pymmcore-plus 0.9.3__tar.gz → 0.13.0__tar.gz

{pymmcore_plus-0.9.3 → pymmcore_plus-0.13.0}/.gitignore

@@ -139,10 +139,11 @@ cython_debug/
 
 Micro-Manager-*
 .vscode
+.idea
 
 docs/_includes/_cmmcore_members.md
 docs/_includes/_cmmcore_table.md
 docs/_includes/_cmmcoreplus_members.md
 
-example_*.ome.tiff
+example_*.some.tiff
 example.zarr

{pymmcore_plus-0.9.3 → pymmcore_plus-0.13.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pymmcore-plus
-Version: 0.9.3
+Version: 0.13.0
 Summary: pymmcore superset providing improved APIs, event handling, and a pure python acquisition engine
 Project-URL: Source, https://github.com/pymmcore-plus/pymmcore-plus
 Project-URL: Tracker, https://github.com/pymmcore-plus/pymmcore-plus/issues
@@ -16,24 +16,24 @@ Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: System :: Hardware
 Classifier: Topic :: System :: Hardware :: Hardware Drivers
 Classifier: Topic :: Utilities
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Requires-Dist: numpy>=1.17.3
 Requires-Dist: platformdirs>=3.0.0
 Requires-Dist: psygnal>=0.7
 Requires-Dist: pymmcore>=10.7.0.71.0
 Requires-Dist: rich>=10.2.0
+Requires-Dist: tensorstore; python_version < '3.13'
 Requires-Dist: typer>=0.4.2
 Requires-Dist: typing-extensions
-Requires-Dist: useq-schema>=0.4.7
-Requires-Dist: wrapt>=1.14
+Requires-Dist: useq-schema>=0.6.2
 Provides-Extra: cli
 Requires-Dist: rich>=10.2.0; extra == 'cli'
 Requires-Dist: typer>=0.4.2; extra == 'cli'
@@ -43,17 +43,27 @@ Requires-Dist: mypy; extra == 'dev'
 Requires-Dist: pdbpp; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: tensorstore-stubs; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: mkdocs-typer==0.0.3; extra == 'docs'
 Requires-Dist: mkdocs>=1.4; extra == 'docs'
 Requires-Dist: mkdocstrings-python==1.1.2; extra == 'docs'
 Requires-Dist: mkdocstrings==0.22.0; extra == 'docs'
 Provides-Extra: io
 Requires-Dist: tifffile>=2021.6.14; extra == 'io'
-Requires-Dist: zarr>=2.2; extra == 'io'
+Requires-Dist: zarr<3,>=2.2; extra == 'io'
+Provides-Extra: pyqt5
+Requires-Dist: pyqt5>=5.15.4; extra == 'pyqt5'
+Provides-Extra: pyqt6
+Requires-Dist: pyqt6<6.8,>=6.4.2; extra == 'pyqt6'
+Provides-Extra: pyside2
+Requires-Dist: pyside2>=5.15; extra == 'pyside2'
+Provides-Extra: pyside6
+Requires-Dist: pyside6<6.8,>=6.4.0; extra == 'pyside6'
 Provides-Extra: test
 Requires-Dist: msgpack; extra == 'test'
-Requires-Dist: pyside6; extra == 'test'
+Requires-Dist: msgspec; (python_version < '3.13') and extra == 'test'
 Requires-Dist: pytest-cov>=4; extra == 'test'
 Requires-Dist: pytest-qt>=4; extra == 'test'
 Requires-Dist: pytest>=7.3.2; extra == 'test'
@@ -61,7 +71,8 @@ Requires-Dist: qtpy>=2; extra == 'test'
 Requires-Dist: rich; extra == 'test'
 Requires-Dist: tifffile>=2021.6.14; extra == 'test'
 Requires-Dist: typer>=0.4.2; extra == 'test'
-Requires-Dist: zarr>=2.2; extra == 'test'
+Requires-Dist: xarray; extra == 'test'
+Requires-Dist: zarr<3,>=2.2; extra == 'test'
 Description-Content-Type: text/markdown
 
 # pymmcore-plus
@@ -70,7 +81,7 @@ Description-Content-Type: text/markdown
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pymmcore-plus)](https://pypi.org/project/pymmcore-plus)
 [![PyPI](https://img.shields.io/pypi/v/pymmcore-plus.svg?color=green)](https://pypi.org/project/pymmcore-plus)
 [![Conda](https://img.shields.io/conda/vn/conda-forge/pymmcore-plus)](https://anaconda.org/conda-forge/pymmcore-plus)
-[![CI](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/test_and_deploy.yml/badge.svg)](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/test_and_deploy.yml)
+[![CI](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/ci.yml/badge.svg)](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/ci.yml)
 [![docs](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/docs.yml/badge.svg)](https://pymmcore-plus.github.io/pymmcore-plus/)
 [![codecov](https://codecov.io/gh/pymmcore-plus/pymmcore-plus/branch/main/graph/badge.svg)](https://codecov.io/gh/pymmcore-plus/pymmcore-plus)
 [![Benchmarks](https://img.shields.io/endpoint?url=https://codspeed.io/badge.json)](https://codspeed.io/pymmcore-plus/pymmcore-plus)
@@ -141,8 +152,7 @@ provides a python API to control the C++ core directly, without the need for
 Java in the loop.  Each has its own advantages and disadvantages!  With
 pycro-manager you immediately get the entire existing micro-manager ecosystem
 and GUI application. With pymmcore-plus you don't need to install Java, and you
-have direct access to the memory buffers used by the C++ core, but the GUI
-side of things is far less mature.
+have direct access to the memory buffers used by the C++ core.
 
 ## Quickstart
 

{pymmcore_plus-0.9.3 → pymmcore_plus-0.13.0}/README.md

@@ -4,7 +4,7 @@
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pymmcore-plus)](https://pypi.org/project/pymmcore-plus)
 [![PyPI](https://img.shields.io/pypi/v/pymmcore-plus.svg?color=green)](https://pypi.org/project/pymmcore-plus)
 [![Conda](https://img.shields.io/conda/vn/conda-forge/pymmcore-plus)](https://anaconda.org/conda-forge/pymmcore-plus)
-[![CI](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/test_and_deploy.yml/badge.svg)](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/test_and_deploy.yml)
+[![CI](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/ci.yml/badge.svg)](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/ci.yml)
 [![docs](https://github.com/pymmcore-plus/pymmcore-plus/actions/workflows/docs.yml/badge.svg)](https://pymmcore-plus.github.io/pymmcore-plus/)
 [![codecov](https://codecov.io/gh/pymmcore-plus/pymmcore-plus/branch/main/graph/badge.svg)](https://codecov.io/gh/pymmcore-plus/pymmcore-plus)
 [![Benchmarks](https://img.shields.io/endpoint?url=https://codspeed.io/badge.json)](https://codspeed.io/pymmcore-plus/pymmcore-plus)
@@ -75,8 +75,7 @@ provides a python API to control the C++ core directly, without the need for
 Java in the loop.  Each has its own advantages and disadvantages!  With
 pycro-manager you immediately get the entire existing micro-manager ecosystem
 and GUI application. With pymmcore-plus you don't need to install Java, and you
-have direct access to the memory buffers used by the C++ core, but the GUI
-side of things is far less mature.
+have direct access to the memory buffers used by the C++ core.
 
 ## Quickstart
 

{pymmcore_plus-0.9.3 → pymmcore_plus-0.13.0}/pyproject.toml

@@ -9,7 +9,7 @@ name = "pymmcore-plus"
 description = "pymmcore superset providing improved APIs, event handling, and a pure python acquisition engine"
 keywords = ["microscope", "micro-manager", "smart-microscopy"]
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = { text = "BSD 3-Clause License" }
 authors = [
     { name = "Talley Lambert", email = "talley.lambert@gmail.com" },
@@ -24,11 +24,11 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: System :: Hardware",
     "Topic :: System :: Hardware :: Hardware Drivers",
     "Topic :: Utilities",
@@ -39,9 +39,9 @@ dependencies = [
     "numpy >=1.17.3",
     "psygnal >=0.7",
     "pymmcore >=10.7.0.71.0",
-    "typing-extensions",      # not actually required at runtime
-    "useq-schema >=0.4.7",
-    "wrapt >=1.14",
+    "typing-extensions",                    # not actually required at runtime
+    "useq-schema >=0.6.2",
+    "tensorstore; python_version < '3.13'",
     # cli requirements included by default for now
     "typer >=0.4.2",
     "rich >=10.2.0",
@@ -51,10 +51,14 @@ dependencies = [
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
 cli = ["typer >=0.4.2", "rich >=10.2.0"]
-io = ["tifffile >=2021.6.14", "zarr >=2.2"]
+io = ["tifffile >=2021.6.14", "zarr >=2.2,<3"]
+PySide2 = ["PySide2 >=5.15"]
+PySide6 = ["PySide6 >=6.4.0,<6.8"]
+PyQt5 = ["PyQt5 >=5.15.4"]
+PyQt6 = ["PyQt6 >=6.4.2,<6.8"]
 test = [
+    "msgspec; python_version < '3.13'",
     "msgpack",
-    "PySide6",
     "pytest-cov >=4",
     "pytest-qt >=4",
     "pytest >=7.3.2",
@@ -62,14 +66,16 @@ test = [
     "rich",
     "typer >=0.4.2",
     "tifffile >=2021.6.14",
-    "zarr >=2.2",
+    "zarr >=2.2,<3",
+    "xarray",
 ]
-dev = ["ipython", "mypy", "pdbpp", "pre-commit", "ruff"]
+dev = ["ipython", "mypy", "pdbpp", "pre-commit", "ruff", "tensorstore-stubs"]
 docs = [
     "mkdocs >=1.4",
     "mkdocs-material",
     "mkdocstrings ==0.22.0",
     "mkdocstrings-python ==1.1.2",
+    "mkdocs-typer ==0.0.3",
     # "griffe @ git+https://github.com/tlambert03/griffe@recursion"
 ]
 
@@ -96,10 +102,10 @@ include = ["/src", "/tests"]
 only-include = ["src"]
 sources = ["src"]
 
-# https://beta.ruff.rs/docs/rules/
+# https://docs.astral.sh/ruff/rules/
 [tool.ruff]
 line-length = 88
-target-version = "py38"
+target-version = "py39"
 
 [tool.ruff.lint]
 pydocstyle = { convention = "numpy" }
@@ -115,7 +121,7 @@ select = [
     "A001", # flake8-builtins
     "RUF",  # ruff-specific rules
     "TID",  # tidy
-    "TCH",  # typecheck
+    "TC",   # typecheck
     "SLF",  # private-access
 ]
 ignore = [
@@ -138,7 +144,8 @@ docstring-code-format = true
 [tool.pytest.ini_options]
 minversion = "6.0"
 testpaths = ["tests"]
-filterwarnings = ["error"]
+filterwarnings = ["error", "ignore:Failed to disconnect::pytestqt"]
+markers = ["run_last: mark a test to run last"]
 
 # https://mypy.readthedocs.io/en/stable/config_file.html
 [tool.mypy]
@@ -149,6 +156,9 @@ disallow_subclassing_any = false
 show_error_codes = true
 pretty = true
 plugins = "pydantic.mypy"
+# see https://github.com/python/mypy/issues/5374 and related discussions
+# it causes more pain than it solves
+disable_error_code = ["type-abstract"]
 
 [[tool.mypy.overrides]]
 module = ["tests.*"]
@@ -181,3 +191,6 @@ ignore = [
     "tests/**/*",
     "tox.ini",
 ]
+
+[tool.typos.default]
+extend-ignore-identifiers-re = ["(?i)nd2?.*", "(?i)ome", "anager"]

{pymmcore_plus-0.9.3 → pymmcore_plus-0.13.0}/src/pymmcore_plus/__init__.py

@@ -9,7 +9,7 @@ except PackageNotFoundError:  # pragma: no cover
 
 
 from ._logger import configure_logging
-from ._util import find_micromanager
+from ._util import find_micromanager, use_micromanager
 from .core import (
     CFGCommand,
     CFGGroup,
@@ -26,6 +26,7 @@ from .core import (
     FocusDirection,
     Keyword,
     Metadata,
+    PixelFormat,
     PortType,
     PropertyType,
 )
@@ -33,7 +34,6 @@ from .core.events import CMMCoreSignaler, PCoreSignaler
 from .mda._runner import GeneratorMDASequence
 
 __all__ = [
-    "__version__",
     "ActionType",
     "CFGCommand",
     "CFGGroup",
@@ -41,7 +41,6 @@ __all__ = [
     "CMMCoreSignaler",
     "ConfigGroup",
     "Configuration",
-    "configure_logging",
     "Device",
     "DeviceAdapter",
     "DeviceDetectionStatus",
@@ -49,12 +48,16 @@ __all__ = [
     "DeviceNotification",
     "DeviceProperty",
     "DeviceType",
-    "find_micromanager",
     "FocusDirection",
     "GeneratorMDASequence",
     "Keyword",
     "Metadata",
     "PCoreSignaler",
+    "PixelFormat",
     "PortType",
     "PropertyType",
+    "__version__",
+    "configure_logging",
+    "find_micromanager",
+    "use_micromanager",
 ]

pymmcore_plus-0.13.0/src/pymmcore_plus/_benchmark.py

@@ -0,0 +1,203 @@
+from __future__ import annotations
+
+import timeit
+import warnings
+from typing import TYPE_CHECKING
+
+from pymmcore_plus import CMMCorePlus, DeviceType
+
+if TYPE_CHECKING:
+    from collections.abc import Iterable, Iterator, Sequence
+
+    from pymmcore_plus.core._device import Device
+
+
+class Benchmark:
+    device_type = DeviceType.Camera
+
+    def __init__(self, core: CMMCorePlus, label: str = "") -> None:
+        self.core = core
+        self.label = label
+
+    def setup(self) -> None:
+        pass
+
+    def device(self) -> Device | None:
+        if self.label is not None:
+            return self.core.getDeviceObject(self.label)
+        return None
+
+    def run(self, number: int) -> Iterator[tuple[str, float | str]]:
+        # get methods in the order of definition, in reverse MRO order
+
+        try:
+            self.setup()
+        except Exception as e:  # pragma: no cover
+            warnings.warn(
+                f"Setup failed on device {self.label!r}: {e}",
+                RuntimeWarning,
+                stacklevel=2,
+            )
+            return
+
+        methods: list[str] = []
+        for base in reversed(type(self).mro()):
+            methods.extend(m for m in base.__dict__ if m.startswith("bench_"))
+
+        for method_name in methods:
+            try:
+                t = timeit.timeit(getattr(self, method_name), number=number)
+                result: float | str = round(1000 * t / number, 3)
+            except Exception as e:
+                result = str(e)
+            yield method_name[6:], result
+
+
+class CoreBenchmark(Benchmark):
+    device_type = DeviceType.Core
+
+    def bench_getDeviceAdapterNames(self) -> None:
+        self.core.getDeviceAdapterNames()
+
+    def bench_getLoadedDevices(self) -> None:
+        self.core.getLoadedDevices()
+
+    def bench_getSystemState(self) -> None:
+        self.core.getSystemState()
+
+
+class CameraBenchmark(Benchmark):
+    device_type = DeviceType.Camera
+
+    def setup(self) -> None:
+        self.core.setCameraDevice(self.label)
+        self.core.setExposure(self.label, 1)
+
+    def bench_getMultiROI(self) -> None:
+        self.core.getMultiROI()
+
+    def bench_getExposure(self) -> None:
+        self.core.getExposure(self.label)
+
+    def bench_snapImage(self) -> None:
+        self.core.snapImage()
+
+    def bench_getImage(self) -> None:
+        self.core.getImage()
+
+    def bench_getImageWidth(self) -> None:
+        self.core.getImageWidth()
+
+    def bench_getImageHeight(self) -> None:
+        self.core.getImageHeight()
+
+    def bench_getImageBufferSize(self) -> None:
+        self.core.getImageBufferSize()
+
+    def bench_getImageBitDepth(self) -> None:
+        self.core.getImageBitDepth()
+
+    def bench_getNumberOfComponents(self) -> None:
+        self.core.getNumberOfComponents()
+
+    def bench_getNumberOfCameraChannels(self) -> None:
+        self.core.getNumberOfCameraChannels()
+
+
+class XYStageBenchmark(Benchmark):
+    device_type = DeviceType.XYStage
+
+    def setup(self) -> None:
+        self.core.setXYStageDevice(self.label)
+        self.position = self.core.getXYPosition(self.label)
+
+    def bench_getXYPosition(self) -> None:
+        self.core.getXYPosition(self.label)
+
+    def bench_getXPosition(self) -> None:
+        self.core.getXPosition(self.label)
+
+    def bench_getYPosition(self) -> None:
+        self.core.getYPosition(self.label)
+
+    def bench_setXYPosition(self) -> None:
+        self.core.setXYPosition(self.label, *self.position)
+
+    def bench_setRelativeXYPosition(self) -> None:
+        self.core.setRelativeXYPosition(self.label, 0, 0)
+
+    def bench_isXYStageSequenceable(self) -> None:
+        self.core.isXYStageSequenceable(self.label)
+
+
+class StageBenchmark(Benchmark):
+    device_type = DeviceType.Stage
+
+    def setup(self) -> None:
+        self.position = self.core.getPosition(self.label)
+
+    def bench_getPosition(self) -> None:
+        self.core.getPosition(self.label)
+
+    def bench_setPosition(self) -> None:
+        self.core.setPosition(self.label, self.position)
+
+    def bench_setRelativePosition(self) -> None:
+        self.core.setRelativePosition(self.label, 0)
+
+    def bench_isStageSequenceable(self) -> None:
+        self.core.isStageSequenceable(self.label)
+
+    def bench_isStageLinearSequenceable(self) -> None:
+        self.core.isStageLinearSequenceable(self.label)
+
+
+class StateBenchmark(Benchmark):
+    device_type = DeviceType.State
+
+    def setup(self) -> None:
+        self.initial_state = self.core.getState(self.label)
+        try:
+            self.labels: Sequence[str] = self.core.getStateLabels(self.label)
+        except Exception:
+            self.labels = []
+
+    def bench_getState(self) -> None:
+        self.core.getState(self.label)
+
+    def bench_setState(self) -> None:
+        self.core.setState(self.label, self.initial_state)
+
+    def bench_getNumberOfStates(self) -> None:
+        self.core.getNumberOfStates(self.label)
+
+    def bench_getStateLabel(self) -> None:
+        self.core.getStateLabel(self.label)
+
+    def bench_getStateFromLabel(self) -> None:
+        for label in self.labels:
+            self.core.getStateFromLabel(self.label, label)
+
+
+def benchmark_core_and_devices(
+    core: CMMCorePlus, number: int = 100
+) -> Iterable[Device | None | tuple[str, float | str]]:
+    """Take an initialized core with devices and benchmark various methods.
+
+    Yields
+    ------
+    Device | None | tuple[str, float | str]
+        If a `Device`, it is the device object being benchmarked.
+        If None, it is the core object being benchmarked.
+        If a tuple, it is the method name and the time taken to run it.
+    """
+    for cls in Benchmark.__subclasses__():
+        if cls.device_type == DeviceType.Core:
+            bench = cls(core, "Core")
+            yield bench.device()
+            yield from bench.run(number)
+        else:
+            for dev in core.getLoadedDevicesOfType(cls.device_type):
+                bench = cls(core, dev)
+                yield bench.device()
+                yield from bench.run(number)

{pymmcore_plus-0.9.3 → pymmcore_plus-0.13.0}/src/pymmcore_plus/_build.py

@@ -1,5 +1,7 @@
 """Clone the micro-manager source code from GitHub and build dev devices."""
 
+from __future__ import annotations
+
 import json
 import os
 import platform
@@ -9,12 +11,15 @@ import subprocess
 import tempfile
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Iterator, Sequence
+from typing import TYPE_CHECKING
 from urllib.request import Request, urlopen
 
 from rich import print
 from rich.prompt import Prompt
 
+if TYPE_CHECKING:
+    from collections.abc import Iterator, Sequence
+
 MM_REPO = "micro-manager/micro-manager"
 MMCORE_AND_DEV = "micro-manager/mmCoreAndDevices"
 MM_REPO_URL = f"https://github.com/{MM_REPO}.git"