mx-bluesky 1.1.0__tar.gz → 1.2.0__tar.gz

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/Dockerfile.release

@@ -31,7 +31,7 @@ RUN git restore .
 
 # Regenerate _version.py with the correct version - this should run quickly since we already have our dependencies
 RUN rm src/mx_bluesky/_version.py
-RUN pip install --no-cache-dir --no-compile -e .
+RUN pip install --no-cache-dir --no-compile --no-deps -e .
 
 ENTRYPOINT /app/hyperion/utility_scripts/docker/entrypoint.sh
 

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mx-bluesky
-Version: 1.1.0
+Version: 1.2.0
 Summary: Bluesky tools for MX Beamlines at DLS
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -238,7 +238,7 @@ Requires-Dist: daq-config-server>=0.1.1
 Requires-Dist: ophyd==1.9.0
 Requires-Dist: ophyd-async>=0.3a5
 Requires-Dist: bluesky>=1.13.0a4
-Requires-Dist: dls-dodal==1.32.0
+Requires-Dist: dls-dodal==1.33.0
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: build; extra == "dev"

mx_bluesky-1.2.0/docs/developer/general/how-to/deploy-a-release.rst

@@ -0,0 +1,84 @@
+Deploy a New Release
+====================
+
+**Remember to discuss any new deployments with the appropriate beamline scientist.**
+
+
+General deployment
+--------------------
+
+The ``utility_scripts/deploy/deploy_mxbluesky.py`` script will deploy the latest mx-bluesky version to a specified beamline. Deployments live in ``/dls_sw/ixx/software/bluesky/mx-bluesky_vX.X.X``. To do a new deployment you should run the deploy script from your mx-bluesky dev environment with e.g.
+
+.. code:: console
+
+    python ./utility_scripts/deploy/deploy_mxbluesky.py --beamline i24
+
+
+If you want to test the script you can run:
+
+.. code:: console
+
+    python ./deploy/deploy_mxbluesky.py --dev-path /your-path/
+
+and a released version will be put in ``/your-path/mxbluesky_release_test``.
+
+If you need a specific beamline test deployment you can also run:
+
+
+.. code:: console
+
+    python ./deploy/deploy_mxbluesky.py --beamline i24 --dev-path /your-path/
+
+which will create the beamline deployment (eg. I24) in the specified test directory ``/your-path/mxbluesky_release_test``.
+
+
+**Note:** When deploying on I24, the edm screens for serial crystallography will be deployed automatically along with the mx-bluesky release. 
+When running a ``dev`` deployment instead, `this script <https://github.com/DiamondLightSource/mx-bluesky/wiki/Serial-Crystallography-on-I24#deploying-a-local-version-of-the-edm-screens>`_ will also need to be run to get the latest version of the screens.
+
+
+Hyperion deployment
+-------------------
+
+The ``utility_scripts/deploy/deploy_hyperion.py`` script will deploy the latest mx-bluesky/Hyperion version to a specified beamline. Deployments live in ``/dls_sw/ixx/software/bluesky/mx-bluesky_vX.X.X``.
+
+If you have just created a release as above, you may need to run git fetch --tags to get the newest release.
+
+To do a new deployment you should run the deploy script from your Hyperion dev environment with e.g.
+
+.. code:: console
+
+    python ./utility_scripts/deploy/deploy_hyperion.py i03
+
+
+If you want to test the script you can run:
+
+
+.. code:: console
+
+    python ./utility_scripts/deploy/deploy_hyperion.py dev
+
+
+and a released version will be put in ``/scratch/30day_tmp/hyperion_release_test``.
+
+For building and deploying a Docker image please see :doc:`../../hyperion/deploying-hyperion`.
+
+
+.. note::
+    
+    On i03 the installation will succeed with error messages due to RedHat7 versions of a dependency being unavailable.
+    This results in the installation being incomplete, thus requiring the following post-installation steps:
+
+    First, on a RedHat8 workstation, run
+
+    .. code:: console
+
+        . ./.venv/bin/activate
+        pip install confluent-kafka
+    
+    Then, on the control machine, run
+
+    .. code:: console
+        
+        . ./.venv/bin/activate
+        pip install -e .
+        pip install -e ../dodal

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/docs/developer/hyperion/reference/param_hierarchy.puml

@@ -8,7 +8,9 @@ package Mixins {
     class WithSample
     class WithScan
     class WithOavCentring
+    class WithOptionalEnergyChange
     class WithSnapshot
+    class WithVisit
     class OptionalXyzStarts
     class XyzStarts
     class OptionalGonioAngleStarts
@@ -22,49 +24,51 @@ package Experiments {
     class DiffractionExperimentWithSample
     class GridCommon
     class GridScanWithEdgeDetect
+    class LoadCentreCollect
     class PinTipCentreThenXrayCentre
     class RotationScan
     class MultiRotationScan
+    class RobotLoadAndEnergyChange
     class RobotLoadThenCentre
     class SpecifiedGridScan
     class ThreeDGridScan
 }
 
 class HyperionParameters
-note bottom: Base class for all experiment parameter models
-
-class TemporaryIspybExtras
-note bottom: To be removed
-
+note top: Base class for all experiment parameter models
 
 BaseModel <|-- HyperionParameters
 BaseModel <|-- SplitScan
 BaseModel <|-- OptionalGonioAngleStarts
 BaseModel <|-- OptionalXyzStarts
-BaseModel <|-- TemporaryIspybExtras
 BaseModel <|-- WithOavCentring
+BaseModel <|-- WithOptionalEnergyChange
 BaseModel <|-- WithSnapshot
 BaseModel <|-- WithSample
 BaseModel <|-- WithScan
+BaseModel <|-- WithVisit
 BaseModel <|-- XyzStarts
 
-RotationScan *-- TemporaryIspybExtras
-MultiRotationScan *-- TemporaryIspybExtras
 OptionalGonioAngleStarts <|-- RotationScanPerSweep
 OptionalXyzStarts  <|-- RotationScanPerSweep
 DiffractionExperimentWithSample <|-- RotationExperiment
 HyperionParameters <|-- DiffractionExperiment
 WithSnapshot <|-- DiffractionExperiment
+WithOptionalEnergyChange <|-- DiffractionExperiment
+WithVisit <|-- DiffractionExperiment
 DiffractionExperiment <|-- DiffractionExperimentWithSample
 WithSample <|-- DiffractionExperimentWithSample
 DiffractionExperimentWithSample <|-- GridCommon
 GridCommon <|-- GridScanWithEdgeDetect
 GridCommon <|-- PinTipCentreThenXrayCentre
 GridCommon <|-- RobotLoadThenCentre
+RobotLoadThenCentre *-- RobotLoadAndEnergyChange
+RobotLoadThenCentre *-- PinTipCentreThenXrayCentre
 GridCommon <|-- SpecifiedGridScan
 WithScan <|-- SpecifiedGridScan
 SpecifiedGridScan <|-- ThreeDGridScan
 SplitScan <|-- ThreeDGridScan
+WithOptionalEnergyChange <|-- ThreeDGridScan
 WithOavCentring <|-- GridCommon
 WithScan <|-- RotationScan
 RotationScanPerSweep <|-- RotationScan
@@ -75,4 +79,8 @@ SplitScan <|-- MultiRotationScan
 XyzStarts <|-- SpecifiedGridScan
 OptionalGonioAngleStarts <|-- GridCommon
 OptionalGonioAngleStarts <|-- RotationScan
+HyperionParameters <|-- RobotLoadAndEnergyChange
+WithSample <|-- RobotLoadAndEnergyChange
+WithSnapshot <|-- RobotLoadAndEnergyChange
+WithOptionalEnergyChange <|-- RobotLoadAndEnergyChange
 @enduml

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/helmchart/templates/deployment.yaml

@@ -57,7 +57,46 @@ spec:
             path: "{{ .Values.hyperion.dataDir }}"
       containers:
       - name: hyperion
-        image: {{ .Values.hyperion.imageRepository}}/hyperion:{{ .Values.hyperion.appVersion }}
+        image: {{ .Values.hyperion.imageRepository}}/mx-bluesky:{{ .Values.hyperion.appVersion }}
+        securityContext:
+          capabilities:
+            # Required for hostNetwork 
+            drop:
+              - AUDIT_WRITE
+              - CHOWN
+              - DAC_OVERRIDE
+              - FOWNER
+              - FSETID
+              - KILL
+              - MKNOD
+              - NET_BIND_SERVICE
+              - NET_RAW
+              - SETFCAP
+              - SETGID
+              - SETPCAP
+              - SETUID
+              - SYS_CHROOT
+              - AUDIT_CONTROL
+              - BLOCK_SUSPEND
+              - DAC_READ_SEARCH
+              - IPC_LOCK
+              - IPC_OWNER
+              - LEASE
+              - LINUX_IMMUTABLE
+              - MAC_ADMIN
+              - MAC_OVERRIDE
+              - SYS_ADMIN
+              - SYS_BOOT
+              - SYS_MODULE
+              - SYS_NICE
+              - SYS_PACCT
+              - SYS_MODULE
+              - SYS_PTRACE
+              - SYS_RESOURCE
+              - SYS_TIME
+              - SYS_TTY_CONFIG
+              - SYSLOG
+              - WAKE_ALARM            
         resources:
           limits:
             cpu: "1"
@@ -111,3 +150,4 @@ spec:
             name: logs
           - mountPath: "/dls/{{ .Values.hyperion.beamline }}/data"
             name: data
+      hostNetwork: true

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/helmchart/values.yaml

@@ -8,7 +8,7 @@ hyperion:
   supplementalGroups: []
   beamline: i03
   dev: false
-  logDir: "/dls_sw/i03/logs/bluesky"
+  logDir: "/dls_sw/i03/logs/bluesky/hyperion-k8s"
   dataDir: "/dls/i03/data"
   # These should be overridden at install time
   projectDir: SET_ON_INSTALL

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/pyproject.toml

@@ -45,7 +45,7 @@ dependencies = [
     "ophyd == 1.9.0",
     "ophyd-async >= 0.3a5",
     "bluesky >= 1.13.0a4",
-    "dls-dodal == 1.32.0",
+    "dls-dodal == 1.33.0",
 ]
 
 

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/src/mx_bluesky/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.1.0'
-__version_tuple__ = version_tuple = (1, 1, 0)
+__version__ = version = '1.2.0'
+__version_tuple__ = version_tuple = (1, 2, 0)

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/src/mx_bluesky/hyperion/device_setup_plans/utils.py

@@ -3,6 +3,10 @@ from collections.abc import Generator
 from bluesky import plan_stubs as bps
 from bluesky import preprocessors as bpp
 from bluesky.utils import Msg
+from dodal.devices.dcm import DCM
+from dodal.devices.detector import (
+    DetectorParams,
+)
 from dodal.devices.detector.detector_motion import DetectorMotion, ShutterState
 from dodal.devices.eiger import EigerDetector
 
@@ -12,6 +16,13 @@ from mx_bluesky.hyperion.device_setup_plans.position_detector import (
 )
 
 
+def fill_in_energy_if_not_supplied(dcm: DCM, detector_params: DetectorParams):
+    if not detector_params.expected_energy_ev:
+        actual_energy_ev = 1000 * (yield from bps.rd(dcm.energy_in_kev))
+        detector_params.expected_energy_ev = actual_energy_ev
+    return detector_params
+
+
 def start_preparing_data_collection_then_do_plan(
     eiger: EigerDetector,
     detector_motion: DetectorMotion,

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/src/mx_bluesky/hyperion/experiment_plans/experiment_registry.py

@@ -7,12 +7,14 @@ import mx_bluesky.hyperion.experiment_plans.flyscan_xray_centre_plan as flyscan_
 import mx_bluesky.hyperion.experiment_plans.rotation_scan_plan as rotation_scan_plan
 from mx_bluesky.hyperion.experiment_plans import (
     grid_detect_then_xray_centre_plan,
+    load_centre_collect_full_plan,
     pin_centre_then_xray_centre_plan,
     robot_load_then_centre_plan,
 )
 from mx_bluesky.hyperion.external_interaction.callbacks.common.callback_util import (
     CallbacksFactory,
     create_gridscan_callbacks,
+    create_load_centre_collect_callbacks,
     create_robot_load_and_centre_callbacks,
     create_rotation_callbacks,
 )
@@ -22,6 +24,7 @@ from mx_bluesky.hyperion.parameters.gridscan import (
     RobotLoadThenCentre,
     ThreeDGridScan,
 )
+from mx_bluesky.hyperion.parameters.load_centre_collect import LoadCentreCollect
 from mx_bluesky.hyperion.parameters.rotation import MultiRotationScan, RotationScan
 
 
@@ -42,6 +45,7 @@ class ExperimentRegistryEntry(TypedDict):
         | MultiRotationScan
         | PinTipCentreThenXrayCentre
         | RobotLoadThenCentre
+        | LoadCentreCollect
     ]
     callbacks_factory: CallbacksFactory
 
@@ -77,6 +81,11 @@ PLAN_REGISTRY: dict[str, ExperimentRegistryEntry] = {
         "param_type": MultiRotationScan,
         "callbacks_factory": create_rotation_callbacks,
     },
+    "load_centre_collect_full_plan": {
+        "setup": load_centre_collect_full_plan.create_devices,
+        "param_type": LoadCentreCollect,
+        "callbacks_factory": create_load_centre_collect_callbacks,
+    },
 }
 
 

{mx_bluesky-1.1.0 → mx_bluesky-1.2.0}/src/mx_bluesky/hyperion/experiment_plans/flyscan_xray_centre_plan.py

@@ -77,6 +77,12 @@ class SmargonSpeedException(Exception):
     pass
 
 
+class CrystalNotFoundException(WarningException):
+    """Raised if grid detection completed normally but no crystal was found."""
+
+    pass
+
+
 @dataclasses.dataclass
 class FlyScanXRayCentreComposite:
     """All devices which are directly or indirectly required by this plan"""
@@ -190,47 +196,50 @@ def run_gridscan_and_move(
 
     LOGGER.info("Grid scan finished, getting results.")
 
-    with TRACER.start_span("wait_for_zocalo"):
-        yield from bps.trigger_and_read(
-            [fgs_composite.zocalo], name=ZOCALO_READING_PLAN_NAME
-        )
-        LOGGER.info("Zocalo triggered and read, interpreting results.")
-        xray_centre, bbox_size = yield from get_processing_result(fgs_composite.zocalo)
-        LOGGER.info(f"Got xray centre: {xray_centre}, bbox size: {bbox_size}")
-        if xray_centre is not None:
-            xray_centre = parameters.FGS_params.grid_position_to_motor_position(
-                xray_centre
+    try:
+        with TRACER.start_span("wait_for_zocalo"):
+            yield from bps.trigger_and_read(
+                [fgs_composite.zocalo], name=ZOCALO_READING_PLAN_NAME
             )
-        else:
-            xray_centre = initial_xyz
-            LOGGER.warning("No X-ray centre received")
-        if bbox_size is not None:
-            with TRACER.start_span("change_aperture"):
-                yield from set_aperture_for_bbox_size(
-                    fgs_composite.aperture_scatterguard, bbox_size
+            LOGGER.info("Zocalo triggered and read, interpreting results.")
+            xray_centre, bbox_size = yield from get_processing_result(
+                fgs_composite.zocalo
+            )
+            LOGGER.info(f"Got xray centre: {xray_centre}, bbox size: {bbox_size}")
+            if xray_centre is not None:
+                xray_centre = parameters.FGS_params.grid_position_to_motor_position(
+                    xray_centre
                 )
-        else:
-            LOGGER.warning("No bounding box size received")
-
-    # once we have the results, go to the appropriate position
-    LOGGER.info("Moving to centre of mass.")
-    with TRACER.start_span("move_to_result"):
-        x, y, z = xray_centre
-        yield from move_x_y_z(fgs_composite.sample_motors, x, y, z, wait=True)
-
-    if parameters.FGS_params.set_stub_offsets:
-        LOGGER.info("Recentring smargon co-ordinate system to this point.")
-        yield from bps.mv(
-            fgs_composite.sample_motors.stub_offsets, StubPosition.CURRENT_AS_CENTER
-        )
-
-    # Turn off dev/shm streaming to avoid filling disk, see https://github.com/DiamondLightSource/hyperion/issues/1395
-    LOGGER.info("Turning off Eiger dev/shm streaming")
-    yield from bps.abs_set(fgs_composite.eiger.odin.fan.dev_shm_enable, 0)
+            else:
+                LOGGER.warning("No X-ray centre received")
+                raise CrystalNotFoundException()
+            if bbox_size is not None:
+                with TRACER.start_span("change_aperture"):
+                    yield from set_aperture_for_bbox_size(
+                        fgs_composite.aperture_scatterguard, bbox_size
+                    )
+            else:
+                LOGGER.warning("No bounding box size received")
+
+        # once we have the results, go to the appropriate position
+        LOGGER.info("Moving to centre of mass.")
+        with TRACER.start_span("move_to_result"):
+            x, y, z = xray_centre
+            yield from move_x_y_z(fgs_composite.sample_motors, x, y, z, wait=True)
+
+        if parameters.FGS_params.set_stub_offsets:
+            LOGGER.info("Recentring smargon co-ordinate system to this point.")
+            yield from bps.mv(
+                fgs_composite.sample_motors.stub_offsets, StubPosition.CURRENT_AS_CENTER
+            )
+    finally:
+        # Turn off dev/shm streaming to avoid filling disk, see https://github.com/DiamondLightSource/hyperion/issues/1395
+        LOGGER.info("Turning off Eiger dev/shm streaming")
+        yield from bps.abs_set(fgs_composite.eiger.odin.fan.dev_shm_enable, 0)
 
-    # Wait on everything before returning to GDA (particularly apertures), can be removed
-    # when we do not return to GDA here
-    yield from bps.wait()
+        # Wait on everything before returning to GDA (particularly apertures), can be removed
+        # when we do not return to GDA here
+        yield from bps.wait()
 
 
 @bpp.set_run_key_decorator(CONST.PLAN.GRIDSCAN_MAIN)

mx_bluesky-1.2.0/src/mx_bluesky/hyperion/experiment_plans/load_centre_collect_full_plan.py

@@ -0,0 +1,46 @@
+import dataclasses
+
+from blueapi.core import BlueskyContext
+from dodal.devices.oav.oav_parameters import OAVParameters
+
+from mx_bluesky.hyperion.experiment_plans.robot_load_then_centre_plan import (
+    RobotLoadThenCentreComposite,
+    robot_load_then_centre,
+)
+from mx_bluesky.hyperion.experiment_plans.rotation_scan_plan import (
+    RotationScanComposite,
+    multi_rotation_scan,
+)
+from mx_bluesky.hyperion.parameters.load_centre_collect import LoadCentreCollect
+from mx_bluesky.hyperion.utils.context import device_composite_from_context
+
+
+@dataclasses.dataclass
+class LoadCentreCollectComposite(RobotLoadThenCentreComposite, RotationScanComposite):
+    """Composite that provides access to the required devices."""
+
+    pass
+
+
+def create_devices(context: BlueskyContext) -> LoadCentreCollectComposite:
+    """Create the necessary devices for the plan."""
+    return device_composite_from_context(context, LoadCentreCollectComposite)
+
+
+def load_centre_collect_full_plan(
+    composite: LoadCentreCollectComposite,
+    params: LoadCentreCollect,
+    oav_params: OAVParameters | None = None,
+):
+    """Attempt a complete data collection experiment, consisting of the following:
+    * Load the sample if necessary
+    * Move to the specified goniometer start angles
+    * Perform optical centring, then X-ray centring
+    * If X-ray centring finds a diffracting centre then move to that centre and
+    * do a collection with the specified parameters.
+    """
+    if not oav_params:
+        oav_params = OAVParameters(context="xrayCentring")
+    yield from robot_load_then_centre(composite, params.robot_load_then_centre)
+
+    yield from multi_rotation_scan(composite, params.multi_rotation_scan, oav_params)