'SoftCode', @@ -44,13 +64,15 @@ CHANNEL_TYPES_OUTPUT = CHANNEL_TYPES_INPUT.copy() CHANNEL_TYPES_OUTPUT.update({b'V': 'Valve', b'P': 'PWM'}) N_SERIAL_EVENTS_DEFAULT = 15 -VALID_OPERATORS = ['exit', '>exit', '>back'] +VALID_OPERATORS = {'exit', '>exit', '>back'} MACHINE_TYPES = {3: 'r2.0-2.5', 4: '2+ r1.0'} +CONFIG_PATH = user_config_path('bpod-core', False) +DISCOVERY_TIMEOUT = 0.11 logger = logging.getLogger(__name__) -class DeviceSettings(msgspec.Struct): +class BpodSettings(msgspec.Struct): """Settings for a specific Bpod device.""" serial_number: str @@ -60,13 +82,30 @@ class DeviceSettings(msgspec.Struct): location: str = '' """User-defined location of the device.""" zmq_port_pub: int | None = None - """Port number for the ZeroMQ PUB service""" + """Port number for the ZeroMQ PUB service.""" zmq_port_rep: int | None = None - """Port number for the ZeroMQ REP service""" + """Port number for the ZeroMQ REP service.""" + + +class BpodInfo(msgspec.Struct): + """Information about a specific Bpod device.""" + + serial_number: str + """Serial number of the device.""" + port: str | None = None + """Port on which the device is connected.""" + name: str = '' + """User-defined name of the device.""" + location: str = '' + """User-defined location of the device.""" + zmq_pub: str | None = None + """ZeroMQ PUB service address.""" + zmq_rep: str | None = None + """ZeroMQ REP service address.""" class VersionInfo(msgspec.Struct, frozen=True): - """Represents the Bpod's on-board hardware configuration.""" + """Data structure representing various version information.""" firmware: tuple[int, int] """Firmware version (major, minor)""" @@ -76,9 +115,8 @@ class VersionInfo(msgspec.Struct, frozen=True): """Machine type (string)""" pcb: int | None """PCB revision, if applicable""" - - def _to_dict(self) -> dict[str, Any]: - return {f: getattr(self, f) for f in self.__struct_fields__} + bpod_core: str + """bpod-core version""" class HardwareConfiguration(msgspec.Struct, frozen=True): @@ -124,8 +162,6 @@ class BpodError(Exception): class FSMThread(threading.Thread): """A thread for managing the execution of a finite state machine on the Bpod.""" - _struct_start = struct.Struct(' None: """ Initialize the FSMThread. @@ -158,8 +195,7 @@ def __init__( # noqa: PLR0913 use_back_op : bool Whether the state machine makes use of the `>back` operator """ - super().__init__() - self.daemon = True + super().__init__(daemon=True) self.serial = serial self._stop_event = threading.Event() self._index = fsm_index @@ -168,8 +204,9 @@ def __init__( # noqa: PLR0913 self._softcode_handler = softcode_handler self._state_transitions = state_transitions self._use_back_op = use_back_op + self._event_names = event_names - def stop(self): + def stop(self) -> None: self._stop_event.set() def run(self) -> None: @@ -178,7 +215,6 @@ def run(self) -> None: serial = self.serial index = self._index cycle_period = self._cycle_period - struct_cycles = self._struct_cycles softcode_handler = self._softcode_handler state_transitions = self._state_transitions previous_state = np.uint8(0) @@ -186,26 +222,22 @@ def run(self) -> None: target_exit = np.uint8(state_transitions.shape[0]) target_back = np.uint8(255) use_back_op = self._use_back_op + event_names = self._event_names # create buffers for repeated serial reads opcode_buf = bytearray(2) # buffer for opcodes event_data_buf = bytearray(259) # max 255 events + 4 bytes for n_cycles - # should we use debug logging? - debug = logger.isEnabledFor(logging.DEBUG) - # confirm the state machine if self._confirm_fsm: if serial.read(1) != b'\x01': raise RuntimeError(f'State machine #{index} was not confirmed by Bpod') - if debug: - logger.debug('State machine #%d confirmed by Bpod', index) - - # read the start time of the state machine (uInt64) - t0 = self._struct_start.unpack(serial.read(8))[0] - if debug: - logger.debug('%d µs: Starting state machine #%d', t0, index) - logger.debug('%d µs: State %d', t0, current_state) + logger.debug('State machine #%d confirmed by Bpod', index) + + # read the start time of the state machine + t0 = serial.read_uint64() + logger.debug('%d µs: Starting state machine #%d', t0, index) + logger.debug('%d µs: State %d', t0, current_state) # TODO: handle start of state machine # TODO: handle start of state @@ -221,14 +253,16 @@ def run(self) -> None: serial.readinto(event_data_view) # unpack the number of cycles, calculate the event's timestamp - n_cycles = struct_cycles.unpack_from(event_data_view, param)[0] + (n_cycles,) = STRUCT_UINT32.unpack_from(event_data_view, param) micros = t0 + n_cycles * cycle_period # handle each event events = event_data_view[:param] for event in events: - if debug: - logger.debug('%d µs: Event %d', micros, event) + if event != 255: + logger.debug( + '%d µs: Event %d - %s)', micros, event, event_names[event] + ) # TODO: handle event # handle state transitions / exit event @@ -248,13 +282,12 @@ def run(self) -> None: previous_state = current_state current_state = target_state # TODO: handle start of state - if debug: - logger.debug('%d µs: State %d', micros, current_state) + logger.debug('%d µs: State %d', micros, current_state) break # only handle the first state transition elif opcode == 2: # handle softcodes - if debug: - logger.debug('Softcode %d', param) + param -= 1 + logger.debug('Softcode %d', param) softcode_handler(param) else: @@ -263,36 +296,66 @@ def run(self) -> None: # exit state machine # read 12 bytes: cycles (uInt32) and micros (uInt64) cycles, micros = self._struct_exit.unpack(serial.read(12)) - if debug: - logger.debug( - '%d µs: Ending state machine #%d (%d cycles)', micros, index, cycles - ) + logger.debug( + '%d µs: Ending state machine #%d (%d cycles)', micros, index, cycles + ) # TODO: handle end of state machine -class AbstractBpod: +class AbstractBpod(DocstringInheritanceMixin, ABC): + """Abstract base class for Bpod objects.""" + _version: VersionInfo _hardware: HardwareConfiguration + _serial_number: str + + @property + @abstractmethod + def name(self) -> str | None: + """The Bpod's user-defined name, or :obj:`None` if not set.""" + + @property + @abstractmethod + def location(self) -> str | None: + """The Bpod's user-defined location, or :obj:`None` if not set.""" @property def version(self) -> VersionInfo: """Version information of the Bpod's firmware and hardware.""" return self._version + @property + def serial_number(self) -> str: + """The Bpod's unique serial number.""" + return self._serial_number + + @abstractmethod + def set_status_led(self, enabled: bool) -> bool: + """ + Enable or disable the Bpod's status LED. + + Parameters + ---------- + enabled : bool + True to enable the status LED, False to disable. + + Returns + ------- + bool + True if the operation was successful, False otherwise. + """ + -class Bpod(AbstractBpod): - """Bpod class for interfacing with the Bpod Finite State Machine.""" +class Bpod(USBSerialDevice, AbstractBpod): + """Class for interfacing with a Bpod Finite State Machine.""" + _device_type = 'Bpod Finite State Machine' _settings: SettingsDict - _name: str | None _fsm_thread: FSMThread | None = None _zmq_service: DualChannelHost _next_fsm_index: int = -1 _serial_buffer = bytearray() # buffer for TrialReader thread - serial0: ExtendedSerial - """Primary serial device for communication with the Bpod.""" - serial1: ExtendedSerial | None = None """Secondary serial device for communication with the Bpod.""" @@ -320,7 +383,7 @@ def __init__( ) -> None: self._finalizer = weakref.finalize(self, self._finalize) logger.info('bpod_core %s', bpod_core_version) - self._settings = SettingsDict(PROJECT_NAME, AUTHOR_NAME) + self._settings = SettingsDict(CONFIG_PATH / 'settings.json') # initialize members self.event_names = [] @@ -329,13 +392,10 @@ def __init__( self._state_transitions: NDArray[np.uint8] = np.empty((0, 255), dtype=np.uint8) self._use_back_op = False - # identify Bpod by port or serial number - port, self._serial_number = self._identify_bpod(port, serial_number) - - # open primary serial port - self.serial0 = ExtendedSerial() - self.serial0.port = port - self.open() + # identify Bpod by port or serial number, open connection + bpod_port, _ = self._identify_bpod(port, serial_number) + super().__init__(bpod_port) + self._serial_number = self._port_info.serial_number or 'unknown' # get firmware version and machine type; enforce version requirements self._get_version_info() @@ -367,15 +427,11 @@ def __init__( self._serial_number, self.version.pcb, ) - # logger.info( - # 'ZeroMQ service started on %s:%d', - # self._zmq_service.bind_address, - # self._zmq_service.port, - # ) - def __enter__(self) -> Self: - """Enter context.""" - return self + @property + def serial0(self) -> ExtendedSerial: + """Primary serial device for communication with the Bpod.""" + return self._serial def __exit__( self, @@ -384,7 +440,7 @@ def __exit__( exc_tb: TracebackType | None, ) -> None: """Exit context and close connection.""" - self.close() + super().__exit__(exc_type, exc_val, exc_tb) self._stop_zmq() def open(self) -> None: @@ -398,25 +454,20 @@ def open(self) -> None: BpodException If the handshake fails. """ - if self.serial0.is_open: - return - self.serial0.open() + super().open() self._handshake() def close(self) -> None: """Close the connection to the Bpod.""" self.stop_state_machine() - if hasattr(self, 'serial0') and self.serial0.is_open: - logger.debug('Closing connection to Bpod on %s', self.port) - self.serial0.write(b'Z') - self.serial0.close() + super().close() def _finalize(self) -> None: self.close() self._stop_zmq() - def _zmq_handler(self, message: dict) -> dict[str, Any]: - msg_type = message.get('type') + def _zmq_handler(self, message: dict[str, Any]) -> dict[str, Any]: + msg_type = message.get('type', 'unknown') if msg_type == 'call': method_name = message.get('method', '') args = message.get('args', ()) @@ -437,8 +488,10 @@ def _zmq_handler(self, message: dict) -> dict[str, Any]: } elif msg_type == 'handshake': response = { - 'bpod-core': bpod_core_version, - 'version': self._version._to_dict(), + 'version': self._version, + 'serial_number': self._serial_number, + 'name': self.name, + 'location': self.location, } else: response = { @@ -447,7 +500,7 @@ def _zmq_handler(self, message: dict) -> dict[str, Any]: } return response - def _start_zmq(self): + def _start_zmq(self) -> None: port_pub = self._get_setting(['devices', self._serial_number, 'port_pub']) port_rep = self._get_setting(['devices', self._serial_number, 'port_rep']) self._zmq_service = DualChannelHost( @@ -466,15 +519,13 @@ def _start_zmq(self): port_rep=cast('int | None', port_rep), ) self._set_setting( - ['devices', self._serial_number, 'port_pub'], - self._zmq_service.pub_tcp_port, + ['devices', self._serial_number, 'port_pub'], self._zmq_service.pub_tcp_port ) self._set_setting( - ['devices', self._serial_number, 'port_rep'], - self._zmq_service.rep_tcp_port, + ['devices', self._serial_number, 'port_rep'], self._zmq_service.rep_tcp_port ) - def _stop_zmq(self): + def _stop_zmq(self) -> None: if hasattr(self, '_zmq_service'): self._zmq_service.close() @@ -484,44 +535,10 @@ def _get_setting(self, keys: list[str], default: Any = None) -> Any: def _set_setting(self, keys: list[str], value: Any = None) -> None: self._settings.set_nested(keys, value) - def _sends_discovery_byte( - self, - port: str, - byte: bytes = b'\xde', - timeout: float = 0.11, - trigger: bytes | None = None, - ) -> bool: - r"""Check if the device on the given port sends a discovery byte. - - Parameters - ---------- - port : str - The name of the serial port to check (e.g., '/dev/ttyUSB0' or 'COM3'). - byte : bytes, optional - The discovery byte to expect from the device. Defaults to b'\\xde'. - timeout : float, optional - Timeout period (in seconds) for the serial read operation. Defaults to 0.11. - trigger : bytes, optional - An optional command to send on serial0 before reading from the given device. - - Returns - ------- - bool - Whether the given device responded with the expected discovery byte or not. - """ - try: - with ExtendedSerial(port, timeout=timeout) as ser: - if trigger is not None and getattr(self, 'serial0', None) is not None: - self.serial0.write(trigger) - return ser.read(1) == byte - except SerialException: - return False - + @staticmethod def _identify_bpod( - self, - port: str | None = None, - serial_number: str | None = None, - ) -> tuple[str, str | None]: + port: str | None = None, serial_number: str | None = None + ) -> tuple[str, str]: """ Try to identify a supported Bpod based on port or serial number. @@ -532,14 +549,14 @@ def _identify_bpod( ---------- port : str | None, optional The port of the device. - serial_number : str | None, optional + serial_number : str, optional The serial number of the device. Returns ------- str the port of the device - str | None + str the serial number of the device Raises @@ -547,41 +564,19 @@ def _identify_bpod( BpodError If no Bpod is found or the indicated device is not supported. """ - # If no port or serial number provided, try to automagically find an idle Bpod - if port is None and serial_number is None: - try: - port_info = next( - p - for p in comports() - if getattr(p, 'vid', None) in VENDOR_IDS_BPOD - and self._sends_discovery_byte(p.device) - ) - except StopIteration as e: - raise BpodError('No available Bpod found') from e - return port_info.device, port_info.serial_number - - # If a serial number was provided, try to match it with a serial device - if serial_number is not None: - try: - port_info = next( - p - for p in comports() - if p.serial_number == serial_number - and self._sends_discovery_byte(p.device) - ) - except (StopIteration, AttributeError) as e: - raise BpodError(f'No device with serial number {serial_number}') from e - - # Else, assure that the provided port exists and the device could be a Bpod - else: - try: - port_info = next(p for p in comports() if p.device == port) - except (StopIteration, AttributeError) as e: - raise BpodError(f'Port not found: {port}') from e - - if port_info.vid not in VENDOR_IDS_BPOD: - raise BpodError('Device is not a supported Bpod') - return port_info.device, port_info.serial_number + try: + port_info = next(discover_bpod(port, serial_number)) + return cast('str', port_info.port), str(port_info.serial_number) + except StopIteration as e: + if port is not None: + if len(find_ports(device=port)) == 0: + raise BpodError(f'Port not found: {port}') from None + else: + raise BpodError(f'Device on {port} is not an idle Bpod') from None + msg = 'No idle Bpod found' + if serial_number is not None: + msg += f' matching serial number {serial_number}' + raise BpodError(msg) from e def _get_version_info(self) -> None: """ @@ -613,7 +608,9 @@ def _get_version_info(self) -> None: f'v{MIN_BPOD_FW_VERSION[0]}.{MIN_BPOD_FW_VERSION[1]} or later.', ) pcv_rev = self.serial0.query_struct(b'v', ' 22 else None - self._version = VersionInfo(v_firmware, machine_type, machine_type_str, pcv_rev) + self._version = VersionInfo( + v_firmware, machine_type, machine_type_str, pcv_rev, bpod_core_version + ) def _get_hardware_configuration(self) -> None: """Retrieve the Bpod's onboard hardware configuration.""" @@ -669,27 +666,26 @@ def _detect_additional_serial_ports(self) -> None: logger.debug('Detecting additional USB-serial ports') # First, assemble a list of candidate ports - candidate_ports = [ - p.device - for p in comports() - if p.serial_number == self._serial_number and p.device != self.port - ] - - # Exclude those devices from the list that are already sending a discovery byte - # NB: this should not be necessary, as we already filter for devices with - # identical USB serial number. - # for port in candidate_ports: - # if self._sends_discovery_byte(port): - # candidate_ports.remove(port) + candidate_ports = find_ports( + vid=VIDS_BPOD, + pid=[PIDsTeensy.DUAL_SERIAL, PIDsTeensy.TRIPLE_SERIAL], + serial_number=self._serial_number, + device=re.compile(rf'^(?!{re.escape(str(self.port))}$).*$'), + ) - # Find secondary USB-serial port + # Then, try to find the secondary USB-serial port if self._version.firmware >= (23, 0): for port in candidate_ports: - if self._sends_discovery_byte(port, bytes([222]), trigger=b'{'): + if verify_serial_discovery( + port.device, + bytes([222]), + timeout=DISCOVERY_TIMEOUT, + trigger=lambda: self.serial0.write(b'{'), + ): self.serial1 = ExtendedSerial() - self.serial1.port = port + self.serial1.port = port.device candidate_ports.remove(port) - logger.debug('Detected secondary USB-serial port: %s', port) + logger.debug('Detected secondary USB-serial port: %s', port.device) break if self.serial1 is None: raise BpodError('Could not detect secondary serial port') @@ -697,10 +693,15 @@ def _detect_additional_serial_ports(self) -> None: # State Machine 2+ uses a third USB-serial port for FlexIO if self.version.machine == 4: for port in candidate_ports: - if self._sends_discovery_byte(port, bytes([223]), trigger=b'}'): + if verify_serial_discovery( + port.device, + bytes([223]), + timeout=DISCOVERY_TIMEOUT, + trigger=lambda: self.serial0.write(b'}'), + ): self.serial2 = ExtendedSerial() - self.serial2.port = port - logger.debug('Detected tertiary USB-serial port: %s', port) + self.serial2.port = port.device + logger.debug('Detected tertiary USB-serial port: %s', port.device) break if self.serial2 is None: raise BpodError('Could not detect tertiary serial port') @@ -767,11 +768,11 @@ def _compile_event_names(self) -> None: if io_key == b'U': # Serial names = self.modules[counters[io_key]].event_names elif io_key == b'X': # SoftCode - names = (f'{name}{i + 1}' for i in range(n_softcodes_per_usb)) + names = (f'{name}{i}' for i in range(n_softcodes_per_usb)) elif io_key == b'Z': # SoftCodeApp - names = (f'{name}{i + 1}' for i in range(n_app_softcodes)) + names = (f'{name}{i}' for i in range(n_app_softcodes)) elif io_key == b'F': # Flex - names = (f'{name}{counters[io_key] + 1}_{i + 1}' for i in range(2)) + names = (f'{name}{counters[io_key] + 1}_{i}' for i in range(2)) elif io_key in b'PBW': # Port, BNC, Wire names = (f'{name}{counters[io_key] + 1}_{s}' for s in ('High', 'Low')) else: @@ -786,7 +787,7 @@ def _compile_event_names(self) -> None: ('GlobalCounter{}_End', self._hardware.n_global_counters), ('Condition{}', self._hardware.n_conditions), ]: - self.event_names.extend(event_name.format(i + 1) for i in range(n)) + self.event_names.extend(event_name.format(i) for i in range(n)) self.event_names.append('Tup') def _compile_output_actions(self) -> None: @@ -814,26 +815,8 @@ def _compile_output_actions(self) -> None: if self.version.machine == 4: self.actions.extend(['AnalogThreshEnable', 'AnalogThreshDisable']) - @property - def port(self) -> str | None: - """The port of the Bpod's primary serial device.""" - return self.serial0.port - @validate_call def set_status_led(self, enabled: bool) -> bool: - """ - Enable or disable the Bpod's status LED. - - Parameters - ---------- - enabled : bool - True to enable the status LED, False to disable. - - Returns - ------- - bool - True if the operation was successful, False otherwise. - """ self.serial0.write_struct(' None: modules = [] for idx in range(self._hardware.n_modules): # check connection state - if not (is_connected := self.serial0.read_struct(' None: while more_info: match self.serial0.read(1): case b'#': - n_events = self.serial0.read_struct('back' operator is being used - targets_used = { - target - for state in state_machine.states.values() - for target in state.transitions.values() - } - self._use_back_op = '>back' in targets_used + # Check if the '>back' operator is being used + self._use_back_op = '>back' in state_machine.states.transition_targets # Validate the number of states, global timers, global counters and conditions. + n_states = len(state_machine.states) n_global_timers = max(state_machine.global_timers.keys(), default=-1) + 1 n_global_counters = max(state_machine.global_counters.keys(), default=-1) + 1 n_conditions = max(state_machine.conditions.keys(), default=-1) + 1 @@ -977,7 +955,7 @@ def send_state_machine( ) # Validate states - valid_targets = list(state_machine.states.keys()) + VALID_OPERATORS + valid_targets = set(state_machine.states.keys()) | VALID_OPERATORS max_state_duration = np.iinfo(np.uint32).max / self._hardware.cycle_frequency for state_name, state in state_machine.states.items(): if state.timer < 0 or state.timer > max_state_duration: @@ -1042,13 +1020,44 @@ def send_state_machine( event_indices = {k: v for v, k in enumerate(self.event_names)} action_indices = {k: v for v, k in enumerate(self.actions)} - # Initialize bytearray. This will be appended to in the following sections. + def append_events(event0: str, event1: str) -> None: + """Append state transitions for a range of events to byte_array. + + For each state, appends: [count] [event_idx, target_idx] ... + where count is the number of transitions, event_idx is relative to + event0, and target_idx is the target state index. + + Parameters + ---------- + event0 : str + First event name (inclusive lower bound). + event1 : str + Last event name (exclusive upper bound). + """ + idx0 = event_indices[event0] + idx1 = event_indices[event1] + for state in state_machine.states.values(): + counter_idx = len(byte_array) + byte_array.append(0) + for event, target in state.transitions.items(): + if idx0 <= (key_idx := event_indices[event]) < idx1: + byte_array[counter_idx] += 1 + byte_array.extend((key_idx - idx0, target_indices[target])) + + # Initialize bytearray for the compiled state machine. + # This will be appended to in the following sections. + # + # HEADER (4 bytes): + # [0] n_states - number of states + # [1] n_global_timers - number of global timers + # [2] n_global_counters - number of global counters + # [3] n_conditions - number of conditions byte_array = bytearray( (n_states, n_global_timers, n_global_counters, n_conditions), ) - # Compile target indices for state timers and append to bytearray - # Target indices default to the respective state's index unless 'Tup' is used + # STATE TIMER TARGET INDICES (n_states bytes): + # Target state index for each state's 'Tup' event (defaults to self) for state_idx, state in enumerate(state_machine.states.values()): for event, target in state.transitions.items(): if event == 'Tup': @@ -1057,42 +1066,27 @@ def send_state_machine( else: byte_array.append(state_idx) - # Helper function for appending events and their target indices to bytearray - def append_events(event0: str, event1: str) -> None: - idx0 = event_indices[event0] - idx1 = event_indices[event1] - for state in state_machine.states.values(): - counter_idx = len(byte_array) - byte_array.append(0) - for event, target in state.transitions.items(): - if idx0 <= (key_idx := event_indices[event]) < idx1: - byte_array[counter_idx] += 1 - byte_array.extend((key_idx - idx0, target_indices[target])) - - # Append input events to bytearray (i.e., events on physical input channels) + # INPUT EVENTS (variable length, per state): + # [count] [event_idx, target_idx] ... for events on physical input channels append_events(self.event_names[0], 'GlobalTimer1_Start') - # Append output actions and their values to bytearray - # TODO: this could be more efficient? + # OUTPUT ACTIONS (variable length, per state): + # [count] [action_idx, value] ... (8-bit on Bpod 0.5-1, 16-bit on Bpod 2+) i1 = action_indices['GlobalTimerTrig'] tmp_list: list[int] = [] for state in state_machine.states.values(): counter_pos = len(tmp_list) tmp_list.append(0) - for invalid_action, value in state.actions.items(): - if (key_idx := action_indices[invalid_action]) < i1: + for action_name, action_value in state.actions.items(): + if (key_idx := action_indices[action_name]) < i1: tmp_list[counter_pos] += 1 - tmp_list.extend((key_idx, value)) - format_string = 'H' if self.version.machine == 4 else 'B' - byte_array.extend( - struct.pack( - f'<{len(tmp_list)}{format_string}', - *tmp_list, - ), - ) + tmp_list.extend( + (key_idx, action_value + ('SoftCode' in action_name)) + ) + extend_packed(byte_array, tmp_list, 'H' if self.version.machine == 4 else 'B') # state transition matrix - n_states = len(state_machine.states) + # TODO: this can be moved elsewhere? self._state_transitions = np.arange(n_states, dtype=np.uint8)[ :, np.newaxis, @@ -1103,19 +1097,15 @@ def append_events(event0: str, event1: str) -> None: self._state_transitions[state_idx][event_indices[event]] = target_idx # Append remaining events - append_events('GlobalTimer1_Start', 'GlobalTimer1_End') # global timer start - append_events('GlobalTimer1_End', 'GlobalCounter1_End') # global timer end - append_events('GlobalCounter1_End', 'Condition1') # global counter end - append_events('Condition1', 'Tup') # conditions + append_events('GlobalTimer0_Start', 'GlobalTimer0_End') # global timer start + append_events('GlobalTimer0_End', 'GlobalCounter0_End') # global timer end + append_events('GlobalCounter0_End', 'Condition0') # global counter end + append_events('Condition0', 'Tup') # conditions # Compile indices for global timers channels timer_channel_indices = {k: v for v, k in enumerate(physical_output_channels)} timer_channel_indices[None] = 254 - # Helper function for packing a collection of integers into byte_array - def pack_values(values: list[int], format_str: str) -> None: - byte_array.extend(struct.pack(f'<{len(values)}{format_str}', *values)) - # Append values for global timer channels to byte_array idx0 = len(byte_array) byte_array.extend(b'\xfe' * n_global_timers) # default: 254 @@ -1126,7 +1116,8 @@ def pack_values(values: list[int], format_str: str) -> None: # Bpod 2+ uses 16-bit values for value_on and value_off format_string = 'H' if self.version.machine == 4 else 'B' for field_name in ('value_on', 'value_off'): - pack_values( + extend_packed( + byte_array, [ getattr(state_machine.global_timers.get(idx), field_name, 0) for idx in range(n_global_timers) @@ -1168,16 +1159,16 @@ def pack_values(values: list[int], format_str: str) -> None: # Append global counter resets if self.version.firmware < (23, 0): byte_array.extend( - s.actions.get('GlobalCounterReset', 0) + s.actions.get('GlobalCounterReset', -1) + 1 for s in state_machine.states.values() ) else: counter_idx = len(byte_array) byte_array.append(0) for state_idx, state in enumerate(state_machine.states.values()): - if (value := state.actions.get('GlobalCounterReset', 0)) > 0: + if (value := state.actions.get('GlobalCounterReset', -1)) >= 0: byte_array[counter_idx] += 1 - byte_array.extend([state_idx, value]) + byte_array.extend([state_idx, value + 1]) # Enable / disable analog thresholds # TODO: this is just a placeholder for now @@ -1194,13 +1185,15 @@ def pack_values(values: list[int], format_str: str) -> None: # Pack global timer triggers and cancels into bytearray for key in ('GlobalTimerTrig', 'GlobalTimerCancel'): - pack_values( - [s.actions.get(key, 0) for s in state_machine.states.values()], + extend_packed( + byte_array, + [s.actions.get(key, -1) + 1 for s in state_machine.states.values()], format_string, ) # Pack global timer onset triggers into bytearray - pack_values( + extend_packed( + byte_array, [ getattr(state_machine.global_timers.get(idx, {}), 'onset_trigger', 0) for idx in range(n_global_timers) @@ -1209,7 +1202,8 @@ def pack_values(values: list[int], format_str: str) -> None: ) # Pack state timers - pack_values( + extend_packed( + byte_array, [ round(s.timer * self._hardware.cycle_frequency) for s in state_machine.states.values() @@ -1219,7 +1213,8 @@ def pack_values(values: list[int], format_str: str) -> None: # Pack global timer durations, onset delays and loop intervals for key in ('duration', 'onset_delay', 'loop_interval'): - pack_values( + extend_packed( + byte_array, [ round( getattr(state_machine.global_timers.get(idx, {}), key, 0) @@ -1231,7 +1226,8 @@ def pack_values(values: list[int], format_str: str) -> None: ) # Pack global counter thresholds - pack_values( + extend_packed( + byte_array, [ getattr(state_machine.global_counters.get(idx, {}), 'threshold', 0) for idx in range(n_global_counters) @@ -1239,12 +1235,12 @@ def pack_values(values: list[int], format_str: str) -> None: 'I', # uint32 ) - # Append additional opcodes - # TODO: why? + # Footer (firmware 23+, 1 byte): + # Reserved for additional opcodes if self.version.firmware > (22, 0): byte_array.append(0) - # Send to state machine + # Send state machine to Bpod self._next_fsm_index += 1 logger.debug('Sending state machine #%d to Bpod', self._next_fsm_index) n_bytes = len(byte_array) @@ -1292,6 +1288,7 @@ def _run_state_machine(self, *, blocking: bool) -> None: self._softcode_handler, self._state_transitions, self._use_back_op, + self.event_names, ) self._fsm_thread.start() self._waiting_for_confirmation = False @@ -1318,26 +1315,26 @@ def name(self) -> str | None: """Get the name of the Bpod device.""" return cast( 'str | None', - self._get_setting(['devices', str(self._serial_number), 'name'], None), + self._get_setting(['devices', self._serial_number, 'name'], None), ) @name.setter def name(self, name: str | None) -> None: """Set the name of the Bpod device.""" - self._set_setting(['devices', str(self._serial_number), 'name'], name) + self._set_setting(['devices', self._serial_number, 'name'], name) @property def location(self) -> str | None: """Get the location of the Bpod device.""" return cast( 'str | None', - self._get_setting(['devices', str(self._serial_number), 'location'], None), + self._get_setting(['devices', self._serial_number, 'location'], None), ) @location.setter def location(self, location: str | None) -> None: """Set the location of the Bpod device.""" - self._set_setting(['devices', str(self._serial_number), 'location'], location) + self._set_setting(['devices', self._serial_number, 'location'], location) class Channel: @@ -1513,7 +1510,7 @@ def _define_event_names(self) -> None: if len(self._custom_event_names) > idx: self.event_names.append(f'{self.name}_{self._custom_event_names[idx]}') else: - self.event_names.append(f'{self.name}_{idx + 1}') + self.event_names.append(f'{self.name}_{idx}') @validate_call def set_relay(self, enable: bool) -> None: @@ -1545,8 +1542,62 @@ def relay(self, state: bool) -> None: """The current state of the serial relay.""" self.set_relay(state) + @validate_call + def load_serial_message( + self, + message_id: int, + message_bytes: bytes, + ) -> bool: + """ + Load a serial message targeting the module. + + Serial messages are byte sequences targeting a specific module that can be + triggered as output actions during a state machine run. Each message is + identified by a ``message_id``. + + Parameters + ---------- + message_id : int + Identifier for the message, in the range ``[0, 254]``. + message_bytes : bytes + The message payload (1 to 3 bytes). + + Returns + ------- + bool + :obj:`True` if the Bpod acknowledged the message, :obj:`False` otherwise. + + Raises + ------ + ValidationError + If the provided parameters cannot be validated or coerced to the expected + type. + ValueError + If ```message_id``, or ``message_bytes`` length is out of range. + """ + if not (0 <= message_id <= 254): + raise ValueError('Message ID must be between 0 and 254') + if not (1 <= (message_length := len(message_bytes)) <= 3): + raise ValueError('Message must be between 1 and 3 bytes long') + + self._bpod.serial0.write_struct( + f' None: properties = { 'address': address, 'name': name, @@ -1569,6 +1620,7 @@ def __init__( address=address, discovery_timeout=timeout, txt_properties=properties, + event_handler=self._event_handler, ) except TimeoutError as e: raise TimeoutError('Failed to discover remote Bpod.') from e @@ -1577,24 +1629,24 @@ def __init__( # log hardware information logger.info( 'Connected to Bpod Finite State Machine %s on %s', - self._version['machine_str'], + self._version.machine_str, self._zmq._address_req, ) - def _request(self, request_type: str, **kwargs) -> dict: + def _request(self, request_type: str, **kwargs: Any) -> dict: return cast('dict', self._zmq.request(type=request_type, **kwargs)) - def _remote_call(self, method: str, *args, **kwargs) -> Any | None: + def _remote_call(self, method: str, *args: Any, **kwargs: Any) -> Any | None: """ - Perform a remote procedure call by sending a 'call' type request. + Perform a remote procedure call. Parameters ---------- method : str The name of the remote method to invoke. - *args + *args : Any Positional arguments to pass to the remote method. - **kwargs + **kwargs : Any Keyword arguments to pass to the remote method. Returns @@ -1605,16 +1657,74 @@ def _remote_call(self, method: str, *args, **kwargs) -> Any | None: reply = self._request('call', method=method, args=args, kwargs=kwargs) if reply.get('success'): return reply['result'] - logger.error(f'Remote {reply["error"]["type"]}: ' + reply['error']['message']) + logger.error( + 'Remote %s: %s, ', reply['error']['type'], reply['error']['message'] + ) return None - def _handshake(self): + def _handshake(self) -> None: reply = self._request('handshake') - self._version = reply['version'] - self._version['bpod_core'] = reply['bpod-core'] - - def set_status_led(self, enabled: bool) -> None: - self._remote_call('set_status_led', enabled) + self._version = VersionInfo(**reply['version']) + self._serial_number = reply['serial_number'] + self._name = reply['name'] + self._location = reply['location'] - def _event_handler(self, message: dict): + def _event_handler(self, message: dict) -> None: pass + + @property + def name(self) -> str | None: + return self._name + + @property + def location(self) -> str | None: + return self._location + + def set_status_led(self, enabled: bool) -> bool: + return self._remote_call('set_status_led', enabled) or False + + +def discover_bpod( + port: str | None = None, serial_number: str | None = None +) -> Iterator[BpodInfo]: + """Identify available Bpod devices connected via USB. + + Scans for USB serial ports matching Bpod vendor/product IDs and verifies each + device responds to a discovery message. Yields information about identified devices. + + Parameters + ---------- + port : str, optional + Filter by specific device path (e.g., '/dev/ttyACM0' or 'COM3'). + serial_number : str, optional + Filter by USB serial number. + + Yields + ------ + BpodInfo + Information structure describing a Bpod device. + + Examples + -------- + Iterate over available Bpods:: + + for device in discover_bpods(): + print(f"Found Bpod at {device}") + + Get as a list:: + + devices = list(discover_bpods()) + """ + # create filter dict + filters: dict[str, str] = {} + if port is not None: + filters['device'] = port + if serial_number is not None: + filters['serial_number'] = serial_number + + # find matching devices + for p in find_ports(vid=VIDS_BPOD, pid=PIDS_BPOD, **filters): + if verify_serial_discovery( + port=p.device, expected_message=b'\xde', timeout=DISCOVERY_TIMEOUT + ): + yield BpodInfo(port=p.device, serial_number=str(p.serial_number)) diff --git a/bpod_core/com.py b/bpod_core/com.py index e25dd5fc..0a034c28 100644 --- a/bpod_core/com.py +++ b/bpod_core/com.py @@ -1,20 +1,108 @@ """Module providing extended serial communication functionality.""" import logging +import re import struct -from collections.abc import Callable -from typing import Any +from collections.abc import Callable, Sequence +from types import TracebackType +from typing import Any, cast -from serial import Serial +from serial import Serial, SerialException from serial.threaded import Protocol, ReaderThread +from serial.tools.list_ports import comports +from serial.tools.list_ports_common import ListPortInfo from typing_extensions import Buffer, Self +from bpod_core.constants import ( + STRUCT_BOOL, + STRUCT_INT8, + STRUCT_INT16, + STRUCT_INT32, + STRUCT_INT64, + STRUCT_UINT8, + STRUCT_UINT16, + STRUCT_UINT32, + STRUCT_UINT64, +) + logger = logging.getLogger(__name__) class ExtendedSerial(Serial): """Enhances :class:`serial.Serial` with additional functionality.""" + def write_int8(self, value: int) -> int | None: + """Write an 8-bit signed integer to the serial port.""" + return self.write(STRUCT_INT8.pack(value)) + + def write_int16(self, value: int) -> int | None: + """Write a 16-bit signed integer to the serial port (little-endian).""" + return self.write(STRUCT_INT16.pack(value)) + + def write_int32(self, value: int) -> int | None: + """Write a 16-bit signed integer to the serial port (little-endian).""" + return self.write(STRUCT_INT32.pack(value)) + + def write_int64(self, value: int) -> int | None: + """Write a 16-bit signed integer to the serial port (little-endian).""" + return self.write(STRUCT_INT64.pack(value)) + + def write_uint8(self, value: int) -> int | None: + """Write an 8-bit unsigned integer to the serial port.""" + return self.write(STRUCT_UINT8.pack(value)) + + def write_uint16(self, value: int) -> int | None: + """Write a 16-bit unsigned integer to the serial port (little-endian).""" + return self.write(STRUCT_UINT16.pack(value)) + + def write_uint32(self, value: int) -> int | None: + """Write a 32-bit unsigned integer to the serial port (little-endian).""" + return self.write(STRUCT_UINT32.pack(value)) + + def write_uint64(self, value: int) -> int | None: + """Write a 64-bit unsigned integer to the serial port (little-endian).""" + return self.write(STRUCT_UINT64.pack(value)) + + def write_bool(self, value: bool) -> int | None: + """Write a boolean value to the serial port.""" + return self.write(STRUCT_BOOL.pack(value)) + + def read_int8(self) -> int: + """Read an 8-bit signed integer from the serial port.""" + return cast('int', STRUCT_INT8.unpack(self.read(1))[0]) + + def read_int16(self) -> int: + """Read a 16-bit signed integer from the serial port (little-endian).""" + return cast('int', STRUCT_INT16.unpack(self.read(2))[0]) + + def read_int32(self) -> int: + """Read a 32-bit signed integer from the serial port (little-endian).""" + return cast('int', STRUCT_INT32.unpack(self.read(4))[0]) + + def read_int64(self) -> int: + """Read a 64-bit signed integer from the serial port (little-endian).""" + return cast('int', STRUCT_INT64.unpack(self.read(8))[0]) + + def read_uint8(self) -> int: + """Read an 8-bit unsigned integer from the serial port.""" + return cast('int', self.read(1)[0]) + + def read_uint16(self) -> int: + """Read a 16-bit unsigned integer from the serial port (little-endian).""" + return cast('int', STRUCT_UINT16.unpack(self.read(2))[0]) + + def read_uint32(self) -> int: + """Read a 32-bit unsigned integer from the serial port (little-endian).""" + return cast('int', STRUCT_UINT32.unpack(self.read(4))[0]) + + def read_uint64(self) -> int: + """Read a 64-bit unsigned integer from the serial port (little-endian).""" + return cast('int', STRUCT_UINT64.unpack(self.read(8))[0]) + + def read_bool(self) -> bool: + """Read a boolean value from the serial port.""" + return cast('bool', STRUCT_BOOL.unpack(self.read(1))[0]) + def write_struct(self, format_string: str, *data: Any) -> int | None: # noqa:ANN401 """ Write structured data to the serial port. @@ -223,3 +311,223 @@ def data_received(self, data: bytes) -> None: while len(self._buffer) >= self._chunk_size: self._callback(self._buffer[: self._chunk_size]) del self._buffer[: self._chunk_size] + + +FilterValue = str | int | re.Pattern[str] | None | Sequence['FilterValue'] + + +def find_ports(**filters: FilterValue) -> list[ListPortInfo]: + r""" + Find serial ports matching specified criteria. + + Multiple filters use AND logic. Iterables within a single filter use OR logic. + + Parameters + ---------- + **filters : FilterValue + Port attributes to filter by. Values can be: + + - Scalar: exact match + - Sequence: match any item (OR logic) + - re.Pattern: regex match (use re.compile()) + + Returns + ------- + list[ListPortInfo] + Ports matching all criteria. + + Examples + -------- + Find by vendor ID:: + + find_ports(vid=0x16C0) + + Find using regex pattern:: + + find_ports(device=re.compile(r'/dev/ttyACM\d+')) + + Find multiple values:: + + find_ports(pid=[0x0483, 0x048B]) + + Combine filters:: + + find_ports(vid=0x16C0, device=re.compile(r'/dev/ttyACM\d+')) + + Notes + ----- + Strings use exact matching. Use re.compile() for regex patterns. + """ + + def matches(key: object, value: FilterValue) -> bool: + if isinstance(value, Sequence) and not isinstance(value, str): + return any(matches(key, v) for v in value) + if isinstance(value, re.Pattern): + return isinstance(key, str) and value.search(key) is not None + return key == value + + return [ + port + for port in comports() + if all(matches(getattr(port, k, None), v) for k, v in filters.items()) + ] + + +def verify_serial_discovery( + port: str, + expected_message: bytes, + timeout: float = 1, + trigger: Callable[[], Any] | None = None, +) -> bool: + r"""Check if a device sends an expected discovery message on a serial port. + + Opens the specified serial port and waits to receive bytes matching the expected + discovery message. Optionally executes a function first, which can be used trigger + the device's discovery routine, e.g., by sending a command. + + Parameters + ---------- + port : str + The serial port to read from (e.g., '/dev/ttyUSB0' or 'COM3'). + expected_message : bytes + The exact byte sequence expected from the device. + timeout : float, default: 1 + Maximum time (in seconds) to wait for the discovery message. Defaults to 1 s. + trigger : Callable, optional + A function to call before reading. Use this to trigger the device's discovery + routine. + + Returns + ------- + bool + True if the device sent the expected message within the timeout period, + False otherwise (including if the port cannot be opened). + """ + try: + with Serial(port, timeout=timeout) as ser: + if trigger is not None: + trigger() + return ser.read(len(expected_message)) == expected_message + except SerialException: + return False + + +class USBSerialDevice: + """Class that interfaces with a USB serial device.""" + + _serial: ExtendedSerial + """The serial connection to the USB device.""" + + _port_info: ListPortInfo + """Information about the serial port associated with the device.""" + + _device_type: str = 'serial device' + """The type of the USB device, e.g., 'Bpod'.""" + + def __init__(self, port: str, open_connection: bool = True, **kwargs: Any) -> None: + """Initialize the USB serial device. + + Parameters + ---------- + port : str + The serial port device path (e.g., '/dev/ttyUSB0' or 'COM3'). + open_connection : bool, optional + Whether to open the connection immediately, by default True. + **kwargs + Additional arguments for compatibility with subclasses. + + Raises + ------ + serial.SerialException + If the specified port does not exist. + """ + try: + self._port_info = next(p for p in comports() if p.device == port) + except StopIteration as e: + raise SerialException(f'Serial port not found: {port}') from e + self._serial = ExtendedSerial() + self._serial.port = port + if open_connection: + self.open() + + def __enter__(self) -> Self: + """Enter the context manager. + + Returns + ------- + Self + The device instance. + """ + return self + + def __exit__( + self, + exc_type: type[BaseException] | None, + exc_val: BaseException | None, + exc_tb: TracebackType | None, + ) -> None: + """Exit the context manager. + + Closes the serial connection. + + Parameters + ---------- + exc_type : type[BaseException] | None + The type of exception raised, if any. + exc_val : BaseException | None + The exception instance raised, if any. + exc_tb : TracebackType | None + The traceback object, if any. + """ + self.close() + + def open(self) -> None: + """Open the serial connection. + + If the connection is already open, this method does nothing. + + Raises + ------ + serial.SerialException + If the connection cannot be opened. + """ + if self._serial.is_open: + return + logger.debug('Opening connection to %s on %s', self._device_type, self.port) + try: + self._serial.open() + except Exception as e: + raise SerialException( + f'Failed to open connection to {self._device_type} on {self.port}' + ) from e + + def close(self) -> None: + """Close the serial connection. + + If the connection is already closed, this method does nothing. + + Raises + ------ + serial.SerialException + If the connection cannot be closed. + """ + if not self._serial.is_open: + return + logger.debug('Closing connection to %s on %s', self._device_type, self.port) + try: + self._serial.close() + except Exception as e: + raise SerialException( + f'Failed to close connection to {self._device_type} on {self.port}' + ) from e + + @property + def port(self) -> str: + """The name of the serial port. + + Returns + ------- + str + The device path of the serial port (e.g., '/dev/ttyACM0'). + """ + return self._port_info.device diff --git a/bpod_core/constants.py b/bpod_core/constants.py new file mode 100644 index 00000000..dde20cd2 --- /dev/null +++ b/bpod_core/constants.py @@ -0,0 +1,42 @@ +"""Constants and identifiers used throughout the package.""" + +from struct import Struct + +# pre-compiled structs for common data types +STRUCT_BOOL = Struct('?') +"""Compiled struct representing a boolean value.""" +STRUCT_UINT8 = Struct('B') +"""Compiled struct representing an unsigned 8-bit integer.""" +STRUCT_UINT16 = Struct(' None: """ - Configure a global timer with the specified parameters. + Configure a global counter with the specified parameters. Parameters ---------- index : int - The index of the global counter. + The index of the global counter. Zero-based. event : str The name of the event to count. threshold : int @@ -494,7 +494,7 @@ def set_condition( Parameters ---------- index : int - The index of the condition. + The index of the condition. Zero-based. channel : str The channel or global timer attached to the condition. value: bool @@ -904,13 +904,13 @@ def check(self) -> None: self._validation_md5_hash = md5_hash def _check(self) -> None: + # Check for empty state machine if len(self.states) == 0: raise ValueError('No states defined') + # Check for unreachable states initial_state = next(iter(self.states.keys())) reachable_states = self.states.transition_targets | {initial_state} - - # Check for unreachable states unreachable_states = [s for s in self.states if s not in reachable_states] if len(unreachable_states) == 1: raise ValueError(f'State "{unreachable_states.pop()}" is unreachable') @@ -920,3 +920,6 @@ def _check(self) -> None: + f' and "{unreachable_states[-1]}"' ) raise ValueError(f'States {missed_states_string} are unreachable') + + # TODO: Check for manipulation of unused timers? + # TODO: Check for manipulation of unused conditions? diff --git a/bpod_core/ipc.py b/bpod_core/ipc.py index baf5a35c..af0f054d 100644 --- a/bpod_core/ipc.py +++ b/bpod_core/ipc.py @@ -26,11 +26,9 @@ ) from bpod_core.com import logger +from bpod_core.constants import IP_ANY, IP_LOOPBACK from bpod_core.misc import convert_to_snake_case, get_local_ipv4 -IP_LOOPBACK = '127.0.0.1' -IP_ANY = '0.0.0.0' - class DualChannelMessage(msgspec.Struct, omit_defaults=True, array_like=True): type: str = msgspec.field(name='T') # message type @@ -67,7 +65,7 @@ def __exit__( return None @abstractmethod - def _event_loop(self): ... + def _event_loop(self) -> None: ... def close(self) -> bool: """ @@ -109,7 +107,7 @@ def __init__( service_name: str, service_type: str, txt_record: dict[str | bytes, str | bytes | None] | None = None, - event_handler: Callable[[Any | None], Any] | None = None, + event_handler: Callable[[Any], Any] | None = None, remote: bool = True, port_pub: int | None = None, port_rep: int | None = None, @@ -380,7 +378,7 @@ def __init__( event_handler: Callable[[dict], Any] | None = None, discovery_timeout: float = 10.0, txt_properties: dict | None = None, - ): + ) -> None: """ Initialize a DualChannelClient instance. @@ -425,16 +423,20 @@ def __init__( self._handshake() # connect SUB channel - self._socket_pub_sub.connect(self._address_sub) - self._socket_pub_sub.setsockopt_string(zmq.SUBSCRIBE, '') - logger.debug("Binding SUB socket to '%s'", self._address_sub) + if event_handler is not None: + self._socket_pub_sub.connect(self._address_sub) + self._socket_pub_sub.setsockopt_string(zmq.SUBSCRIBE, '') + logger.debug("Binding SUB socket to '%s'", self._address_sub) + else: + logger.debug('Not binding SUB socket for lack of event handler') # start event loop for subscription handling self._event_handler = event_handler self._event_thread = threading.Thread(target=self._event_loop, daemon=True) - self._event_thread.start() + if event_handler is not None: + self._event_thread.start() - def _event_loop(self): + def _event_loop(self) -> None: """Process incoming PUB messages.""" while not self._stop_event_loop.is_set(): if not self._socket_pub_sub.poll(100): @@ -442,11 +444,11 @@ def _event_loop(self): msg = self._socket_pub_sub.recv() msg = self._decoder.decode(msg) try: - self._event_handler(msg) + cast('Callable', self._event_handler)(msg) except Exception as e: logger.exception('Subscription handler raised an exception', exc_info=e) - def _handshake(self): + def _handshake(self) -> None: """Perform handshake with the host.""" reply_type, reply_data = self._req('H') if ( @@ -505,13 +507,13 @@ def _req(self, request_type: str, data: Any | None = None) -> tuple[str, Any]: # return reply type and data return reply.type, reply.data - def request(self, **kwargs) -> Any: + def request(self, **kwargs: Any) -> Any: """ Send a generic request to the server. Parameters ---------- - **kwargs : dict + **kwargs : Any Key-value pairs to be sent as the request payload. Returns @@ -571,7 +573,9 @@ def discover( event = threading.Event() txt_record = {} - def on_state_change(*, name: str, state_change: ServiceStateChange, **_): + def on_state_change( + *, name: str, state_change: ServiceStateChange, **_: Any + ) -> None: nonlocal address, protocol, txt_record, event if state_change is ServiceStateChange.Added: info = zeroconf.get_service_info(service_type, name) diff --git a/bpod_core/misc.py b/bpod_core/misc.py index 5e528464..68c0bedb 100644 --- a/bpod_core/misc.py +++ b/bpod_core/misc.py @@ -3,37 +3,50 @@ import difflib import errno import json +import logging import re import socket -from collections.abc import ( - Iterator, - Mapping, - MutableMapping, - Sequence, -) +import struct +from collections.abc import Iterable, Iterator, Mapping, MutableMapping, Sequence +from os import PathLike from pathlib import Path -from typing import ( - TYPE_CHECKING, - Any, - Generic, - TypeVar, - cast, -) +from typing import TYPE_CHECKING, Any, Generic, TypeVar, cast import msgspec -from appdirs import user_config_dir +from filelock import FileLock from pydantic import Field, RootModel +logger = logging.getLogger(__name__) + K = TypeVar('K') V = TypeVar('V') - RE_SANITIZE = re.compile(r'[^a-zA-Z0-9_]') RE_SNAKE_CASE = re.compile(r'(?<=[a-z])(?=[A-Z])|(?<=\D)(?=\d)|(?<=\d)(?=\D)') RE_UNDERSCORES = re.compile(r'_{2,}') -def sanitize_string(string: str, substitute='_'): +class DocstringInheritanceMixin: + """Mixin that automatically inherits docstrings from parent classes. + + When a subclass overrides a method or property without providing its own docstring, + this mixin copies the docstring from the nearest parent class that defines one. This + avoids having to duplicate docstrings across abstract methods and their concrete + implementations. + """ + + def __init_subclass__(cls, **kwargs: Any) -> None: + super().__init_subclass__(**kwargs) + for name, attr in vars(cls).items(): + if (callable(attr) or isinstance(attr, property)) and not attr.__doc__: + for base in cls.__mro__[1:]: + base_attr = vars(base).get(name) + if base_attr is not None and base_attr.__doc__: + attr.__doc__ = base_attr.__doc__ + break + + +def sanitize_string(string: str, substitute: str = '_') -> str: """ Replace non-alphanumeric characters in a string with a given substitute. @@ -84,23 +97,23 @@ def convert_to_snake_case(string: str) -> str: def suggest_similar( invalid_string: str, - valid_strings: list[str], + valid_strings: Iterable[str], format_string: str = " - did you mean '{}'?", cutoff: float = 0.6, ) -> str: """ Suggest a similar valid string based on the given invalid string. - This function uses a similarity matching algorithm to find the closest match from a - list of valid strings. If a match is found above the specified cutoff, it returns a - formatted suggestion string. + This function uses a similarity matching algorithm to find the closest match from an + iterable of valid strings. If a match is found above the specified cutoff, it + returns a formatted suggestion string. Parameters ---------- invalid_string : str The string that is invalid or misspelled. - valid_strings : list[str] - A list of valid strings to compare against. + valid_strings : Iterable[str] + An iterable of valid strings to compare against. format_string : str, optional The format string for the suggestion. Defaults to " - did you mean '{}'?". cutoff : float, optional @@ -196,46 +209,33 @@ def get_local_ipv4() -> str: class SettingsDict(MutableMapping): """ - Represents a dictionary-like persistent settings storage. - - This class is a mutable mapping implementation that stores and retrieves key-value - pairs, persisting them to a JSON configuration file. The settings are associated - with a specific application name and, optionally, an application author to organize - the file path appropriately. You can use this class to manage configuration data - that needs to be saved and reused across sessions. Changes to the dictionary are - automatically saved to the file. - - This class supports standard dictionary operations such as getting, setting, - deleting items, checking for the existence of keys, and iterating over keys. - Additionally, it provides functionality for accessing nested values using a sequence - of keys. + A dictionary-like persistent settings storage backed by a JSON file. + + This class implements the MutableMapping interface, storing key-value pairs that are + automatically persisted to a JSON file on every write. It supports standard + dictionary operations (get, set, delete, iterate) as well as nested key access. + + File access is protected by a file lock for safe concurrent access from multiple + processes. """ - def __init__( - self, - app_name: str, - app_author: str | None = None, - filename: str = 'settings.json', - ) -> None: + def __init__(self, json_path: PathLike | str) -> None: """Initialize the SettingsDict instance. Parameters ---------- - app_name : str - Name of the application. - app_author : str, optional - Name of the application author. - filename : str, optional - Name of the settings file. Defaults to 'settings.json'. + json_path : PathLike or str + Path to the JSON configuration file. """ - config_path = Path(user_config_dir(app_name, app_author)) - self._path = config_path / filename + self._json_path = Path(json_path).resolve() + self._lock_path = self._json_path.with_suffix('.lock') + self._file_lock = FileLock(self._lock_path) self._state = self._load_from_file() def _load_from_file(self) -> dict: - if not self._path.exists(): + if not self._json_path.exists(): return {} - with self._path.open('r') as f: + with self._file_lock, self._json_path.open('r') as f: data = f.read() try: return cast('dict', msgspec.json.decode(data)) @@ -244,19 +244,16 @@ def _load_from_file(self) -> dict: def _save_to_file(self) -> None: dictionary = msgspec.to_builtins(self._state) - if not self._path.exists(): - self._path.parent.mkdir(parents=True, exist_ok=True) - self._path.touch(exist_ok=True) - with self._path.open('w') as f: + self._json_path.parent.mkdir(parents=True, exist_ok=True) + with self._file_lock, self._json_path.open('w') as f: json.dump(dictionary, f, indent=2) def __getitem__(self, key: Any) -> Any: - if key in self._state: - return self._state.get(key) - else: - raise KeyError(key) + return self._state[key] def __setitem__(self, key: Any, value: Any) -> None: + if self._state.get(key) == value: + return self._state[key] = value self._save_to_file() @@ -264,14 +261,11 @@ def __contains__(self, key: Any) -> bool: return key in self._state def __delitem__(self, key: Any) -> None: - if key in self._state: - del self._state[key] - self._save_to_file() - else: - raise KeyError(key) + del self._state[key] + self._save_to_file() def __iter__(self) -> Iterator[Any]: - return iter(self._state) + return iter(list(self._state)) def __len__(self) -> int: return len(self._state) @@ -285,7 +279,7 @@ def get_nested(self, keys: Sequence[Any], default: Any | None = None) -> Any: Parameters ---------- keys : Sequence - An sequence of keys representing the nested path. + A sequence of keys representing the nested path. default : Any, optional The value to return if the path does not exist. Defaults to None. @@ -302,10 +296,12 @@ def set_nested(self, keys: Sequence[Any], value: Any) -> None: Parameters ---------- keys : Sequence - An sequence of keys representing the nested path. + A sequence of keys representing the nested path. value : Any The value to set at the nested path. """ + if get_nested(d=self._state, keys=keys) == value: + return set_nested(d=self._state, keys=keys, value=value) self._save_to_file() @@ -373,3 +369,45 @@ def __init__(self, root: Mapping[K, V] | None = ...) -> None: ... def __hash__(self) -> int: ... else: __hash__ = None + + +def extend_packed( + byte_array: bytearray, + values: Sequence[int], + fmt: str, +) -> None: + """Extend a bytearray with packed binary values. + + This function takes a sequence of integers, converts each one to bytes using the + specified struct format character, and appends the result to the given bytearray. + All values use the same format character and are packed in little-endian byte order. + + Parameters + ---------- + byte_array : bytearray + The bytearray that will be modified in-place by appending the packed binary + data. + values : Sequence[int] + Integer values to convert to binary. The number of values determines how many + times the format character is repeated. + fmt : str + A single struct format character that defines how each value is encoded. + Common options: 'b' (int8), 'h' (int16), 'i' (int32), 'q' (int64), 'B' (uint8), + 'H' (uint16), 'I' (uint32), 'Q' (uint64). + + Examples + -------- + >>> from bpod_core.misc import extend_packed + >>> buffer = bytearray() + >>> extend_packed(buffer, [1, 2, 3], 'i') + >>> len(buffer) + 12 + >>> buffer.hex() + '010000000200000003000000' + + References + ---------- + https://docs.python.org/3/library/struct.html#format-characters + """ + if values: + byte_array.extend(struct.pack(f'<{len(values)}{fmt}', *values)) diff --git a/docs/source/_templates/custom-class-template.rst b/docs/source/_templates/custom-class-template.rst index 064ac716..ad6dfb11 100644 --- a/docs/source/_templates/custom-class-template.rst +++ b/docs/source/_templates/custom-class-template.rst @@ -6,7 +6,17 @@ .. currentmodule:: {{ module }} +{% if objname in ["RemoteBpod", "Bpod"] %} .. autoclass:: {{ objname }} :members: :undoc-members: :show-inheritance: + :member-order: groupwise + :inherited-members: +{% else %} +.. autoclass:: {{ objname }} + :members: + :undoc-members: + :show-inheritance: + :member-order: groupwise +{% endif %} diff --git a/docs/source/conf.py b/docs/source/conf.py index c6a34404..7684a527 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -19,12 +19,10 @@ def generate_fsm_examples(app): return # Create docs/source/state_machines/examples/ with one page per example - examples_source_path = project_root / 'examples' + examples_source_path = project_root / 'examples' / 'state_machines' examples_target_path = docs_source_path / 'state_machines' / 'examples' examples_target_path.mkdir(parents=True, exist_ok=True) - example_files = sorted( - [f for f in examples_source_path.glob('*.py')], key=lambda f: f.name - ) + example_files = sorted(examples_source_path.glob('*.py'), key=lambda f: f.name) for fn in example_files: # Import the example file as a module @@ -48,7 +46,7 @@ def generate_fsm_examples(app): json = [' ' * 7 + line for line in json] # Generate YAML - yaml = state_machine.to_yaml(indent=2).splitlines() + yaml = state_machine.to_yaml().splitlines() yaml = [' ' * 7 + line for line in yaml] page_path = examples_target_path.joinpath(f'{fn.stem}.rst') @@ -65,7 +63,7 @@ def generate_fsm_examples(app): '', ' .. tab-item:: Python', '', - f' .. literalinclude:: ../../../../examples/{fn.name}', + f' .. literalinclude:: ../../../../examples/state_machines/{fn.name}', ' :language: python', ' :start-at: from bpod_core.', '', diff --git a/docs/source/developer_guide.rst b/docs/source/developer_guide.rst index 04c40199..a16a863f 100644 --- a/docs/source/developer_guide.rst +++ b/docs/source/developer_guide.rst @@ -2,36 +2,12 @@ Developer Guide =============== -Versioning Scheme ------------------ - -bpod-core uses `Semantic Versioning `_. -Its version string (currently |version_code|) is a combination of three fields, separated by dots: - -.. centered:: ``MAJOR`` . ``MINOR`` . ``PATCH`` - -* The ``MAJOR`` field is only incremented for breaking changes, i.e., changes that are not backward compatible with previous changes. -* The ``MINOR`` field will be incremented upon adding new, backward compatible features. -* The ``PATCH`` field will be incremented with each new, backward compatible bugfix release that does not implement a new feature. - -On the developer side, these 3 fields are manually controlled by, both - - 1. adjusting the variable ``__version__`` in ``bpod-core/__init__.py``, and - 2. adding the corresponding version string to a commit as a `git tag `_, - for instance: - - .. code-block:: console +Setting Up the Development Environment +-------------------------------------- - $ git tag 1.2.3 - $ git push origin --tags - - -Installing UV -------------- - -This project is utilizing `UV `_ as its package -manager for managing dependencies and ensuring consistent and reproducible environments. -To install UV: +This project uses `UV `_ as its package manager for +managing dependencies and ensuring consistent and reproducible environments. To install +UV: .. tab-set:: @@ -49,86 +25,85 @@ To install UV: See `UV's documentation `_ for details. - -Installing developer dependencies ---------------------------------- - -To set up your development environment, you need to install the necessary -dependencies. The following command will synchronize your environment with the -dependencies specified in the ``pyproject.toml`` file, including development -dependencies and Qt: +Once UV is installed, synchronize your environment with the dependencies specified in +the ``pyproject.toml`` file, including development dependencies: .. code-block:: console $ uv sync -Running the unit-tests ----------------------- +.. _unit_tests: +Testing and Code Quality +------------------------ + +We use `tox `_ to automate all testing and code quality checks. +Running tox will execute the full suite of checks across several Python versions: -We use `tox `_ to automate our unit-tests. This allows us to -verify that our code works with various versions of Qt for Python. To run the -unit tests, execute the following command: +* `pytest `_ — unit-tests (located in the ``tests`` directory) +* `mypy `_ — static type checking +* `ruff `_ — linting and formatting checks + +To run all checks, execute: .. code-block:: console $ uv run tox -p -Tox will create isolated environments for each specified version of Qt and run -the tests in those environments. You can find the results of the tests in the -terminal output, which will indicate whether the tests passed or failed. +Tox will create isolated environments for each check and Python version. The terminal +output will indicate whether the checks passed or failed. -Alternatively, if you want to run unit-tests for your current environment, run +To run individual tools against your current environment: .. code-block:: console - $ uv run pytest - + $ uv run pytest # run unit-tests + $ uv run mypy # run type checking + $ uv run ruff check # check for linting issues + $ uv run ruff format # auto-format code -Coverage report ---------------- +Adding ``--fix`` to ``ruff check`` will automatically correct fixable issues. -After running ``tox`` or ``pytest`` (see above), you can generate a coverage report -to assess how much of the code is covered by the unit tests: +After running ``tox`` or ``pytest``, you can generate a coverage report to assess how +much of the code is covered by the unit-tests: .. code-block:: console $ uv run coverage report -If you need a more detailed representation of your code coverage, generate an HTML -report: +For a more detailed representation, generate an HTML report: .. code-block:: console $ uv run coverage html -You'll find the HTML report in the folder ``htmlcov``, where you can open -``index.html`` in a web browser to view detailed coverage statistics. +You'll find the HTML report in the folder ``htmlcov``, where you can open ``index.html`` +in a web browser to view detailed coverage statistics. -Checking and formatting of code -------------------------------- +Pull Requests +------------- -We use `ruff `_ to ensure our code -adheres to style guidelines and is free of common issues. To format your code -automatically, run: +All development work should be based on the ``develop`` branch. To contribute: -.. code-block:: console +1. Create a new branch from ``develop``: - $ uv run ruff format + .. code-block:: console -This command will apply formatting changes to your codebase according to the -specified style rules. To check your code for issues, use: + $ git checkout develop + $ git checkout -b your-branch-name -.. code-block:: console +2. Make your changes, keeping each pull request focused on a single topic (feature, + bugfix, refactor, etc.). - $ uv run ruff check +3. Before opening a pull request, ensure that all tests pass and the code is properly + formatted (see :ref:`unit_tests`) -This command will analyze your code and report any issues it finds. If you want -ruff to attempt to fix any issues it identifies, you can add the ``--fix`` -flag, which will automatically correct fixable problems. +4. Open your pull request against the ``develop`` branch. The ``main`` branch only + receives merges from ``develop`` as part of the release process. -Building the documentation + +Building the Documentation -------------------------- We use `Sphinx `_ to build our documentation and @@ -141,15 +116,44 @@ API reference. To build the documentation, run the following command: After running this command, you can view the generated documentation in your web browser by opening ``docs/build/index.html``. -Building the package + +Building the Package -------------------- -To build the package, execute the following command: +To build bpod-core as a distributable Python package, execute the following command: .. code-block:: console $ uv build -This command will create a distributable package of your project, in the form -of a source distribution (sdist) and a wheel (bdist_wheel). The generated -package files will be located in the ``dist`` directory. +This command will create a distributable package of bpod-core, in the form of a source +distribution (sdist) and a wheel (bdist_wheel). The generated package files will be +located in the ``dist`` directory. + + +Versioning Scheme +----------------- + +bpod-core uses `Semantic Versioning `_. Its version +string (currently |version_code|) is a combination of three fields, separated by dots: + +.. centered:: ``MAJOR`` . ``MINOR`` . ``PATCH`` + +* The ``MAJOR`` field is only incremented for breaking changes, i.e., changes that are + not backward compatible with previous changes. +* The ``MINOR`` field will be incremented upon adding new, backward compatible features. +* The ``PATCH`` field will be incremented with each new, backward compatible bugfix + release that does not implement a new feature. +* Optionally appended letters can be used to indicate an alpha release (``a``), a beta + release (``b``) or a release candidate (``rc``). + +On the developer side, these fields are controlled by both + + 1. adjusting the variable ``version`` field in ``pyproject.toml``, and + 2. adding the corresponding version string to a commit as a + `git tag `_, for instance: + + .. code-block:: console + + $ git tag 1.2.3 + $ git push origin --tags diff --git a/docs/source/faq.rst b/docs/source/faq.rst new file mode 100644 index 00000000..ac13230e --- /dev/null +++ b/docs/source/faq.rst @@ -0,0 +1,24 @@ +Frequently Asked Questions +========================== + +I can't connect to a Bpod on Linux +---------------------------------- +If you're experiencing "Permission denied" errors, slow or unreliable connections, +missing data, or timeout errors when trying to connect to your Bpod on Linux, you likely +need to install additional udev rules. + +By default, Linux restricts access to USB serial devices to root and members of the +``dialout`` group for security reasons. Additionally, system services like +`ModemManager `__ automatically probe serial devices to +detect modems, which can interfere with normal communication. Bpod devices use +`Teensy microcontrollers `__, which appear as USB serial +devices that are subject to these restrictions. + +Installing the `Teensy udev rules `__ +should solve these issues by: + +- Granting all users read/write access to Teensy devices without requiring ``dialout`` + group membership +- Preventing `ModemManager `__ from probing and interfering + with the connection +- Configuring serial ports with appropriate low-level settings (raw mode, no echo) diff --git a/docs/source/index.rst b/docs/source/index.rst index c8883310..4eaff828 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -9,6 +9,7 @@ :hidden: state_machines/index + faq api schema developer_guide diff --git a/docs/source/schema.rst b/docs/source/schema.rst index 3ef5d0cc..71285ef7 100644 --- a/docs/source/schema.rst +++ b/docs/source/schema.rst @@ -2,3 +2,7 @@ JSON Schema =========== .. jsonschema:: ../../schema/statemachine.json + :lift_description: + :lift_definitions: + :auto_reference: + :auto_target: diff --git a/examples/ipython_notebooks/graph_state_machine.ipynb b/examples/ipython_notebooks/graph_state_machine.ipynb new file mode 100644 index 00000000..180d71fb --- /dev/null +++ b/examples/ipython_notebooks/graph_state_machine.ipynb @@ -0,0 +1,99 @@ +{ + "cells": [ + { + "cell_type": "code", + "id": "e8a973cd", + "metadata": {}, + "source": [ + "from bpod_core.fsm import StateMachine" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "markdown", + "id": "09331e75", + "metadata": {}, + "source": [ + "### Define a state machine" + ] + }, + { + "cell_type": "code", + "id": "1dfc3950", + "metadata": {}, + "source": [ + "fsm = StateMachine()\n", + "\n", + "fsm.set_global_timer(\n", + " index=0,\n", + " duration=5\n", + ")\n", + "\n", + "fsm.add_state(\n", + " name='StartGlobalTimer',\n", + " timer=0.25,\n", + " transitions={'Tup': 'Port1Light'},\n", + " actions={'GlobalTimerTrig': 0},\n", + ")\n", + "fsm.add_state(\n", + " name='Port1Light',\n", + " timer=0.25,\n", + " transitions={\n", + " 'Tup': 'Port3Light',\n", + " 'GlobalTimer0_End': '>exit',\n", + " },\n", + " actions={'PWM1': 255},\n", + ")\n", + "fsm.add_state(\n", + " name='Port3Light',\n", + " timer=0.25,\n", + " transitions={\n", + " 'Tup': 'Port1Light',\n", + " 'GlobalTimer0_End': '>exit',\n", + " },\n", + " actions={'PWM3': 255},\n", + ")" + ], + "outputs": [], + "execution_count": null + }, + { + "cell_type": "markdown", + "id": "a32cfda8", + "metadata": {}, + "source": [ + "### Display the statemechine for easy verification" + ] + }, + { + "cell_type": "code", + "id": "2c77e81e", + "metadata": {}, + "source": "fsm.to_digraph()", + "outputs": [], + "execution_count": null + } + ], + "metadata": { + "kernelspec": { + "display_name": "bpod-core", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.7" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/examples/minimal_examples/run_global_timer.py b/examples/minimal_examples/run_global_timer.py new file mode 100644 index 00000000..b3e6fc1b --- /dev/null +++ b/examples/minimal_examples/run_global_timer.py @@ -0,0 +1,49 @@ +"""Global Timer Example. + +This example demonstrates how to define a state machine with a global timer and run it +on a Bpod with debug logging enabled. The state machine alternates LEDs of Port 1 and +Port 3 every 250 ms until a 5-second global timer expires, then exits the state machine. +""" + +import logging + +from bpod_core.bpod import Bpod +from bpod_core.fsm import StateMachine + +# configure debug logging +logging.basicConfig(level=logging.DEBUG) + +# create a new StateMachine instance and configure a 5-second global timer +fsm = StateMachine() +fsm.set_global_timer(index=0, duration=5) + +# define the state machine's states +fsm.add_state( + name='StartGlobalTimer', + timer=0.25, + transitions={'Tup': 'Port1Light'}, + actions={'GlobalTimerTrig': 0}, +) +fsm.add_state( + name='Port1Light', + timer=0.25, + transitions={ + 'Tup': 'Port3Light', + 'GlobalTimer0_End': '>exit', + }, + actions={'PWM1': 255}, +) +fsm.add_state( + name='Port3Light', + timer=0.25, + transitions={ + 'Tup': 'Port1Light', + 'GlobalTimer0_End': '>exit', + }, + actions={'PWM3': 255}, +) + +# connect to the Bpod, send the state machine, and run it +with Bpod() as bpod: + bpod.send_state_machine(fsm) + bpod.run_state_machine() diff --git a/examples/back_operator.py b/examples/state_machines/back_operator.py similarity index 100% rename from examples/back_operator.py rename to examples/state_machines/back_operator.py diff --git a/examples/bnc_triggered_state_change.py b/examples/state_machines/bnc_triggered_state_change.py similarity index 100% rename from examples/bnc_triggered_state_change.py rename to examples/state_machines/bnc_triggered_state_change.py diff --git a/examples/conditions.py b/examples/state_machines/conditions.py similarity index 100% rename from examples/conditions.py rename to examples/state_machines/conditions.py diff --git a/examples/global_counters.py b/examples/state_machines/global_counters.py similarity index 85% rename from examples/global_counters.py rename to examples/state_machines/global_counters.py index 77534b58..3ce22293 100644 --- a/examples/global_counters.py +++ b/examples/state_machines/global_counters.py @@ -9,7 +9,7 @@ fsm = StateMachine() fsm.set_global_counter( - index=1, + index=0, event='Port1High', threshold=5, ) @@ -23,14 +23,14 @@ fsm.add_state( name='ResetGlobalCounter', transitions={'Tup': 'Port1Light'}, - actions={'GlobalCounterReset': 1}, + actions={'GlobalCounterReset': 0}, ) fsm.add_state( name='Port1Light', timer=0.25, transitions={ 'Tup': 'Port3Light', - 'GlobalCounter1_End': '>exit', + 'GlobalCounter0_End': '>exit', }, actions={'PWM1': 255}, ) @@ -39,7 +39,7 @@ timer=0.25, transitions={ 'Tup': 'Port1Light', - 'GlobalCounter1_End': '>exit', + 'GlobalCounter0_End': '>exit', }, actions={'PWM3': 255}, ) diff --git a/examples/state_machines/global_timers.py b/examples/state_machines/global_timers.py new file mode 100644 index 00000000..21ab25c7 --- /dev/null +++ b/examples/state_machines/global_timers.py @@ -0,0 +1,38 @@ +"""Global Timers. + +A global timer ends an infinite loop when 5 seconds have passed. +""" + +from bpod_core.fsm import StateMachine + +fsm = StateMachine() + +fsm.set_global_timer( + index=0, + duration=5, +) + +fsm.add_state( + name='StartGlobalTimer', + timer=0.25, + transitions={'Tup': 'Port1Light'}, + actions={'GlobalTimerTrig': 0}, +) +fsm.add_state( + name='Port1Light', + timer=0.25, + transitions={ + 'Tup': 'Port3Light', + 'GlobalTimer0_End': '>exit', + }, + actions={'PWM1': 255}, +) +fsm.add_state( + name='Port3Light', + timer=0.25, + transitions={ + 'Tup': 'Port1Light', + 'GlobalTimer0_End': '>exit', + }, + actions={'PWM3': 255}, +) diff --git a/examples/light_chasing.py b/examples/state_machines/light_chasing.py similarity index 100% rename from examples/light_chasing.py rename to examples/state_machines/light_chasing.py diff --git a/examples/two_choice.py b/examples/state_machines/two_choice.py similarity index 100% rename from examples/two_choice.py rename to examples/state_machines/two_choice.py diff --git a/pyproject.toml b/pyproject.toml index b6cf39a9..a2944e37 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,10 +23,11 @@ dependencies = [ "graphviz>=0.20.0", "pyzmq>=27.0.0", "zeroconf>=0.147.0", - "appdirs>=1.4.0", "msgspec>=0.19.0", "packaging>=25.0", "pyyaml>=6.0.0", + "platformdirs>=4.4.0", + "filelock>=3.20.0", ] license = { text = "MIT" } readme = "README.md" @@ -45,7 +46,7 @@ doc = [ "sphinx-autodoc-typehints>=3.0.1", "sphinx-copybutton>=0.5.2", "sphinx-rtd-theme>=3.0.2", - "sphinx>=8.1.3", + "sphinx<=8.2.3", "sphinx-jsonschema>=1.19.1", "sphinx-design>=0.6.1", "sphinx-toolbox>=4.0.0", @@ -99,7 +100,7 @@ source-include = [ "tests/*.py", "schema/*.json", "docs/source/**/*", - "examples/*" + "examples/**/*" ] source-exclude = [ "docs/source/api", @@ -127,12 +128,16 @@ ignore = [ "PLR0913", # Too many arguments "PLR0915", # Too many statements "PLR2004", # Magic value used in comparison, consider replacing with a constant variable + "ANN401" # Dynamically typed expressions (typing.Any) are disallowed in {name} ] select = [ + "ANN", # flake8-annotations "A", # flake8-builtins "B", # flake8-bugbear + "C4", # flake8-comprehensions "ICN", # flake8-import-conventions "LOG", # flake8-logging + "G", # flake8-logging-format "PIE", # flake8-pie "SIM", # flake8-simplify "TID", # flake8-tidy-imports @@ -148,6 +153,9 @@ select = [ "FURB", # refurb ] +[tool.ruff.lint.per-file-ignores] +"!bpod_core/**.py" = [ "D", "ANN" ] + [tool.ruff.lint.pydocstyle] convention = "numpy" diff --git a/tests/conftest.py b/tests/conftest.py index c213a209..5b2028da 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,10 +1,11 @@ import re -from unittest.mock import MagicMock, PropertyMock +from unittest.mock import PropertyMock import pytest from bpod_core.bpod import Bpod from bpod_core.com import ExtendedSerial +from bpod_core.constants import VID_TEENSY, PIDsTeensy fixture_bpod_all = { b'6': b'5', @@ -45,13 +46,19 @@ @pytest.fixture -def mock_comports(mocker): +def mock_serial_discovery(mocker): + return mocker.patch('bpod_core.bpod.verify_serial_discovery', return_value=True) + + +@pytest.fixture +def mock_comports(mocker, mock_serial_discovery): """Fixture to mock available COM ports.""" - mock_port_info = MagicMock() + mock_port_info = mocker.MagicMock() mock_port_info.device = 'COM3' mock_port_info.serial_number = '12345' - mock_port_info.vid = 0x16C0 # supported VID - mock_comports = mocker.patch('bpod_core.bpod.comports') + mock_port_info.vid = VID_TEENSY + mock_port_info.pid = PIDsTeensy.SERIAL + mock_comports = mocker.patch('bpod_core.com.comports') mock_comports.return_value = [mock_port_info] return mock_comports @@ -93,48 +100,45 @@ def in_waiting() -> int: @pytest.fixture -def mock_bpod(mock_ext_serial, mock_settings): - mock_bpod = MagicMock(spec=Bpod) +def mock_bpod(mocker, mock_ext_serial, mock_settings): + mock_bpod = mocker.MagicMock(spec=Bpod) mock_bpod.serial0 = mock_ext_serial mock_bpod._identify_bpod.side_effect = lambda *args, **kwargs: Bpod._identify_bpod( mock_bpod, *args, **kwargs, ) - mock_bpod._sends_discovery_byte.side_effect = ( - lambda *args, **kwargs: Bpod._sends_discovery_byte(mock_bpod, *args, **kwargs) - ) return mock_bpod @pytest.fixture def mock_settings(mocker): - mock_settings = MagicMock() + mock_settings = mocker.MagicMock() mocker.patch('bpod_core.bpod.SettingsDict', return_value=mock_settings) @pytest.fixture -def mock_bpod_20(mock_comports, mock_ext_serial, mock_settings, mocker): # noqa: ARG001 +def mock_bpod_20(mock_comports, mock_ext_serial, mock_settings, mocker): mock_ext_serial.mock_responses.update(fixture_bpod_20) - mocker.patch('bpod_core.bpod.ExtendedSerial', return_value=mock_ext_serial) + mocker.patch('bpod_core.com.ExtendedSerial', return_value=mock_ext_serial) mocker.patch('bpod_core.bpod.Bpod._detect_additional_serial_ports') mocker.patch('bpod_core.bpod.DualChannelHost') return Bpod('COM3') @pytest.fixture -def mock_bpod_25(mock_comports, mock_ext_serial, mock_settings, mocker): # noqa: ARG001 +def mock_bpod_25(mock_comports, mock_ext_serial, mock_settings, mocker): mock_ext_serial.mock_responses.update(fixture_bpod_25) - mocker.patch('bpod_core.bpod.ExtendedSerial', return_value=mock_ext_serial) + mocker.patch('bpod_core.com.ExtendedSerial', return_value=mock_ext_serial) mocker.patch('bpod_core.bpod.Bpod._detect_additional_serial_ports') mocker.patch('bpod_core.bpod.DualChannelHost') return Bpod('COM3') @pytest.fixture -def mock_bpod_2p(mock_comports, mock_ext_serial, mock_settings, mocker): # noqa: ARG001 +def mock_bpod_2p(mock_comports, mock_ext_serial, mock_settings, mocker): mock_ext_serial.mock_responses.update(fixture_bpod_2p) - mocker.patch('bpod_core.bpod.ExtendedSerial', return_value=mock_ext_serial) + mocker.patch('bpod_core.com.ExtendedSerial', return_value=mock_ext_serial) mocker.patch('bpod_core.bpod.Bpod._detect_additional_serial_ports') mocker.patch('bpod_core.bpod.DualChannelHost') return Bpod('COM3') diff --git a/tests/test_bpod.py b/tests/test_bpod.py index d5307d56..ff7cfb50 100644 --- a/tests/test_bpod.py +++ b/tests/test_bpod.py @@ -19,85 +19,67 @@ def mock_bpod(self, mock_bpod): @pytest.mark.usefixtures('mock_comports') def test_automatic_success(self, mock_bpod): """Test successful identification of Bpod without specifying port or serial.""" - assert Bpod._identify_bpod(mock_bpod) == ('COM3', '12345') - mock_bpod.serial0.__init__.assert_called_once_with('COM3', timeout=0.11) + assert Bpod._identify_bpod() == ('COM3', '12345') def test_automatic_unsupported_vid(self, mock_bpod, mock_comports): """Test failure to auto identify Bpod when only device has unsupported VID.""" mock_port_info = mock_comports.return_value mock_port_info[0].vid = 0x0000 # unsupported VID with pytest.raises(BpodError, match=r'No .* Bpod found'): - Bpod._identify_bpod(mock_bpod) - mock_bpod.serial0.__init__.assert_not_called() + Bpod._identify_bpod() def test_automatic_no_devices(self, mock_bpod, mock_comports): """Test failure to auto identify Bpod when no COM ports are available.""" mock_comports.return_value = [] with pytest.raises(BpodError, match=r'No .* Bpod found'): - Bpod._identify_bpod(mock_bpod) - mock_bpod.serial0.__init__.assert_not_called() + Bpod._identify_bpod() @pytest.mark.usefixtures('mock_comports') - def test_automatic_no_discovery_byte(self, mock_bpod): + def test_automatic_no_discovery_byte(self, mock_bpod, mock_serial_discovery): """Test failure to auto identify Bpod when no discovery byte is received.""" - mock_bpod.serial0.response_buffer = bytearray() + mock_serial_discovery.return_value = False with pytest.raises(BpodError, match='No .* Bpod found'): - Bpod._identify_bpod(mock_bpod) - mock_bpod.serial0.__init__.assert_called_once_with('COM3', timeout=0.11) - - @pytest.mark.usefixtures('mock_comports') - def test_automatic_serial_exception(self, mock_bpod): - """Test failure to auto identify Bpod when serial read raises exception.""" - mock_bpod.serial0.read.side_effect = SerialException - with pytest.raises(BpodError, match='No .* Bpod found'): - Bpod._identify_bpod(mock_bpod) - mock_bpod.serial0.__init__.assert_called_once_with('COM3', timeout=0.11) + Bpod._identify_bpod() @pytest.mark.usefixtures('mock_comports') def test_serial_success(self, mock_bpod): """Test successful identification of Bpod when specifying serial.""" - port, serial_number = Bpod._identify_bpod(mock_bpod, serial_number='12345') + port, serial_number = Bpod._identify_bpod(serial_number='12345') assert port == 'COM3' assert serial_number == '12345' # existing serial - mock_bpod.serial0.__init__.assert_called_once_with('COM3', timeout=0.11) @pytest.mark.usefixtures('mock_comports') def test_serial_incorrect_serial(self, mock_bpod): """Test failure to identify Bpod when specifying incorrect serial.""" with pytest.raises(BpodError, match='No .* serial number'): - Bpod._identify_bpod(mock_bpod, serial_number='00000') - mock_bpod.serial0.__init__.assert_not_called() + Bpod._identify_bpod(serial_number='00000') def test_serial_unsupported_vid(self, mock_bpod, mock_comports): """Test failure to identify Bpod by serial if device has incompatible VID.""" mock_port_info = mock_comports.return_value mock_port_info[0].vid = 0x0000 # unsupported VID - with pytest.raises(BpodError, match='.* not a supported Bpod'): - Bpod._identify_bpod(mock_bpod, serial_number='12345') - mock_bpod.serial0.__init__.assert_called_once_with('COM3', timeout=0.11) + with pytest.raises(BpodError, match='No .* Bpod found matching serial number'): + Bpod._identify_bpod(serial_number='12345') @pytest.mark.usefixtures('mock_comports') def test_port_success(self, mock_bpod): """Test successful identification of Bpod when specifying port.""" - port, serial_number = Bpod._identify_bpod(mock_bpod, port='COM3') + port, serial_number = Bpod._identify_bpod(port='COM3') assert port == 'COM3' assert serial_number == '12345' # existing serial - mock_bpod.serial0.__init__.assert_not_called() @pytest.mark.usefixtures('mock_comports') def test_port_incorrect_port(self, mock_bpod): """Test failure to identify Bpod when specifying incorrect port.""" with pytest.raises(BpodError, match='Port not found'): - Bpod._identify_bpod(mock_bpod, port='incorrect_port') - mock_bpod.serial0.__init__.assert_not_called() + Bpod._identify_bpod(port='incorrect_port') def test_port_unsupported_vid(self, mock_bpod, mock_comports): """Test failure to identify Bpod when specifying incorrect port.""" mock_port_info = mock_comports.return_value mock_port_info[0].vid = 0x0000 # unsupported VID - with pytest.raises(BpodError, match='.* not .* supported Bpod'): - Bpod._identify_bpod(mock_bpod, port='COM3') - mock_bpod.serial0.__init__.assert_not_called() + with pytest.raises(BpodError, match='not an .* Bpod'): + Bpod._identify_bpod(port='COM3') class TestGetVersionInfo: @@ -252,8 +234,8 @@ def fsm_basic(self): def fsm_global_timers(self): fsm = StateMachine() fsm.set_global_timer(2, 3, 1.5, 'PWM1', 128, 64, 1, 1, 3, 0) - fsm.add_state('a', 1, {'GlobalTimer3_Start': 'b'}, {'GlobalTimerTrig': 4}) - fsm.add_state('b', 1, {'GlobalTimer3_End': '>exit'}) + fsm.add_state('a', 1, {'GlobalTimer2_Start': 'b'}, {'GlobalTimerTrig': 3}) + fsm.add_state('b', 1, {'GlobalTimer2_End': '>exit'}) return fsm @pytest.fixture @@ -261,8 +243,8 @@ def fsm_global_counters(self): fsm = StateMachine() fsm.set_global_counter(2, 'Port1_High', 5) fsm.add_state('a', 2, {'Tup': 'b'}, {'PWM2': 255}) - fsm.add_state('b', 0, {'Tup': 'c'}, {'GlobalCounterReset': 3}) - fsm.add_state('c', 0, {'GlobalCounter3_End': '>exit'}, {'PWM1': 255}) + fsm.add_state('b', 0, {'Tup': 'c'}, {'GlobalCounterReset': 2}) + fsm.add_state('c', 0, {'GlobalCounter2_End': '>exit'}, {'PWM1': 255}) return fsm @pytest.fixture @@ -270,7 +252,7 @@ def fsm_conditions(self): fsm = StateMachine() fsm.set_condition(1, 'Port2', 1) fsm.add_state('a', 1, {'Tup': 'b'}, {'PWM1': 255}) - fsm.add_state('b', 1, {'Tup': '>exit', 'Condition2': '>exit'}, {'PWM2': 255}) + fsm.add_state('b', 1, {'Tup': '>exit', 'Condition1': '>exit'}, {'PWM2': 255}) return fsm def test_send_state_machine_basic_25(self, fsm_basic, mock_bpod_25): diff --git a/tests/test_com.py b/tests/test_com.py index 02d0f8f6..a5ceb322 100644 --- a/tests/test_com.py +++ b/tests/test_com.py @@ -1,7 +1,10 @@ import logging +import re from unittest.mock import MagicMock, call +import numpy as np import pytest +from serial import SerialException from bpod_core import com @@ -59,6 +62,71 @@ def test_verify(self, mock_serial): result = mock_serial.verify(b'x', b'\x01') assert result is False + @pytest.mark.parametrize( + 'fcn', + [ + 'write_int8', + 'write_int16', + 'write_int32', + 'write_int64', + 'write_uint8', + 'write_uint16', + 'write_uint32', + 'write_uint64', + ], + ) + def test_write_int(self, mock_serial, fcn): + """Test writing integer values.""" + dtype = getattr(np, fcn.split('_')[1]) + info = np.iinfo(dtype) + length = info.bits // 8 + signed = info.kind == 'i' + for value_type in ['min', 'max']: + value = getattr(info, value_type) + expected = value.to_bytes(length, 'little', signed=signed) + getattr(mock_serial, fcn)(value) + mock_serial.super_write.assert_called_with(expected) + + @pytest.mark.parametrize( + 'fcn', + [ + 'read_int8', + 'read_int16', + 'read_int32', + 'read_int64', + 'read_uint8', + 'read_uint16', + 'read_uint32', + 'read_uint64', + ], + ) + def test_read_int(self, mock_serial, fcn): + """Test reading integer values.""" + dtype = getattr(np, fcn.split('_')[1]) + info = np.iinfo(dtype) + length = info.bits // 8 + signed = info.kind == 'i' + for value_type in ['min', 'max']: + value = getattr(info, value_type) + mock_serial.super_read.return_value = value.to_bytes( + length, 'little', signed=signed + ) + value_out = getattr(mock_serial, fcn)() + mock_serial.super_read.assert_called_with(length) + assert value_out == value + + def test_write_bool(self, mock_serial): + """Test reading single character.""" + mock_serial.write_bool(True) + mock_serial.super_write.assert_called_with(b'\x01') + + def test_read_bool(self, mock_serial): + """Test reading single character.""" + mock_serial.super_read.return_value = b'\x01' + value_out = mock_serial.read_bool() + mock_serial.super_read.assert_called_with(1) + assert value_out is True + class TestChunkedSerialReader: """Tests for ChunkedSerialReader buffer and processing behavior.""" @@ -149,3 +217,256 @@ def test_non_multiple_chunk_data(self): reader.data_received(b'\x01\x02\x03\x04\x05') callback.assert_called_once_with(b'\x01\x02\x03\x04') assert reader._buffer == bytearray(b'\x05') + + +class TestFindPorts: + """Tests for find_ports() filtering functionality.""" + + @pytest.fixture + def mock_ports(self, mocker): + """Fixture providing mock serial ports.""" + port1 = MagicMock() + port1.device = '/dev/ttyACM0' + port1.vid = 0x16C0 + port1.pid = 0x0483 + port1.serial_number = 'ABC123' + + port2 = MagicMock() + port2.device = '/dev/ttyUSB0' + port2.vid = 0x0403 + port2.pid = 0x6001 + port2.serial_number = 'DEF456' + + port3 = MagicMock() + port3.device = '/dev/ttyACM1' + port3.vid = 0x16C0 + port3.pid = 0x048B + port3.serial_number = 'GHI789' + + ports = [port1, port2, port3] + mocker.patch('bpod_core.com.comports', return_value=ports) + return ports + + def test_no_filters(self, mock_ports): + """Returns all ports when no filters specified.""" + result = com.find_ports() + assert result == mock_ports + + def test_scalar_filter(self, mock_ports): + """Exact match on single attribute returns matching ports.""" + result = com.find_ports(vid=0x16C0) + assert len(result) == 2 + assert mock_ports[0] in result + assert mock_ports[2] in result + + def test_scalar_filter_no_match(self, mock_ports): + """Returns empty list when no ports match filter.""" + result = com.find_ports(vid=0x9999) + assert result == [] + + def test_list_filter(self, mock_ports): + """List filter matches any item (OR logic).""" + result = com.find_ports(pid=[0x0483, 0x6001]) + assert len(result) == 2 + assert mock_ports[0] in result + assert mock_ports[1] in result + + def test_regex_filter(self, mock_ports): + """Regex pattern filter matches ports with matching strings.""" + result = com.find_ports(device=re.compile(r'/dev/ttyACM\d+')) + assert len(result) == 2 + assert mock_ports[0] in result + assert mock_ports[2] in result + + def test_combined_filters(self, mock_ports): + """Multiple filters combine with AND logic.""" + result = com.find_ports(vid=0x16C0, pid=0x0483) + assert len(result) == 1 + assert mock_ports[0] in result + + def test_nonexistent_attribute(self, mock_ports): + """Filter on missing attribute matches None values.""" + result = com.find_ports(nonexistent_attr='value') + assert result == [] + + def test_regex_on_non_string(self, mock_ports): + """Regex filter on non-string attribute returns no match.""" + result = com.find_ports(vid=re.compile(r'16C0')) + assert result == [] + + def test_list_with_regex(self, mock_ports): + """List can contain regex patterns.""" + result = com.find_ports(device=[re.compile(r'ttyACM'), '/dev/ttyUSB0']) + assert len(result) == 3 + + +class TestVerifySerialDiscovery: + @pytest.fixture() + def mock_serial(self, mocker): + mock_serial = mocker.MagicMock() + mock_serial.read.return_value = b'A' + mock_serial.__enter__.return_value = mock_serial + mocker.patch('bpod_core.com.Serial', return_value=mock_serial) + return mock_serial + + def test_success(self, mock_serial): + result = com.verify_serial_discovery( + port='COM1', + expected_message=b'A', + ) + assert result is True + mock_serial.read.assert_called_once_with(1) + + def test_wrong_message(self, mock_serial): + result = com.verify_serial_discovery( + port='COM1', + expected_message=b'B', + ) + assert result is False + + def test_trigger_called(self, mock_serial, mocker): + trigger = mocker.Mock() + result = com.verify_serial_discovery( + port='COM1', + expected_message=b'A', + trigger=trigger, + ) + assert result is True + trigger.assert_called_once() + + def test_serial_exception(self, mock_serial): + mock_serial.read.side_effect = SerialException() + result = com.verify_serial_discovery( + port='COM1', + expected_message=b'A', + ) + assert result is False + + +class TestUSBSerialDevice: + """Tests for USBSerialDevice class.""" + + @pytest.fixture + def mock_port_info(self, mocker): + """Fixture to create a mock port info object.""" + port_info = mocker.MagicMock() + port_info.device = '/dev/ttyACM0' + port_info.serial_number = '12345' + port_info.vid = 0x16C0 + port_info.pid = 0x0483 + return port_info + + @pytest.fixture + def mock_comports(self, mocker, mock_port_info): + """Fixture to mock available COM ports.""" + mock = mocker.patch('bpod_core.com.comports') + mock.return_value = [mock_port_info] + return mock + + @pytest.fixture + def mock_extended_serial(self, mocker): + """Fixture to mock ExtendedSerial.""" + mock = mocker.MagicMock(spec=com.ExtendedSerial) + mock.is_open = False + mocker.patch('bpod_core.com.ExtendedSerial', return_value=mock) + return mock + + def test_init_opens_connection_by_default( + self, mock_comports, mock_extended_serial + ): + """Device opens serial connection by default on init.""" + device = com.USBSerialDevice('/dev/ttyACM0') + mock_extended_serial.open.assert_called_once() + assert device.port == '/dev/ttyACM0' + + def test_init_without_opening_connection(self, mock_comports, mock_extended_serial): + """Device can be initialized without opening connection.""" + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + mock_extended_serial.open.assert_not_called() + assert device.port == '/dev/ttyACM0' + + def test_init_port_not_found(self, mock_comports): + """Raises SerialException when port does not exist.""" + mock_comports.return_value = [] + with pytest.raises(SerialException, match='Serial port not found'): + com.USBSerialDevice('/dev/ttyACM0') + + def test_context_manager_enter(self, mock_comports, mock_extended_serial): + """Context manager __enter__ returns the device instance.""" + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + result = device.__enter__() + assert result is device + + def test_context_manager_exit(self, mock_comports, mock_extended_serial): + """Context manager __exit__ closes the connection.""" + mock_extended_serial.is_open = True + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + device.__exit__(None, None, None) + mock_extended_serial.close.assert_called_once() + + def test_context_manager_with_statement(self, mock_comports, mock_extended_serial): + """Device works correctly with 'with' statement.""" + mock_extended_serial.is_open = True + with com.USBSerialDevice('/dev/ttyACM0', open_connection=False) as device: + assert device.port == '/dev/ttyACM0' + mock_extended_serial.close.assert_called_once() + + def test_open_when_closed(self, mock_comports, mock_extended_serial, caplog): + """open() opens connection when not already open.""" + mock_extended_serial.is_open = False + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + with caplog.at_level(logging.DEBUG): + device.open() + mock_extended_serial.open.assert_called_once() + assert 'Opening connection' in caplog.text + + def test_open_when_already_open(self, mock_comports, mock_extended_serial): + """open() does nothing when connection is already open.""" + mock_extended_serial.is_open = True + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + device.open() + mock_extended_serial.open.assert_not_called() + + def test_open_raises_on_failure(self, mock_comports, mock_extended_serial): + """open() raises SerialException when connection fails.""" + mock_extended_serial.is_open = False + mock_extended_serial.open.side_effect = Exception('Connection failed') + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + with pytest.raises(SerialException, match='Failed to open connection'): + device.open() + + def test_close_when_open(self, mock_comports, mock_extended_serial, caplog): + """close() closes connection when open.""" + mock_extended_serial.is_open = True + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + with caplog.at_level(logging.DEBUG): + device.close() + mock_extended_serial.close.assert_called_once() + assert 'Closing connection' in caplog.text + + def test_close_when_already_closed(self, mock_comports, mock_extended_serial): + """close() does nothing when connection is already closed.""" + mock_extended_serial.is_open = False + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + device.close() + mock_extended_serial.close.assert_not_called() + + def test_close_raises_on_failure(self, mock_comports, mock_extended_serial): + """close() raises SerialException when closing fails.""" + mock_extended_serial.is_open = True + mock_extended_serial.close.side_effect = Exception('Close failed') + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + with pytest.raises(SerialException, match='Failed to close connection'): + device.close() + + def test_port_property(self, mock_comports, mock_extended_serial): + """port property returns the device path.""" + device = com.USBSerialDevice('/dev/ttyACM0', open_connection=False) + assert device.port == '/dev/ttyACM0' + + def test_accepts_kwargs(self, mock_comports, mock_extended_serial): + """Extra kwargs are accepted for subclass compatibility.""" + device = com.USBSerialDevice( + '/dev/ttyACM0', open_connection=False, custom_arg='value' + ) + assert device.port == '/dev/ttyACM0' diff --git a/tests/test_misc.py b/tests/test_misc.py index 4544d041..cf1a864d 100644 --- a/tests/test_misc.py +++ b/tests/test_misc.py @@ -1,6 +1,7 @@ """Tests for bpod_core.misc utilities and helpers.""" import errno +import struct import pytest from pydantic import ValidationError @@ -229,8 +230,7 @@ class TestSettingsDict: @pytest.fixture def temp_settings(self, tmp_path, mocker): """Fixture to create a SettingsDict pointing to a temporary directory.""" - mocker.patch('bpod_core.misc.user_config_dir', return_value=str(tmp_path)) - settings = misc.SettingsDict('test_app', 'test_author', 'test_settings.json') + settings = misc.SettingsDict(tmp_path / 'settings.json') yield settings def test_set_and_get(self, temp_settings): @@ -285,8 +285,7 @@ def test_corrupted_file(self, tmp_path, mocker): """Test behavior with a corrupted JSON file.""" corrupted_file = tmp_path / 'test_settings.json' corrupted_file.write_text('corrupted json') - mocker.patch('bpod_core.misc.user_config_dir', return_value=str(tmp_path)) - settings = misc.SettingsDict('test_app', 'test_author', 'test_settings.json') + settings = misc.SettingsDict(corrupted_file) assert len(settings) == 0 # Should recover with an empty dict def test_repr(self, temp_settings): @@ -297,12 +296,11 @@ def test_repr(self, temp_settings): def test_persistence_across_instances(self, tmp_path, mocker): """Values should persist to disk and be readable by a new instance.""" - mocker.patch('bpod_core.misc.user_config_dir', return_value=str(tmp_path)) - s1 = misc.SettingsDict('test_app', 'test_author', 'persist.json') + s1 = misc.SettingsDict(tmp_path / 'persist.json') s1['a'] = 1 s1.set_nested(['nested', 'x'], 42) # New instance should read previous state - s2 = misc.SettingsDict('test_app', 'test_author', 'persist.json') + s2 = misc.SettingsDict(tmp_path / 'persist.json') assert s2['a'] == 1 assert s2.get_nested(['nested', 'x']) == 42 @@ -316,11 +314,9 @@ def test_set_and_get_nested_methods(self, temp_settings): def test_missing_file_initialization_and_creation_on_write(self, tmp_path, mocker): """Dict starts empty and file is created upon first write.""" - mocker.patch('bpod_core.misc.user_config_dir', return_value=str(tmp_path)) - file_name = 'new_settings.json' - s = misc.SettingsDict('test_app', 'test_author', file_name) + path = tmp_path / 'new_settings.json' + s = misc.SettingsDict(path) assert len(s) == 0 - path = tmp_path / file_name assert not path.exists() s['created'] = True assert path.exists() @@ -331,6 +327,100 @@ def test_contains_operator(self, temp_settings): assert 'present' in temp_settings assert 'absent' not in temp_settings + def test_setitem_skips_write_when_value_unchanged(self, temp_settings, mocker): + """Setting the same value should not trigger a file write.""" + temp_settings['key'] = 'value' + spy = mocker.spy(temp_settings, '_save_to_file') + temp_settings['key'] = 'value' # same value + spy.assert_not_called() + + def test_setitem_writes_when_value_changed(self, temp_settings, mocker): + """Setting a different value should trigger a file write.""" + temp_settings['key'] = 'value' + spy = mocker.spy(temp_settings, '_save_to_file') + temp_settings['key'] = 'new_value' + spy.assert_called_once() + + def test_set_nested_skips_write_when_value_unchanged(self, temp_settings, mocker): + """set_nested with the same value should not trigger a file write.""" + temp_settings.set_nested(['a', 'b'], 42) + spy = mocker.spy(temp_settings, '_save_to_file') + temp_settings.set_nested(['a', 'b'], 42) # same value + spy.assert_not_called() + + def test_set_nested_writes_when_value_changed(self, temp_settings, mocker): + """set_nested with a different value should trigger a file write.""" + temp_settings.set_nested(['a', 'b'], 42) + spy = mocker.spy(temp_settings, '_save_to_file') + temp_settings.set_nested(['a', 'b'], 99) + spy.assert_called_once() + + def test_setitem_writes_for_new_key(self, temp_settings, mocker): + """Setting a new key should always trigger a file write.""" + spy = mocker.spy(temp_settings, '_save_to_file') + temp_settings['new_key'] = 'value' + spy.assert_called_once() + + def test_set_nested_writes_for_new_path(self, temp_settings, mocker): + """set_nested with a new path should always trigger a file write.""" + spy = mocker.spy(temp_settings, '_save_to_file') + temp_settings.set_nested(['new', 'path'], 'value') + spy.assert_called_once() + + +class TestExtendPacked: + """Tests for misc.extend_packed().""" + + def test_pack_unsigned_bytes(self): + """Packs a list of unsigned bytes.""" + buf = bytearray() + misc.extend_packed(buf, [1, 2, 255], 'B') + assert buf == b'\x01\x02\xff' + + def test_pack_unsigned_shorts(self): + """Packs a list of unsigned 16-bit integers (little-endian).""" + buf = bytearray() + misc.extend_packed(buf, [1, 256, 65535], 'H') + assert buf == b'\x01\x00\x00\x01\xff\xff' + + def test_pack_unsigned_ints(self): + """Packs a list of unsigned 32-bit integers (little-endian).""" + buf = bytearray() + misc.extend_packed(buf, [1, 0x01020304], 'I') + assert buf == b'\x01\x00\x00\x00\x04\x03\x02\x01' + + def test_empty_values(self, mocker): + """Empty list results in no bytes added.""" + pack = mocker.spy(struct, 'pack') + buf = bytearray() + misc.extend_packed(buf, [], 'I') + assert buf == b'' + assert not pack.called + + def test_extends_existing_buffer(self): + """Appends to an existing bytearray without overwriting.""" + buf = bytearray(b'\xaa\xbb') + misc.extend_packed(buf, [1, 2], 'B') + assert buf == b'\xaa\xbb\x01\x02' + + def test_invalid_format_raises_struct_error(self): + """Raises struct.error for an invalid format character.""" + buf = bytearray() + with pytest.raises(struct.error): + misc.extend_packed(buf, [1], 'Z') + + def test_value_out_of_range_raises_struct_error(self): + """Raises struct.error when value exceeds format range.""" + buf = bytearray() + with pytest.raises(struct.error): + misc.extend_packed(buf, [256], 'B') # max for 'B' is 255 + + def test_negative_for_unsigned_raises_struct_error(self): + """Raises struct.error for negative value with unsigned format.""" + buf = bytearray() + with pytest.raises(struct.error): + misc.extend_packed(buf, [-1], 'B') + class TestValidatedDict: @pytest.fixture @@ -398,3 +488,65 @@ def test_missing_key(self, validated_dict): _ = validated_dict['missing'] with pytest.raises(KeyError): del validated_dict['missing'] + + +class TestDocstringInheritanceMixin: + """Tests for DocstringInheritanceMixin.""" + + def test_inherits_method_docstring(self): + """Subclass method without docstring inherits from parent.""" + + class Base(misc.DocstringInheritanceMixin): + def foo(self): + """Base docstring.""" + + class Child(Base): + def foo(self): + pass + + assert Child.foo.__doc__ == 'Base docstring.' + + def test_does_not_overwrite_existing_docstring(self): + """Subclass method with its own docstring is not overwritten.""" + + class Base(misc.DocstringInheritanceMixin): + def foo(self): + """Base docstring.""" + + class Child(Base): + def foo(self): + """Child docstring.""" + + assert Child.foo.__doc__ == 'Child docstring.' + + def test_inherits_property_docstring(self): + """Subclass property without docstring inherits from parent.""" + + class Base(misc.DocstringInheritanceMixin): + @property + def bar(self): + """Base property docstring.""" + return 1 + + class Child(Base): + @property + def bar(self): + return 2 + + assert Child.bar.__doc__ == 'Base property docstring.' + + def test_inherits_from_grandparent(self): + """Docstring is inherited across multiple levels of inheritance.""" + + class Base(misc.DocstringInheritanceMixin): + def foo(self): + """Base docstring.""" + + class Middle(Base): + pass + + class Child(Middle): + def foo(self): + pass + + assert Child.foo.__doc__ == 'Base docstring.' diff --git a/uv.lock b/uv.lock index 000ffb36..c665224d 100644 --- a/uv.lock +++ b/uv.lock @@ -3,7 +3,8 @@ revision = 3 requires-python = ">=3.10" resolution-markers = [ "python_full_version >= '3.13'", - "python_full_version >= '3.11' and python_full_version < '3.13'", + "python_full_version == '3.12.*'", + "python_full_version == '3.11.*'", "python_full_version < '3.11'", ] required-markers = [ @@ -32,17 +33,16 @@ 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