dls-dodal 1.36.2__tar.gz → 1.37.0__tar.gz

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dls-dodal
-Version: 1.36.2
+Version: 1.37.0
 Summary: Ophyd devices and other utils that could be used across DLS beamlines
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -216,7 +216,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: click
 Requires-Dist: ophyd
-Requires-Dist: ophyd-async>=0.8.0a5
+Requires-Dist: ophyd-async>=0.9.0a1
 Requires-Dist: bluesky
 Requires-Dist: pyepics
 Requires-Dist: dataclasses-json
@@ -228,7 +228,7 @@ Requires-Dist: pydantic>=2.0
 Requires-Dist: opencv-python-headless
 Requires-Dist: aioca
 Requires-Dist: p4p
-Requires-Dist: numpy<2.0
+Requires-Dist: numpy
 Requires-Dist: aiofiles
 Requires-Dist: aiohttp
 Requires-Dist: redis

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/conftest.py

@@ -1,5 +1,4 @@
 import asyncio
-import importlib
 import logging
 import os
 import sys
@@ -18,14 +17,13 @@ from ophyd_async.core import (
     PathProvider,
 )
 
-from dodal.common.beamlines import beamline_parameters, beamline_utils
+from dodal.common.beamlines import beamline_utils
 from dodal.common.visit import (
     DirectoryServiceClient,
     LocalDirectoryServiceClient,
     StaticVisitPathProvider,
 )
 from dodal.log import LOGGER, GELFTCPHandler, set_up_all_logging_handlers
-from dodal.utils import make_all_devices
 
 MOCK_DAQ_CONFIG_PATH = "tests/devices/unit_tests/test_daq_configuration"
 mock_paths = [
@@ -55,9 +53,9 @@ def patch_open_to_prevent_dls_reads_in_tests():
         requested_path = Path(args[0])
         if requested_path.is_absolute():
             for p in BANNED_PATHS:
-                assert not requested_path.is_relative_to(
-                    p
-                ), f"Attempt to open {requested_path} from inside a unit test"
+                assert not requested_path.is_relative_to(p), (
+                    f"Attempt to open {requested_path} from inside a unit test"
+                )
         return unpatched_open(*args, **kwargs)
 
     with patch("builtins.open", side_effect=patched_open):
@@ -82,31 +80,6 @@ if os.getenv("PYTEST_RAISE", "0") == "1":
         raise excinfo.value
 
 
-def mock_beamline_module_filepaths(bl_name, bl_module):
-    if mock_attributes := mock_attributes_table.get(bl_name):
-        [bl_module.__setattr__(attr[0], attr[1]) for attr in mock_attributes]
-        beamline_parameters.BEAMLINE_PARAMETER_PATHS[bl_name] = (
-            "tests/test_data/i04_beamlineParameters"
-        )
-
-
-@pytest.fixture(scope="function")
-def module_and_devices_for_beamline(request):
-    beamline = request.param
-    with patch.dict(os.environ, {"BEAMLINE": beamline}, clear=True):
-        bl_mod = importlib.import_module("dodal.beamlines." + beamline)
-        importlib.reload(bl_mod)
-        mock_beamline_module_filepaths(beamline, bl_mod)
-        devices, exceptions = make_all_devices(
-            bl_mod,
-            include_skipped=True,
-            fake_with_ophyd_sim=True,
-        )
-        yield (bl_mod, devices, exceptions)
-        beamline_utils.clear_devices()
-        del bl_mod
-
-
 def pytest_runtest_setup(item):
     beamline_utils.clear_devices()
     if LOGGER.handlers == []:

dls_dodal-1.37.0/docs/how-to/zocalo.rst

@@ -0,0 +1,71 @@
+Zocalo Interaction
+==================
+
+.. image:: ../assets/zocalo.png
+  :alt: Diagram of zocalo
+
+Zocalo jobs are triggered based on their ISPyB DCID using the ``ZocaloTrigger`` class in a callback subscribed to the 
+Bluesky plan or ``RunEngine``. These can trigger processing for any kind of job, as zocalo infers the necessary 
+processing from data in ISPyB.
+
+Results are received using the ``ZocaloResults`` device, so that they can be read into a plan and used for 
+decision-making. Currently the ``ZocaloResults`` device is only made to handle X-ray centring results. It subscribes to 
+a given zocalo RabbitMQ channel the first time that it is triggered.
+
+Zocalo Service
+==============
+
+The Zocalo service processes incoming messages using recipes which describe routing of messages between processing 
+steps. You can see `source for the recipes here`_.
+
+.. _source for the recipes here: https://gitlab.diamond.ac.uk/scisoft/zocalo/-/tree/master/recipes
+
+You can find more information about Zocalo at https://confluence.diamond.ac.uk/display/SSCC/How+to+create+an+MX+processing+pipeline
+
+Gridscans
+---------
+
+The Zocalo Service receives messages of the following form for both the xy and xz gridscans::
+
+    {
+        'recipes': ['mimas'],
+        'parameters': {
+            'ispyb_dcid': 16085800,
+            'filename': 'ins_10_31',
+            'start_frame_index': 0,
+            'number_of_frames': 1140,
+            'message_index': 0,
+            'event': 'start',
+            'guid': 'd6f117bb-c856-4df8-b9bc-2d3c625e9fd5'
+        }
+    }
+
+Zocalo is then sent stop messages::
+
+   {
+        'recipes': ['mimas'],
+        'parameters': {
+            'event': 'end',
+            'ispyb_dcid': 16085800,
+            'guid': '9a96e59c-da30-494c-8380-c7a5c828c2c9'
+        },
+   }
+
+these tell zocalo that the data is now ready to be processed.
+
+Zocalo then uses the ISPyB DataCollection ID to fetch the corresponding info from ISPyB
+
+The messages that zocalo receives can be found in Graylog in the Zocalo stream, from there you can find the log of 
+the recipe processing using the path to the logbook that comes from messages like these::
+    Message saved in logbook at /dls/tmp/zocalo/dispatcher/2024-12/cb/62d35b-7cc9-4f1b-868b-712e82aa0271
+
+From the zocalo graylog you can also see that once the gridscan nexus file is picked up (for the CPU gridscan) it 
+starts a recipe::
+
+    {'recipes': ['per-image-analysis-gridscan-i03-no-really'], 'parameters': {'ispyb_dcid': 16085803, 'filename': '{filename}', 'start_frame_index': '{start_frame_index}', 'number_of_frames': '{number_of_frames}', 'message_index': '{message_index}', 'guid': 'd10f8b8c-57a5-4dc4-acaf-a22f8d2bbf60'}, 'recipe': <workflows.recipe.recipe.Recipe object at 0x7f0587f13110>}
+
+
+If you look at the recipe json, Zocalo then runs Per-Image-Analysis on each frame and then assembles the results in 
+the `DLS X-Ray Centring service`_.
+
+.. _DLS X-Ray Centring service: https://github.com/DiamondLightSource/python-dlstbx/blob/a8fcbd30335bf13f5e35df78badfc60397500535/src/dlstbx/services/xray_centering.py

dls_dodal-1.37.0/docs/reference/api.md

@@ -0,0 +1,28 @@
+# API
+
+```{eval-rst}
+.. autosummary::
+    :recursive:
+    :toctree: generated
+
+    dodal.beamlines
+    dodal.common
+    dodal.devices
+    dodal.parameters
+    dodal.plan_stubs
+    dodal.plans
+
+.. automodule:: dodal
+
+    ``dodal``
+    -----------------------------------
+```
+
+This is the internal API reference for dodal
+
+```{eval-rst}
+.. data:: dodal.__version__
+    :type: str
+
+    Version number as calculated by https://github.com/pypa/setuptools_scm
+```

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/docs/reference.md

@@ -6,7 +6,7 @@ Technical reference material including APIs and release notes.
 :maxdepth: 1
 :glob:
 
-API <_api/dodal>
+reference/*
 genindex
 Release Notes <https://github.com/DiamondLightSource/dodal/releases>
 ```

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/pyproject.toml

@@ -15,7 +15,7 @@ description = "Ophyd devices and other utils that could be used across DLS beaml
 dependencies = [
     "click",
     "ophyd",
-    "ophyd-async >= 0.8.0a5",
+    "ophyd-async >= 0.9.0a1",
     "bluesky",
     "pyepics",
     "dataclasses-json",
@@ -27,7 +27,7 @@ dependencies = [
     "opencv-python-headless", # For pin-tip detection.
     "aioca",                  # Required for CA support with ophyd-async.
     "p4p",                    # Required for PVA support with ophyd-async.
-    "numpy<2.0",              # Unpin when https://github.com/bluesky/ophyd-async/issues/387 resolved
+    "numpy",
     "aiofiles",
     "aiohttp",
     "redis",

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/src/dls_dodal.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dls-dodal
-Version: 1.36.2
+Version: 1.37.0
 Summary: Ophyd devices and other utils that could be used across DLS beamlines
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -216,7 +216,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: click
 Requires-Dist: ophyd
-Requires-Dist: ophyd-async>=0.8.0a5
+Requires-Dist: ophyd-async>=0.9.0a1
 Requires-Dist: bluesky
 Requires-Dist: pyepics
 Requires-Dist: dataclasses-json
@@ -228,7 +228,7 @@ Requires-Dist: pydantic>=2.0
 Requires-Dist: opencv-python-headless
 Requires-Dist: aioca
 Requires-Dist: p4p
-Requires-Dist: numpy<2.0
+Requires-Dist: numpy
 Requires-Dist: aiofiles
 Requires-Dist: aiohttp
 Requires-Dist: redis

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/src/dls_dodal.egg-info/SOURCES.txt

@@ -29,7 +29,6 @@ pyproject.toml
 .vscode/launch.json
 .vscode/settings.json
 .vscode/tasks.json
-docs/_api.rst
 docs/conf.py
 docs/explanations.md
 docs/genindex.md
@@ -67,6 +66,7 @@ docs/how-to/write-tests.md
 docs/how-to/zocalo.rst
 docs/images/dls-logo.svg
 docs/images/excalidraw-example.svg
+docs/reference/api.md
 docs/reference/device-standards.rst
 docs/reference/standards.rst
 docs/tutorials/get_started.rst
@@ -90,6 +90,7 @@ src/dodal/beamlines/README.md
 src/dodal/beamlines/__init__.py
 src/dodal/beamlines/adsim.py
 src/dodal/beamlines/b01_1.py
+src/dodal/beamlines/i02_1.py
 src/dodal/beamlines/i03.py
 src/dodal/beamlines/i04.py
 src/dodal/beamlines/i10.py
@@ -120,8 +121,8 @@ src/dodal/devices/adsim.py
 src/dodal/devices/aperture.py
 src/dodal/devices/aperturescatterguard.py
 src/dodal/devices/apple2_undulator.py
-src/dodal/devices/attenuator.py
 src/dodal/devices/backlight.py
+src/dodal/devices/bimorph_mirror.py
 src/dodal/devices/cryostream.py
 src/dodal/devices/dcm.py
 src/dodal/devices/diamond_filter.py
@@ -160,6 +161,15 @@ src/dodal/devices/zebra.py
 src/dodal/devices/zebra_controlled_shutter.py
 src/dodal/devices/areadetector/plugins/CAM.py
 src/dodal/devices/areadetector/plugins/MJPG.py
+src/dodal/devices/attenuator/attenuator.py
+src/dodal/devices/attenuator/filter.py
+src/dodal/devices/attenuator/filter_selections.py
+src/dodal/devices/current_amplifiers/__init__.py
+src/dodal/devices/current_amplifiers/current_amplifier.py
+src/dodal/devices/current_amplifiers/current_amplifier_detector.py
+src/dodal/devices/current_amplifiers/femto.py
+src/dodal/devices/current_amplifiers/sr570.py
+src/dodal/devices/current_amplifiers/struck_scaler_counter.py
 src/dodal/devices/detector/__init__.py
 src/dodal/devices/detector/det_dim_constants.py
 src/dodal/devices/detector/det_dist_to_beam_converter.py
@@ -167,9 +177,15 @@ src/dodal/devices/detector/det_resolution.py
 src/dodal/devices/detector/detector.py
 src/dodal/devices/detector/detector_motion.py
 src/dodal/devices/i03/__init__.py
+src/dodal/devices/i03/beamstop.py
 src/dodal/devices/i04/transfocator.py
 src/dodal/devices/i10/i10_apple2.py
 src/dodal/devices/i10/i10_setting_data.py
+src/dodal/devices/i10/mirrors.py
+src/dodal/devices/i10/slits.py
+src/dodal/devices/i10/rasor/rasor_current_amp.py
+src/dodal/devices/i10/rasor/rasor_motors.py
+src/dodal/devices/i10/rasor/rasor_scaler_cards.py
 src/dodal/devices/i20_1/__init__.py
 src/dodal/devices/i22/dcm.py
 src/dodal/devices/i22/fswitch.py
@@ -238,6 +254,7 @@ system_tests/test_undulator_system.py
 system_tests/test_zebra_system.py
 system_tests/test_zocalo_results.py
 tests/__init__.py
+tests/conftest.py
 tests/fake_beamline.py
 tests/fake_beamline_all_devices_raise_exception.py
 tests/fake_beamline_broken_dependency.py
@@ -266,6 +283,8 @@ tests/common/beamlines/test_device_helpers.py
 tests/common/beamlines/test_device_instantiation.py
 tests/devices/__init__.py
 tests/devices/test_diamond_filter.py
+tests/devices/i03/__init__.py
+tests/devices/i03/test_beamstop.py
 tests/devices/i04/__init__.py
 tests/devices/i04/test_transfocator.py
 tests/devices/i10/test_i10Apple2.py
@@ -290,6 +309,7 @@ tests/devices/unit_tests/test_backlight.py
 tests/devices/unit_tests/test_bart_robot.py
 tests/devices/unit_tests/test_beam_converter.py
 tests/devices/unit_tests/test_beamline_undulator_to_gap_lookup_table.txt
+tests/devices/unit_tests/test_bimorph_mirror.py
 tests/devices/unit_tests/test_dcm.py
 tests/devices/unit_tests/test_display.configuration
 tests/devices/unit_tests/test_eiger.py
@@ -320,6 +340,8 @@ tests/devices/unit_tests/test_xspress3.py
 tests/devices/unit_tests/test_zebra.py
 tests/devices/unit_tests/test_zocalo_interaction.py
 tests/devices/unit_tests/test_zocalo_results.py
+tests/devices/unit_tests/current_amplifier/test_femto.py
+tests/devices/unit_tests/current_amplifier/test_sr570.py
 tests/devices/unit_tests/detector/test_det_dim_constants.py
 tests/devices/unit_tests/detector/test_det_resolution.py
 tests/devices/unit_tests/detector/test_detector.py

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/src/dls_dodal.egg-info/requires.txt

@@ -1,6 +1,6 @@
 click
 ophyd
-ophyd-async>=0.8.0a5
+ophyd-async>=0.9.0a1
 bluesky
 pyepics
 dataclasses-json
@@ -12,7 +12,7 @@ pydantic>=2.0
 opencv-python-headless
 aioca
 p4p
-numpy<2.0
+numpy
 aiofiles
 aiohttp
 redis

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/src/dodal/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.36.2'
-__version_tuple__ = version_tuple = (1, 36, 2)
+__version__ = version = '1.37.0'
+__version_tuple__ = version_tuple = (1, 37, 0)

dls_dodal-1.37.0/src/dodal/beamlines/i02_1.py

@@ -0,0 +1,37 @@
+"""Beamline i02-1 is also known as VMXm, or I02J"""
+
+from dodal.common.beamlines.beamline_utils import (
+    device_factory,
+)
+from dodal.common.beamlines.beamline_utils import set_beamline as set_utils_beamline
+from dodal.devices.attenuator.attenuator import EnumFilterAttenuator
+from dodal.devices.attenuator.filter_selections import (
+    I02_1FilterFourSelections,
+    I02_1FilterOneSelections,
+    I02_1FilterThreeSelections,
+    I02_1FilterTwoSelections,
+)
+from dodal.log import set_beamline as set_log_beamline
+from dodal.utils import BeamlinePrefix, get_beamline_name
+
+BL = get_beamline_name("i02-1")
+PREFIX = BeamlinePrefix(BL, suffix="J")
+set_log_beamline(BL)
+set_utils_beamline(BL)
+
+
+@device_factory()
+def attenuator() -> EnumFilterAttenuator:
+    """Get the i02-1 attenuator device, instantiate it if it hasn't already been.
+    If this is called when already instantiated in i02-1, it will return the existing object.
+    """
+
+    return EnumFilterAttenuator(
+        f"{PREFIX.beamline_prefix}-OP-ATTN-01:",
+        (
+            I02_1FilterOneSelections,
+            I02_1FilterTwoSelections,
+            I02_1FilterThreeSelections,
+            I02_1FilterFourSelections,
+        ),
+    )

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/src/dodal/beamlines/i03.py

@@ -13,7 +13,7 @@ from dodal.devices.aperturescatterguard import (
     ApertureScatterguard,
     load_positions_from_beamline_parameters,
 )
-from dodal.devices.attenuator import Attenuator
+from dodal.devices.attenuator.attenuator import BinaryFilterAttenuator
 from dodal.devices.backlight import Backlight
 from dodal.devices.cryostream import CryoStream
 from dodal.devices.dcm import DCM
@@ -24,6 +24,7 @@ from dodal.devices.eiger import EigerDetector
 from dodal.devices.fast_grid_scan import PandAFastGridScan, ZebraFastGridScan
 from dodal.devices.flux import Flux
 from dodal.devices.focusing_mirror import FocusingMirrorWithStripes, MirrorVoltages
+from dodal.devices.i03.beamstop import Beamstop
 from dodal.devices.motors import XYZPositioner
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.oav_parameters import OAVConfig
@@ -80,12 +81,12 @@ def aperture_scatterguard(
 
 def attenuator(
     wait_for_connection: bool = True, fake_with_ophyd_sim: bool = False
-) -> Attenuator:
+) -> BinaryFilterAttenuator:
     """Get the i03 attenuator device, instantiate it if it hasn't already been.
     If this is called when already instantiated in i03, it will return the existing object.
     """
     return device_instantiation(
-        Attenuator,
+        BinaryFilterAttenuator,
         "attenuator",
         "-EA-ATTN-01:",
         wait_for_connection,
@@ -93,6 +94,22 @@ def attenuator(
     )
 
 
+def beamstop(
+    wait_for_connection: bool = True, fake_with_ophyd_sim: bool = False
+) -> Beamstop:
+    """Get the i03 beamstop device, instantiate it if it hasn't already been.
+    If this is called when already instantiated in i03, it will return the existing object.
+    """
+    return device_instantiation(
+        Beamstop,
+        "beamstop",
+        "-MO-BS-01:",
+        wait_for_connection,
+        fake_with_ophyd_sim,
+        beamline_parameters=get_beamline_parameters(),
+    )
+
+
 def dcm(wait_for_connection: bool = True, fake_with_ophyd_sim: bool = False) -> DCM:
     """Get the i03 DCM device, instantiate it if it hasn't already been.
     If this is called when already instantiated in i03, it will return the existing object.

{dls_dodal-1.36.2 → dls_dodal-1.37.0}/src/dodal/beamlines/i04.py

@@ -6,7 +6,7 @@ from dodal.devices.aperturescatterguard import (
     ApertureScatterguard,
     load_positions_from_beamline_parameters,
 )
-from dodal.devices.attenuator import Attenuator
+from dodal.devices.attenuator.attenuator import BinaryFilterAttenuator
 from dodal.devices.backlight import Backlight
 from dodal.devices.dcm import DCM
 from dodal.devices.detector import DetectorParams
@@ -138,12 +138,12 @@ def sample_shutter(
 
 def attenuator(
     wait_for_connection: bool = True, fake_with_ophyd_sim: bool = False
-) -> Attenuator:
+) -> BinaryFilterAttenuator:
     """Get the i04 attenuator device, instantiate it if it hasn't already been.
     If this is called when already instantiated in i04, it will return the existing object.
     """
     return device_instantiation(
-        Attenuator,
+        BinaryFilterAttenuator,
         "attenuator",
         "-EA-ATTN-01:",
         wait_for_connection,