pymmcore-plus 0.11.0__tar.gz → 0.12.0__tar.gz

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pymmcore-plus
-Version: 0.11.0
+Version: 0.12.0
 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
@@ -16,7 +16,6 @@ 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
@@ -24,7 +23,7 @@ Classifier: Programming Language :: Python :: 3.12
 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
@@ -33,7 +32,7 @@ Requires-Dist: rich>=10.2.0
 Requires-Dist: tensorstore
 Requires-Dist: typer>=0.4.2
 Requires-Dist: typing-extensions
-Requires-Dist: useq-schema>=0.4.7
+Requires-Dist: useq-schema>=0.5.0
 Requires-Dist: wrapt>=1.14
 Provides-Extra: cli
 Requires-Dist: rich>=10.2.0; extra == 'cli'
@@ -53,7 +52,7 @@ 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: test
 Requires-Dist: msgpack; extra == 'test'
 Requires-Dist: msgspec; extra == 'test'
@@ -65,7 +64,7 @@ Requires-Dist: rich; extra == 'test'
 Requires-Dist: tifffile>=2021.6.14; extra == 'test'
 Requires-Dist: typer>=0.4.2; extra == 'test'
 Requires-Dist: xarray; extra == 'test'
-Requires-Dist: zarr>=2.2; extra == 'test'
+Requires-Dist: zarr<3,>=2.2; extra == 'test'
 Description-Content-Type: text/markdown
 
 # pymmcore-plus

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/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" },
@@ -24,7 +24,6 @@ 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",
@@ -40,7 +39,7 @@ dependencies = [
     "psygnal >=0.7",
     "pymmcore >=10.7.0.71.0",
     "typing-extensions",      # not actually required at runtime
-    "useq-schema >=0.4.7",
+    "useq-schema >=0.5.0",
     "wrapt >=1.14",
     "tensorstore",
     # cli requirements included by default for now
@@ -52,7 +51,7 @@ 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"]
 test = [
     "msgspec",
     "msgpack",
@@ -63,7 +62,7 @@ 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", "tensorstore-stubs"]
@@ -72,7 +71,7 @@ docs = [
     "mkdocs-material",
     "mkdocstrings ==0.22.0",
     "mkdocstrings-python ==1.1.2",
-    "mkdocs-typer ==0.0.3"
+    "mkdocs-typer ==0.0.3",
     # "griffe @ git+https://github.com/tlambert03/griffe@recursion"
 ]
 
@@ -102,7 +101,7 @@ sources = ["src"]
 # https://beta.ruff.rs/docs/rules/
 [tool.ruff]
 line-length = 88
-target-version = "py38"
+target-version = "py39"
 
 [tool.ruff.lint]
 pydocstyle = { convention = "numpy" }

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/_build.py

@@ -11,12 +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"

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/_cli.py

@@ -6,7 +6,7 @@ import sys
 import time
 from contextlib import suppress
 from pathlib import Path
-from typing import List, Optional, Union, cast
+from typing import Optional, Union, cast
 
 try:
     import typer
@@ -31,7 +31,7 @@ def _show_version_and_exit(value: bool) -> None:
         import pymmcore
 
         typer.echo(f"pymmcore-plus v{pymmcore_plus.__version__}")
-        typer.echo(f"pymmcore v{pymmcore.__version__}")  # type: ignore [attr-defined]
+        typer.echo(f"pymmcore v{pymmcore.__version__}")
         typer.echo(f"MMCore v{pymmcore.CMMCore().getAPIVersionInfo()}")
         raise typer.Exit()
 
@@ -53,7 +53,7 @@ def _main(
     # fix for windows CI encoding and emoji printing
     if getattr(sys.stdout, "encoding", None) != "utf-8":
         with suppress(AttributeError):
-            sys.stdout.reconfigure(encoding="utf-8")  # type: ignore [attr-defined]
+            sys.stdout.reconfigure(encoding="utf-8")  # type: ignore [union-attr]
 
 
 if "mkdocs" in sys.argv[0]:  # pragma: no cover
@@ -190,10 +190,10 @@ def run(
         None, help="Asymmetric range of z-stack below position."
     ),
     z_step: Optional[float] = typer.Option(None, help="Step size of z-stack."),
-    z_relative: Optional[List[float]] = typer.Option(
+    z_relative: Optional[list[float]] = typer.Option(
         None, "-zr", help="Relative z-positions to acquire (may use multiple times)."
     ),
-    z_absolute: Optional[List[float]] = typer.Option(
+    z_absolute: Optional[list[float]] = typer.Option(
         None, "-za", help="Absolute z-positions to acquire (may use multiple times)."
     ),
     t_interval: Optional[float] = typer.Option(
@@ -207,7 +207,7 @@ def run(
     axis_order: Optional[str] = typer.Option(
         None, help="Order of axes to acquire (e.g. 'TPCZ')."
     ),
-    channel: Optional[List[str]] = typer.Option(
+    channel: Optional[list[str]] = typer.Option(
         None,
         help="\bChannel to acquire. Argument is a string of the following form:\n"
         '\b - name: "DAPI"\n'
@@ -294,7 +294,7 @@ def run(
 
 @app.command()
 def build_dev(
-    devices: Optional[List[str]] = typer.Argument(
+    devices: Optional[list[str]] = typer.Argument(
         None, help=f"Device adapters to build. Defaults to {DEFAULT_PACKAGES}"
     ),
     dest: Path = typer.Option(

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/_logger.py

@@ -6,7 +6,10 @@ import sys
 from contextlib import contextmanager
 from logging.handlers import RotatingFileHandler
 from pathlib import Path
-from typing import ClassVar, Iterator
+from typing import TYPE_CHECKING, ClassVar
+
+if TYPE_CHECKING:
+    from collections.abc import Iterator
 
 __all__ = ["logger"]
 

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/_util.py

@@ -18,8 +18,9 @@ from typing import TYPE_CHECKING, cast, overload
 from platformdirs import user_data_dir
 
 if TYPE_CHECKING:
+    from collections.abc import Iterator
     from re import Pattern
-    from typing import Any, Callable, Iterator, Literal, TypeVar
+    from typing import Any, Callable, Literal, TypeVar
 
     QtConnectionType = Literal["AutoConnection", "DirectConnection", "QueuedConnection"]
 

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/_config.py

@@ -3,15 +3,17 @@
 from __future__ import annotations
 
 from collections import defaultdict
-from typing import TYPE_CHECKING, Any, Iterable, Iterator, Tuple, overload
+from typing import TYPE_CHECKING, Any, overload
 
 import pymmcore
 
 if TYPE_CHECKING:
+    from collections.abc import Iterable, Iterator
+
     from typing_extensions import TypeAlias  # py310
 
-DevPropValueTuple: TypeAlias = Tuple[str, str, str]
-DevPropTuple: TypeAlias = Tuple[str, str]
+DevPropValueTuple: TypeAlias = tuple[str, str, str]
+DevPropTuple: TypeAlias = tuple[str, str]
 
 
 class Configuration(pymmcore.Configuration):

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/_config_group.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Iterator, Literal, MutableMapping, overload
+from collections.abc import Iterator, MutableMapping
+from typing import TYPE_CHECKING, Any, Literal, overload
 
 import pymmcore
 

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/_metadata.py

@@ -1,8 +1,8 @@
 """pythonic wrapper on pymmcore.Metadata object."""
 
-from collections.abc import Mapping
+from collections.abc import ItemsView, Iterator, KeysView, Mapping, ValuesView
 from types import new_class
-from typing import Any, ItemsView, Iterator, KeysView, ValuesView, cast
+from typing import Any, cast
 
 import pymmcore
 

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/_mmcore_plus.py

@@ -10,17 +10,14 @@ from collections import defaultdict
 from contextlib import contextmanager, suppress
 from datetime import datetime
 from pathlib import Path
+from re import Pattern
 from textwrap import dedent
 from threading import RLock, Thread
 from typing import (
     TYPE_CHECKING,
     Any,
     Callable,
-    Iterable,
-    Iterator,
     NamedTuple,
-    Pattern,
-    Sequence,
     TypeVar,
     overload,
 )
@@ -51,6 +48,7 @@ from ._sequencing import can_sequence_events
 from .events import CMMCoreSignaler, PCoreSignaler, _get_auto_core_callback_class
 
 if TYPE_CHECKING:
+    from collections.abc import Iterable, Iterator, Sequence
     from typing import Literal, TypedDict
 
     import numpy as np
@@ -1594,7 +1592,7 @@ class CMMCorePlus(pymmcore.CMMCore):
 
         try:
             channel_group = self.getPropertyFromCache("Core", "ChannelGroup")
-            channel = self.getCurrentConfigFromCache(channel_group)
+            channel: str = self.getCurrentConfigFromCache(channel_group)
         except Exception:
             channel = "Default"
         tags["Channel"] = channel
@@ -2010,7 +2008,7 @@ class CMMCorePlus(pymmcore.CMMCore):
 
         :sparkles: *This method is new in `CMMCorePlus`.*
         """
-        _current = {
+        _current: dict[str, str] = {
             self.getCameraDevice(): "Camera",
             self.getXYStageDevice(): "XYStage",
             self.getFocusDevice(): "Focus",

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/_property.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from functools import cached_property
-from typing import TYPE_CHECKING, Any, Sequence, TypedDict
+from typing import TYPE_CHECKING, Any, TypedDict
 
 from pymmcore import g_Keyword_Label, g_Keyword_State
 
@@ -9,6 +9,8 @@ from ._constants import DeviceType, PropertyType
 from .events._device_signal_view import _DevicePropValueSignal
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
+
     from ._mmcore_plus import CMMCorePlus
 
 

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/_sequencing.py

@@ -1,13 +1,15 @@
 from __future__ import annotations
 
 from itertools import product
-from typing import TYPE_CHECKING, Literal, Sequence, Tuple, overload
+from typing import TYPE_CHECKING, Literal, overload
 
 from useq import AcquireImage, MDAEvent
 
 from pymmcore_plus.core._constants import DeviceType
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
+
     from pymmcore_plus import CMMCorePlus
 
 
@@ -18,12 +20,12 @@ class SequencedEvent(MDAEvent):
     calculate sequences for x, y, z, and exposure based on an a sequence of events.
     """
 
-    events: Tuple[MDAEvent, ...]  # noqa: UP006
+    events: tuple[MDAEvent, ...]
 
-    exposure_sequence: Tuple[float, ...]  # noqa: UP006
-    x_sequence: Tuple[float, ...]  # noqa: UP006
-    y_sequence: Tuple[float, ...]  # noqa: UP006
-    z_sequence: Tuple[float, ...]  # noqa: UP006
+    exposure_sequence: tuple[float, ...]
+    x_sequence: tuple[float, ...]
+    y_sequence: tuple[float, ...]
+    z_sequence: tuple[float, ...]
 
     # technically this is more like a field, but it requires a core instance
     # to getConfigData for channels, so we leave it as a method.

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/events/__init__.py

@@ -1,4 +1,4 @@
-from typing import TYPE_CHECKING, Any, List, Type
+from typing import TYPE_CHECKING, Any
 
 from pymmcore_plus._util import signals_backend
 
@@ -18,7 +18,7 @@ __all__ = [
 ]
 
 
-def _get_auto_core_callback_class() -> Type[PCoreSignaler]:
+def _get_auto_core_callback_class() -> type[PCoreSignaler]:
     if signals_backend() == "qt":
         from ._qsignals import QCoreSignaler
 
@@ -26,7 +26,7 @@ def _get_auto_core_callback_class() -> Type[PCoreSignaler]:
     return CMMCoreSignaler
 
 
-def __dir__() -> List[str]:  # pragma: no cover
+def __dir__() -> list[str]:  # pragma: no cover
     return [*list(globals()), "QCoreSignaler"]
 
 

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/events/_device_signal_view.py

@@ -1,14 +1,16 @@
-from typing import TYPE_CHECKING, Any, Optional
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Any
 
 if TYPE_CHECKING:
     from pymmcore_plus.core import CMMCorePlus
 
-from ._prop_event_mixin import _C
+    from ._prop_event_mixin import _C
 
 
 class _DevicePropValueSignal:
     def __init__(
-        self, device_label: str, property_name: Optional[str], mmcore: "CMMCorePlus"
+        self, device_label: str, property_name: str | None, mmcore: CMMCorePlus
     ) -> None:
         self._dev = device_label
         self._prop = property_name
@@ -18,13 +20,13 @@ class _DevicePropValueSignal:
         sig = self._mmc.events.devicePropertyChanged(self._dev, self._prop)
         return sig.connect(callback)  # type: ignore
 
-    def disconnect(self, callback: _C) -> None:
+    def disconnect(self, callback: _C | None = None) -> None:
         sig = self._mmc.events.devicePropertyChanged(self._dev, self._prop)
-        return sig.disconnect(callback)  # type: ignore
+        sig.disconnect(callback)
 
     def emit(self, *args: Any) -> Any:
         """Emits the signal with the given arguments."""
         self._mmc.events.devicePropertyChanged(self._dev, self._prop).emit(*args)
 
-    def __call__(self, property: str) -> "_DevicePropValueSignal":
+    def __call__(self, property: str) -> _DevicePropValueSignal:
         return _DevicePropValueSignal(self._dev, property, self._mmc)

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/events/_norm_slot.py

@@ -8,13 +8,11 @@ from types import MethodType
 from typing import TYPE_CHECKING, Any, Callable, Union
 
 if TYPE_CHECKING:
-    from typing import Tuple
-
     from typing_extensions import TypeGuard  # py310
 
-    MethodRef = Tuple[weakref.ReferenceType[object], str, Callable | None]
+    MethodRef = tuple[weakref.ReferenceType[object], str, Callable | None]
     NormedCallback = Union[MethodRef, Callable]
-    StoredSlot = Tuple[NormedCallback, int | None]
+    StoredSlot = tuple[NormedCallback, int | None]
     ReducerFunc = Callable[[tuple, tuple], tuple]
 
 

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/events/_prop_event_mixin.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Callable, ClassVar, Dict, Tuple, TypeVar
+from typing import TYPE_CHECKING, Any, Callable, ClassVar, TypeVar
 
 from ._norm_slot import denormalize_slot, normalize_slot
 from ._protocol import PCoreSignaler
@@ -8,8 +8,8 @@ from ._protocol import PCoreSignaler
 if TYPE_CHECKING:
     from ._norm_slot import NormedCallback
 
-    PropKey = Tuple[str, str | None, NormedCallback]
-    PropKeyDict = Dict[PropKey, Callable]
+    PropKey = tuple[str, str | None, NormedCallback]
+    PropKeyDict = dict[PropKey, Callable]
 
 
 _C = TypeVar("_C", bound=Callable[..., Any])
@@ -64,8 +64,11 @@ class _PropertySignal:
         self._events.propertyChanged.connect(_wrapper)
         return callback
 
-    def disconnect(self, callback: Callable) -> None:
+    def disconnect(self, callback: Callable | None = None) -> None:
         """Disconnect `callback` from this device and/or property."""
+        if callback is None:
+            self._events.propertyChanged.disconnect()
+            return
         key = (self._device, self._property, normalize_slot(callback))
         cb = self._events.property_callbacks.pop(key, None)
         if cb is None:

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/core/events/_protocol.py

@@ -12,8 +12,11 @@ class PSignalInstance(Protocol):
     def connect(self, slot: Callable) -> Any:
         """Connect slot to this signal."""
 
-    def disconnect(self, slot: Callable) -> Any:
-        """Disconnect slot from this signal."""
+    def disconnect(self, slot: Optional[Callable] = None) -> Any:
+        """Disconnect slot from this signal.
+
+        If `None`, all slots should be disconnected.
+        """
 
     def emit(self, *args: Any) -> Any:
         """Emits the signal with the given arguments."""

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/install.py

@@ -10,7 +10,7 @@ import tempfile
 from contextlib import contextmanager, nullcontext
 from pathlib import Path
 from platform import system
-from typing import TYPE_CHECKING, Callable, ContextManager, Iterator, Protocol
+from typing import TYPE_CHECKING, Callable, Protocol
 from urllib.request import urlopen, urlretrieve
 
 import typer
@@ -18,6 +18,8 @@ import typer
 from pymmcore_plus._util import USER_DATA_MM_PATH
 
 if TYPE_CHECKING:
+    from collections.abc import Iterator
+    from contextlib import AbstractContextManager
 
     class _MsgLogger(Protocol):
         def __call__(self, text: str, color: str = "", emoji: str = "") -> None: ...
@@ -70,7 +72,7 @@ def _get_download_name(url: str) -> str:
     return ""
 
 
-def _get_spinner(log_msg: _MsgLogger) -> Callable[[str], ContextManager]:
+def _get_spinner(log_msg: _MsgLogger) -> Callable[[str], AbstractContextManager]:
     if log_msg is _pretty_print:
         spinner = _spinner
     else:

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/mda/_engine.py

@@ -5,10 +5,7 @@ from contextlib import suppress
 from itertools import product
 from typing import (
     TYPE_CHECKING,
-    Iterable,
-    Iterator,
     NamedTuple,
-    Sequence,
     cast,
 )
 
@@ -29,6 +26,8 @@ from pymmcore_plus.metadata import (
 from ._protocol import PMDAEngine
 
 if TYPE_CHECKING:
+    from collections.abc import Iterable, Iterator, Sequence
+
     from numpy.typing import NDArray
 
     from pymmcore_plus.core import CMMCorePlus
@@ -54,12 +53,11 @@ class MDAEngine(PMDAEngine):
         attempt to combine MDAEvents into a single `SequencedEvent` if
         [`core.canSequenceEvents()`][pymmcore_plus.CMMCorePlus.canSequenceEvents]
         reports that the events can be sequenced. This can be set after instantiation.
-        By default, this is `False`, in order to avoid unexpected behavior, particularly
-        in testing and demo scenarios.  But in many "real world" scenarios, this can be
-        set to `True` to improve performance.
+        By default, this is `True`, however in various testing and demo scenarios, you
+        may wish to set it to `False` in order to avoid unexpected behavior.
     """
 
-    def __init__(self, mmc: CMMCorePlus, use_hardware_sequencing: bool = False) -> None:
+    def __init__(self, mmc: CMMCorePlus, use_hardware_sequencing: bool = True) -> None:
         self._mmc = mmc
         self.use_hardware_sequencing = use_hardware_sequencing
 

{pymmcore_plus-0.11.0 → pymmcore_plus-0.12.0}/src/pymmcore_plus/mda/_protocol.py

@@ -4,7 +4,7 @@ from abc import abstractmethod
 from typing import TYPE_CHECKING, Protocol, runtime_checkable
 
 if TYPE_CHECKING:
-    from typing import Iterable, Iterator
+    from collections.abc import Iterable, Iterator
 
     from numpy.typing import NDArray
     from useq import MDAEvent, MDASequence