diff --git a/.envrc b/.envrc new file mode 100644 index 00000000..fa6b8405 --- /dev/null +++ b/.envrc @@ -0,0 +1,2 @@ +export VIRTUAL_ENV=.venv +layout python diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs new file mode 100644 index 00000000..3b6d32f6 --- /dev/null +++ b/.git-blame-ignore-revs @@ -0,0 +1,4 @@ +# chore: format files with ruff. Add pre-commit-config. +5b4c220154d33cac15a75d3d7d978a75e67f2b8a +# Ran `black` formatter on entire codebase and fixed non-standard line-endings with `dos2unix`. +4e4f20be40a73f2162a565732bae76ea0c812739 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 00000000..668eca62 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,37 @@ +name: Test package + +on: + push: + branches: [main] + pull_request: + branches: [main] + workflow_dispatch: + +jobs: + build: + strategy: + matrix: + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + os: + - "ubuntu-latest" + - "windows-latest" + - "macos-latest" + runs-on: ${{matrix.os}} + + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v2 + with: + enable-cache: true + cache-dependency-glob: "uv.lock" + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + + - name: Install the project + run: uv sync --all-extras --dev + + - name: Run tests + run: uv run pytest tests diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 00000000..742a547f --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,28 @@ +name: Upload Python Package + +on: + release: + types: [published] + workflow_dispatch: + +permissions: + contents: read + +jobs: + deploy: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v2 + + - name: Build Package + run: uv build + + - name: Publish Package + env: + TWINE_USERNAME: __token__ + TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} + run: uvx twine upload dist/* diff --git a/.github/workflows/python-publish-ezmsg.yml b/.github/workflows/python-publish-ezmsg.yml deleted file mode 100644 index 69030485..00000000 --- a/.github/workflows/python-publish-ezmsg.yml +++ /dev/null @@ -1,40 +0,0 @@ -# This workflow will upload a Python Package using Twine when a release is created -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries - -# This workflow uses actions that are not certified by GitHub. -# They are provided by a third-party and are governed by -# separate terms of service, privacy policy, and support -# documentation. - -name: Upload Python Package - ezmsg - -on: - release: - types: [published] - workflow_dispatch: - -permissions: - contents: read - -jobs: - deploy: - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.8" - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install build - - - name: Build ezmsg - run: python -m build - - name: Publish ezmsg - uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 - with: - password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml deleted file mode 100644 index 3407af48..00000000 --- a/.github/workflows/python-tests.yml +++ /dev/null @@ -1,51 +0,0 @@ -name: Test package - -on: - push: - branches: [main] - pull_request: - branches: [main] - workflow_dispatch: - -jobs: - build: - strategy: - matrix: - python-version: [3.8, 3.9, "3.10"] - os: - - "ubuntu-latest" - - "windows-latest" - - "macos-latest" - runs-on: ${{matrix.os}} - - steps: - - uses: actions/checkout@v4 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade pip and install pipx - run: | - python -m pip install --upgrade pip pipx flake8 - - - name: Install Poetry via pipx - run: | - pipx install poetry - echo "$HOME/.local/bin/" >> $GITHUB_PATH - - - name: Install dependencies with Poetry - run: | - poetry install --with test - - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - - name: Test ezmsg - run: | - poetry run python -m pytest -v tests diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..6f694649 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,10 @@ +repos: + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.5.0 + hooks: + # Run the linter. + - id: ruff + args: [--fix] + # Run the formatter. + - id: ruff-format diff --git a/.python-version b/.python-version new file mode 100644 index 00000000..902b2c90 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py index 4f4d9b51..0b74dcc2 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -18,7 +18,7 @@ "sphinx.ext.autosummary", "sphinx.ext.intersphinx", "sphinx.ext.linkcode", - "sphinx.ext.napoleon" + "sphinx.ext.napoleon", ] intersphinx_mapping = { @@ -46,15 +46,14 @@ def linkcode_resolve(domain, info): - if domain != 'py': + if domain != "py": return None - if not info['module']: + if not info["module"]: return None - filename = info['module'].replace('.', '/') + filename = info["module"].replace(".", "/") if "sigproc" in filename: return f"{sigproc_code_url}src/{filename}.py" elif "core" in filename: return f"{code_url}src/ezmsg/core/__init__.py" else: return f"{code_url}src/{filename}.py" - diff --git a/docs/source/extensions/sigproc.rst b/docs/source/extensions/sigproc.rst index 1d3853c0..e41ecb14 100644 --- a/docs/source/extensions/sigproc.rst +++ b/docs/source/extensions/sigproc.rst @@ -1,6 +1,21 @@ ezmsg-sigproc ============= +Timeseries signal processing implementations in ezmsg, leveraging numpy and scipy. +Most of the methods and classes in this extension are intended to be used in building signal processing pipelines. +They use :class:`ezmsg.util.messages.axisarray.AxisArray` as the primary data structure for passing signals between components. +The message's data are expected to be a numpy array. + +Note for offline processing: some generators might yield valid :class:`AxisArray` messages with ``.data`` size of 0. +This may occur when the generator receives inadequate data to produce a valid output, such as when windowing or buffering. + +ezmsg.sigproc.activation +----------------------------- + +.. automodule:: ezmsg.sigproc.activation + :members: + + ezmsg.sigproc.affinetransform ----------------------------- @@ -57,6 +72,25 @@ ezmsg.sigproc.ewmfilter :members: +ezmsg.sigproc.math +----------------------- + +.. automodule:: ezmsg.sigproc.math.clip + :members: + +.. automodule:: ezmsg.sigproc.math.difference + :members: + +.. automodule:: ezmsg.sigproc.math.invert + :members: + +.. automodule:: ezmsg.sigproc.math.log + :members: + +.. automodule:: ezmsg.sigproc.math.scale + :members: + + ezmsg.sigproc.sampler --------------------- diff --git a/examples/ezmsg_configs.py b/examples/ezmsg_configs.py index 883e0d02..ffa9d767 100644 --- a/examples/ezmsg_configs.py +++ b/examples/ezmsg_configs.py @@ -14,7 +14,7 @@ class TerminatorSettings(ez.Settings): class Terminator(ez.Unit): - SETTINGS: TerminatorSettings + SETTINGS = TerminatorSettings @ez.task async def terminate(self) -> None: @@ -31,7 +31,7 @@ class GeneratorSettings(ez.Settings): class Generator(ez.Unit): - SETTINGS: GeneratorSettings + SETTINGS = GeneratorSettings OUTPUT = ez.OutputStream(int) @@ -51,7 +51,7 @@ class ModulusSettings(ez.Settings): class Modulus(ez.Unit): - SETTINGS: ModulusSettings + SETTINGS = ModulusSettings INPUT = ez.InputStream(int) OUTPUT = ez.OutputStream(int) @@ -70,7 +70,7 @@ class ListenerState(ez.State): class Listener(ez.Unit): - STATE: ListenerState + STATE = ListenerState INPUT = ez.InputStream(int) @@ -93,8 +93,7 @@ def network(self) -> ez.NetworkDefinition: # CORNER CASES -class EmptySystem(ez.Collection): - ... +class EmptySystem(ez.Collection): ... class EmptyTerminateSystem(ez.Collection): diff --git a/examples/ezmsg_count.py b/examples/ezmsg_count.py index 4d3e120b..7d524ed2 100644 --- a/examples/ezmsg_count.py +++ b/examples/ezmsg_count.py @@ -1,4 +1,5 @@ import asyncio +import time import array from dataclasses import dataclass import ezmsg.core as ez @@ -20,7 +21,7 @@ class CountSettings(ez.Settings): class Count(ez.Unit): - SETTINGS: CountSettings + SETTINGS = CountSettings OUTPUT = ez.OutputStream(int) @@ -29,14 +30,23 @@ async def count(self) -> AsyncGenerator: count = 0 while True: await asyncio.sleep(0.1) - yield self.OUTPUT, CountMessage( - value=count, arr=array.array("b", [0x00] * (2**count)) + yield ( + self.OUTPUT, + CountMessage(value=count, arr=array.array("b", [0x00] * (2**count))), ) count = count + 1 if count >= self.SETTINGS.num_msgs: raise ez.Complete + @ez.thread + def hello_world(self): + i = 0 + while True: + print(f"Hello world {i}") + i += 1 + time.sleep(1) + class CountSystem(ez.Collection): COUNT = Count() @@ -61,4 +71,4 @@ def process_components(self): # multiprocessing.set_start_method('spawn', force=True) system = CountSystem() - ez.run(SYSTEM = system) + ez.run(SYSTEM=system) diff --git a/examples/ezmsg_generator.py b/examples/ezmsg_generator.py index 748b3091..d60e3d91 100644 --- a/examples/ezmsg_generator.py +++ b/examples/ezmsg_generator.py @@ -46,7 +46,7 @@ class PowSettings(ez.Settings): class Pow(Gen): - SETTINGS: PowSettings + SETTINGS = PowSettings def construct_generator(self): self.STATE.gen = pow(self.SETTINGS.n) @@ -66,7 +66,7 @@ class AddSettings(ez.Settings): class Add(Gen): - SETTINGS: AddSettings + SETTINGS = AddSettings def construct_generator(self): self.STATE.gen = add(self.SETTINGS.n) @@ -123,10 +123,7 @@ def network(self): (self.POW_0_5.OUTPUT, self.LOG_OUT.INPUT), ) - ez.run( - SYSTEM=GenOneExample() - ) - + ez.run(SYSTEM=GenOneExample()) # This example will show the type-hint based introspection to construct ezmsg Units # at runtime, which simplifies the integration of generators into Units, reducing @@ -158,6 +155,4 @@ def network(self): (self.POW_0_5.OUTPUT, self.LOG_OUT.INPUT), ) - ez.run( - SYSTEM=GenTwoExample() - ) + ez.run(SYSTEM=GenTwoExample()) diff --git a/examples/ezmsg_intro.py b/examples/ezmsg_intro.py index 44903f5e..1ad2b073 100644 --- a/examples/ezmsg_intro.py +++ b/examples/ezmsg_intro.py @@ -61,7 +61,7 @@ class Count(ez.Unit): # We do this because this unit may receive settings objects # from parent collections. Also, SETTINGS is a special/reserved # class attribute for Components (ez.Unit, and ez.Collection) - SETTINGS: CountSettings + SETTINGS = CountSettings OUTPUT_COUNT = ez.OutputStream(CountMessage) @@ -115,7 +115,7 @@ class PrintState(ez.State): class PrintValue(ez.Unit): - SETTINGS: PrintSettings + SETTINGS = PrintSettings # As with settings, only provide a state type, do not instantiate. # We do this because this unit may end up living in a different @@ -123,7 +123,7 @@ class PrintValue(ez.Unit): # pickled/sent to subprocesses (e.g. open file-handles, asyncio # and threading primitives, etc.) STATE is a special/reserved # class attribute for Units - STATE: PrintState + STATE = PrintState INPUT = ez.InputStream(CountMessage) @@ -148,7 +148,7 @@ class CountSystemSettings(ez.Settings): class CountSystem(ez.Collection): - SETTINGS: CountSystemSettings + SETTINGS = CountSystemSettings # Define member units COUNT = Count() diff --git a/examples/ezmsg_normalterm.py b/examples/ezmsg_normalterm.py index d1737aba..8c5c7905 100644 --- a/examples/ezmsg_normalterm.py +++ b/examples/ezmsg_normalterm.py @@ -23,7 +23,7 @@ class MessageGeneratorSettings(ez.Settings): class MessageGenerator(ez.Unit): - SETTINGS: MessageGeneratorSettings + SETTINGS = MessageGeneratorSettings OUTPUT = ez.OutputStream(SimpleMessage) @@ -47,8 +47,8 @@ class MessageReceiverState(ez.State): class MessageReceiver(ez.Unit): - STATE: MessageReceiverState - SETTINGS: MessageReceiverSettings + STATE = MessageReceiverState + SETTINGS = MessageReceiverSettings INPUT = ez.InputStream(SimpleMessage) @@ -71,7 +71,7 @@ class ToySystemSettings(ez.Settings): class ToySystem(ez.Collection): - SETTINGS: ToySystemSettings + SETTINGS = ToySystemSettings # Publishers SIMPLE_PUB = MessageGenerator() @@ -104,12 +104,12 @@ def process_components(self): def main(): test_filename = "./test.txt" num_messages = 5 - with open(test_filename, "w") as f: + with open(test_filename, "w") as _: ... system = ToySystem( ToySystemSettings(num_msgs=num_messages, output_fn=test_filename) ) - ez.run(SYSTEM = system) + ez.run(SYSTEM=system) results = [] with open(test_filename, "r") as file: diff --git a/examples/ezmsg_stop.py b/examples/ezmsg_stop.py index 17efebe4..65975fed 100644 --- a/examples/ezmsg_stop.py +++ b/examples/ezmsg_stop.py @@ -23,7 +23,7 @@ class MessageGeneratorSettings(ez.Settings): class MessageGenerator(ez.Unit): - SETTINGS: MessageGeneratorSettings + SETTINGS = MessageGeneratorSettings OUTPUT = ez.OutputStream(SimpleMessage) @@ -47,8 +47,8 @@ class MessageReceiverState(ez.State): class MessageReceiver(ez.Unit): - STATE: MessageReceiverState - SETTINGS: MessageReceiverSettings + STATE = MessageReceiverState + SETTINGS = MessageReceiverSettings INPUT = ez.InputStream(SimpleMessage) @@ -71,7 +71,7 @@ class ToySystemSettings(ez.Settings): class ToySystem(ez.Collection): - SETTINGS: ToySystemSettings + SETTINGS = ToySystemSettings # Publishers SIMPLE_PUB = MessageGenerator() @@ -98,12 +98,12 @@ def network(self) -> ez.NetworkDefinition: def main(): test_filename = "./test.txt" num_messages = 5 - with open(test_filename, "w") as f: + with open(test_filename, "w") as _: ... system = ToySystem( ToySystemSettings(num_msgs=num_messages, output_fn=test_filename) ) - ez.run(SYSTEM = system) + ez.run(SYSTEM=system) results = [] with open(test_filename, "r") as file: diff --git a/examples/ezmsg_toy.py b/examples/ezmsg_toy.py index 47885b8e..3c4238d0 100644 --- a/examples/ezmsg_toy.py +++ b/examples/ezmsg_toy.py @@ -18,17 +18,18 @@ class CombinedMessage: # LFO: Low Frequency Oscillator + class LFOSettings(ez.Settings): freq: float = 0.2 # Hz, sinus frequency update_rate: float = 2.0 # Hz, update rate class LFO(ez.Unit): - SETTINGS: LFOSettings + SETTINGS = LFOSettings OUTPUT = ez.OutputStream(float) - def initialize(self) -> None: + async def initialize(self) -> None: self.start_time = time.time() @ez.publisher(OUTPUT) @@ -45,7 +46,7 @@ class MessageGeneratorSettings(ez.Settings): class MessageGenerator(ez.Unit): - SETTINGS: MessageGeneratorSettings + SETTINGS = MessageGeneratorSettings OUTPUT = ez.OutputStream(str) @@ -68,7 +69,7 @@ class DebugOutputSettings(ez.Settings): class DebugOutput(ez.Unit): - SETTINGS: DebugOutputSettings + SETTINGS = DebugOutputSettings INPUT = ez.InputStream(str) @@ -85,7 +86,7 @@ class MessageModifierState(ez.State): class MessageModifier(ez.Unit): """Store number input, and append it to message""" - STATE: MessageModifierState + STATE = MessageModifierState MESSAGE = ez.InputStream(str) NUMBER = ez.InputStream(float) @@ -93,7 +94,7 @@ class MessageModifier(ez.Unit): JOINED = ez.OutputStream(str) REPUB = ez.OutputStream(CombinedMessage) - def initialize(self): + async def initialize(self): self.STATE.number = 0.0 @ez.subscriber(NUMBER) @@ -149,7 +150,7 @@ class TestSystemSettings(ez.Settings): class TestSystem(ez.Collection): - 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-[extras] -all-ext = ["ezmsg-sigproc", "ezmsg-vispy", "ezmsg-websocket", "ezmsg-zmq"] -sigproc = ["ezmsg-sigproc"] -vispy = ["ezmsg-vispy"] -websocket = ["ezmsg-websocket"] -zmq = ["ezmsg-zmq"] - -[metadata] -lock-version = "2.0" -python-versions = "^3.8" -content-hash = "ba3e62a6e7a812d508784cb7cd9cb627d05db306fda4a5ee44be0a1f56848e7d" diff --git a/pyproject.toml b/pyproject.toml index 9ec8fcd6..48ed129d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,73 +1,34 @@ -[tool.poetry] +[project] name = "ezmsg" -version = "3.4.0" +version = "3.5.0" description = "A simple DAG-based computation model" authors = [ - "Milsap, Griffin ", - "Peranich, Preston ", + { name = "Griffin Milsap", email = "griffin.milsap@gmail.com" }, + { name = "Preston Peranich", email = "pperanich@gmail.com" }, + { name = "Chadwick Boulay", email = "chadwick.boulay@gmail.com" }, ] license = "MIT" readme = "README.md" -packages = [{ include = "ezmsg", from = "src" }] classifiers = [ "Programming Language :: Python :: 3", "Operating System :: OS Independent", ] +requires-python = ">=3.8" +dependencies = ["typing-extensions >= 4.9.0"] + +[project.optional-dependencies] +test = [ + "pytest>=7.0.0", + "numpy>=1.24.2", + "pytest-asyncio>=0.23.8", + "pytest-cov>=5.0.0", + "flake8>=5.0.4", +] +docs = ["sphinx<=7.2", "sphinx-rtd-theme==2.0.0", "ezmsg-sigproc>=1.2.3"] -[tool.poetry.scripts] -ezmsg = "ezmsg.core.command:cmdline" - -[tool.poetry.dependencies] -python = "^3.8" -typing-extensions = "^4.9.0" -ezmsg-sigproc = { version = "*", source = "pypi", optional = true } -ezmsg-websocket = { version = "*", source = "pypi", optional = true } -ezmsg-zmq = { version = "*", source = "pypi", optional = true } -ezmsg-vispy = { version = "*", source = "pypi", optional = true } -# ezmsg-panel = { git = "https://github.com/griffinmilsap/ezmsg-panel.git", rev = "main", optional = true } -# ezmsg-blackrock = { python = "^3.9", git = "https://github.com/CerebusOSS/ezmsg-blackrock.git", rev = "main", optional = true } -# ezmsg-unicorn = { git = "https://github.com/griffinmilsap/ezmsg-unicorn.git", rev = "main", optional = true } -# ezmsg-gadget = { git = "https://github.com/griffinmilsap/ezmsg-gadget.git", rev = "main", optional = true } -# ezmsg-openbci = { git = "https://github.com/griffinmilsap/ezmsg-openbci.git", rev = "main", optional = true } -# ezmsg-ssvep = { git = "https://github.com/griffinmilsap/ezmsg-ssvep.git", rev = "main", optional = true } - - -[tool.poetry.group.test.dependencies] -pytest = "^7.0.0" -pytest-asyncio = "*" -pytest-cov = "*" -numpy = "^1.24.2" -flake8 = "*" - - -[tool.poetry.group.docs.dependencies] -sphinx = "<7.2" -sphinx-rtd-theme = "^2.0.0" -ezmsg-sigproc = { version = "*", source = "pypi" } -[tool.poetry.extras] -sigproc = ["ezmsg-sigproc"] -websocket = ["ezmsg-websocket"] -zmq = ["ezmsg-zmq"] -# panel = ["ezmsg-panel"] -# blackrock = ["ezmsg-blackrock"] -# unicorn = ["ezmsg-unicorn"] -# gadget = ["ezmsg-gadget"] -# openbci = ["ezmsg-openbci"] -# ssvep = ["ezmsg-ssvep"] -vispy = ["ezmsg-vispy"] -all_ext = [ - "ezmsg-sigproc", - "ezmsg-websocket", - "ezmsg-zmq", - # "ezmsg-panel", - # "ezmsg-blackrock", - # "ezmsg-unicorn", - # "ezmsg-gadget", - # "ezmsg-openbci", - # "ezmsg-ssvep", - "ezmsg-vispy", -] +[project.scripts] +ezmsg = "ezmsg.core.command:cmdline" [tool.pytest.ini_options] addopts = ["--import-mode=importlib"] @@ -75,5 +36,15 @@ pythonpath = ["src", "tests"] testpaths = "tests" [build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling"] +build-backend = "hatchling.build" + +[tool.hatch.metadata] +allow-direct-references = true + +[tool.hatch.build.targets.wheel] +packages = ["src/ezmsg"] + +[tool.hatch.build.hooks.version] +path = "src/ezmsg/core/__init__.py" +pattern = true diff --git a/src/ezmsg/core/__init__.py b/src/ezmsg/core/__init__.py index 6697b3a7..6e8f387e 100644 --- a/src/ezmsg/core/__init__.py +++ b/src/ezmsg/core/__init__.py @@ -1,7 +1,4 @@ -import importlib.metadata - - -__version__ = importlib.metadata.version("ezmsg") +__version__ = "3.5.0" __all__ = [ "task", @@ -10,6 +7,7 @@ "main", "timeit", "process", + "thread", "Component", "Settings", "Collection", @@ -35,12 +33,11 @@ from .state import State from .settings import Settings from .collection import Collection, NetworkDefinition -from .unit import Unit, task, publisher, subscriber, main, timeit, process +from .unit import Unit, task, publisher, subscriber, main, timeit, process, thread from .stream import InputStream, OutputStream from .backend import run from .backendprocess import Complete, NormalTermination -from .graphserver import GraphServer, GraphService -from .shmserver import SHMService +from .graphserver import GraphServer from .graphcontext import GraphContext from .command import run_command @@ -65,4 +62,4 @@ LOGLEVEL = os.environ.get("EZMSG_LOGLEVEL", "INFO").upper() logger.setLevel(LOGLEVEL) -logger.debug(f'Log level set to {LOGLEVEL}') +logger.debug(f"Log level set to {LOGLEVEL}") diff --git a/src/ezmsg/core/backend.py b/src/ezmsg/core/backend.py index 1752e1f5..00e85008 100644 --- a/src/ezmsg/core/backend.py +++ b/src/ezmsg/core/backend.py @@ -203,7 +203,6 @@ def run( raise ValueError("Must supply at least one component to run") with new_threaded_event_loop() as loop: - execution_context = ExecutionContext.setup( components, graph_service, @@ -286,7 +285,6 @@ def collect_processes( collection: typing.Union[Collection, typing.Iterable[Component]], process_components: typing.Optional[typing.Collection[Component]] = None, ) -> typing.List[typing.List[Unit]]: - if isinstance(collection, Collection): process_units, units = _collect_processes( collection._components.values(), collection.process_components() @@ -311,7 +309,6 @@ def _collect_processes( units: typing.List[Unit] = [] for comp in comps: - if isinstance(comp, Collection): r_process_units, r_units = _collect_processes( comp.components.values(), comp.process_components() diff --git a/src/ezmsg/core/backendprocess.py b/src/ezmsg/core/backendprocess.py index e185cc2f..3d855ed1 100644 --- a/src/ezmsg/core/backendprocess.py +++ b/src/ezmsg/core/backendprocess.py @@ -16,7 +16,7 @@ from concurrent.futures import TimeoutError from .stream import Stream, InputStream, OutputStream -from .unit import Unit, TIMEIT_ATTR, PUBLISHES_ATTR, SUBSCRIBES_ATTR, ZERO_COPY_ATTR +from .unit import Unit, TIMEIT_ATTR, SUBSCRIBES_ATTR, ZERO_COPY_ATTR from .graphcontext import GraphContext from .graphserver import GraphService @@ -24,6 +24,7 @@ from .pubclient import Publisher from .subclient import Subscriber from .messagecache import MessageCache +from abc import abstractmethod from typing import ( List, @@ -31,6 +32,7 @@ Callable, Any, Optional, + Sequence, Set, Coroutine, DefaultDict, @@ -45,6 +47,7 @@ class Complete(Exception): A type of ``Exception`` which signals to ``ezmsg`` that the function can be shut down gracefully. If all functions in all :obj:`Units` raise ``Complete``, the entire pipeline will terminate execution. """ + pass @@ -52,6 +55,7 @@ class NormalTermination(Exception): """ A type of ``Exception`` which signals to ``ezmsg`` that the pipeline can be shut down gracefully. """ + pass @@ -89,6 +93,7 @@ def run(self) -> None: except KeyboardInterrupt: logger.debug("Process Interrupted.") + @abstractmethod def process(self, loop: asyncio.AbstractEventLoop) -> None: raise NotImplementedError @@ -121,7 +126,7 @@ async def setup_state(): for unit, main_fn in main_funcs ] ) - suggestion = f"Use a Collection and define process_components to separate these units." + suggestion = "Use a Collection and define process_components to separate these units." raise Exception( "Process has more than one main-thread functions\n" + details @@ -172,7 +177,7 @@ async def setup_state(): ), loop=loop, ).result() - except: + except Exception: self.start_barrier.abort() logger.error(f"{traceback.format_exc()}") @@ -195,12 +200,10 @@ async def coro_wrapper(coro): complete_tasks = [ asyncio.run_coroutine_threadsafe(coro_wrapper(coro()), loop) - for name, coro in coro_callables.items() + for coro in coro_callables.values() ] - monitor = loop.run_in_executor( - None, self.monitor_termination, complete_tasks, loop - ) + loop.run_in_executor(None, self.monitor_termination, complete_tasks, loop) if main_func is not None: unit, fn = main_func @@ -229,7 +232,7 @@ async def coro_wrapper(coro): # This stop barrier prevents publishers/subscribers # from getting destroyed before all other processes have # drained communication channels - logger.debug(f"Waiting at stop barrier") + logger.debug("Waiting at stop barrier") while True: try: self.stop_barrier.wait() @@ -248,14 +251,14 @@ async def coro_wrapper(coro): # for thread in threads: # thread.result() - logger.debug(f"Shutting down Units") + logger.debug("Shutting down Units") async def shutdown_units() -> None: for unit in self.units: if inspect.iscoroutinefunction(unit.shutdown): await unit.shutdown() else: - unit.shutdown() # type: ignore + unit.shutdown() # type: ignore asyncio.run_coroutine_threadsafe(shutdown_units(), loop=loop).result() @@ -275,10 +278,12 @@ async def shutdown_units() -> None: # ) def monitor_termination( - self, tasks: List[asyncio.Task], loop: asyncio.AbstractEventLoop + self, + tasks: Sequence[concurrent.futures.Future[None]], + loop: asyncio.AbstractEventLoop, ): self.term_ev.wait() - logger.debug(f"Detected term_ev") + logger.debug("Detected term_ev") for task in tasks: loop.call_soon_threadsafe(task.cancel) @@ -301,15 +306,18 @@ async def perf_publish(stream: Stream, obj: Any) -> None: ) pub_fn = perf_publish if hasattr(task, TIMEIT_ATTR) else publish - - call_fn = lambda _: task(unit) + signature = inspect.signature(task) if len(signature.parameters) == 1: - call_fn = lambda _: task(unit) + + def call_fn(_): # type: ignore + return task(unit) elif len(signature.parameters) == 2: - call_fn = lambda msg: task(unit, msg) + + def call_fn(msg): + return task(unit, msg) else: - logger.error(f'Incompatible call signature on task: {task.__name__}') + logger.error(f"Incompatible call signature on task: {task.__name__}") @wraps(task) async def wrapped_task(msg: Any = None) -> None: diff --git a/src/ezmsg/core/collection.py b/src/ezmsg/core/collection.py index 7de4dd0c..1c73eb22 100644 --- a/src/ezmsg/core/collection.py +++ b/src/ezmsg/core/collection.py @@ -6,16 +6,18 @@ from .settings import Settings -NetworkDefinition = typing.Iterable[typing.Tuple[typing.Union[Stream, str], typing.Union[Stream, str]]] +NetworkDefinition = typing.Iterable[ + typing.Tuple[typing.Union[Stream, str], typing.Union[Stream, str]] +] class CollectionMeta(ComponentMeta): def __init__( - cls, - name: str, - bases: typing.Tuple[type, ...], - fields: typing.Dict[str, typing.Any], - **kwargs: typing.Any + cls, + name: str, + bases: typing.Tuple[type, ...], + fields: typing.Dict[str, typing.Any], + **kwargs: typing.Any, ) -> None: super(CollectionMeta, cls).__init__(name, bases, fields) diff --git a/src/ezmsg/core/command.py b/src/ezmsg/core/command.py index 9c25e971..364f31fb 100644 --- a/src/ezmsg/core/command.py +++ b/src/ezmsg/core/command.py @@ -103,9 +103,9 @@ async def run_command(cmd: str, graph_address: Address, shm_address: Address) -> while True: try: - reader, writer = await graph_service.open_connection() + _, writer = await graph_service.open_connection() await close_stream_writer(writer) - reader, writer = await shm_service.open_connection() + _, writer = await shm_service.open_connection() await close_stream_writer(writer) break except ConnectionRefusedError: @@ -188,12 +188,12 @@ def tree(): def recurse_graph(g: defaultdict): out = "" for leaf in g: - if type(g[leaf]) == defaultdict: + if isinstance(g[leaf], defaultdict): out += indent( "\n".join( [ f"subgraph {leaf.lower()} {{", - indent(f"cluster = true;", IND), + indent("cluster = true;", IND), indent(f'label = "{leaf}";', IND), f"{recurse_graph(g[leaf])}}};", "", @@ -281,7 +281,7 @@ def tree(): def recurse_graph(g: defaultdict): out = "" for leaf in g: - if type(g[leaf]) == defaultdict: + if isinstance(g[leaf], defaultdict): out += indent( "\n".join( [ diff --git a/src/ezmsg/core/component.py b/src/ezmsg/core/component.py index d0f187ff..58490c27 100644 --- a/src/ezmsg/core/component.py +++ b/src/ezmsg/core/component.py @@ -9,6 +9,10 @@ from typing import List, Optional, Dict, Tuple, Any, Callable +import logging + +logger = logging.getLogger("ezmsg") + class ComponentMeta(ABCMeta): def __init__( @@ -16,59 +20,78 @@ def __init__( ) -> None: super(ComponentMeta, cls).__init__(name, bases, fields) - cls.__settings_type__ = Settings - cls.__state_type__ = State - - for base in bases: - if ( - cls.__settings_type__ is not Settings - and hasattr(base, "__settings_type__") - and getattr(base, "__settings_type__") is not Settings - ): - # This means class settings has already been set by a base class. - raise Exception( - f"Class {name} already has settings of type {cls.__settings_type__}, " - + f"but is trying to be set to {getattr(base, '__settings_type__')}" - ) - if ( - hasattr(base, "__settings_type__") - and getattr(base, "__settings_type__") is not Settings - ): - cls.__settings_type__ = getattr(base, "__settings_type__") - if ( - cls.__state_type__ is not State - and hasattr(base, "__state_type__") - and getattr(base, "__state_type__") is not State - ): - # This means class state has already been set by a base class. - raise Exception( - f"Class {name} already has state of type {cls.__state_type__}, " - + f"but is trying to be set to {getattr(base, '__state_type__')}" - ) - if ( - hasattr(base, "__state_type") - and getattr(base, "__state_type__") is not State - ): - cls.__state_type__ = getattr(base, "__state_type__") + cls.__streams__ = {} if "SETTINGS" in cls.__annotations__: - cls.__settings_type__ = cls.__annotations__["SETTINGS"] - + settings_cls = cls.__annotations__["SETTINGS"].__name__ + logger.warning( + f"{name} SETTINGS should be assigned rather than annotated: `SETTINGS = {settings_cls}` -> `SETTINGS = {settings_cls}`" + ) + fields["SETTINGS"] = cls.__annotations__["SETTINGS"] if "STATE" in cls.__annotations__: - cls.__state_type__ = cls.__annotations__["STATE"] - - cls.__streams__ = {} - + state_cls = cls.__annotations__["STATE"].__name__ + logger.warning( + f"{name} STATE should be assigned rather than annotated: `STATE = {state_cls}` -> `STATE = {state_cls}`" + ) + fields["STATE"] = cls.__annotations__["STATE"] + + base_settings_types = [] + base_state_types = [] for base in bases: if hasattr(base, "__streams__"): streams = getattr(base, "__streams__") for stream_name, stream in streams.items(): cls.__streams__[stream_name] = stream + if hasattr(base, "__settings_type__"): + base_settings_types.append(base.__settings_type__) + if hasattr(base, "__state_type__"): + base_state_types.append(base.__state_type__) for field_name, field_value in fields.items(): if isinstance(field_value, Stream): field_value._set_name(field_name) cls.__streams__[field_name] = field_value + continue + + if field_name == "SETTINGS": + if not issubclass(field_value, Settings): + logger.error( + f"{name} Settings must be a subclass of `ez.Settings`!" + ) + + for settings_type in base_settings_types: + if not issubclass(field_value, settings_type): + logger.error( + f"{name} Settings of type {field_value.__name__} must be a subclass of {settings_type.__name__}" + ) + cls.__settings_type__ = field_value + + if field_name == "STATE": + if not issubclass(field_value, State): + logger.error(f"{name} State must be a subclass of `ez.State`!") + + for state_type in base_state_types: + if not issubclass(field_value, state_type): + logger.error( + f"{name} State of type {field_value.__name__} must be a subclass of {state_type.__name__}" + ) + cls.__state_type__ = field_value + + if not hasattr(cls, "__state_type__"): + if len(base_state_types) == 1: + cls.__state_type__ = base_state_types[0] + elif len(base_state_types) > 1: + logger.error("More than one state base class inherited!") + else: + cls.__state_type__ = State + + if not hasattr(cls, "__settings_type__"): + if len(base_settings_types) == 1: + cls.__settings_type__ = base_settings_types[0] + elif len(base_settings_types) > 1: + logger.error("More than one settings base class inherited!") + else: + cls.__settings_type__ = Settings class Component(Addressable, metaclass=ComponentMeta): @@ -76,9 +99,6 @@ class Component(Addressable, metaclass=ComponentMeta): Metaclass which :obj:`Unit` and :obj:`Collection` inherit from. """ - SETTINGS: Settings - STATE: State - _tasks: Dict[str, Callable] # Only Units will have tasks _streams: Dict[str, Stream] # All Components can have streams _components: Dict[str, "Component"] # Only Collections will have components @@ -88,8 +108,8 @@ class Component(Addressable, metaclass=ComponentMeta): def __init__(self, *args, settings: Optional[Settings] = None, **kwargs): super(Component, self).__init__() - self.SETTINGS = None # type: ignore - self.STATE = None # type: ignore + self.SETTINGS = None + self.STATE = None self._settings_applied = False self._components = {} self._tasks = {} @@ -102,7 +122,7 @@ def __init__(self, *args, settings: Optional[Settings] = None, **kwargs): if settings is None: # settings not supplied as a kwarg. Try to build it. - if len(args) > 0 and type(args[0]) == self.__class__.__settings_type__: + if len(args) > 0 and isinstance(args[0], self.__class__.__settings_type__): settings = args[0] elif len(args) > 0 or len(kwargs) > 0: settings = self.__class__.__settings_type__(*args, **kwargs) diff --git a/src/ezmsg/core/dag.py b/src/ezmsg/core/dag.py index aefa4bea..e6ace550 100644 --- a/src/ezmsg/core/dag.py +++ b/src/ezmsg/core/dag.py @@ -5,8 +5,7 @@ from typing import List, Set, DefaultDict -class CyclicException(Exception): - ... +class CyclicException(Exception): ... GraphType = DefaultDict[str, Set[str]] diff --git a/src/ezmsg/core/graphserver.py b/src/ezmsg/core/graphserver.py index c2812971..d31d3b65 100644 --- a/src/ezmsg/core/graphserver.py +++ b/src/ezmsg/core/graphserver.py @@ -92,8 +92,9 @@ async def api( info = SubscriberInfo(id, writer, pid, topic) self.clients[id] = info self._client_tasks[id] = asyncio.create_task( - self._handle_client(id, reader, writer)) - iface = writer.transport.get_extra_info('sockname')[0] + self._handle_client(id, reader, writer) + ) + iface = writer.transport.get_extra_info("sockname")[0] await self._notify_subscriber(info, iface) elif req == Command.PUBLISH.value: @@ -101,8 +102,9 @@ async def api( info = PublisherInfo(id, writer, pid, topic, address) self.clients[id] = info self._client_tasks[id] = asyncio.create_task( - self._handle_client(id, reader, writer)) - iface = writer.transport.get_extra_info('peername')[0] + self._handle_client(id, reader, writer) + ) + iface = writer.transport.get_extra_info("peername")[0] for sub in self._downstream_subs(info.topic): await self._notify_subscriber(sub, iface) @@ -187,19 +189,23 @@ async def _handle_client( del self.clients[id] await close_stream_writer(writer) - async def _notify_subscriber(self, sub: SubscriberInfo, iface: typing.Optional[str] = None) -> None: + async def _notify_subscriber( + self, sub: SubscriberInfo, iface: typing.Optional[str] = None + ) -> None: try: notification = [] for pub in self._upstream_pubs(sub.topic): address = pub.address - if address != None: + if address is not None: if iface is not None: notification.append(f"{str(pub.id)}@{iface}:{address.port}") else: - notification.append(f"{str(pub.id)}@{address.host}:{address.port}") + notification.append( + f"{str(pub.id)}@{address.host}:{address.port}" + ) async with sub.sync_writer() as writer: - notify_str = ','.join(notification) + notify_str = ",".join(notification) writer.write(Command.UPDATE.value) writer.write(encode_str(notify_str)) diff --git a/src/ezmsg/core/message.py b/src/ezmsg/core/message.py index 691231b1..b9c597e6 100644 --- a/src/ezmsg/core/message.py +++ b/src/ezmsg/core/message.py @@ -21,7 +21,7 @@ def __new__( name: str, bases: Tuple[type, ...], classdict: Dict[str, Any], - **kwargs: Any + **kwargs: Any, ) -> Type["Message"]: new_cls = super().__new__(cls, name, bases, classdict) return dataclass(unsafe_hash=True, frozen=True)(new_cls) # type: ignore @@ -39,6 +39,7 @@ def __init__(self): @dataclass class Flag: """Message with no contents""" + ... diff --git a/src/ezmsg/core/messagecache.py b/src/ezmsg/core/messagecache.py index 9be7f12e..bd1a4f7d 100644 --- a/src/ezmsg/core/messagecache.py +++ b/src/ezmsg/core/messagecache.py @@ -11,8 +11,7 @@ logger = logging.getLogger("ezmsg") -class CacheMiss(Exception): - ... +class CacheMiss(Exception): ... class Cache: diff --git a/src/ezmsg/core/messagemarshal.py b/src/ezmsg/core/messagemarshal.py index 681733e8..537dc9e0 100644 --- a/src/ezmsg/core/messagemarshal.py +++ b/src/ezmsg/core/messagemarshal.py @@ -17,8 +17,7 @@ def __init__(self, *args: object, req_size: int = 0) -> None: self.req_size = req_size -class UninitializedMemory(Exception): - ... +class UninitializedMemory(Exception): ... class Marshal: diff --git a/src/ezmsg/core/netprotocol.py b/src/ezmsg/core/netprotocol.py index a4a4fc35..efa8b651 100644 --- a/src/ezmsg/core/netprotocol.py +++ b/src/ezmsg/core/netprotocol.py @@ -2,7 +2,6 @@ import socket import typing import enum -import os from uuid import UUID from dataclasses import field, dataclass @@ -91,8 +90,7 @@ class PublisherInfo(ClientInfo): @dataclass -class SubscriberInfo(ClientInfo): - ... +class SubscriberInfo(ClientInfo): ... def uint64_to_bytes(i: int) -> bytes: diff --git a/src/ezmsg/core/pubclient.py b/src/ezmsg/core/pubclient.py index fad89cbb..0f17530f 100644 --- a/src/ezmsg/core/pubclient.py +++ b/src/ezmsg/core/pubclient.py @@ -32,8 +32,8 @@ logger = logging.getLogger("ezmsg") -BACKPRESSURE_WARNING = not ("EZMSG_DISABLE_BACKPRESSURE_WARNING" in os.environ) -BACKPRESSURE_REFRACTORY = 5.0 # sec +BACKPRESSURE_WARNING = "EZMSG_DISABLE_BACKPRESSURE_WARNING" not in os.environ +BACKPRESSURE_REFRACTORY = 5.0 # sec class Publisher: diff --git a/src/ezmsg/core/server.py b/src/ezmsg/core/server.py index 1879d98b..f925a8f2 100644 --- a/src/ezmsg/core/server.py +++ b/src/ezmsg/core/server.py @@ -86,11 +86,9 @@ async def monitor_shutdown() -> None: with suppress(asyncio.CancelledError): await monitor_task - async def setup(self) -> None: - ... + async def setup(self) -> None: ... - async def shutdown(self) -> None: - ... + async def shutdown(self) -> None: ... async def api( self, reader: asyncio.StreamReader, writer: asyncio.StreamWriter diff --git a/src/ezmsg/core/settings.py b/src/ezmsg/core/settings.py index 9bc6203b..9b839304 100644 --- a/src/ezmsg/core/settings.py +++ b/src/ezmsg/core/settings.py @@ -21,7 +21,7 @@ def __new__( name: str, bases: typing.Tuple[type, ...], classdict: typing.Dict[str, typing.Any], - **kwargs: typing.Any + **kwargs: typing.Any, ) -> typing.Type["Settings"]: new_cls = super().__new__(cls, name, bases, classdict) return dataclass(frozen=True)(new_cls) # type: ignore @@ -43,7 +43,7 @@ class YourSettings(Settings): class YourUnit(Unit): - SETTINGS: YourSettings + SETTINGS = YourSettings A ``Unit`` can accept a ``Settings`` object as a parameter on instantiation. @@ -62,4 +62,5 @@ class YourCollection(Collection): ``Settings`` uses type hints to define member variables, but does not enforce type checking. """ + ... diff --git a/src/ezmsg/core/state.py b/src/ezmsg/core/state.py index b4937d29..0513fb14 100644 --- a/src/ezmsg/core/state.py +++ b/src/ezmsg/core/state.py @@ -15,7 +15,7 @@ def __new__( name: str, bases: Tuple[type, ...], classdict: Dict[str, Any], - **kwargs: Any + **kwargs: Any, ) -> Type["State"]: new_cls = super().__new__(cls, name, bases, classdict) return dataclass(unsafe_hash=True, frozen=False, init=False)(new_cls) # type: ignore @@ -44,13 +44,14 @@ class YourState(State): class YourUnit(Unit): - STATE: YourState + STATE = YourState - def initialize(self): + async def initialize(self): this.STATE.state1 = 0 this.STATE.state2 = 0.0 .. note:: ``State`` uses type hints to define member variables, but does not enforce type checking. """ + ... diff --git a/src/ezmsg/core/stream.py b/src/ezmsg/core/stream.py index 7b5e8414..52d2aae2 100644 --- a/src/ezmsg/core/stream.py +++ b/src/ezmsg/core/stream.py @@ -1,17 +1,15 @@ -from typing import Type, Optional +from typing import Any, Optional from .netprotocol import DEFAULT_SHM_SIZE from .addressable import Addressable class Stream(Addressable): - """ - - """ + """ """ - msg_type: Type + msg_type: Any - def __init__(self, msg_type: Type): + def __init__(self, msg_type: Any): super().__init__() self.msg_type = msg_type @@ -24,6 +22,7 @@ class InputStream(Stream): """ Can be added to any ``Component`` as a member variable. Methods may subscribe to it. """ + def __repr__(self) -> str: return f"Input{super().__repr__()}()" @@ -32,6 +31,7 @@ class OutputStream(Stream): """ Can be added to any ``Component`` as a member variable. Methods may publish to it. """ + host: Optional[str] port: Optional[int] num_buffers: int @@ -40,7 +40,7 @@ class OutputStream(Stream): def __init__( self, - msg_type: Type, + msg_type: Any, host: Optional[str] = None, port: Optional[int] = None, num_buffers: int = 32, diff --git a/src/ezmsg/core/subclient.py b/src/ezmsg/core/subclient.py index af85eed6..be71ed7b 100644 --- a/src/ezmsg/core/subclient.py +++ b/src/ezmsg/core/subclient.py @@ -14,7 +14,6 @@ from .netprotocol import ( Address, - AddressType, UINT64_SIZE, uint64_to_bytes, bytes_to_uint, diff --git a/src/ezmsg/core/unit.py b/src/ezmsg/core/unit.py index 05bc5d73..48c089ac 100644 --- a/src/ezmsg/core/unit.py +++ b/src/ezmsg/core/unit.py @@ -1,7 +1,7 @@ import time import inspect import functools -from .stream import Stream, InputStream, OutputStream +from .stream import InputStream, OutputStream from .component import ComponentMeta, Component from .settings import Settings @@ -84,7 +84,7 @@ async def setup(self): if inspect.iscoroutinefunction(self.initialize): await self.initialize() else: - self.initialize() # type: ignore + self.initialize() # type: ignore self._check_state() diff --git a/src/ezmsg/core/util.py b/src/ezmsg/core/util.py index 1ca0426e..4102787b 100644 --- a/src/ezmsg/core/util.py +++ b/src/ezmsg/core/util.py @@ -18,9 +18,11 @@ T = typing.TypeVar("T") + def is_dict_like(value: typing.Any) -> TypeGuard[typing.Mapping]: return hasattr(value, "keys") and hasattr(value, "__getitem__") + def either_dict_or_kwargs( pos_kwargs: typing.Optional[typing.Mapping[str, T]], kw_kwargs: typing.Mapping[str, T], diff --git a/src/ezmsg/util/debuglog.py b/src/ezmsg/util/debuglog.py index 6ad3ccdc..ce89bc9f 100644 --- a/src/ezmsg/util/debuglog.py +++ b/src/ezmsg/util/debuglog.py @@ -13,6 +13,7 @@ class DebugLogSettings(ez.Settings): max_length: Sets a maximum number of chars which will be printed from the message. If the message is longer, the log message will be truncated. """ + name: str = "DEBUG" max_length: Optional[int] = 400 @@ -22,7 +23,7 @@ class DebugLog(ez.Unit): Logs messages that pass through. """ - SETTINGS: DebugLogSettings + SETTINGS = DebugLogSettings INPUT = ez.InputStream(Any) """Send messages to log here.""" diff --git a/src/ezmsg/util/gen_to_unit.py b/src/ezmsg/util/gen_to_unit.py index 90ff463e..60d57be4 100644 --- a/src/ezmsg/util/gen_to_unit.py +++ b/src/ezmsg/util/gen_to_unit.py @@ -5,6 +5,7 @@ However, please be aware that any changes made to the `ezmsg` core may potentially impact the functionality of `gen_to_unit`. """ + import ezmsg.core as ez import asyncio import sys @@ -62,18 +63,20 @@ def gen_to_unit( for param in sig.parameters.values(): if param.default is not inspect.Parameter.empty: _defaults[param.name] = param.default - _type_hints[param.name] = param.annotation # OK if empty, needed for untyped params + _type_hints[param.name] = ( + param.annotation + ) # OK if empty, needed for untyped params settings = args_to_settings(func.__name__, _type_hints, _defaults) # Create State state = args_to_state(func.__name__, _type_hints, publish_type, subscribe_type) - def initialize(self): + async def initialize(self): self.STATE.gen = func(**asdict(self.SETTINGS)) for field in fields(self.SETTINGS): setattr(self.STATE, field.name, getattr(self.SETTINGS, field.name)) - def shutdown(self): + async def shutdown(self): self.STATE.gen.close() def check_fields(self, msg): @@ -91,7 +94,9 @@ def check_fields(self, msg): setattr(self.STATE, state_field_name, getattr(msg, msg_field_name)) self.STATE.gen = func(**asdict(self.STATE)) - stream_suffix = {AxisArray: "_SIGNAL"} # Add more message types if accessible in core. + stream_suffix = { + AxisArray: "_SIGNAL" + } # Add more message types if accessible in core. streams = {} ez_task: Callable if subscribe_type is type(None) and publish_type is type(None): @@ -106,12 +111,12 @@ async def task(self) -> None: elif subscribe_type is type(None) and publish_type is not type(None): _output = ez.OutputStream(publish_type, **output_stream_kwargs) - streams["OUTPUT" + stream_suffix.get(publish_type, "")] = _output + streams["OUTPUT" + stream_suffix.get(publish_type, "")] = _output @ez.publisher(_output) async def publish(self): while True: - OUTPUT = self.streams["OUTPUT" + stream_suffix.get(publish_type, "")] + OUTPUT = self.streams["OUTPUT" + stream_suffix.get(publish_type, "")] yield OUTPUT, next(self.STATE.gen) await asyncio.sleep(sleep_time) @@ -119,7 +124,7 @@ async def publish(self): elif subscribe_type is not type(None) and publish_type is type(None): _input = ez.InputStream(subscribe_type) - streams["INPUT"+ stream_suffix.get(subscribe_type, "")] = _input + streams["INPUT" + stream_suffix.get(subscribe_type, "")] = _input @ez.subscriber(_input) async def subscribe(self, msg) -> None: @@ -131,15 +136,15 @@ async def subscribe(self, msg) -> None: else: _input = ez.InputStream(subscribe_type) _output = ez.OutputStream(publish_type, **output_stream_kwargs) - streams["INPUT" + stream_suffix.get(subscribe_type, "")] = _input - streams["OUTPUT" + stream_suffix.get(publish_type, "")] = _output + streams["INPUT" + stream_suffix.get(subscribe_type, "")] = _input + streams["OUTPUT" + stream_suffix.get(publish_type, "")] = _output @ez.subscriber(_input) @ez.publisher(_output) async def subscribe_publish(self, msg): self.check_fields(msg) res = self.STATE.gen.send(msg) - OUTPUT = self.streams["OUTPUT" + stream_suffix.get(publish_type, "")] + OUTPUT = self.streams["OUTPUT" + stream_suffix.get(publish_type, "")] yield OUTPUT, res ez_task = subscribe_publish diff --git a/src/ezmsg/util/generator.py b/src/ezmsg/util/generator.py index 72801296..ecdfa9f7 100644 --- a/src/ezmsg/util/generator.py +++ b/src/ezmsg/util/generator.py @@ -1,5 +1,4 @@ import ezmsg.core as ez -from ezmsg.util.messages.axisarray import AxisArray import traceback from typing import Any, AsyncGenerator, Generator, Callable, TypeVar from typing_extensions import ParamSpec @@ -12,7 +11,7 @@ def consumer( - func: Callable[P, Generator[Y, S, None]] + func: Callable[P, Generator[Y, S, None]], ) -> Callable[P, Generator[Y, S, None]]: """ A decorator that primes a generator by advancing it to the first yield statement. @@ -62,12 +61,12 @@ class GenState(ez.State): # Abstract Unit class that uses a generator for processing messages class Gen(ez.Unit): - STATE: GenState + STATE = GenState INPUT = ez.InputStream(Any) OUTPUT = ez.OutputStream(Any) - def initialize(self) -> None: + async def initialize(self) -> None: self.construct_generator() # Method to be implemented by subclasses to construct the specific generator @@ -87,36 +86,3 @@ async def on_message(self, message: Any) -> AsyncGenerator: ez.logger.debug(f"Generator closed in {self.address}") except Exception: ez.logger.info(traceback.format_exc()) - - -class GenAxisArray(ez.Unit): - STATE: GenState - - INPUT_SIGNAL = ez.InputStream(AxisArray) - OUTPUT_SIGNAL = ez.OutputStream(AxisArray) - INPUT_SETTINGS = ez.InputStream(ez.Settings) - - def initialize(self) -> None: - self.construct_generator() - - # Method to be implemented by subclasses to construct the specific generator - def construct_generator(self): - raise NotImplementedError - - @ez.subscriber(INPUT_SETTINGS) - async def on_settings(self, msg: ez.Settings) -> None: - self.apply_settings(msg) - self.construct_generator() - - @ez.subscriber(INPUT_SIGNAL) - @ez.publisher(OUTPUT_SIGNAL) - async def on_message(self, message: AxisArray) -> AsyncGenerator: - try: - ret = self.STATE.gen.send(message) - if ret is not None: - yield self.OUTPUT_SIGNAL, ret - except (StopIteration, GeneratorExit): - ez.logger.debug(f"Generator closed in {self.address}") - except Exception: - ez.logger.info(traceback.format_exc()) - diff --git a/src/ezmsg/util/messagecodec.py b/src/ezmsg/util/messagecodec.py index 08643064..1de61d48 100644 --- a/src/ezmsg/util/messagecodec.py +++ b/src/ezmsg/util/messagecodec.py @@ -1,5 +1,4 @@ import json -import time import pickle import base64 import typing @@ -26,8 +25,7 @@ @dataclass -class LogStart: - ... +class LogStart: ... def type_str(obj: typing.Any) -> str: @@ -124,8 +122,8 @@ def message_log( fname: Path, return_object: bool = True ) -> typing.Generator[typing.Any, None, None]: with open(fname, "r") as f: - for l in f: - obj = json.loads(l, cls=MessageDecoder) + for line in f: + obj = json.loads(line, cls=MessageDecoder) if isinstance(obj["obj"], LogStart): continue if return_object is True: diff --git a/src/ezmsg/util/messagegate.py b/src/ezmsg/util/messagegate.py index 94a95e84..7e259f01 100644 --- a/src/ezmsg/util/messagegate.py +++ b/src/ezmsg/util/messagegate.py @@ -7,6 +7,7 @@ @dataclass class GateMessage: """Send this message to ``INPUT_GATE`` to open or close the gate.""" + open: bool @@ -21,6 +22,7 @@ class MessageGateSettings(ez.Settings): ``True`` will allow messages to flow through, ``False`` will discard messages. default_after: sets the number of messages after which the `default_open` state will be applied. """ + start_open: bool = False default_open: bool = False default_after: typing.Optional[int] = None @@ -37,8 +39,8 @@ class MessageGate(ez.Unit): Can be set as open, closed, open after n messages, or closed after n messages. """ - SETTINGS: MessageGateSettings - STATE: MessageGateState + SETTINGS = MessageGateSettings + STATE = MessageGateState INPUT_GATE = ez.InputStream(GateMessage) """ @@ -52,7 +54,7 @@ class MessageGate(ez.Unit): OUTPUT = ez.OutputStream(typing.Any) """Publishes messages which flow through.""" - def initialize(self) -> None: + async def initialize(self) -> None: self.STATE.gate_open = self.SETTINGS.start_open def set_gate(self, set_open: bool) -> None: @@ -77,4 +79,4 @@ async def on_input(self, msg: typing.Any) -> typing.AsyncGenerator: and (self.STATE.gate_open != self.SETTINGS.default_open) and (self.STATE.msgs >= self.SETTINGS.default_after) ): - self.set_gate(self.SETTINGS.default_open) \ No newline at end of file + self.set_gate(self.SETTINGS.default_open) diff --git a/src/ezmsg/util/messagelogger.py b/src/ezmsg/util/messagelogger.py index 52c9c45c..547c1c6d 100644 --- a/src/ezmsg/util/messagelogger.py +++ b/src/ezmsg/util/messagelogger.py @@ -24,6 +24,7 @@ class MessageLoggerSettings(ez.Settings): output: :py:class:`pathlib.Path` for a file where the messages will be logged. If the file path already exists, the existing file will be truncated to 0 length. """ + output: Optional[Path] = None @@ -38,8 +39,8 @@ class MessageLogger(ez.Unit): :py:class:`pathlib.Path` to ``INPUT_START``. """ - SETTINGS: MessageLoggerSettings - STATE: MessageLoggerState + SETTINGS = MessageLoggerSettings + STATE = MessageLoggerState INPUT_START = ez.InputStream(Path) """ diff --git a/src/ezmsg/util/messagequeue.py b/src/ezmsg/util/messagequeue.py index bffac8a8..d2330edb 100644 --- a/src/ezmsg/util/messagequeue.py +++ b/src/ezmsg/util/messagequeue.py @@ -12,6 +12,7 @@ class MessageQueueSettings(ez.Settings): maxsize: The maximum number of items which the queue will hold. leaky: Whether the queue will drop new messages when it reaches its maxsize, or whether it will wait for space to open for them. """ + maxsize: int = 0 leaky: bool = False log_above_n: Optional[int] = None @@ -28,8 +29,8 @@ class MessageQueue(ez.Unit): Place between two other ``Units`` to induce backpressure. """ - SETTINGS: MessageQueueSettings - STATE: MessageQueueState + SETTINGS = MessageQueueSettings + STATE = MessageQueueState INPUT = ez.InputStream(Any) """Send messages to queue here.""" @@ -37,7 +38,7 @@ class MessageQueue(ez.Unit): OUTPUT = ez.OutputStream(Any) """Subscribe to pull messages out of the queue.""" - def initialize(self): + async def initialize(self): self.STATE.leaky = self.SETTINGS.leaky if self.SETTINGS.leaky is True and self.SETTINGS.maxsize <= 0: ez.logger.warning( @@ -80,4 +81,3 @@ async def send_message(self) -> AsyncGenerator: yield self.OUTPUT, msg if rate is not None: await rate.sleep() - diff --git a/src/ezmsg/util/messagereplay.py b/src/ezmsg/util/messagereplay.py index 97e1b094..0a3170ca 100644 --- a/src/ezmsg/util/messagereplay.py +++ b/src/ezmsg/util/messagereplay.py @@ -22,6 +22,7 @@ class ReplayStatusMessage: total: Number of messages in the file. done: Whether the file has finished replaying. """ + filename: Path idx: int total: int @@ -39,6 +40,7 @@ class FileReplayMessage: 0 = realtime (if timestamps in file) If not specified, messages will publish as fast as possible. """ + filename: typing.Optional[Path] = None rate: typing.Optional[float] = None # Hz @@ -50,6 +52,7 @@ class MessageReplaySettings(ez.Settings, FileReplayMessage): Args: progress: will use tqdm to indicate progress through the file. tqdm must be installed. """ + progress: bool = False @@ -65,8 +68,8 @@ class MessageReplay(ez.Unit): Stores a queue of files to stream and streams from them in order. """ - SETTINGS: MessageReplaySettings - STATE: MessageReplayState + SETTINGS = MessageReplaySettings + STATE = MessageReplayState INPUT_FILE = ez.InputStream(FileReplayMessage) """Add a new file to the queue.""" @@ -213,7 +216,7 @@ class MessageCollector(ez.Unit): Collects ``Messages`` into a local list. """ - STATE: MessageCollectorState + STATE = MessageCollectorState INPUT_MESSAGE = ez.InputStream(typing.Any) """Send messages here to be collected.""" diff --git a/src/ezmsg/util/messages/axisarray.py b/src/ezmsg/util/messages/axisarray.py index 6d0b5f2c..7c58f092 100644 --- a/src/ezmsg/util/messages/axisarray.py +++ b/src/ezmsg/util/messages/axisarray.py @@ -1,5 +1,4 @@ import math -import time import typing from contextlib import contextmanager @@ -11,7 +10,7 @@ from ezmsg.core.util import either_dict_or_kwargs -# TODO: Typehinting is all wrong in this and +# TODO: Typehinting needs continued help # concatenate/transpose should probably not be staticmethods @@ -20,9 +19,13 @@ class AxisArray: """ A lightweight message class comprising a numpy ndarray and its metadata. """ + data: npt.NDArray dims: typing.List[str] axes: typing.Dict[str, "AxisArray.Axis"] = field(default_factory=dict) + key: str = "" + + T = typing.TypeVar("T", bound="AxisArray") @dataclass class Axis: @@ -69,19 +72,18 @@ def __post_init__(self): raise ValueError("dims contains repeated dim names") def isel( - self, + self: T, indexers: typing.Optional[typing.Any] = None, - **indexers_kwargs: typing.Any - ) -> "AxisArray": - - indexers = either_dict_or_kwargs(indexers, indexers_kwargs, 'isel') + **indexers_kwargs: typing.Any, + ) -> T: + indexers = either_dict_or_kwargs(indexers, indexers_kwargs, "isel") out_axes = {an: a for an, a in self.axes.items()} out_data = self.data for axis_name, ix in indexers.items(): if not isinstance(ix, (np.ndarray, int, slice)): - raise ValueError('isel only accepts arrays, ints, or slices') + raise ValueError("isel only accepts arrays, ints, or slices") ax = self.ax(axis_name) indices = np.arange(len(ax)) @@ -99,12 +101,11 @@ def isel( return replace(self, data=out_data, axes=out_axes) def sel( - self, + self: T, indexers: typing.Optional[typing.Any] = None, - **indexers_kwargs: typing.Any - ) -> "AxisArray": - - indexers = either_dict_or_kwargs(indexers, indexers_kwargs, 'sel') + **indexers_kwargs: typing.Any, + ) -> T: + indexers = either_dict_or_kwargs(indexers, indexers_kwargs, "sel") out_indexers = dict() for axis_name, ix in indexers.items(): @@ -115,7 +116,7 @@ def sel( stop = int(axis.index(ix.stop)) if ix.stop is not None else None step = int(ix.step / axis.gain) if ix.step is not None else None out_indexers[axis_name] = slice(start, stop, step) - + return self.isel(**out_indexers) @property @@ -156,6 +157,23 @@ def _axis_idx(self, dim: typing.Union[str, int]) -> int: def as2d(self, dim: typing.Union[str, int]) -> npt.NDArray: return as2d(self.data, self.axis_idx(dim)) + def iter_over_axis( + self: T, axis: typing.Union[str, int] + ) -> typing.Generator[T, None, None]: + axis_idx = self.axis_idx(axis) + dim_name = self.dims[axis_idx] + new_dims = [d for i, d in enumerate(self.dims) if i != axis_idx] + new_axes = {d: a for d, a in self.axes.items() if d != dim_name} + + for it_data in np.moveaxis(self.data, axis_idx, 0): + it_aa = replace( + self, + data=it_data, + dims=new_dims, + axes=new_axes, + ) + yield it_aa + @contextmanager def view2d( self, dim: typing.Union[str, int] @@ -168,8 +186,14 @@ def shape2d(self, dim: typing.Union[str, int]) -> typing.Tuple[int, int]: @staticmethod def concatenate( - *aas: "AxisArray", dim: str, axis: typing.Optional[Axis] = None - ) -> "AxisArray": + *aas: T, + dim: str, + axis: typing.Optional[Axis] = None, + filter_key: typing.Optional[str] = None + ) -> T: + if filter_key is not None: + aas = [aa for aa in aas if aa.key == filter_key] + aa_0 = aas[0] for aa in aas[1:]: if aa.dims != aa_0.dims: @@ -177,6 +201,7 @@ def concatenate( new_dims = [d for d in aa_0.dims] new_axes = {ax_name: ax for ax_name, ax in aa_0.axes.items()} + new_key = aa_0.key if all(aa.key == aa_0.key for aa in aas) else "" if axis is not None: new_axes[dim] = axis @@ -186,20 +211,20 @@ def concatenate( if dim in aa_0.dims: dim_idx = aa_0.axis_idx(dim=dim) new_data = np.concatenate(all_data, axis=dim_idx) - return replace(aa_0, data=new_data, dims=new_dims, axes=new_axes) + return replace(aa_0, data=new_data, dims=new_dims, axes=new_axes, key=new_key) else: new_data = np.array(all_data) new_dims = [dim] + new_dims - return replace(aa_0, data=new_data, dims=new_dims, axes=new_axes) + return replace(aa_0, data=new_data, dims=new_dims, axes=new_axes, key=new_key) @staticmethod def transpose( - aa: "AxisArray", + aa: T, dims: typing.Optional[ typing.Union[typing.Iterable[str], typing.Iterable[int]] ] = None, - ) -> "AxisArray": + ) -> T: dims = reversed(range(aa.data.ndim)) if dims is None else dims dim_indices = [aa.axis_idx(d) for d in dims] new_dims = [aa.dims[d] for d in dim_indices] @@ -207,7 +232,9 @@ def transpose( return replace(aa, data=new_data, dims=new_dims, axes=aa.axes) -def slice_along_axis(in_arr: npt.NDArray, sl: typing.Union[slice, int], axis: int) -> npt.NDArray: +def slice_along_axis( + in_arr: npt.NDArray, sl: typing.Union[slice, int], axis: int +) -> npt.NDArray: """ Slice the input array along a specified axis using the given slice object or integer index. Integer arguments to `sl` will cause the sliced dimension to be dropped. @@ -225,10 +252,14 @@ def slice_along_axis(in_arr: npt.NDArray, sl: typing.Union[slice, int], axis: in ValueError: If the axis value is invalid for the input array. """ if axis < -in_arr.ndim or axis >= in_arr.ndim: - raise ValueError(f"Invalid axis value {axis} for input array with {in_arr.ndim} dimensions.") + raise ValueError( + f"Invalid axis value {axis} for input array with {in_arr.ndim} dimensions." + ) if -in_arr.ndim <= axis < 0: axis = in_arr.ndim + axis - all_slice = (slice(None),) * axis + (sl,) + (slice(None),) * (in_arr.ndim - axis - 1) + all_slice = ( + (slice(None),) * axis + (sl,) + (slice(None),) * (in_arr.ndim - axis - 1) + ) return in_arr[all_slice] @@ -260,14 +291,21 @@ def sliding_win_oneaxis(in_arr: npt.NDArray, nwin: int, axis: int) -> npt.NDArra """ if -in_arr.ndim <= axis < 0: axis = in_arr.ndim + axis - out_strides = in_arr.strides[:axis] + (in_arr.strides[axis],) * 2 + in_arr.strides[axis+1:] - out_shape = in_arr.shape[:axis] + (in_arr.shape[axis]-(nwin-1),) + (nwin,) + in_arr.shape[axis+1:] + out_strides = ( + in_arr.strides[:axis] + (in_arr.strides[axis],) * 2 + in_arr.strides[axis + 1 :] + ) + out_shape = ( + in_arr.shape[:axis] + + (in_arr.shape[axis] - (nwin - 1),) + + (nwin,) + + in_arr.shape[axis + 1 :] + ) return nps.as_strided(in_arr, strides=out_strides, shape=out_shape, writeable=False) def _as2d( in_arr: npt.NDArray, axis: int = 0 -) -> typing.Tuple[npt.NDArray, typing.Tuple[int]]: +) -> typing.Tuple[npt.NDArray, typing.Tuple[int, ...]]: arr = in_arr if arr.ndim == 0: arr = arr.reshape(1, 1) diff --git a/src/ezmsg/util/messages/chunker.py b/src/ezmsg/util/messages/chunker.py new file mode 100644 index 00000000..408fa328 --- /dev/null +++ b/src/ezmsg/util/messages/chunker.py @@ -0,0 +1,100 @@ +import asyncio +from dataclasses import replace +import traceback +import typing + +import numpy as np +import numpy.typing as npt + +import ezmsg.core as ez +from .axisarray import AxisArray, slice_along_axis +from ..generator import GenState + + +def array_chunker( + data: npt.ArrayLike, + chunk_len: int, + axis: int = 0, + fs: float = 1000.0, + tzero: float = 0.0, +) -> typing.Generator[AxisArray, None, None]: + """ + Create a generator that yields chunks of an array along a specified axis. + The generator should be useful for quick offline analyses, tests, or examples. + This generator probably is not useful for online streaming applications. + + Parameters: + data: An array_like object to iterate over, chunk-by-chunk. + chunk_len: The length of the chunk returned in each iteration (except the last). + axis: The axis along which to chunk the array. + fs: The sampling frequency of the data. Will only be used to make the time axis. + tzero: The time offset of the first chunk. Will only be used to make the time axis. + + Returns: + A generator that yields AxisArrays containing chunks of the input array. + """ + + if not type(data) == np.ndarray: + data = np.array(data) + n_chunks = int(np.ceil(data.shape[axis] / chunk_len)) + tvec = np.arange(n_chunks, dtype=float) * chunk_len / fs + tzero + out_dims = [f"d{_}" for _ in range(data.ndim)] + out_dims[axis] = "time" + template = AxisArray( + slice_along_axis(data, slice(None, 0), axis), + dims=out_dims, + axes={"time": AxisArray.Axis.TimeAxis(fs=fs, offset=tvec[0])} + ) + + for chunk_ix in range(n_chunks): + view = slice_along_axis(data, slice(chunk_ix*chunk_len, (chunk_ix+1)*chunk_len), axis) + axis_arr_out = replace( + template, + data=view, + axes={"time": AxisArray.Axis.TimeAxis(fs=fs, offset=tvec[chunk_ix])} + ) + yield axis_arr_out + + +class ArrayChunkerSettings(ez.Settings): + data: npt.ArrayLike + chunk_len: int + axis: int = 0 + fs: float = 1000.0 + tzero: float = 0.0 + + +class ArrayChunker(ez.Unit): + SETTINGS = ArrayChunkerSettings + STATE = GenState + + INPUT_SETTINGS = ez.InputStream(ArrayChunkerSettings) + OUTPUT_SIGNAL = ez.OutputStream(AxisArray) + + async def initialize(self) -> None: + self.construct_generator() + + def construct_generator(self): + self.STATE.gen = array_chunker( + data=self.SETTINGS.data, + chunk_len=self.SETTINGS.chunk_len, + axis=self.SETTINGS.axis, + fs=self.SETTINGS.fs, + tzero=self.SETTINGS.tzero + ) + + @ez.subscriber(INPUT_SETTINGS) + async def on_settings(self, msg: ez.Settings) -> None: + self.apply_settings(msg) + self.construct_generator() + + @ez.publisher(OUTPUT_SIGNAL) + async def send_chunk(self) -> typing.AsyncGenerator: + try: + while True: + yield self.OUTPUT_SIGNAL, next(self.STATE.gen) + await asyncio.sleep(0) + except (StopIteration, GeneratorExit): + ez.logger.debug(f"ArrayChunker closed in {self.address}") + except Exception: + ez.logger.info(traceback.format_exc()) diff --git a/src/ezmsg/util/messages/key.py b/src/ezmsg/util/messages/key.py new file mode 100644 index 00000000..cd7825fd --- /dev/null +++ b/src/ezmsg/util/messages/key.py @@ -0,0 +1,89 @@ +from dataclasses import replace +import traceback +import typing + +import numpy as np + +import ezmsg.core as ez +from .axisarray import AxisArray +from ..generator import consumer, GenState + + +@consumer +def set_key( + key: str = "" +) -> typing.Generator[AxisArray, AxisArray, None]: + """ + Set the key of an AxisArray. + + Args: + key: The string to set as the key. + + Returns: + A primed generator object ready to yield an AxisArray with the key set for each .send(axis_array) + """ + # State variables + axis_arr_in = AxisArray(np.array([]), dims=[""]) + axis_arr_out = AxisArray(np.array([]), dims=[""]) + + while True: + axis_arr_in = yield axis_arr_out + + axis_arr_out = replace(axis_arr_in, key=key) + + +class KeySettings(ez.Settings): + key: str = "" + + +class SetKey(ez.Unit): + STATE = GenState + SETTINGS = KeySettings + + INPUT_SIGNAL = ez.InputStream(AxisArray) + OUTPUT_SIGNAL = ez.OutputStream(AxisArray) + INPUT_SETTINGS = ez.InputStream(ez.Settings) + + async def initialize(self) -> None: + self.construct_generator() + + def construct_generator(self): + self.STATE.gen = set_key(key=self.SETTINGS.key) + + @ez.subscriber(INPUT_SETTINGS) + async def on_settings(self, msg: ez.Settings) -> None: + self.apply_settings(msg) + self.construct_generator() + + @ez.subscriber(INPUT_SIGNAL, zero_copy=True) + @ez.publisher(OUTPUT_SIGNAL) + async def on_message(self, message: AxisArray) -> typing.AsyncGenerator: + try: + ret = self.STATE.gen.send(message) + if ret is not None: + yield self.OUTPUT_SIGNAL, ret + except (StopIteration, GeneratorExit): + ez.logger.debug(f"SetKey closed in {self.address}") + except Exception: + ez.logger.info(traceback.format_exc()) + + +class FilterOnKey(ez.Unit): + """ + Filter an AxisArray based on its key. + Note: There is no associated generator method for this Unit because messages that fail the filter + would still be yielded (as None), which complicates downstream processing. For contexts where filtering + on key is desired but the ezmsg framework is not used, use normal Python functional programming. + See https://github.com/ezmsg-org/ezmsg/issues/142#issuecomment-2323110318 + """ + SETTINGS = KeySettings + + INPUT_SIGNAL = ez.InputStream(AxisArray) + OUTPUT_SIGNAL = ez.OutputStream(AxisArray) + + @ez.subscriber(INPUT_SIGNAL, zero_copy=True) + @ez.publisher(OUTPUT_SIGNAL) + async def on_message(self, message: AxisArray) -> typing.AsyncGenerator: + if message.key == self.SETTINGS.key: + out = replace(message, key=message.key) # Minimal 'touch' to prevent deepcopy by framework + yield self.OUTPUT_SIGNAL, out diff --git a/src/ezmsg/util/messages/modify.py b/src/ezmsg/util/messages/modify.py index 197251b5..5a9a0939 100644 --- a/src/ezmsg/util/messages/modify.py +++ b/src/ezmsg/util/messages/modify.py @@ -1,17 +1,28 @@ from dataclasses import replace +import traceback import typing import numpy as np import ezmsg.core as ez -from ezmsg.util.messages.axisarray import AxisArray -from ezmsg.util.generator import consumer, GenAxisArray +from .axisarray import AxisArray +from ..generator import consumer, GenState @consumer def modify_axis( - name_map: typing.Optional[typing.Dict[str, str]] = None + name_map: typing.Optional[typing.Dict[str, str]] = None, ) -> typing.Generator[AxisArray, AxisArray, None]: + """ + Modify an AxisArray's axes and dims according to a name_map. + + Args: + name_map: A dictionary where the keys are the names of the old dims and the values are the new names. + Use None as a value to drop the dimension. If the dropped dimension is not len==1 then an error is raised. + + Returns: + A primed generator object ready to yield an AxisArray with modified axes for each .send(axis_array) + """ # State variables axis_arr_in = AxisArray(np.array([]), dims=[""]) axis_arr_out = AxisArray(np.array([]), dims=[""]) @@ -21,8 +32,24 @@ def modify_axis( if name_map is not None: new_dims = [name_map.get(old_k, old_k) for old_k in axis_arr_in.dims] - new_axes = {name_map.get(old_k, old_k): v for old_k, v in axis_arr_in.axes.items()} - axis_arr_out = replace(axis_arr_in, dims=new_dims, axes=new_axes) + new_axes = { + name_map.get(old_k, old_k): v for old_k, v in axis_arr_in.axes.items() + } + drop_ax_ix = [ix for ix, old_dim in enumerate(axis_arr_in.dims) if new_dims[ix] is None] + if len(drop_ax_ix) > 0: + # Rewrite new_dims and new_axes without the dropped axes + new_dims = [_ for _ in new_dims if _ is not None] + new_axes.pop(None, None) + # Reshape data + # np.squeeze will raise ValueError if not len==1 + axis_arr_out = replace( + axis_arr_in, + data=np.squeeze(axis_arr_in.data, axis=tuple(drop_ax_ix)), + dims=new_dims, + axes=new_axes + ) + else: + axis_arr_out = replace(axis_arr_in, dims=new_dims, axes=new_axes) else: axis_arr_out = axis_arr_in @@ -31,8 +58,33 @@ class ModifyAxisSettings(ez.Settings): name_map: typing.Optional[typing.Dict[str, str]] = None -class ModifyAxis(GenAxisArray): - SETTINGS: ModifyAxisSettings +class ModifyAxis(ez.Unit): + STATE = GenState + SETTINGS = ModifyAxisSettings + + INPUT_SIGNAL = ez.InputStream(AxisArray) + OUTPUT_SIGNAL = ez.OutputStream(AxisArray) + INPUT_SETTINGS = ez.InputStream(ModifyAxisSettings) + + async def initialize(self) -> None: + self.construct_generator() def construct_generator(self): self.STATE.gen = modify_axis(name_map=self.SETTINGS.name_map) + + @ez.subscriber(INPUT_SETTINGS) + async def on_settings(self, msg: ez.Settings) -> None: + self.apply_settings(msg) + self.construct_generator() + + @ez.subscriber(INPUT_SIGNAL, zero_copy=True) + @ez.publisher(OUTPUT_SIGNAL) + async def on_message(self, message: AxisArray) -> typing.AsyncGenerator: + try: + ret = self.STATE.gen.send(message) + if ret is not None: + yield self.OUTPUT_SIGNAL, ret + except (StopIteration, GeneratorExit): + ez.logger.debug(f"ModifyAxis closed in {self.address}") + except Exception: + ez.logger.info(traceback.format_exc()) diff --git a/tests/test_perf.py b/src/ezmsg/util/perf_test.py similarity index 87% rename from tests/test_perf.py rename to src/ezmsg/util/perf_test.py index 4c5bc20d..18434a7c 100644 --- a/tests/test_perf.py +++ b/src/ezmsg/util/perf_test.py @@ -4,7 +4,6 @@ import os import platform import time -import pytest from typing import List, Tuple, AsyncGenerator @@ -49,9 +48,9 @@ class LoadTestSample: class LoadTestPublisher(ez.Unit): OUTPUT = ez.OutputStream(LoadTestSample) - SETTINGS: LoadTestSettings + SETTINGS = LoadTestSettings - def initialize(self) -> None: + async def initialize(self) -> None: self.running = True self.counter = 0 self.OUTPUT.num_buffers = self.SETTINGS.buffers @@ -65,18 +64,21 @@ async def publish(self) -> AsyncGenerator: if current_time - start_time >= self.SETTINGS.duration: break - yield self.OUTPUT, LoadTestSample( - _timestamp=time.time(), - counter=self.counter, - dynamic_data=np.zeros( - int(self.SETTINGS.dynamic_size // 8), dtype=np.float32 + yield ( + self.OUTPUT, + LoadTestSample( + _timestamp=time.time(), + counter=self.counter, + dynamic_data=np.zeros( + int(self.SETTINGS.dynamic_size // 8), dtype=np.float32 + ), ), ) self.counter += 1 ez.logger.info("Exiting publish") raise ez.Complete - def shutdown(self) -> None: + async def shutdown(self) -> None: self.running = False ez.logger.info(f"Samples sent: {self.counter}") @@ -91,8 +93,8 @@ class LoadTestSubscriberState(ez.State): class LoadTestSubscriber(ez.Unit): INPUT = ez.InputStream(LoadTestSample) - SETTINGS: LoadTestSettings - STATE: LoadTestSubscriberState + SETTINGS = LoadTestSettings + STATE = LoadTestSubscriberState @ez.subscriber(INPUT, zero_copy=True) async def receive(self, sample: LoadTestSample) -> None: @@ -111,7 +113,7 @@ async def log_result(self) -> None: # Wait for the duration of the load test await asyncio.sleep(self.SETTINGS.duration) - # logger.info(f"STATE: {self.STATE.received_data}") + # logger.info(f"STATE = {self.STATE.received_data}") # Log some useful summary statistics min_timestamp = min(timestamp for timestamp, _, _ in self.STATE.received_data) @@ -148,7 +150,7 @@ async def log_result(self) -> None: class LoadTest(ez.Collection): - SETTINGS: LoadTestSettings + SETTINGS = LoadTestSettings PUBLISHER = LoadTestPublisher() SUBSCRIBER = LoadTestSubscriber() @@ -173,19 +175,12 @@ def get_time() -> float: return time.time() if PLATFORM == "win" else time.perf_counter() -@pytest.mark.parametrize("duration", [2]) -@pytest.mark.parametrize("buffers", [2, 32]) -@pytest.mark.parametrize("size", [2**i for i in range(5, 22, 4)]) def test_performance(duration, size, buffers) -> None: ez.logger.info(f"Running load test for dynamic size: {size} bytes") system = LoadTest( - LoadTestSettings( - dynamic_size=int(size), - duration=duration, - buffers=buffers - ) + LoadTestSettings(dynamic_size=int(size), duration=duration, buffers=buffers) ) - ez.run(SYSTEM = system) + ez.run(SYSTEM=system) def run_many_dynamic_sizes(duration, buffers) -> None: diff --git a/src/ezmsg/util/terminate.py b/src/ezmsg/util/terminate.py index bc3fa91c..4bdf2b00 100644 --- a/src/ezmsg/util/terminate.py +++ b/src/ezmsg/util/terminate.py @@ -1,8 +1,6 @@ import asyncio import time -from dataclasses import dataclass - import ezmsg.core as ez from typing import Optional, Any @@ -16,6 +14,7 @@ class TerminateOnTimeoutSettings(ez.Settings): time: Terminate if no message has been received in this time (sec) poll_rate: Hz. """ + time: float = 2.0 poll_rate: float = 4.0 @@ -29,8 +28,8 @@ class TerminateOnTimeout(ez.Unit): End a pipeline execution when a certain amount of time has passed without receiving a message. """ - SETTINGS: TerminateOnTimeoutSettings - STATE: TerminateOnTimeoutState + SETTINGS = TerminateOnTimeoutSettings + STATE = TerminateOnTimeoutState INPUT = ez.InputStream(Any) """Send messages here.""" @@ -58,6 +57,7 @@ class TerminateOnTotalSettings(ez.Settings): Args: total: The total number of messages to terminate after. """ + total: Optional[int] = None @@ -71,8 +71,8 @@ class TerminateOnTotal(ez.Unit): End a pipeline execution once a certain number of messages have been received. """ - SETTINGS: TerminateOnTotalSettings - STATE: TerminateOnTotalState + SETTINGS = TerminateOnTotalSettings + STATE = TerminateOnTotalState INPUT_MESSAGE = ez.InputStream(Any) """Send messages here.""" @@ -83,7 +83,7 @@ class TerminateOnTotal(ez.Unit): If this number has already been reached, termination will occur immediately. """ - def initialize(self) -> None: + async def initialize(self) -> None: self.STATE.total = self.SETTINGS.total @ez.subscriber(INPUT_TOTAL) diff --git a/tests/ez_test_utils.py b/tests/ez_test_utils.py index 8ca42c2d..abf6af20 100644 --- a/tests/ez_test_utils.py +++ b/tests/ez_test_utils.py @@ -41,7 +41,7 @@ class MessageGeneratorSettings(ez.Settings): class MessageGenerator(ez.Unit): - SETTINGS: MessageGeneratorSettings + SETTINGS = MessageGeneratorSettings OUTPUT = ez.OutputStream(SimpleMessage) @@ -63,8 +63,8 @@ class MessageReceiverState(ez.State): class MessageReceiver(ez.Unit): - STATE: MessageReceiverState - SETTINGS: MessageReceiverSettings + STATE = MessageReceiverState + SETTINGS = MessageReceiverSettings INPUT = ez.InputStream(SimpleMessage) diff --git a/tests/messages/test_axisarray.py b/tests/messages/test_axisarray.py index 94137b3c..1d051b48 100644 --- a/tests/messages/test_axisarray.py +++ b/tests/messages/test_axisarray.py @@ -3,7 +3,12 @@ from dataclasses import dataclass, field -from ezmsg.util.messages.axisarray import AxisArray, shape2d, slice_along_axis, sliding_win_oneaxis +from ezmsg.util.messages.axisarray import ( + AxisArray, + shape2d, + slice_along_axis, + sliding_win_oneaxis, +) from typing import Generator, List @@ -28,6 +33,7 @@ def test_axes() -> None: "x": AxisArray.Axis(unit="mm", gain=0.2, offset=-13.0), "y": AxisArray.Axis(unit="mm", gain=0.2, offset=-13.0), }, + key="spatial_sensor_array", ch_names=["a", "b"], ) @@ -45,6 +51,7 @@ def msg_gen( x=AxisArray.Axis(unit="mm"), y=AxisArray.Axis(unit="mm"), ), + key="spatial_sensor_array", ch_names=["a", "b"], ) @@ -79,6 +86,23 @@ def test_concat() -> None: assert isinstance(batch_cat, MultiChannelData) + # Test filtering based on key + gen = msg_gen(fs, x_size, y_size) + single_batch = [next(gen) for _ in range(batch_size)] + # All messages pass + single_batch_cat = AxisArray.concatenate(*single_batch, dim="time", filter_key="spatial_sensor_array") + assert single_batch_cat.key == "spatial_sensor_array" + assert single_batch_cat.shape[single_batch_cat.get_axis_idx("time")] == batch_size + # Exclude one message based on filter_key + single_batch[0].key = "wrong key" + filter_batch_cat = AxisArray.concatenate(*single_batch, dim="time", filter_key="spatial_sensor_array") + assert filter_batch_cat.key == "spatial_sensor_array" + assert filter_batch_cat.shape[filter_batch_cat.get_axis_idx("time")] == (batch_size - 1) + # No filtering, but key is reset because it is not consistent + nofilter_batch_cat = AxisArray.concatenate(*single_batch, dim="time") + assert nofilter_batch_cat.key == "" + assert nofilter_batch_cat.shape[nofilter_batch_cat.get_axis_idx("time")] == batch_size + @pytest.mark.parametrize( "data", @@ -121,19 +145,26 @@ def test_sel(): data, dims=["dim0"], axes=dict(dim0=AxisArray.Axis(gain=gain, offset=offset)) ) - aa_sl = aa.sel(dim0=slice(None, -10.75, 1.5)) # slice based on axis info - aa_idx = aa.isel(dim0=-1) # index slice of last index + aa_sl = aa.sel(dim0=slice(-10.75, 1.5)) # slice based on axis info + assert np.allclose( + aa_sl.data, + data[np.argmin(np.abs(data - -10.75)) : np.argmin(np.abs(data - 1.5))], + ) + aa_idx = aa.isel(dim0=-1) # index slice of last index assert aa_idx.data == data[-1] - + @pytest.mark.parametrize("axis", [0, 1, 2, -1, 3, -4]) -@pytest.mark.parametrize("sl", [ - 3, - slice(None, None, 2), - slice(2, 4, None), - slice(-3, -1, None), - slice(3, 10, None) -]) +@pytest.mark.parametrize( + "sl", + [ + 3, + slice(None, None, 2), + slice(2, 4, None), + slice(-3, -1, None), + slice(3, 10, None), + ], +) def test_slice_along_axis(axis: int, sl): dims = [4, 5, 6] data = np.arange(np.prod(dims)).reshape(dims) diff --git a/tests/messages/test_chunker.py b/tests/messages/test_chunker.py new file mode 100644 index 00000000..b12d7fda --- /dev/null +++ b/tests/messages/test_chunker.py @@ -0,0 +1,31 @@ +import time +import pytest + +import numpy as np + +from ezmsg.util.messages.axisarray import AxisArray +from ezmsg.util.messages.chunker import array_chunker + + +@pytest.mark.parametrize("axis", [0, 1, 2]) +def test_array_chunker(axis: int): + tzero = time.time() + dshape = [3, 4, 5] + dshape[axis] = 10_000 + dshape = tuple(dshape) + fs = 1_000.0 + chunk_len = 19 + data = np.arange(np.prod(dshape)).reshape(dshape) + tvec = np.arange(dshape[axis]) / fs + tzero + + chunker = array_chunker(data, chunk_len=chunk_len, axis=axis, fs=fs, tzero=tzero) + chunks = list(chunker) + + assert len(chunks) == int(np.ceil(dshape[axis] / chunk_len)) + assert all(isinstance(chunk, AxisArray) for chunk in chunks) + assert all(chunk.data.ndim == data.ndim for chunk in chunks) + assert all(chunk.data.shape[axis] == chunk_len for chunk in chunks[:-1]) + assert chunks[-1].data.shape[axis] == dshape[axis] % chunk_len + assert np.array_equal([_.axes["time"].offset for _ in chunks], tvec[::chunk_len]) + assert np.array_equal(np.concatenate([chunk.data for chunk in chunks], axis=axis), data) + assert all(np.may_share_memory(chunk.data, data) for chunk in chunks) diff --git a/tests/messages/test_key.py b/tests/messages/test_key.py new file mode 100644 index 00000000..df02ced2 --- /dev/null +++ b/tests/messages/test_key.py @@ -0,0 +1,134 @@ +import copy +import json +import os +import typing + +import numpy as np + +import ezmsg.core as ez +from ezmsg.util.messages.axisarray import AxisArray +from ezmsg.util.messages.key import set_key, SetKey, FilterOnKey +from ..ez_test_utils import ( + get_test_fn, + MessageGeneratorSettings, + MessageReceiverSettings, + MessageReceiverState, +) + + +def test_set_key(): + input_ax_arr = AxisArray( + data=np.arange(60).reshape(3, 5, 4), + dims=["step", "freq", "ch"], + axes={"step": AxisArray.Axis.TimeAxis(fs=10.0, offset=0.0)}, + key="old key" + ) + backup = copy.deepcopy(input_ax_arr) + + gen = set_key(key="new key") + res = gen.send(input_ax_arr) + + # Make sure the input hasn't changed + assert np.array_equal(input_ax_arr.data, backup.data) + assert input_ax_arr.dims == backup.dims + assert list(input_ax_arr.axes.keys()) == list(backup.axes.keys()) + for k, v in input_ax_arr.axes.items(): + assert v == backup.axes[k] + + # We don't want the data to be copied + assert res.data is input_ax_arr.data + + assert res.key == "new key" + + +class KeyedAxarrGenerator(ez.Unit): + SETTINGS = MessageGeneratorSettings + OUTPUT_SIGNAL = ez.OutputStream(AxisArray) + + @ez.publisher(OUTPUT_SIGNAL) + async def spawn(self) -> typing.AsyncGenerator: + for i in range(self.SETTINGS.num_msgs): + yield self.OUTPUT_SIGNAL, AxisArray(data=np.arange(i), dims=["time"], key="odd" if i % 2 else "even") + raise ez.Complete + + +class AxarrReceiver(ez.Unit): + STATE = MessageReceiverState + SETTINGS = MessageReceiverSettings + INPUT_SIGNAL = ez.InputStream(AxisArray) + + @ez.subscriber(INPUT_SIGNAL) + async def on_message(self, msg: AxisArray) -> None: + self.STATE.num_received += 1 + with open(self.SETTINGS.output_fn, "a") as output_file: + payload = {self.STATE.num_received: msg.key} + output_file.write(json.dumps(payload) + "\n") + if self.STATE.num_received == self.SETTINGS.num_msgs: + raise ez.NormalTermination + + +def test_set_key_unit(): + num_msgs = 20 + test_fn_raw = get_test_fn() + test_fn_keyed = test_fn_raw.parent / (test_fn_raw.stem + "_keyed" + test_fn_raw.suffix) + + comps = { + "SRC": KeyedAxarrGenerator(num_msgs=num_msgs), + "KEYSETTER": SetKey(key="new key"), + "SINK_RAW": AxarrReceiver(num_msgs=1e9, output_fn=test_fn_raw), + "SINK_KEYED": AxarrReceiver(num_msgs=num_msgs, output_fn=test_fn_keyed), + } + conns = [ + (comps["SRC"].OUTPUT_SIGNAL, comps["SINK_RAW"].INPUT_SIGNAL), + (comps["SRC"].OUTPUT_SIGNAL, comps["KEYSETTER"].INPUT_SIGNAL), + (comps["KEYSETTER"].OUTPUT_SIGNAL, comps["SINK_KEYED"].INPUT_SIGNAL), + ] + ez.run( + components=comps, + connections=conns + ) + + with open(test_fn_raw, "r") as file: + raw_results = [json.loads(_) for _ in file.readlines()] + os.remove(test_fn_raw) + assert len(raw_results) == num_msgs + assert all([_[str(ix + 1)] == ("odd" if ix % 2 else "even") for ix, _ in enumerate(raw_results)]) + + with open(test_fn_keyed, "r") as file: + keyed_results = [json.loads(_) for _ in file.readlines()] + os.remove(test_fn_keyed) + assert len(keyed_results) == num_msgs + assert all([_[str(ix + 1)] == "new key" for ix, _ in enumerate(keyed_results)]) + + +def test_filter_key(): + num_msgs = 20 + test_fn_raw = get_test_fn() + test_fn_filtered = test_fn_raw.parent / (test_fn_raw.stem + "_keyed" + test_fn_raw.suffix) + + comps = { + "SRC": KeyedAxarrGenerator(num_msgs=num_msgs), + "FILTER": FilterOnKey(key="odd"), + "SINK_RAW": AxarrReceiver(num_msgs=1e9, output_fn=test_fn_raw), + "SINK_FILTERED": AxarrReceiver(num_msgs=num_msgs // 2, output_fn=test_fn_filtered), + } + conns = [ + (comps["SRC"].OUTPUT_SIGNAL, comps["SINK_RAW"].INPUT_SIGNAL), + (comps["SRC"].OUTPUT_SIGNAL, comps["FILTER"].INPUT_SIGNAL), + (comps["FILTER"].OUTPUT_SIGNAL, comps["SINK_FILTERED"].INPUT_SIGNAL), + ] + ez.run( + components=comps, + connections=conns + ) + + with open(test_fn_raw, "r") as file: + raw_results = [json.loads(_) for _ in file.readlines()] + os.remove(test_fn_raw) + assert len(raw_results) == num_msgs + + with open(test_fn_filtered, "r") as file: + filtered_results = [json.loads(_) for _ in file.readlines()] + os.remove(test_fn_filtered) + assert len(filtered_results) == num_msgs // 2 + assert all([_[str(ix + 1)] == "odd" for ix, _ in enumerate(filtered_results)]) diff --git a/tests/messages/test_modify.py b/tests/messages/test_modify.py index 022727d2..04546f0f 100644 --- a/tests/messages/test_modify.py +++ b/tests/messages/test_modify.py @@ -1,9 +1,11 @@ +import copy +import typing + import numpy as np import pytest -import typing from ezmsg.util.messages.axisarray import AxisArray -from ezmsg.util.messages.modify import modify_axis, ModifyAxis, ModifyAxisSettings +from ezmsg.util.messages.modify import modify_axis @pytest.mark.parametrize("name_map", [None, {"step": "time"}]) @@ -13,9 +15,19 @@ def test_modify_axis(name_map: typing.Optional[typing.Dict[str, str]]): dims=["step", "freq", "ch"], axes={"step": AxisArray.Axis.TimeAxis(fs=10.0, offset=0.0)}, ) + backup = copy.deepcopy(input_ax_arr) gen = modify_axis(name_map) res = gen.send(input_ax_arr) + + # Make sure the input hasn't changed + assert np.array_equal(input_ax_arr.data, backup.data) + assert input_ax_arr.dims == backup.dims + assert list(input_ax_arr.axes.keys()) == list(backup.axes.keys()) + for k, v in input_ax_arr.axes.items(): + assert v == backup.axes[k] + + assert res.data is input_ax_arr.data if name_map is None: assert res is input_ax_arr else: @@ -23,3 +35,22 @@ def test_modify_axis(name_map: typing.Optional[typing.Dict[str, str]]): assert k not in res.axes assert v in res.axes assert input_ax_arr.axes[k] is res.axes[v] + + +@pytest.mark.parametrize("targ_dim_len", [1, 3]) +def test_drop_axis(targ_dim_len: int): + input_ax_arr = AxisArray( + data=np.arange(targ_dim_len * 5 * 4).reshape(targ_dim_len, 5, 4), + dims=["step", "freq", "ch"], + axes={"step": AxisArray.Axis.TimeAxis(fs=10.0, offset=0.0)}, + ) + gen = modify_axis({"step": None}) + if targ_dim_len != 1: + with pytest.raises(ValueError): + res = gen.send(input_ax_arr) + else: + res = gen.send(input_ax_arr) + assert "step" not in res.dims + assert "step" not in res.axes + assert res.data.shape == (5, 4) + diff --git a/tests/test_attach.py b/tests/test_attach.py index 048f4354..86414048 100644 --- a/tests/test_attach.py +++ b/tests/test_attach.py @@ -17,8 +17,8 @@ class TransmitReceiveState(ez.State): class TransmitReceive(ez.Unit): - SETTINGS: TransmitReceiveSettings - STATE: TransmitReceiveState + SETTINGS = TransmitReceiveSettings + STATE = TransmitReceiveState OUTPUT = ez.OutputStream(str) INPUT = ez.InputStream(str) @@ -105,13 +105,12 @@ def run(self) -> None: @pytest.mark.asyncio @pytest.mark.skip(reason="canonical port isn't always available") async def test_attach(): - event_loop = asyncio.get_running_loop() graph_service = ez.GraphService(address=ez.GraphService.default_address()) shm_service = ez.SHMService(address=ez.SHMService.default_address()) graph_server = graph_service.create_server() shm_server = shm_service.create_server() - async with ez.GraphContext(graph_service, shm_service) as context: + async with ez.GraphContext(graph_service, shm_service): settings = TransmitReceiveSettings() txrx_process = TransmitReceiveProcess(settings) diff --git a/tests/test_connections.py b/tests/test_connections.py index 23ed1233..4289a5fd 100644 --- a/tests/test_connections.py +++ b/tests/test_connections.py @@ -41,4 +41,4 @@ def network(self) -> ez.NetworkDefinition: if __name__ == "__main__": - ez.run(SYSTEM = SplitSystem()) + ez.run(SYSTEM=SplitSystem()) diff --git a/tests/test_generator.py b/tests/test_generator.py index d4de1b7e..ba3ee77b 100644 --- a/tests/test_generator.py +++ b/tests/test_generator.py @@ -13,16 +13,15 @@ from ez_test_utils import ( get_test_fn, - MessageGenerator, MessageGeneratorSettings, - MessageReceiverSettings, MessageReceiverState + MessageGenerator, + MessageGeneratorSettings, + MessageReceiverSettings, + MessageReceiverState, ) def undecorated_generator( - arg_untyped, - arg_typed: int, - kwarg_untyped=None, - kwarg_typed: bool = True + arg_untyped, arg_typed: int, kwarg_untyped=None, kwarg_typed: bool = True ) -> typing.Generator[typing.Any, typing.Any, None]: """ Do-nothing generator to test func inspection. @@ -37,14 +36,11 @@ def undecorated_generator( @consumer def decorated_generator( - arg_untyped, - arg_typed: int, - kwarg_untyped=None, - kwarg_typed: bool = True + arg_untyped, arg_typed: int, kwarg_untyped=None, kwarg_typed: bool = True ) -> typing.Generator[typing.Any, typing.Any, None]: """ - Do-nothing generator to test func inspection. - """ + Do-nothing generator to test func inspection. + """ msg_in = None msg_out = None @@ -60,7 +56,7 @@ def test_gen_to_unit_settings(): assert isinstance(MyUnit, ez.unit.UnitMeta) # Why not ez.Unit? with pytest.raises(TypeError): # Fails on missing positional arguments - def_settings = MySettings() + MySettings() settings = MySettings(None, 0) assert settings.arg_untyped is None @@ -77,7 +73,7 @@ def test_gen_to_unit_settings(): @consumer def my_gen_func( - append_right: bool = True, + append_right: bool = True, ) -> typing.Generator[typing.List[typing.Any], typing.Any, None]: """ Basic generator function used for testing. It returns the accumulated inputs. @@ -100,7 +96,7 @@ def my_gen_func( @consumer def my_gen_func_axarr( - axis: str = "time", + axis: str = "time", ) -> typing.Generator[AxisArray, AxisArray, None]: """ Basic generator function used for testing. It returns the accumulated inputs @@ -139,8 +135,8 @@ def test_gen_funcs(): class MessageAnyReceiver(ez.Unit): - STATE: MessageReceiverState - SETTINGS: MessageReceiverSettings + STATE = MessageReceiverState + SETTINGS = MessageReceiverSettings INPUT = ez.InputStream(typing.List[typing.Any]) @@ -170,14 +166,14 @@ def test_gen_to_unit_any(): comps = { "SIMPLE_PUB": MessageGenerator(num_msgs=num_msgs), "MYUNIT": MyUnit(), - "SIMPLE_SUB": MessageAnyReceiver(num_msgs=num_msgs, output_fn=test_filename) + "SIMPLE_SUB": MessageAnyReceiver(num_msgs=num_msgs, output_fn=test_filename), } ez.run( components=comps, connections=( (comps["SIMPLE_PUB"].OUTPUT, comps["MYUNIT"].INPUT), - (comps["MYUNIT"].OUTPUT, comps["SIMPLE_SUB"].INPUT) - ) + (comps["MYUNIT"].OUTPUT, comps["SIMPLE_SUB"].INPUT), + ), ) results = [] with open(test_filename, "r") as file: @@ -191,7 +187,7 @@ def test_gen_to_unit_any(): class AxarrGenerator(ez.Unit): - SETTINGS: MessageGeneratorSettings + SETTINGS = MessageGeneratorSettings OUTPUT_SIGNAL = ez.OutputStream(AxisArray) @ez.publisher(OUTPUT_SIGNAL) @@ -202,8 +198,8 @@ async def spawn(self) -> typing.AsyncGenerator: class AxarrReceiver(ez.Unit): - STATE: MessageReceiverState - SETTINGS: MessageReceiverSettings + STATE = MessageReceiverState + SETTINGS = MessageReceiverSettings INPUT_SIGNAL = ez.InputStream(AxisArray) @ez.subscriber(INPUT_SIGNAL) @@ -231,14 +227,14 @@ def test_gen_to_unit_axarr(): comps = { "SIMPLE_PUB": AxarrGenerator(num_msgs=num_msgs), "MYUNIT": MyUnit(), - "SIMPLE_SUB": AxarrReceiver(num_msgs=num_msgs, output_fn=test_filename) + "SIMPLE_SUB": AxarrReceiver(num_msgs=num_msgs, output_fn=test_filename), } ez.run( components=comps, connections=( (comps["SIMPLE_PUB"].OUTPUT_SIGNAL, comps["MYUNIT"].INPUT_SIGNAL), - (comps["MYUNIT"].OUTPUT_SIGNAL, comps["SIMPLE_SUB"].INPUT_SIGNAL) - ) + (comps["MYUNIT"].OUTPUT_SIGNAL, comps["SIMPLE_SUB"].INPUT_SIGNAL), + ), ) results = [] with open(test_filename, "r") as file: @@ -246,8 +242,10 @@ def test_gen_to_unit_axarr(): for line in lines: results.append(json.loads(line)) os.remove(test_filename) - assert np.array_equal(results[-1][f"{num_msgs}"], np.hstack([np.arange(_) for _ in range(num_msgs)])) + assert np.array_equal( + results[-1][f"{num_msgs}"], np.hstack([np.arange(_) for _ in range(num_msgs)]) + ) assert len(results) == num_msgs -# TODO: test compose, GenState, Gen, GenAxisArray +# TODO: test compose, GenState, Gen diff --git a/tests/test_graph.py b/tests/test_graph.py index 3c940f90..b7b414ac 100644 --- a/tests/test_graph.py +++ b/tests/test_graph.py @@ -22,14 +22,14 @@ @pytest.mark.asyncio async def test_graph(): async with GraphContext() as context: - a_pub = await context.publisher("a") - e_sub = await context.subscriber("e") + await context.publisher("a") + await context.subscriber("e") for edge in simple_graph_1: await context.connect(*edge) - c_sub = await context.subscriber("c") - b_pub = await context.publisher("b") + await context.subscriber("c") + await context.publisher("b") for edge in simple_graph_2: await context.connect(*edge) @@ -99,7 +99,7 @@ async def test_comms(): async def test_order(): async with GraphContext() as context: b_pub = await context.publisher("b") - c_sub = await context.subscriber("c") + await context.subscriber("c") e_sub = await context.subscriber("e") for edge in simple_graph_1: diff --git a/tests/test_run.py b/tests/test_run.py index 24c616da..97ea52af 100644 --- a/tests/test_run.py +++ b/tests/test_run.py @@ -1,4 +1,3 @@ - import json import os import pytest @@ -7,8 +6,10 @@ from ez_test_utils import ( get_test_fn, - MessageGenerator, MessageGeneratorSettings, - MessageReceiver, MessageReceiverSettings + MessageGenerator, + MessageGeneratorSettings, + MessageReceiver, + MessageReceiverSettings, ) @@ -19,7 +20,7 @@ class ToySystemSettings(ez.Settings): class ToySystem(ez.Collection): - SETTINGS: ToySystemSettings + SETTINGS = ToySystemSettings # Publishers SIMPLE_PUB = MessageGenerator() @@ -66,7 +67,7 @@ def test_local_system(toy_system_fixture, num_messages): system = toy_system_fixture( ToySystemSettings(num_msgs=num_messages, output_fn=test_filename) ) - ez.run(SYSTEM = system) + ez.run(SYSTEM=system) results = [] with open(test_filename, "r") as file: @@ -84,18 +85,20 @@ def test_run_comps_conns(passthrough_settings, num_messages): if passthrough_settings: comps = { "SIMPLE_PUB": MessageGenerator(num_msgs=num_messages), - "SIMPLE_SUB": MessageReceiver(num_msgs=num_messages, output_fn=test_filename) + "SIMPLE_SUB": MessageReceiver( + num_msgs=num_messages, output_fn=test_filename + ), } else: comps = { - "SIMPLE_PUB": MessageGenerator(MessageGeneratorSettings(num_msgs=num_messages)), - "SIMPLE_SUB": MessageReceiver(MessageReceiverSettings( - num_msgs=num_messages, output_fn=test_filename - )) + "SIMPLE_PUB": MessageGenerator( + MessageGeneratorSettings(num_msgs=num_messages) + ), + "SIMPLE_SUB": MessageReceiver( + MessageReceiverSettings(num_msgs=num_messages, output_fn=test_filename) + ), } - conns = ( - (comps["SIMPLE_PUB"].OUTPUT, comps["SIMPLE_SUB"].INPUT), - ) + conns = ((comps["SIMPLE_PUB"].OUTPUT, comps["SIMPLE_SUB"].INPUT),) ez.run(components=comps, connections=conns) diff --git a/tests/test_state.py b/tests/test_state.py index c288f63f..945e8d1a 100644 --- a/tests/test_state.py +++ b/tests/test_state.py @@ -24,10 +24,10 @@ class ToySettings(ez.Settings): class ToyUnit(ez.Unit): - STATE: ToyState - SETTINGS: ToySettings + STATE = ToyState + SETTINGS = ToySettings - def initialize(self) -> None: + async def initialize(self) -> None: if self.SETTINGS.override_integer is not None: self.STATE.integer = self.SETTINGS.override_integer if self.SETTINGS.override_string is not None: diff --git a/tests/test_test.py b/tests/test_test.py index 1157c61a..4793fd4a 100644 --- a/tests/test_test.py +++ b/tests/test_test.py @@ -1,6 +1,3 @@ -import pytest - - def test_test(): """ Tests that testing works 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