mx-bluesky 0.0.1__py3-none-any.whl → 0.3.1__py3-none-any.whl

mx_bluesky/parameters/components.py

@@ -0,0 +1,200 @@
+from __future__ import annotations
+
+from abc import abstractmethod
+from collections.abc import Sequence
+from enum import Enum
+from pathlib import Path
+from typing import SupportsInt, TypeVar
+
+from dodal.devices.aperturescatterguard import AperturePositionGDANames
+from dodal.devices.detector import (
+    DetectorParams,
+    TriggerMode,
+)
+from pydantic import BaseModel, Field, root_validator
+from scanspec.core import AxesPoints
+from semver import Version
+
+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"])
+
+
+class RotationAxis(str, Enum):
+    OMEGA = "omega"
+    PHI = "phi"
+    CHI = "chi"
+    KAPPA = "kappa"
+
+
+class XyzAxis(str, Enum):
+    X = "sam_x"
+    Y = "sam_y"
+    Z = "sam_z"
+
+
+class IspybExperimentType(str, Enum):
+    # 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 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(WithSnapshot):
+    """For all experiments which use beam"""
+
+    visit: str = Field(min_length=5, regex=r"[\w]{2}[\d]+-[\d]+")
+    file_name: str
+    exposure_time_s: float = Field(gt=0)
+    comment: str = Field(default="")
+    beamline: str = Field(regex=r"BL\d{2}[BIJS]")
+    insertion_prefix: str = Field(regex=r"SR\d{2}[BIJS]")
+    det_dist_to_beam_converter_path: str
+    zocalo_environment: str
+    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 num_images(self) -> int:
+        return 0
+
+    @property
+    @abstractmethod
+    def detector_params(self) -> DetectorParams: ...
+
+
+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 WithOavCentring(BaseModel):
+    oav_centring_file: str
+
+
+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

{mx_bluesky-0.0.1.dist-info → mx_bluesky-0.3.1.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: mx-bluesky
-Version: 0.0.1
-Summary: Bluesky tools for MX Beamlines
+Version: 0.3.1
+Summary: Bluesky tools for MX Beamlines at DLS
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License: Apache License
                                    Version 2.0, January 2004
@@ -205,30 +205,42 @@ License: Apache License
            See the License for the specific language governing permissions and
            limitations under the License.
         
-Project-URL: GitHub, https://github.com/DiamondLightSource/mx_bluesky
+Project-URL: GitHub, https://github.com/DiamondLightSource/mx-bluesky
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.9
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: bluesky
 Requires-Dist: ophyd
 Requires-Dist: pyepics
+Requires-Dist: caproto
 Requires-Dist: jupyterlab
 Requires-Dist: matplotlib
 Requires-Dist: requests
 Requires-Dist: opencv-python
-Requires-Dist: dls-dodal ==1.8.0
+Requires-Dist: pydantic
+Requires-Dist: semver
+Requires-Dist: fastapi[all]
+Requires-Dist: dls-dodal ==1.30.0
+Requires-Dist: blueapi ==0.4.4
 Provides-Extra: dev
 Requires-Dist: black ; extra == 'dev'
+Requires-Dist: copier ; extra == 'dev'
+Requires-Dist: GitPython ; extra == 'dev'
 Requires-Dist: mypy ; extra == 'dev'
+Requires-Dist: myst-parser ; extra == 'dev'
 Requires-Dist: pipdeptree ; extra == 'dev'
 Requires-Dist: pre-commit ; extra == 'dev'
 Requires-Dist: pydata-sphinx-theme >=0.12 ; extra == 'dev'
+Requires-Dist: pyright ; extra == 'dev'
+Requires-Dist: pytest-asyncio ; extra == 'dev'
 Requires-Dist: pytest-cov ; extra == 'dev'
+Requires-Dist: pytest-random-order ; extra == 'dev'
+Requires-Dist: pytest ; extra == 'dev'
 Requires-Dist: ruff ; extra == 'dev'
 Requires-Dist: sphinx-autobuild ; extra == 'dev'
 Requires-Dist: sphinx-copybutton ; extra == 'dev'
@@ -237,45 +249,44 @@ Requires-Dist: tox-direct ; extra == 'dev'
 Requires-Dist: types-mock ; extra == 'dev'
 Requires-Dist: types-requests ; extra == 'dev'
 
-mx_bluesky
+mx-bluesky
 ===========================
 
-|code_ci| |docs_ci| |coverage| |pypi_version| |license|
+|ci| |coverage| |pypi_version| |license|
 
 Contains code for working with Bluesky on MX beamlines at Diamond
 
 ============== ==============================================================
-PyPI           ``pip install mx_bluesky``
-Source code    https://github.com/DiamondLightSource/mx_bluesky
-Documentation  https://DiamondLightSource.github.io/mx_bluesky
-Releases       https://github.com/DiamondLightSource/mx_bluesky/releases
+PyPI           ``pip install mx-bluesky``
+Source code    https://github.com/DiamondLightSource/mx-bluesky
+Documentation  https://DiamondLightSource.github.io/mx-bluesky
+Releases       https://github.com/DiamondLightSource/mx-bluesky/releases
 ============== ==============================================================
 
 Getting Started
 ===============
 
-To get started with developing this repo at DLS run ```dls_dev_setup.sh``.
+To get started with developing this repo at DLS run ``dls_dev_setup.sh``.
 
-We recommend developing with VSCode. You can do this at DLS by running::
+If you want to develop interactively at the beamline we recommend using jupyter notebooks. You can get started with this by running::
 
+    $ ./start_jupyter.sh
+
+If you're doing more in-depth development we recommend developing with VSCode. You can do this at DLS by running::
 
     $ module load vscode
-    $ code .
+    $ code .vscode/mx-bluesky.code-workspace
 
-.. |code_ci| image:: https://github.com/DiamondLightSource/mx_bluesky/actions/workflows/code.yml/badge.svg?branch=main
-    :target: https://github.com/DiamondLightSource/mx_bluesky/actions/workflows/code.yml
+.. |ci| image:: https://github.com/DiamondLightSource/mx-bluesky/actions/workflows/ci.yml/badge.svg?branch=main
+    :target: https://github.com/DiamondLightSource/mx-bluesky/actions/workflows/ci.yml
     :alt: Code CI
 
-.. |docs_ci| image:: https://github.com/DiamondLightSource/mx_bluesky/actions/workflows/docs.yml/badge.svg?branch=main
-    :target: https://github.com/DiamondLightSource/mx_bluesky/actions/workflows/docs.yml
-    :alt: Docs CI
-
-.. |coverage| image:: https://codecov.io/gh/DiamondLightSource/mx_bluesky/branch/main/graph/badge.svg
-    :target: https://codecov.io/gh/DiamondLightSource/mx_bluesky
+.. |coverage| image:: https://codecov.io/gh/DiamondLightSource/mx-bluesky/branch/main/graph/badge.svg
+    :target: https://codecov.io/gh/DiamondLightSource/mx-bluesky
     :alt: Test Coverage
 
-.. |pypi_version| image:: https://img.shields.io/pypi/v/mx_bluesky.svg
-    :target: https://pypi.org/project/mx_bluesky
+.. |pypi_version| image:: https://img.shields.io/pypi/v/mx-bluesky.svg
+    :target: https://pypi.org/project/mx-bluesky
     :alt: Latest PyPI version
 
 .. |license| image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
@@ -286,4 +297,4 @@ We recommend developing with VSCode. You can do this at DLS by running::
     Anything below this line is used when viewing README.rst and will be replaced
     when included in index.rst
 
-See https://DiamondLightSource.github.io/mx_bluesky for more detailed documentation.
+See https://DiamondLightSource.github.io/mx-bluesky for more detailed documentation.

mx_bluesky-0.3.1.dist-info/RECORD

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+mx_bluesky/i24/serial/setup_beamline/setup_zebra_plans.py,sha256=dzkml6AbJovQr4znygV4yg2wrUffNQcRpgAQqGx0siY,17019
+mx_bluesky/parameters/__init__.py,sha256=JfT3Y5XiAQAD2IHedVxb5KVZzC9B47HVe6GPuiCCS1U,583
+mx_bluesky/parameters/components.py,sha256=3D2ww7xV3AY47lASqqOq8JXuiFafb4ZBbHuauAGa_-k,5659
+mx_bluesky-0.3.1.dist-info/LICENSE,sha256=tAkwu8-AdEyGxGoSvJ2gVmQdcicWw3j1ZZueVV74M-E,11357
+mx_bluesky-0.3.1.dist-info/METADATA,sha256=BA3YdXE-z6zmKD2FK2S1Wa0YxmEQJuzHSjHetcfLe7Q,16677
+mx_bluesky-0.3.1.dist-info/WHEEL,sha256=nCVcAvsfA9TDtwGwhYaRrlPhTLV9m-Ga6mdyDtuwK18,91
+mx_bluesky-0.3.1.dist-info/entry_points.txt,sha256=LHs220CM6hOrmptR6i9pLzyWZfJ0_PZ4Mvyp2VFNsgY,186
+mx_bluesky-0.3.1.dist-info/top_level.txt,sha256=S4rrzXIUef58ulf_04wn01XGZ3xeJjXs4LPEJ_xoF-I,11
+mx_bluesky-0.3.1.dist-info/RECORD,,

{mx_bluesky-0.0.1.dist-info → mx_bluesky-0.3.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (73.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

mx_bluesky-0.3.1.dist-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+mx-bluesky = mx_bluesky.__main__:main
+run_extruder = mx_bluesky.i24.serial.run_serial:run_extruder
+run_fixed_target = mx_bluesky.i24.serial.run_serial:run_fixed_target