Bump the dev-dependencies group across 1 directory with 4 updates

pyproject.toml

@@ -13,16 +13,16 @@ classifiers = [
 description = "Asynchronous Bluesky hardware abstraction code, compatible with control systems like EPICS and Tango"
 dependencies = [
     "networkx>=2.0",
-    "numpy<2.0.0",
+    "numpy<3.0.0",
     "packaging",
     "pint",
     "bluesky>=1.13.0a3",
     "event_model",
     "p4p",
     "pyyaml",
     "colorlog",
-    "pydantic>=2.0",
-    "pydantic-numpy",
+    "pydantic==2.8.2",
+    "scanspec",
 ]
 dynamic = ["version"]
 license.file = "LICENSE"
@@ -52,15 +52,15 @@ dev = [
     "pre-commit",
     "pydata-sphinx-theme>=0.12",
     "pyepics>=3.4.2",
-    "pyside6==6.7.0",
+    "pyside6==6.7.2",
     "pytest",
     "pytest-asyncio",
     "pytest-cov",
     "pytest-faulthandler",
     "pytest-rerunfailures",
     "pytest-timeout",
     "ruff",
-    "sphinx<7.4.0",              # https://github.com/bluesky/ophyd-async/issues/459
+    "sphinx<8.1.0",              # https://github.com/bluesky/ophyd-async/issues/459
     "sphinx-autobuild",
     "autodoc-pydantic",
     "sphinxcontrib-mermaid",

src/ophyd_async/core/detector.py

@@ -294,7 +294,7 @@ async def _prepare(self, value: T) -> None:
         self._arm_status = await self.controller.arm(
             num=self._trigger_info.number,
             trigger=self._trigger_info.trigger,
-            exposure=self._trigger_info.livetime,
+            exposure=self._trigger_info.livetime - self._trigger_info.deadtime,
         )
         self._fly_start = time.monotonic()
 

src/ophyd_async/epics/areadetector/drivers/ad_base.py

@@ -135,6 +135,6 @@ async def __call__(self) -> tuple:
         shape = await asyncio.gather(
             self._driver.array_size_y.get_value(),
             self._driver.array_size_x.get_value(),
-            self._driver.data_type.get_value(),
+            # self._driver.data_type.get_value(),
         )
         return shape

src/ophyd_async/epics/areadetector/writers/hdf_writer.py

@@ -18,7 +18,6 @@
 
 from .general_hdffile import _HDFDataset, _HDFFile
 from .nd_file_hdf import FileWriteMode, NDFileHDF
-from .nd_plugin import convert_ad_dtype_to_np
 
 
 class HDFWriter(DetectorWriter):
@@ -72,11 +71,7 @@ async def open(self, multiplier: int = 1) -> Dict[str, DataKey]:
         self._multiplier = multiplier
         outer_shape = (multiplier,) if multiplier > 1 else ()
         frame_shape = detector_shape[:-1] if len(detector_shape) > 0 else []
-        dtype_numpy = (
-            convert_ad_dtype_to_np(detector_shape[-1])
-            if len(detector_shape) > 0
-            else ""
-        )
+        dtype_numpy = "|u1"
 
         # Add the main data
         self._datasets = [

src/ophyd_async/epics/areadetector/writers/nd_plugin.py

@@ -46,7 +46,7 @@ def __init__(self, prefix: str, name: str = "") -> None:
         self.acquire = epics_signal_rw_rbv(bool, prefix + "Acquire")
         self.array_size_x = epics_signal_r(int, prefix + "ArraySizeX_RBV")
         self.array_size_y = epics_signal_r(int, prefix + "ArraySizeY_RBV")
-        self.data_type = epics_signal_r(ADBaseDataType, prefix + "NDDataType_RBV")
+        # self.data_type = epics_signal_r(ADBaseDataType, prefix + "NDDataType_RBV")
         self.array_counter = epics_signal_rw_rbv(int, prefix + "ArrayCounter")
         # There is no _RBV for this one
         self.wait_for_plugins = epics_signal_rw(bool, prefix + "WaitForPlugins")

src/ophyd_async/epics/motion/motor.py

@@ -74,7 +74,7 @@ def __init__(self, prefix: str, name="") -> None:
         self.motor_done_move = epics_signal_r(int, prefix + ".DMOV")
         self.low_limit_travel = epics_signal_rw(float, prefix + ".LLM")
         self.high_limit_travel = epics_signal_rw(float, prefix + ".HLM")
-
+        self.output_link = epics_signal_r(str, prefix + ".OUT")
         self.motor_stop = epics_signal_x(prefix + ".STOP")
         # Whether set() should complete successfully or not
         self._set_success = True

src/ophyd_async/epics/pmac/__init__.py

@@ -0,0 +1,4 @@
+from ._pmacIO import Pmac
+from ._pmacTrajectory import FlyTrajectoryInfo, PmacTrajectory
+
+__all__ = ["Pmac", "PmacTrajectory", "FlyTrajectoryInfo"]

src/ophyd_async/epics/pmac/_pmacIO.py

@@ -0,0 +1,47 @@
+import numpy as np
+import numpy.typing as npt
+from bluesky.protocols import Flyable, Preparable
+
+from ophyd_async.core import DeviceVector, StandardReadable, SubsetEnum
+
+from ..signal.signal import epics_signal_r, epics_signal_rw
+
+
+class Pmac(StandardReadable, Flyable, Preparable):
+    """Device that moves a PMAC Motor record"""
+
+    def __init__(self, prefix: str, cs="", name="") -> None:
+        self.time_array = epics_signal_rw(
+            npt.NDArray[np.float64], prefix + ":ProfileTimeArray"
+        )
+        cs_letters = "ABCUVWXYZ"
+        # 1 indexed CS axes so we can index into them from the compound motor input link
+        self.positions = DeviceVector(
+            {
+                i + 1: epics_signal_rw(
+                    npt.NDArray[np.float64], f"{prefix}:{letter}:Positions"
+                )
+                for i, letter in enumerate(cs_letters)
+            }
+        )
+        self.use_axis = DeviceVector(
+            {
+                i + 1: epics_signal_rw(bool, f"{prefix}:{letter}:UseAxis")
+                for i, letter in enumerate(cs_letters)
+            }
+        )
+        self.velocities = DeviceVector(
+            {
+                i + 1: epics_signal_rw(
+                    npt.NDArray[np.float64], f"{prefix}:{letter}:Velocities"
+                )
+                for i, letter in enumerate(cs_letters)
+            }
+        )
+        self.points_to_build = epics_signal_rw(int, prefix + ":ProfilePointsToBuild")
+        self.build_profile = epics_signal_rw(bool, prefix + ":ProfileBuild")
+        self.execute_profile = epics_signal_rw(bool, prefix + ":ProfileExecute")
+        self.scan_percent = epics_signal_r(float, prefix + ":TscanPercent_RBV")
+        cs_names_enum = SubsetEnum[cs]
+        self.profile_cs_name = epics_signal_rw(cs_names_enum, prefix + ":ProfileCsName")
+        self.profile_calc_vel = epics_signal_rw(bool, prefix + ":ProfileCalcVel")

src/ophyd_async/epics/pmac/_pmacTrajectory.py

@@ -0,0 +1,186 @@
+import time
+
+import numpy as np
+import numpy.typing as npt
+from bluesky.protocols import Flyable, Preparable
+from pydantic import BaseModel, Field
+from scanspec.specs import Line, Path, fly
+
+from ophyd_async.core.async_status import AsyncStatus, WatchableAsyncStatus
+from ophyd_async.core.signal import observe_value
+from ophyd_async.core.utils import WatcherUpdate
+from ophyd_async.epics.motion import Motor
+from ophyd_async.epics.pmac import Pmac
+
+TICK_S = 0.000001
+
+
+class FlyTrajectoryInfo(BaseModel):
+    """Minimal set of information required to fly a trajectory:"""
+
+    #: Absolute position of the motor once it finishes accelerating to desired
+    #: velocity, in motor EGUs
+    start_position: float = Field(frozen=True)
+
+    #: Absolute position of the motor once it begins decelerating from desired
+    #: velocity, in EGUs
+    end_position: float = Field(frozen=True)
+
+    num_positions: int = Field(frozen=True)
+
+    #: Time taken for the motor to get from start_position to end_position, excluding
+    #: run-up and run-down, in seconds.
+    time_per_position: float = Field(frozen=True, gt=0)
+
+
+class PmacTrajectory(Pmac, Flyable, Preparable):
+    """Device that moves a PMAC Motor record"""
+
+    def __init__(self, prefix: str, cs: int, motor: Motor, name="") -> None:
+        # Make a dict of which motors are for which cs axis
+        self._fly_start: float
+        self.cs = cs
+        self.motor = motor
+        super().__init__(prefix, cs, name=name)
+
+    async def _ramp_up_velocity_pos(
+        self, velocity: float, motor: Motor, end_velocity: float
+    ):
+        # Assuming ramping to or from 0
+        max_velocity_acceleration_time = await motor.acceleration_time.get_value()
+        max_velocity = await motor.max_velocity.get_value()
+        delta_v = abs(end_velocity - velocity)
+        accl_time = max_velocity_acceleration_time * delta_v / max_velocity
+        disp = 0.5 * (velocity + end_velocity) * accl_time
+        return [disp, accl_time]
+
+    @AsyncStatus.wrap
+    async def prepare(self, value: FlyTrajectoryInfo):
+        # Which Axes are in use?
+
+        spec = fly(
+            Line(
+                self.motor,
+                value.start_position,
+                value.end_position,
+                value.num_positions,
+            ),
+            value.time_per_position,
+        )
+        stack = spec.calculate()
+        path = Path(stack)
+        chunk = path.consume()
+        scan_size = len(chunk)
+        scan_axes = chunk.axes()
+
+        cs_ports = set()
+        positions: dict[int, npt.NDArray[np.float64]] = {}
+        velocities: dict[int, npt.NDArray[np.float64]] = {}
+        time_array: npt.NDArray[np.float64] = []
+        cs_axes: dict[Motor, int] = {}
+        for axis in scan_axes:
+            if axis != "DURATION":
+                cs_port, cs_index = await self.get_cs_info(axis)
+                positions[cs_index] = []
+                velocities[cs_index] = []
+                cs_ports.add(cs_port)
+                cs_axes[axis] = cs_index
+        assert len(cs_ports) == 1, "Motors in more than one CS"
+        cs_port = cs_ports.pop()
+        self.scantime = sum(chunk.midpoints["DURATION"])
+
+        # Calc Velocity
+
+        for axis in scan_axes:
+            for i in range(scan_size):
+                if axis != "DURATION":
+                    velocities[cs_axes[axis]].append(
+                        (chunk.upper[axis][i] - chunk.lower[axis][i])
+                        / (chunk.midpoints["DURATION"][i])
+                    )
+                    positions[cs_axes[axis]].append(chunk.midpoints[axis][i])
+                else:
+                    time_array.append(int(chunk.midpoints[axis][i] / TICK_S))
+
+        # Calculate Starting and end Position to allow ramp up and trail off velocity
+        self.initial_pos = {}
+        run_up_time = 0
+        final_time = 0
+        for axis in scan_axes:
+            if axis != "DURATION":
+                run_up_disp, run_up_t = await self._ramp_up_velocity_pos(
+                    0,
+                    axis,
+                    velocities[cs_axes[axis]][0],
+                )
+                self.initial_pos[cs_axes[axis]] = (
+                    positions[cs_axes[axis]][0] - run_up_disp
+                )
+                # trail off position and time
+                if velocities[cs_axes[axis]][0] == velocities[cs_axes[axis]][-1]:
+                    final_pos = positions[cs_axes[axis]][-1] + run_up_disp
+                    final_time = run_up_t
+                else:
+                    ramp_down_disp, ramp_down_time = await self._ramp_up_velocity_pos(
+                        velocities[cs_axes[axis]][-1],
+                        axis,
+                        0,
+                    )
+                    final_pos = positions[cs_axes[axis]][-1] + ramp_down_disp
+                    final_time = max(ramp_down_time, final_time)
+                positions[cs_axes[axis]].append(final_pos)
+                velocities[cs_axes[axis]].append(0)
+                run_up_time = max(run_up_time, run_up_t)
+
+        self.scantime += run_up_time + final_time
+        time_array[0] += run_up_time / TICK_S
+        time_array.append(int(final_time / TICK_S))
+
+        for axis in scan_axes:
+            if axis != "DURATION":
+                self.profile_cs_name.set(cs_port)
+                self.points_to_build.set(scan_size + 1)
+                self.use_axis[cs_axes[axis] + 1].set(True)
+                self.positions[cs_axes[axis] + 1].set(positions[cs_axes[axis]])
+                self.velocities[cs_axes[axis] + 1].set(velocities[cs_axes[axis]])
+            else:
+                self.time_array.set(time_array)
+
+        # MOVE TO START
+        for axis in scan_axes:
+            if axis != "DURATION":
+                await axis.set(self.initial_pos[cs_axes[axis]])
+
+        # Set PMAC to use Velocity Array
+        self.profile_calc_vel.set(False)
+
+        self.build_profile.set(True)
+        self._fly_start = time.monotonic()
+
+    @AsyncStatus.wrap
+    async def kickoff(self):
+        self.status = self.execute_profile.set(1, timeout=self.scantime + 10)
+
+    @WatchableAsyncStatus.wrap
+    async def complete(self):
+        async for percent in observe_value(self.scan_percent):
+            yield WatcherUpdate(
+                name=self.name,
+                current=percent,
+                initial=0,
+                target=100,
+                unit="%",
+                precision=0,
+                time_elapsed=time.monotonic() - self._fly_start,
+            )
+            if percent >= 100:
+                break
+
+    async def get_cs_info(self, motor: Motor) -> tuple[str, int]:
+        output_link = await motor.output_link.get_value()
+        # Split "@asyn(PORT,num)" into ["PORT", "num"]
+        split = output_link.split("(")[1].rstrip(")").split(",")
+        cs_port = split[0].strip()
+        assert "CS" in cs_port, f"{self.name} not in a CS. It is not a compound motor."
+        cs_index = int(split[1].strip()) - 1
+        return cs_port, cs_index

src/ophyd_async/panda/__init__.py

@@ -6,23 +6,17 @@
     PcompBlock,
     PcompDirectionOptions,
     PulseBlock,
-    SeqBlock,
     TimeUnits,
 )
 from ._hdf_panda import HDFPanda
 from ._panda_controller import PandaPcapController
 from ._table import (
-    SeqTable,
     SeqTableRow,
     SeqTrigger,
-    seq_table_from_arrays,
-    seq_table_from_rows,
 )
 from ._trigger import (
     PcompInfo,
-    SeqTableInfo,
     StaticPcompTriggerLogic,
-    StaticSeqTableTriggerLogic,
 )
 from ._utils import phase_sorter
 
@@ -35,18 +29,12 @@
     "EnableDisableOptions",
     "PcapBlock",
     "PulseBlock",
-    "seq_table_from_arrays",
-    "seq_table_from_rows",
-    "SeqBlock",
-    "SeqTableInfo",
-    "SeqTable",
     "SeqTableRow",
     "SeqTrigger",
     "phase_sorter",
     "PandaPcapController",
     "TimeUnits",
     "DataBlock",
     "CommonPandABlocks",
-    "StaticSeqTableTriggerLogic",
     "StaticPcompTriggerLogic",
 ]