pymmcore-plus 0.13.4__tar.gz → 0.13.6__tar.gz

{pymmcore_plus-0.13.4 → pymmcore_plus-0.13.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymmcore-plus
-Version: 0.13.4
+Version: 0.13.6
 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
@@ -30,7 +30,7 @@ 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: tensorstore<=0.1.71
 Requires-Dist: typer>=0.4.2
 Requires-Dist: typing-extensions
 Requires-Dist: useq-schema>=0.7.0
@@ -40,11 +40,12 @@ Requires-Dist: typer>=0.4.2; extra == 'cli'
 Provides-Extra: dev
 Requires-Dist: ipython; extra == 'dev'
 Requires-Dist: mypy; extra == 'dev'
-Requires-Dist: pdbpp; extra == 'dev'
+Requires-Dist: pdbpp; (sys_platform != 'win32') and 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-autorefs==1.3.1; extra == 'docs'
 Requires-Dist: mkdocs-material; extra == 'docs'
 Requires-Dist: mkdocs-typer==0.0.3; extra == 'docs'
 Requires-Dist: mkdocs>=1.4; extra == 'docs'
@@ -62,8 +63,10 @@ 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: mm-device-adapters; (sys_platform == 'darwin' and platform_machine == 'x86_64') and extra == 'test'
+Requires-Dist: mm-device-adapters; (sys_platform == 'win32') and extra == 'test'
 Requires-Dist: msgpack; extra == 'test'
-Requires-Dist: msgspec; (python_version < '3.13') and extra == 'test'
+Requires-Dist: msgspec; extra == 'test'
 Requires-Dist: pytest-cov>=4; extra == 'test'
 Requires-Dist: pytest-qt>=4; extra == 'test'
 Requires-Dist: pytest>=7.3.2; extra == 'test'
@@ -99,7 +102,7 @@ environments**.
   [CMMCorePlus
   documentation](https://pymmcore-plus.github.io/pymmcore-plus/api/cmmcoreplus/)
   for details.
-- `pymmcore-plus` includes an [acquisition engine](https://pymmcore-plus.github.io/pymmcore-plus/guides/mda_engine/) 
+- `pymmcore-plus` includes an [acquisition engine](https://pymmcore-plus.github.io/pymmcore-plus/guides/mda_engine/)
   that drives micro-manager for conventional multi-dimensional experiments. It accepts an
   [MDASequence](https://pymmcore-plus.github.io/useq-schema/schema/sequence/)
   from [useq-schema](https://pymmcore-plus.github.io/useq-schema/) for
@@ -112,7 +115,7 @@ environments**.
 
 ## Documentation
 
-https://pymmcore-plus.github.io/pymmcore-plus/
+<https://pymmcore-plus.github.io/pymmcore-plus/>
 
 ## Why not just use `pymmcore` directly?
 
@@ -139,20 +142,22 @@ python users are accustomed to. This library:
 
 ## How does this relate to `Pycro-Manager`?
 
-[Pycro-Manager](https://github.com/micro-manager/pycro-manager) is an impressive
-library written by Henry Pinkard designed to make it easier to work with and
-control the Java Micro-manager application using python. As such, it requires
-Java to be installed and running in the background (either via the micro-manager
-GUI application directly, or via a headless process). The python half
-communicates with the Java half using ZeroMQ messaging.
+[Pycro-Manager](https://github.com/micro-manager/pycro-manager) is designed to
+make it easier to work with and control the Java Micro-manager application
+(MMStudio) using python. As such, it requires Java to be installed and for
+MMStudio to be running a server in another process. The python half communicates
+with the Java half using ZeroMQ messaging.
 
 **In brief**: while `Pycro-Manager` provides a python API to control the Java
 Micro-manager application (which in turn controls the C++ core), `pymmcore-plus`
 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.
+Java in the loop. Each has its own advantages and disadvantages! With
+pycro-manager you retain the entire existing micro-manager ecosystem
+and GUI application. With pymmcore-plus, the entire thing is python: you
+don't need to install Java, and you have direct access to the memory buffers
+used by the C++ core.  Work on recreating the gui application in python
+being done in [`pymmcore-widgets`](https://github.com/pymmcore-plus/pymmcore-widgets)
+and [`pymmcore-gui`](https://github.com/pymmcore-plus/pymmcore-gui).
 
 ## Quickstart
 
@@ -191,7 +196,7 @@ mmcore install
 
 (you can also download these manually from [micro-manager.org](https://micro-manager.org/Micro-Manager_Nightly_Builds))
 
-_See [installation documentation ](https://pymmcore-plus.github.io/pymmcore-plus/install/) for more details._
+_See [installation documentation](https://pymmcore-plus.github.io/pymmcore-plus/install/) for more details._
 
 ### Usage
 

{pymmcore_plus-0.13.4 → pymmcore_plus-0.13.6}/README.md

@@ -22,7 +22,7 @@ environments**.
   [CMMCorePlus
   documentation](https://pymmcore-plus.github.io/pymmcore-plus/api/cmmcoreplus/)
   for details.
-- `pymmcore-plus` includes an [acquisition engine](https://pymmcore-plus.github.io/pymmcore-plus/guides/mda_engine/) 
+- `pymmcore-plus` includes an [acquisition engine](https://pymmcore-plus.github.io/pymmcore-plus/guides/mda_engine/)
   that drives micro-manager for conventional multi-dimensional experiments. It accepts an
   [MDASequence](https://pymmcore-plus.github.io/useq-schema/schema/sequence/)
   from [useq-schema](https://pymmcore-plus.github.io/useq-schema/) for
@@ -35,7 +35,7 @@ environments**.
 
 ## Documentation
 
-https://pymmcore-plus.github.io/pymmcore-plus/
+<https://pymmcore-plus.github.io/pymmcore-plus/>
 
 ## Why not just use `pymmcore` directly?
 
@@ -62,20 +62,22 @@ python users are accustomed to. This library:
 
 ## How does this relate to `Pycro-Manager`?
 
-[Pycro-Manager](https://github.com/micro-manager/pycro-manager) is an impressive
-library written by Henry Pinkard designed to make it easier to work with and
-control the Java Micro-manager application using python. As such, it requires
-Java to be installed and running in the background (either via the micro-manager
-GUI application directly, or via a headless process). The python half
-communicates with the Java half using ZeroMQ messaging.
+[Pycro-Manager](https://github.com/micro-manager/pycro-manager) is designed to
+make it easier to work with and control the Java Micro-manager application
+(MMStudio) using python. As such, it requires Java to be installed and for
+MMStudio to be running a server in another process. The python half communicates
+with the Java half using ZeroMQ messaging.
 
 **In brief**: while `Pycro-Manager` provides a python API to control the Java
 Micro-manager application (which in turn controls the C++ core), `pymmcore-plus`
 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.
+Java in the loop. Each has its own advantages and disadvantages! With
+pycro-manager you retain the entire existing micro-manager ecosystem
+and GUI application. With pymmcore-plus, the entire thing is python: you
+don't need to install Java, and you have direct access to the memory buffers
+used by the C++ core.  Work on recreating the gui application in python
+being done in [`pymmcore-widgets`](https://github.com/pymmcore-plus/pymmcore-widgets)
+and [`pymmcore-gui`](https://github.com/pymmcore-plus/pymmcore-gui).
 
 ## Quickstart
 
@@ -114,7 +116,7 @@ mmcore install
 
 (you can also download these manually from [micro-manager.org](https://micro-manager.org/Micro-Manager_Nightly_Builds))
 
-_See [installation documentation ](https://pymmcore-plus.github.io/pymmcore-plus/install/) for more details._
+_See [installation documentation](https://pymmcore-plus.github.io/pymmcore-plus/install/) for more details._
 
 ### Usage
 

{pymmcore_plus-0.13.4 → pymmcore_plus-0.13.6}/pyproject.toml

@@ -39,9 +39,10 @@ dependencies = [
     "numpy >=1.17.3",
     "psygnal >=0.7",
     "pymmcore >=10.7.0.71.0",
-    "typing-extensions",                    # not actually required at runtime
+    "typing-extensions",      # not actually required at runtime
     "useq-schema >=0.7.0",
-    "tensorstore; python_version < '3.13'",
+    # until https://github.com/google/tensorstore/issues/217 is resolved
+    "tensorstore <= 0.1.71",
     # cli requirements included by default for now
     "typer >=0.4.2",
     "rich >=10.2.0",
@@ -57,7 +58,7 @@ 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'",
+    "msgspec",
     "msgpack",
     "pytest-cov >=4",
     "pytest-qt >=4",
@@ -68,12 +69,22 @@ test = [
     "tifffile >=2021.6.14",
     "zarr >=2.2,<3",
     "xarray",
+    "mm-device-adapters; sys_platform == 'win32'",
+    "mm-device-adapters; sys_platform == 'darwin' and platform_machine == 'x86_64'",
+]
+dev = [
+    "ipython",
+    "mypy",
+    "pdbpp; sys_platform != 'win32'",
+    "pre-commit",
+    "ruff",
+    "tensorstore-stubs",
 ]
-dev = ["ipython", "mypy", "pdbpp", "pre-commit", "ruff", "tensorstore-stubs"]
 docs = [
     "mkdocs >=1.4",
     "mkdocs-material",
     "mkdocstrings ==0.22.0",
+    "mkdocs-autorefs ==1.3.1",
     "mkdocstrings-python ==1.1.2",
     "mkdocs-typer ==0.0.3",
     # "griffe @ git+https://github.com/tlambert03/griffe@recursion"
@@ -193,4 +204,4 @@ ignore = [
 ]
 
 [tool.typos.default]
-extend-ignore-identifiers-re = ["(?i)nd2?.*", "(?i)ome", "anager"]
+extend-ignore-identifiers-re = ["(?i)nd2?.*", "(?i)ome", "anager", "ba"]

{pymmcore_plus-0.13.4 → pymmcore_plus-0.13.6}/src/pymmcore_plus/_cli.py

@@ -8,6 +8,7 @@ from contextlib import suppress
 from pathlib import Path
 from typing import Optional, Union, cast
 
+from pymmcore_plus._util import get_device_interface_version
 from pymmcore_plus.core._device import Device
 from pymmcore_plus.core._mmcore_plus import CMMCorePlus
 
@@ -114,9 +115,15 @@ def _list() -> None:
         for parent, items in found.items():
             print(f":file_folder:[bold green] {parent}")
             for item in items:
+                version = ""
+                for _lib in (parent / item).glob("*_dal_*"):
+                    with suppress(Exception):
+                        div = get_device_interface_version(_lib)
+                        version = f" (Dev. Interface {div})"
+                        break
                 bullet = "   [bold yellow]*" if first else "   •"
                 using = " [bold blue](active)" if first else ""
-                print(f"{bullet} [cyan]{item}{using}")
+                print(f"{bullet} [cyan]{item}{version}{using}")
                 first = False
     else:
         print(":x: [bold red]There are no pymmcore-plus Micro-Manager files.")
@@ -157,7 +164,7 @@ def install(
         help="Installation directory.",
     ),
     release: str = typer.Option(
-        "latest", "-r", "--release", help="Release date. e.g. 20210201"
+        "latest-compatible", "-r", "--release", help="Release date. e.g. 20210201"
     ),
     plain_output: bool = typer.Option(
         False,
@@ -289,7 +296,7 @@ def run(
         mda.setdefault("channels", []).append(_c)
     if channel_group is not None:
         for c in mda.get("channels", []):
-            cast(dict, c)["group"] = channel_group
+            cast("dict", c)["group"] = channel_group
 
     # this will raise if anything has gone wrong.
     _mda = MDASequence(**mda)

pymmcore_plus-0.13.6/src/pymmcore_plus/_pymmcore.py

@@ -0,0 +1,30 @@
+"""Internal module to choose between pymmcore and pymmcore-nano."""
+
+import re
+from typing import NamedTuple
+
+try:
+    from pymmcore_nano import *  # noqa F403
+    from pymmcore_nano import __version__
+
+    BACKEND = "pymmcore-nano"
+    NANO = True
+except ImportError:
+    from pymmcore import *  # noqa F403
+    from pymmcore import __version__
+
+    BACKEND = "pymmcore"
+    NANO = False
+
+
+class VersionInfo(NamedTuple):
+    """Version info for the backend."""
+
+    major: int
+    minor: int
+    micro: int
+    device_interface: int
+    build: int
+
+
+version_info = VersionInfo(*(int(x) for x in re.findall(r"\d+", __version__)))

{pymmcore_plus-0.13.4 → pymmcore_plus-0.13.6}/src/pymmcore_plus/_util.py

@@ -94,7 +94,7 @@ def find_micromanager(return_first: bool = True) -> str | None | list[str]:
     """
     from ._logger import logger
 
-    # we use a dict here to avoid duplicates
+    # we use a dict here to avoid duplicates, while retaining order
     full_list: dict[str, None] = {}
 
     # environment variable takes precedence
@@ -114,13 +114,42 @@ def find_micromanager(return_first: bool = True) -> str | None | list[str]:
                 return path
             full_list[path] = None
 
+    # then look for mm-device-adapters
+    with suppress(ImportError):
+        import mm_device_adapters
+
+        from . import _pymmcore
+
+        mm_dev_div = mm_device_adapters.__version__.split(".")[0]
+        pymm_div = str(_pymmcore.version_info.device_interface)
+
+        if pymm_div != mm_dev_div:  # pragma: no cover
+            warnings.warn(
+                "mm-device-adapters installed, but its device interface "
+                f"version ({mm_dev_div}) "
+                f"does not match the device interface version of {_pymmcore.BACKEND}"
+                f"({pymm_div}). You may wish to run"
+                f" `pip install --force-reinstall mm-device-adapters=={pymm_div}`. "
+                "mm-device-adapters will be ignored.",
+                stacklevel=2,
+            )
+        else:
+            path = mm_device_adapters.device_adapter_path()
+            if return_first:
+                logger.debug("using MM path from mm-device-adapters: %s", path)
+                return str(path)
+            full_list[path] = None
+
     # then look in user_data_dir
     _folders = (p for p in USER_DATA_MM_PATH.glob("Micro-Manager*") if p.is_dir())
-    user_install = sorted(_folders, reverse=True)
-    if user_install:
-        if return_first:
-            logger.debug("using MM path from user install: %s", user_install[0])
-            return str(user_install[0])
+    if user_install := sorted(_folders, reverse=True):
+        if return_first and (
+            first := next(
+                (x for x in user_install if _mm_path_has_compatible_div(x)), None
+            )
+        ):
+            logger.debug("using MM path from user install: %s", first)
+            return str(first)
         for x in user_install:
             full_list[str(x)] = None
 
@@ -130,9 +159,13 @@ def find_micromanager(return_first: bool = True) -> str | None | list[str]:
         p for p in PYMMCORE_PLUS_PATH.glob(f"**/Micro-Manager*{sfx}") if p.is_dir()
     ]
     if local_install:
-        if return_first:
-            logger.debug("using MM path from local install: %s", local_install[0])
-            return str(local_install[0])
+        if return_first and (
+            first := next(
+                (x for x in local_install if _mm_path_has_compatible_div(x)), None
+            )
+        ):  # pragma: no cover
+            logger.debug("using MM path from local install: %s", first)
+            return str(first)
         for x in local_install:
             full_list[str(x)] = None
 
@@ -153,8 +186,9 @@ def find_micromanager(return_first: bool = True) -> str | None | list[str]:
                 "could not find micromanager directory. Please run 'mmcore install'"
             )
             return None
-        logger.debug("using MM path found in applications: %s", pth)
-        return str(pth)
+        if _mm_path_has_compatible_div(pth):  # pragma: no cover
+            logger.debug("using MM path found in applications: %s", pth)
+            return str(pth)
     if pth is not None:
         full_list[str(pth)] = None
     return list(full_list)
@@ -229,15 +263,15 @@ def _qt_app_is_running() -> bool:
     return False  # pragma: no cover
 
 
-MMCORE_PLUS_SIGNALS_BACKEND = "MMCORE_PLUS_SIGNALS_BACKEND"
+PYMM_SIGNALS_BACKEND = "PYMM_SIGNALS_BACKEND"
 
 
 def signals_backend() -> Literal["qt", "psygnal"]:
     """Return the name of the event backend to use."""
-    env_var = os.environ.get(MMCORE_PLUS_SIGNALS_BACKEND, "auto").lower()
+    env_var = os.environ.get(PYMM_SIGNALS_BACKEND, "auto").lower()
     if env_var not in {"qt", "psygnal", "auto"}:
         warnings.warn(
-            f"{MMCORE_PLUS_SIGNALS_BACKEND} must be one of ['qt', 'psygnal', 'auto']. "
+            f"{PYMM_SIGNALS_BACKEND} must be one of ['qt', 'psygnal', 'auto']. "
             f"not: {env_var!r}. Using 'auto'.",
             stacklevel=1,
         )
@@ -250,7 +284,7 @@ def signals_backend() -> Literal["qt", "psygnal"]:
         if qt_app_running or list(_imported_qt_modules()):
             return "qt"
         warnings.warn(
-            f"{MMCORE_PLUS_SIGNALS_BACKEND} set to 'qt', but no Qt app is running. "
+            f"{PYMM_SIGNALS_BACKEND} set to 'qt', but no Qt app is running. "
             "Falling back to 'psygnal'.",
             stacklevel=1,
         )
@@ -618,3 +652,34 @@ def timestamp() -> str:
     with suppress(Exception):
         now = now.astimezone()
     return now.isoformat()
+
+
+def get_device_interface_version(lib_path: str | Path) -> int:
+    """Return the device interface version from the given library path."""
+    import ctypes
+
+    if sys.platform.startswith("win"):
+        lib = ctypes.WinDLL(lib_path)
+    else:
+        lib = ctypes.CDLL(lib_path)
+
+    try:
+        func = lib.GetDeviceInterfaceVersion
+    except AttributeError:
+        raise RuntimeError(
+            f"Function 'GetDeviceInterfaceVersion' not found in {lib_path}"
+        ) from None
+
+    func.restype = ctypes.c_long
+    func.argtypes = []
+    return func()  # type: ignore[no-any-return]
+
+
+def _mm_path_has_compatible_div(folder: Path | str) -> bool:
+    from . import _pymmcore
+
+    div = _pymmcore.version_info.device_interface
+    for lib_path in Path(folder).glob("*mmgr_dal*"):
+        with suppress(Exception):
+            return get_device_interface_version(lib_path) == div
+    return False  # pragma: no cover

{pymmcore_plus-0.13.4 → pymmcore_plus-0.13.6}/src/pymmcore_plus/core/_constants.py

@@ -94,6 +94,14 @@ class CFGCommand(str, Enum):
     PixelSizeAffine = pymmcore.g_CFGCommand_PixelSizeAffine
     ParentID = pymmcore.g_CFGCommand_ParentID
     FocusDirection = pymmcore.g_CFGCommand_FocusDirection
+
+    if hasattr(pymmcore, "g_CFGCommand_PixelSizedxdz"):
+        PixelSize_dxdz = pymmcore.g_CFGCommand_PixelSizedxdz
+    if hasattr(pymmcore, "g_CFGCommand_PixelSizedydz"):
+        PixelSize_dydz = pymmcore.g_CFGCommand_PixelSizedydz
+    if hasattr(pymmcore, "g_CFGCommand_PixelSizeOptimalZUm"):
+        PixelSize_OptimalZUm = pymmcore.g_CFGCommand_PixelSizeOptimalZUm
+
     #
     FieldDelimiters = pymmcore.g_FieldDelimiters
 

{pymmcore_plus-0.13.4 → pymmcore_plus-0.13.6}/src/pymmcore_plus/core/_metadata.py

@@ -20,8 +20,7 @@ class Metadata(pymmcore.Metadata):
     def __init__(self, *args: Any, **kwargs: Any) -> None:
         super().__init__()
         if args and isinstance(args[0], Mapping):
-            for k, v in args[0].items():
-                self[k] = v
+            kwargs = {**args[0], **kwargs}
         for k, v in kwargs.items():
             self[k] = v
 
@@ -76,15 +75,19 @@ class Metadata(pymmcore.Metadata):
         return json.dumps(dict(self))
 
     def keys(self) -> KeysView[str]:
-        return cast(KeysView, metadata_keys(self))
+        return cast("KeysView", metadata_keys(self))
 
     def items(self) -> ItemsView[str, str]:
-        return cast(ItemsView, metadata_items(self))
+        return cast("ItemsView", metadata_items(self))
 
     def values(self) -> ValuesView[str]:
-        return cast(ValuesView, metadata_values(self))
+        return cast("ValuesView", metadata_values(self))
 
 
 metadata_keys = new_class("metadata_keys", (KeysView,), {})
 metadata_items = new_class("metadata_items", (ItemsView,), {})
 metadata_values = new_class("metadata_values", (ValuesView,), {})
+
+# Register the new classes with the `collections.abc` module
+# so that isistance() works as expected.
+Mapping.register(Metadata)