pymmcore-plus 0.11.1__py3-none-any.whl → 0.12.0__py3-none-any.whl

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/_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
@@ -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/_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/_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/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/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/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/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

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/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/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/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/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/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/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/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/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

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

pymmcore_plus/mda/_runner.py

@@ -2,17 +2,10 @@ from __future__ import annotations
 
 import time
 import warnings
-from contextlib import nullcontext
+from collections.abc import Iterable, Iterator, Sequence
+from contextlib import AbstractContextManager, nullcontext
 from pathlib import Path
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    ContextManager,
-    Iterable,
-    Iterator,
-    Sequence,
-    Tuple,
-)
+from typing import TYPE_CHECKING, Any
 from unittest.mock import MagicMock
 
 from useq import MDASequence
@@ -39,7 +32,7 @@ MSG = (
 
 
 class GeneratorMDASequence(MDASequence):
-    axis_order: Tuple[str, ...] = ()  # noqa: UP006
+    axis_order: tuple[str, ...] = ()
 
     @property
     def sizes(self) -> dict[str, int]:  # pragma: no cover
@@ -77,7 +70,10 @@ class MDARunner:
 
         self._canceled = False
         self._sequence: MDASequence | None = None
-        self._reset_timer()
+        # timer for the full sequence, reset only once at the beginning of the sequence
+        self._sequence_t0: float = 0.0
+        # event clock, reset whenever `event.reset_event_timer` is True
+        self._t0: float = 0.0
 
     def set_engine(self, engine: PMDAEngine) -> PMDAEngine | None:
         """Set the [`PMDAEngine`][pymmcore_plus.mda.PMDAEngine] to use for the MDA run."""  # noqa: E501
@@ -212,11 +208,19 @@ class MDARunner:
 
     def seconds_elapsed(self) -> float:
         """Return the number of seconds since the start of the acquisition."""
+        return time.perf_counter() - self._sequence_t0
+
+    def event_seconds_elapsed(self) -> float:
+        """Return the number of seconds on the "event clock".
+
+        This is the time since either the start of the acquisition or the last
+        event with `reset_event_timer` set to `True`.
+        """
         return time.perf_counter() - self._t0
 
     def _outputs_connected(
         self, output: SingleOutput | Sequence[SingleOutput] | None
-    ) -> ContextManager:
+    ) -> AbstractContextManager:
         """Context in which output handlers are connected to the frameReady signal."""
         if output is None:
             return nullcontext()
@@ -272,9 +276,12 @@ class MDARunner:
         teardown_event = getattr(engine, "teardown_event", lambda e: None)
         event_iterator = getattr(engine, "event_iterator", iter)
         _events: Iterator[MDAEvent] = event_iterator(events)
-        self._reset_timer()
+        self._reset_event_timer()
+        self._sequence_t0 = self._t0
 
         for event in _events:
+            if event.reset_event_timer:
+                self._reset_event_timer()
             # If cancelled break out of the loop
             if self._wait_until_event(event) or not self._running:
                 break
@@ -284,17 +291,18 @@ class MDARunner:
             engine.setup_event(event)
 
             try:
-                elapsed_ms = self.seconds_elapsed() * 1000
+                runner_time_ms = self.seconds_elapsed() * 1000
                 # this is a bit of a hack to pass the time into the engine
-                # it is used for intra-event time calculations
+                # it is used for intra-event time calculations inside the engine.
                 # we pop it off after the event is executed.
-                event.metadata["runner_t0"] = self._t0
+                event.metadata["runner_t0"] = self._sequence_t0
                 output = engine.exec_event(event) or ()  # in case output is None
                 for payload in output:
                     img, event, meta = payload
                     event.metadata.pop("runner_t0", None)
+                    # if the engine calculated its own time, don't overwrite it
                     if "runner_time_ms" not in meta:
-                        meta["runner_time_ms"] = elapsed_ms
+                        meta["runner_time_ms"] = runner_time_ms
                     with exceptions_logged():
                         self._signals.frameReady.emit(img, event, meta)
             finally:
@@ -321,7 +329,7 @@ class MDARunner:
         logger.info("MDA Started: %s", sequence)
         return self._engine
 
-    def _reset_timer(self) -> None:
+    def _reset_event_timer(self) -> None:
         self._t0 = time.perf_counter()  # reference time, in seconds
 
     def _check_canceled(self) -> bool:
@@ -374,7 +382,7 @@ class MDARunner:
             go_at = event.min_start_time + self._paused_time
             # We need to enter a loop here checking paused and canceled.
             # otherwise you'll potentially wait a long time to cancel
-            remaining_wait_time = go_at - self.seconds_elapsed()
+            remaining_wait_time = go_at - self.event_seconds_elapsed()
             while remaining_wait_time > 0:
                 self._signals.awaitingEvent.emit(event, remaining_wait_time)
                 while self._paused and not self._canceled:
@@ -385,7 +393,7 @@ class MDARunner:
                 if self._canceled:
                     break
                 time.sleep(min(remaining_wait_time, 0.5))
-                remaining_wait_time = go_at - self.seconds_elapsed()
+                remaining_wait_time = go_at - self.event_seconds_elapsed()
 
         # check canceled again in case it was canceled
         # during the waiting loop

pymmcore_plus/mda/_thread_relay.py

@@ -11,7 +11,9 @@ from pymmcore_plus._util import listeners_connected
 from .events import _get_auto_MDA_callback_class
 
 if TYPE_CHECKING:
-    from typing import Any, ContextManager, Iterator
+    from collections.abc import Iterator
+    from contextlib import AbstractContextManager
+    from typing import Any
 
     from pymmcore_plus.core.events._protocol import PSignalInstance
     from pymmcore_plus.mda import PMDASignaler
@@ -24,7 +26,7 @@ def mda_listeners_connected(
     name_map: dict[str, str] | None = ...,
     asynchronous: Literal[False],
     wait_on_exit: bool = ...,
-) -> ContextManager[None]: ...
+) -> AbstractContextManager[None]: ...
 
 
 @overload
@@ -34,7 +36,7 @@ def mda_listeners_connected(
     name_map: dict[str, str] | None = ...,
     asynchronous: Literal[True] = ...,
     wait_on_exit: bool = ...,
-) -> ContextManager[MDARelayThread]: ...
+) -> AbstractContextManager[MDARelayThread]: ...
 
 
 @contextmanager

pymmcore_plus/mda/handlers/_5d_writer_base.py

@@ -3,11 +3,13 @@ from __future__ import annotations
 import warnings
 from abc import abstractmethod
 from collections import defaultdict
-from typing import TYPE_CHECKING, Generic, Mapping, Protocol, TypeVar
+from typing import TYPE_CHECKING, Generic, Protocol, TypeVar
 
 from ._util import position_sizes
 
 if TYPE_CHECKING:
+    from collections.abc import Mapping
+
     import numpy as np
     import useq
 

pymmcore_plus/mda/handlers/_img_sequence_writer.py

@@ -7,9 +7,10 @@ provided.
 
 from __future__ import annotations
 
+from collections.abc import Mapping, Sequence
 from itertools import count
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Callable, ClassVar, Mapping, Sequence, cast
+from typing import TYPE_CHECKING, Any, Callable, ClassVar, cast
 
 from pymmcore_plus.metadata.serialize import json_dumps
 

pymmcore_plus/mda/handlers/_ome_zarr_writer.py

@@ -6,7 +6,7 @@ import os.path
 import shutil
 import tempfile
 from contextlib import suppress
-from typing import TYPE_CHECKING, Any, Literal, MutableMapping, Protocol
+from typing import TYPE_CHECKING, Any, Literal, Protocol
 
 import numpy as np
 
@@ -15,8 +15,10 @@ from pymmcore_plus.metadata.serialize import to_builtins
 from ._5d_writer_base import _5DWriterBase
 
 if TYPE_CHECKING:
+    from collections.abc import MutableMapping, Sequence
+    from contextlib import AbstractAsyncContextManager
     from os import PathLike
-    from typing import ContextManager, Sequence, TypedDict
+    from typing import TypedDict
 
     import xarray as xr
     import zarr
@@ -24,7 +26,7 @@ if TYPE_CHECKING:
     from numcodecs.abc import Codec
 
     class ZarrSynchronizer(Protocol):
-        def __getitem__(self, key: str) -> ContextManager: ...
+        def __getitem__(self, key: str) -> AbstractAsyncContextManager: ...
 
     class ArrayCreationKwargs(TypedDict, total=False):
         compressor: str | Codec
@@ -276,9 +278,7 @@ class OMEZarrWriter(_5DWriterBase["zarr.Array"]):
         self._group.attrs["multiscales"] = scales
         ary.attrs["_ARRAY_DIMENSIONS"] = dims
         if seq := self.current_sequence:
-            ary.attrs["useq_MDASequence"] = to_builtins(
-                seq.model_dump(exclude_unset=True)
-            )
+            ary.attrs["useq_MDASequence"] = to_builtins(seq)
 
         return ary
 

pymmcore_plus/mda/handlers/_tensorstore_handler.py

@@ -14,7 +14,8 @@ from pymmcore_plus.metadata.serialize import json_dumps, json_loads
 from ._util import position_sizes
 
 if TYPE_CHECKING:
-    from typing import Literal, Mapping, Sequence, TypeAlias
+    from collections.abc import Mapping, Sequence
+    from typing import Literal, TypeAlias
 
     import numpy as np
     import tensorstore as ts
@@ -258,7 +259,7 @@ class TensorStoreHandler:
             # expand the sizes to include the largest size we encounter for each axis
             # in the case of positions with subsequences, we'll still end up with a
             # jagged array, but it won't take extra space, and we won't get index errors
-            max_sizes = seq.sizes.copy()
+            max_sizes = dict(seq.sizes)
             for psize in position_sizes(seq):
                 for k, v in psize.items():
                     max_sizes[k] = max(max_sizes.get(k, 0), v)

pymmcore_plus/mda/handlers/_util.py

@@ -29,7 +29,7 @@ def position_sizes(seq: useq.MDASequence) -> list[dict[str, int]]:
     `{dim: size}` pairs for each dimension in the sequence. Dimensions with no size
     will be omitted, though singletons will be included.
     """
-    main_sizes = seq.sizes.copy()
+    main_sizes = dict(seq.sizes)
     main_sizes.pop("p", None)  # remove position
 
     if not seq.stage_positions:

pymmcore_plus/metadata/schema.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, List, Literal, Optional, Tuple, TypedDict, Union
+from typing import Any, Literal, Optional, TypedDict, Union
 
 import useq
 from typing_extensions import NotRequired
@@ -17,7 +17,7 @@ __all__ = [
     "SystemInfo",
 ]
 
-AffineTuple = Tuple[float, float, float, float, float, float]
+AffineTuple = tuple[float, float, float, float, float, float]
 
 
 class PropertyInfo(TypedDict):
@@ -53,9 +53,9 @@ class PropertyInfo(TypedDict):
     value: Optional[str]
     data_type: Literal["undefined", "float", "int", "str"]
     is_read_only: bool
-    allowed_values: NotRequired[Tuple[str, ...]]
+    allowed_values: NotRequired[tuple[str, ...]]
     is_pre_init: NotRequired[bool]
-    limits: NotRequired[Tuple[float, float]]
+    limits: NotRequired[tuple[float, float]]
     sequenceable: NotRequired[bool]
     sequence_max_length: NotRequired[int]
     # device_label: str
@@ -104,14 +104,14 @@ class DeviceInfo(TypedDict):
     name: str
     type: str
     description: str
-    properties: Tuple[PropertyInfo, ...]
+    properties: tuple[PropertyInfo, ...]
 
     # hub devices and non-peripheral devices will have no parent_label
     parent_label: NotRequired[str]
     # state device only
-    labels: NotRequired[Tuple[str, ...]]
+    labels: NotRequired[tuple[str, ...]]
     # hub device only
-    child_names: NotRequired[Tuple[str, ...]]
+    child_names: NotRequired[tuple[str, ...]]
     # stage/focus device only
     is_continuous_focus_drive: NotRequired[bool]
     focus_direction: NotRequired[Literal["Unknown", "TowardSample", "AwayFromSample"]]
@@ -159,7 +159,7 @@ class SystemInfo(TypedDict):
     pymmcore_plus_version: str
     mmcore_version: str
     device_api_version: str
-    device_adapter_search_paths: Tuple[str, ...]
+    device_adapter_search_paths: tuple[str, ...]
     system_configuration_file: Optional[str]
     primary_log_file: str
     sequence_buffer_size_mb: int
@@ -215,7 +215,7 @@ class ImageInfo(TypedDict):
     """  # noqa: E501
 
     camera_label: str
-    plane_shape: Tuple[int, ...]
+    plane_shape: tuple[int, ...]
     dtype: str
 
     height: int
@@ -238,8 +238,8 @@ class ImageInfo(TypedDict):
     pixel_size_um: float
     magnification_factor: NotRequired[float]
     pixel_size_affine: NotRequired[AffineTuple]
-    roi: NotRequired[Tuple[int, int, int, int]]
-    multi_roi: NotRequired[Tuple[List[int], List[int], List[int], List[int]]]
+    roi: NotRequired[tuple[int, int, int, int]]
+    multi_roi: NotRequired[tuple[list[int], list[int], list[int], list[int]]]
 
     # # this will be != 1 for things like multi-camera device,
     # # or any "single" device adapter that manages multiple detectors, like PMTs, etc..
@@ -250,7 +250,7 @@ class StagePosition(TypedDict):
     """Represents the position of a single stage device."""
 
     device_label: str
-    position: Union[float, Tuple[float, float]]
+    position: Union[float, tuple[float, float]]
 
 
 class Position(TypedDict):
@@ -276,7 +276,7 @@ class Position(TypedDict):
     x: NotRequired[float]
     y: NotRequired[float]
     z: NotRequired[float]
-    all_stages: NotRequired[List[StagePosition]]
+    all_stages: NotRequired[list[StagePosition]]
 
 
 class PropertyValue(TypedDict):
@@ -312,7 +312,7 @@ class ConfigPreset(TypedDict):
     """
 
     name: str
-    settings: Tuple[PropertyValue, ...]
+    settings: tuple[PropertyValue, ...]
 
 
 class PixelSizeConfigPreset(ConfigPreset):
@@ -350,7 +350,7 @@ class ConfigGroup(TypedDict):
     """
 
     name: str
-    presets: Tuple[ConfigPreset, ...]
+    presets: tuple[ConfigPreset, ...]
 
 
 class SummaryMetaV1(TypedDict):
@@ -395,14 +395,14 @@ class SummaryMetaV1(TypedDict):
     format: Literal["summary-dict"]
     version: Literal["1.0"]
     datetime: NotRequired[str]
-    devices: Tuple[DeviceInfo, ...]
+    devices: tuple[DeviceInfo, ...]
     system_info: SystemInfo
-    image_infos: Tuple[ImageInfo, ...]
-    config_groups: Tuple[ConfigGroup, ...]
-    pixel_size_configs: Tuple[PixelSizeConfigPreset, ...]
+    image_infos: tuple[ImageInfo, ...]
+    config_groups: tuple[ConfigGroup, ...]
+    pixel_size_configs: tuple[PixelSizeConfigPreset, ...]
     position: Position
     mda_sequence: NotRequired[useq.MDASequence]
-    extra: NotRequired[Dict[str, Any]]
+    extra: NotRequired[dict[str, Any]]
 
 
 class FrameMetaV1(TypedDict):
@@ -462,10 +462,10 @@ class FrameMetaV1(TypedDict):
     camera_device: Optional[str]
     exposure_ms: float
     position: Position
-    property_values: Tuple[PropertyValue, ...]
+    property_values: tuple[PropertyValue, ...]
     runner_time_ms: float
     mda_event: NotRequired[useq.MDAEvent]
     hardware_triggered: NotRequired[bool]
     images_remaining_in_buffer: NotRequired[int]
-    camera_metadata: NotRequired[Dict[str, Any]]
-    extra: NotRequired[Dict[str, Any]]
+    camera_metadata: NotRequired[dict[str, Any]]
+    extra: NotRequired[dict[str, Any]]

pymmcore_plus/metadata/serialize.py

@@ -2,10 +2,12 @@ from __future__ import annotations
 
 import json
 import sys
+from collections.abc import Mapping, Sequence
 from contextlib import suppress
 from datetime import timedelta
+from enum import Enum
 from types import MappingProxyType
-from typing import TYPE_CHECKING, Any, Mapping, Sequence
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 
@@ -35,6 +37,8 @@ def encode_hook(obj: Any, raises: bool = True) -> Any:
         return obj.item()
     if isinstance(obj, timedelta):
         return obj.total_seconds()
+    if isinstance(obj, Enum):
+        return obj.value
     if raises:
         raise NotImplementedError(f"Cannot serialize object of type {type(obj)}")
     return obj

pymmcore_plus/model/_config_file.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 import warnings
-from typing import TYPE_CHECKING, Any, Callable, Iterable, Sequence
+from typing import TYPE_CHECKING, Any, Callable
 
 from pymmcore_plus import CFGCommand, DeviceType, FocusDirection, Keyword
 from pymmcore_plus._util import timestamp
@@ -15,6 +15,7 @@ from ._pixel_size_config import DEFAULT_AFFINE, PixelSizePreset
 
 if TYPE_CHECKING:
     import io
+    from collections.abc import Iterable, Sequence
     from typing import TypeAlias
 
     Executor: TypeAlias = Callable[[Microscope, Sequence[str]], None]

pymmcore_plus/model/_config_group.py

@@ -4,7 +4,8 @@ from dataclasses import dataclass, field
 from typing import TYPE_CHECKING, NamedTuple
 
 if TYPE_CHECKING:
-    from typing import Container, Final, MutableMapping
+    from collections.abc import Container, MutableMapping
+    from typing import Final
 
     from typing_extensions import Self  # py311
 

pymmcore_plus/model/_core_device.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from dataclasses import dataclass, field
-from typing import TYPE_CHECKING, Container
+from typing import TYPE_CHECKING
 
 from pymmcore_plus import CMMCorePlus, DeviceType, Keyword
 
@@ -9,6 +9,8 @@ from ._device import Device
 from ._property import Property
 
 if TYPE_CHECKING:
+    from collections.abc import Container
+
     from pymmcore_plus.model._core_link import ErrCallback
 
 CORE = Keyword.CoreDevice.value

pymmcore_plus/model/_core_link.py

@@ -5,8 +5,9 @@ from dataclasses import fields
 from typing import TYPE_CHECKING, Protocol
 
 if TYPE_CHECKING:
+    from collections.abc import Container, Iterable
     from dataclasses import Field
-    from typing import Any, Callable, ClassVar, Container, Iterable, TypeVar
+    from typing import Any, Callable, ClassVar, TypeVar
 
     from typing_extensions import TypeAlias  # py310
 

pymmcore_plus/model/_device.py

@@ -12,7 +12,8 @@ from ._core_link import CoreObject
 from ._property import Property
 
 if TYPE_CHECKING:
-    from typing import Any, Callable, Container, Iterable
+    from collections.abc import Container, Iterable
+    from typing import Any, Callable
 
     from typing_extensions import (
         Self,  # py311

pymmcore_plus/model/_microscope.py

@@ -4,7 +4,7 @@ import os
 from copy import deepcopy
 from dataclasses import dataclass, field, fields
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Callable, Container, Iterable
+from typing import TYPE_CHECKING, Any, Callable
 
 from pymmcore_plus import DeviceType, Keyword
 
@@ -14,6 +14,8 @@ from ._device import AvailableDevice, Device, get_available_devices
 from ._pixel_size_config import PixelSizeGroup
 
 if TYPE_CHECKING:
+    from collections.abc import Container, Iterable
+
     from pymmcore_plus import CMMCorePlus
     from pymmcore_plus.metadata.schema import SummaryMetaV1
 

pymmcore_plus/model/_pixel_size_config.py

@@ -6,7 +6,8 @@ from typing import TYPE_CHECKING
 from ._config_group import ConfigGroup, ConfigPreset, Setting
 
 if TYPE_CHECKING:
-    from typing import Any, Container, Final, Iterable, MutableMapping
+    from collections.abc import Container, Iterable, MutableMapping
+    from typing import Any, Final
 
     from typing_extensions import (
         Self,  # py311

pymmcore_plus/model/_property.py

@@ -8,7 +8,8 @@ from pymmcore_plus import CMMCorePlus, PropertyType
 from ._core_link import CoreObject
 
 if TYPE_CHECKING:
-    from typing import Any, Callable, Container
+    from collections.abc import Container
+    from typing import Any, Callable
 
     from typing_extensions import TypeAlias  # py310
 

{pymmcore_plus-0.11.1.dist-info → pymmcore_plus-0.12.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pymmcore-plus
-Version: 0.11.1
+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'

pymmcore_plus-0.12.0.dist-info/RECORD

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pymmcore_plus-0.11.1.dist-info/RECORD

@@ -1,59 +0,0 @@
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