Move the basic parameter model components to MXB (#1537)

* add mxb workspace

* move parameter components to mx-bluesky

* remove dependency on semver

* update mxb pin

.vscode/hyperion-mx-bluesky.code-workspace

@@ -0,0 +1,23 @@
+{
+ "folders": [
+ {
+ "path": ".."
+ },
+ {
+ "path": "../../dodal"
+ },
+ {
+ "path": "../../mx-bluesky"
+ }
+ ],
+ "settings": {
+ "python.languageServer": "Pylance",
+ "terminal.integrated.gpuAcceleration": "off",
+ "esbonio.sphinx.confDir": "",
+ "[python]": {
+ "editor.defaultFormatter": "ms-python.black-formatter"
+ },
+ "python.formatting.provider": "none",
+ "python.analysis.enablePytestExtra": false
+ }
+}

setup.cfg

@@ -31,7 +31,6 @@ install_requires =
  pyzmq
  scanspec
  scipy
- semver
  #
  # These dependencies may be issued as pre-release versions and should have a pin constraint
  # as by default pip-install will not upgrade to a pre-release.
@@ -41,6 +40,7 @@ install_requires =
  ophyd-async >= 0.3a5
  bluesky >= 1.13.0a4
  blueapi >= 0.4.3-rc1
+ mx-bluesky @ git+https://github.com/DiamondLightSource/mx-bluesky.git@0492e92f75eefa8885be59dde3eff323c1ea81c2
  dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git
 
 [options.entry_points]

src/hyperion/experiment_plans/oav_snapshot_plan.py

@@ -8,9 +8,9 @@
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.oav_parameters import OAVParameters
 from dodal.devices.smargon import Smargon
+from mx_bluesky.parameters import WithSnapshot
 
 from hyperion.device_setup_plans.setup_oav import setup_general_oav_params
-from hyperion.parameters.components import WithSnapshot
 from hyperion.parameters.constants import DocDescriptorNames
 
 OAV_SNAPSHOT_SETUP_GROUP = "oav_snapshot_setup"

src/hyperion/external_interaction/callbacks/rotation/ispyb_callback.py

@@ -3,6 +3,8 @@
 from collections.abc import Sequence
 from typing import TYPE_CHECKING, Any, Callable, Optional
 
+from mx_bluesky.parameters import IspybExperimentType
+
 from hyperion.external_interaction.callbacks.common.ispyb_mapping import (
  populate_data_collection_group,
  populate_remaining_data_collection_info,
@@ -23,7 +25,6 @@
  StoreInIspyb,
 )
 from hyperion.log import ISPYB_LOGGER, set_dcgid_tag
-from hyperion.parameters.components import IspybExperimentType
 from hyperion.parameters.constants import CONST
 from hyperion.parameters.rotation import RotationScan
 

src/hyperion/parameters/components.py

@@ -3,19 +3,15 @@
 import datetime
 import json
 from abc import abstractmethod
-from enum import StrEnum
 from pathlib import Path
-from typing import Sequence, SupportsInt, TypeVar
+from typing import TypeVar
 
-from dodal.devices.aperturescatterguard import AperturePositionGDANames
 from dodal.devices.detector import (
- DetectorParams,
  TriggerMode,
 )
+from mx_bluesky.parameters import DiffractionExperiment, ParameterVersion, WithSample
 from numpy.typing import NDArray
-from pydantic import BaseModel, Extra, Field, root_validator, validator
-from scanspec.core import AxesPoints
-from semver import Version
+from pydantic import BaseModel, Extra, Field, validator
 
 from hyperion.external_interaction.config_server import FeatureFlags
 from hyperion.external_interaction.ispyb.ispyb_dataclass import (
@@ -26,85 +22,9 @@
 T = TypeVar("T")
 
 
-class ParameterVersion(Version):
- @classmethod
- def _parse(cls, version):
- if isinstance(version, cls):
- return version
- return cls.parse(version)
-
- @classmethod
- def __get_validators__(cls):
- """Return a list of validator methods for pydantic models."""
- yield cls._parse
-
- @classmethod
- def __modify_schema__(cls, field_schema):
- """Inject/mutate the pydantic field schema in-place."""
- field_schema.update(examples=["1.0.2", "2.15.3-alpha", "21.3.15-beta+12345"])
-
-
 PARAMETER_VERSION = ParameterVersion.parse("5.0.0")
 
 
-class RotationAxis(StrEnum):
- OMEGA = "omega"
- PHI = "phi"
- CHI = "chi"
- KAPPA = "kappa"
-
-
-class XyzAxis(StrEnum):
- X = "sam_x"
- Y = "sam_y"
- Z = "sam_z"
-
-
-class IspybExperimentType(StrEnum):
- # Enum values from ispyb column data type
- SAD = "SAD" # at or slightly above the peak
- SAD_INVERSE_BEAM = "SAD - Inverse Beam"
- OSC = "OSC" # "native" (in the absence of a heavy atom)
- COLLECT_MULTIWEDGE = (
- "Collect - Multiwedge" # "poorly determined" ~ EDNA complex strategy???
- )
- MAD = "MAD"
- HELICAL = "Helical"
- MULTI_POSITIONAL = "Multi-positional"
- MESH = "Mesh"
- BURN = "Burn"
- MAD_INVERSE_BEAM = "MAD - Inverse Beam"
- CHARACTERIZATION = "Characterization"
- DEHYDRATION = "Dehydration"
- TOMO = "tomo"
- EXPERIMENT = "experiment"
- EM = "EM"
- PDF = "PDF"
- PDF_BRAGG = "PDF+Bragg"
- BRAGG = "Bragg"
- SINGLE_PARTICLE = "single particle"
- SERIAL_FIXED = "Serial Fixed"
- SERIAL_JET = "Serial Jet"
- STANDARD = "Standard" # Routine structure determination experiment
- TIME_RESOLVED = "Time Resolved" # Investigate the change of a system over time
- DLS_ANVIL_HP = "Diamond Anvil High Pressure" # HP sample environment pressure cell
- CUSTOM = "Custom" # Special or non-standard data collection
- XRF_MAP = "XRF map"
- ENERGY_SCAN = "Energy scan"
- XRF_SPECTRUM = "XRF spectrum"
- XRF_MAP_XAS = "XRF map xas"
- MESH_3D = "Mesh3D"
- SCREENING = "Screening"
- STILL = "Still"
- SSX_CHIP = "SSX-Chip"
- SSX_JET = "SSX-Jet"
-
- # Aliases for historic hyperion experiment type mapping
- ROTATION = "SAD"
- GRIDSCAN_2D = "mesh"
- GRIDSCAN_3D = "Mesh3D"
-
-
 class HyperionParameters(BaseModel):
  class Config:
  arbitrary_types_allowed = True
@@ -140,128 +60,32 @@ def from_json(cls, input: str | None, *, allow_extras: bool = False):
  return params
 
 
-class WithSnapshot(BaseModel):
- snapshot_directory: Path
- snapshot_omegas_deg: list[float] | None
-
- @property
- def take_snapshots(self) -> bool:
- return bool(self.snapshot_omegas_deg)
-
-
-class DiffractionExperiment(HyperionParameters, WithSnapshot):
+class HyperionDiffractionExperiment(DiffractionExperiment, HyperionParameters):
  """For all experiments which use beam"""
 
- visit: str = Field(min_length=1)
- file_name: str = Field(pattern=r"[\w]{2}[\d]+-[\d]+")
- exposure_time_s: float = Field(gt=0)
- comment: str = Field(default="")
- beamline: str = Field(default=CONST.I03.BEAMLINE, pattern=r"BL\d{2}[BIJS]")
+ beamline: str = Field(default=CONST.I03.BEAMLINE, regex=r"BL\d{2}[BIJS]")
  insertion_prefix: str = Field(
- default=CONST.I03.INSERTION_PREFIX, pattern=r"SR\d{2}[BIJS]"
+ default=CONST.I03.INSERTION_PREFIX, regex=r"SR\d{2}[BIJS]"
  )
  det_dist_to_beam_converter_path: str = Field(
  default=CONST.PARAM.DETECTOR.BEAM_XY_LUT_PATH
  )
  zocalo_environment: str = Field(default=CONST.ZOCALO_ENV)
  trigger_mode: TriggerMode = Field(default=TriggerMode.FREE_RUN)
- detector_distance_mm: float | None = Field(default=None, gt=0)
- demand_energy_ev: float | None = Field(default=None, gt=0)
- run_number: int | None = Field(default=None, ge=0)
- selected_aperture: AperturePositionGDANames | None = Field(default=None)
- transmission_frac: float = Field(default=0.1)
- ispyb_experiment_type: IspybExperimentType
- storage_directory: str
-
- @root_validator(pre=True)
- def validate_snapshot_directory(cls, values):
- snapshot_dir = values.get(
- "snapshot_directory", Path(values["storage_directory"], "snapshots")
- )
- values["snapshot_directory"] = (
- snapshot_dir if isinstance(snapshot_dir, Path) else Path(snapshot_dir)
- )
- return values
 
  @property
  def visit_directory(self) -> Path:
  return (
  Path(CONST.I03.BASE_DATA_DIR) / str(datetime.date.today().year) / self.visit
  )
 
- @property
- def num_images(self) -> int:
- return 0
-
- @property
- @abstractmethod
- def detector_params(self) -> DetectorParams: ...
-
  @property
  @abstractmethod
  def ispyb_params(self) -> IspybParams: # Soon to remove
  ...
 
 
-class WithScan(BaseModel):
- """For experiments where the scan is known"""
-
- @property
- @abstractmethod
- def scan_points(self) -> AxesPoints: ...
-
- @property
- @abstractmethod
- def num_images(self) -> int: ...
-
-
-class SplitScan(BaseModel):
- @property
- @abstractmethod
- def scan_indices(self) -> Sequence[SupportsInt]:
- """Should return the first index of each scan (i.e. for each nexus file)"""
- ...
-
-
-class WithSample(BaseModel):
- sample_id: int
- sample_puck: int | None = None
- sample_pin: int | None = None
-
-
-class DiffractionExperimentWithSample(DiffractionExperiment, WithSample): ...
-
-
-class WithOavCentring(BaseModel):
- oav_centring_file: str = Field(default=CONST.I03.OAV_CENTRING_FILE)
-
-
-class OptionalXyzStarts(BaseModel):
- x_start_um: float | None = None
- y_start_um: float | None = None
- z_start_um: float | None = None
-
-
-class XyzStarts(BaseModel):
- x_start_um: float
- y_start_um: float
- z_start_um: float
-
- def _start_for_axis(self, axis: XyzAxis) -> float:
- match axis:
- case XyzAxis.X:
- return self.x_start_um
- case XyzAxis.Y:
- return self.y_start_um
- case XyzAxis.Z:
- return self.z_start_um
-
-
-class OptionalGonioAngleStarts(BaseModel):
- omega_start_deg: float | None = None
- phi_start_deg: float | None = None
- chi_start_deg: float | None = None
- kappa_start_deg: float | None = None
+class DiffractionExperimentWithSample(HyperionDiffractionExperiment, WithSample): ...
 
 
 class TemporaryIspybExtras(BaseModel):

src/hyperion/parameters/gridscan.py

@@ -11,28 +11,29 @@
  PandAGridScanParams,
  ZebraGridScanParams,
 )
-from pydantic import Field, PrivateAttr
-from scanspec.core import Path as ScanPath
-from scanspec.specs import Line, Static
-
-from hyperion.external_interaction.ispyb.ispyb_dataclass import (
- GridscanIspybParams,
-)
-from hyperion.parameters.components import (
- DiffractionExperimentWithSample,
+from mx_bluesky.parameters import (
  IspybExperimentType,
  OptionalGonioAngleStarts,
  SplitScan,
  WithOavCentring,
  WithScan,
  XyzStarts,
 )
+from pydantic import Field, PrivateAttr
+from scanspec.core import Path as ScanPath
+from scanspec.specs import Line, Static
+
+from hyperion.external_interaction.ispyb.ispyb_dataclass import (
+ GridscanIspybParams,
+)
+from hyperion.parameters.components import DiffractionExperimentWithSample
 from hyperion.parameters.constants import CONST, I03Constants
 
 
 class GridCommon(
  DiffractionExperimentWithSample, OptionalGonioAngleStarts, WithOavCentring
 ):
+ oav_centring_file: str = Field(default=CONST.I03.OAV_CENTRING_FILE)
  grid_width_um: float = Field(default=CONST.PARAM.GRIDSCAN.WIDTH_UM)
  exposure_time_s: float = Field(default=CONST.PARAM.GRIDSCAN.EXPOSURE_TIME_S)
  use_roi_mode: bool = Field(default=CONST.PARAM.GRIDSCAN.USE_ROI)

src/hyperion/parameters/rotation.py

@@ -13,6 +13,14 @@
 from dodal.devices.zebra import (
  RotationDirection,
 )
+from mx_bluesky.parameters import (
+ IspybExperimentType,
+ OptionalGonioAngleStarts,
+ OptionalXyzStarts,
+ RotationAxis,
+ SplitScan,
+ WithScan,
+)
 from pydantic import Field, root_validator
 from scanspec.core import AxesPoints
 from scanspec.core import Path as ScanPath
@@ -21,13 +29,7 @@
 from hyperion.external_interaction.ispyb.ispyb_dataclass import RotationIspybParams
 from hyperion.parameters.components import (
  DiffractionExperimentWithSample,
- IspybExperimentType,
- OptionalGonioAngleStarts,
- OptionalXyzStarts,
- RotationAxis,
- SplitScan,
  TemporaryIspybExtras,
- WithScan,
 )
 from hyperion.parameters.constants import CONST, I03Constants