Merge branch 'main' into 574_make_common_logging

.pre-commit-config.yaml

@@ -26,6 +26,14 @@ repos:
         types: [python]
         require_serial: true
 
+      - id: import-contracts
+        name: Ensure import directionality
+        pass_filenames: false
+        language: system
+        entry: lint-imports
+        types: [python]
+        require_serial: false
+
   # Type checking
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.4.1

hyperion_other/workflows/code.yml

@@ -28,6 +28,12 @@ jobs:
       - name: Run ruff
         run: ruff check .
 
+      - name: Install import linter
+        run: pip install import-linter
+
+      - name: Run import linter
+        run: lint-imports
+
   tests:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
     runs-on: ubuntu-latest

pyproject.toml

@@ -14,7 +14,7 @@ description = "Bluesky tools for MX Beamlines at DLS"
 dependencies = [
     #
     # If a constraint is not set here or if the dependency is pinned to a hash
-    # it will be auto-pinned to the latest release version by the pre-release workflow   
+    # it will be auto-pinned to the latest release version by the pre-release workflow
     #
     "annotated_types",
     "caproto",
@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib",
     "nexgen",
     "numpy",
-    "opencv-python",               # Needed for I24 ssx moveonclick. To be changed to headless once this is moved to separate ui. 
+    "opencv-python",               # Needed for I24 ssx moveonclick. To be changed to headless once this is moved to separate ui.
     "opentelemetry-distro",
     "opentelemetry-exporter-otlp",
     "pydantic",
@@ -39,13 +39,13 @@ dependencies = [
     #
     # 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.
-    # 
+    #
     "blueapi >= 0.5.0",
     "daq-config-server >= 0.1.1",
     "ophyd == 1.9.0",
     "ophyd-async >= 0.3a5",
     "bluesky >= 1.13.0a4",
-    "dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git",
+    "dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@main",
 ]
 
 
@@ -62,6 +62,7 @@ dev = [
     # "copier",
     "diff-cover",
     "GitPython",
+    "import-linter",
     "ipython",
     "mypy",
     "myst-parser",
@@ -122,8 +123,6 @@ addopts = """
 # https://iscinumpy.gitlab.io/post/bound-version-constraints/#watch-for-warnings
 filterwarnings = [
     "error",
-    # Ignore incorrect errors from bluesky (remove when https://github.com/bluesky/bluesky/issues/1797 is released)
-    "ignore:((.|\n)*)was never iterated.*:RuntimeWarning",
     # Ignore deprecation warning from sqlalchemy
     "ignore::sqlalchemy.exc.MovedIn20Warning",
     # Ignore deprecation warning from setuptools_dso (remove when https://github.com/epics-base/setuptools_dso/issues/36 is released)
@@ -134,10 +133,6 @@ filterwarnings = [
     "ignore:(.*)unclosed file(.*)name='(.*)dodal.log'(.*):ResourceWarning",
     "ignore:(.*)unclosed <socket(.*):ResourceWarning",
     "ignore:(.*)unclosed event loop(.*):ResourceWarning",
-    # Ignore pydantic 2 issues from blueapi, see https://github.com/DiamondLightSource/blueapi/issues/622
-    "ignore::DeprecationWarning:blueapi",
-    # Ignore deprecation warning from python-workflows https://github.com/DiamondLightSource/python-workflows/issues/180
-    "ignore:.*pkg_resources.*:DeprecationWarning",
 ]
 # Doctest python code in docs, python code in src docstrings, test functions in tests
 testpaths = "docs src tests/unit_tests"
@@ -198,3 +193,23 @@ lint.extend-ignore = [
 
 [tool.mypy]
 plugins = ["pydantic.mypy"]
+
+[tool.importlinter]
+root_package = "mx_bluesky"
+
+[[tool.importlinter.contracts]]
+name = "Common does not import from apps"
+type = "forbidden"
+source_modules = "mx_bluesky.common"
+forbidden_modules = ["mx_bluesky.beamlines", "mx_bluesky.hyperion"]
+
+[[tool.importlinter.contracts]]
+name = "Beamlines do not import from each other"
+type = "independence"
+modules = "mx_bluesky.beamlines.*"
+
+[[tool.importlinter.contracts]]
+name = "Beamlines do not import from hyperion"
+type = "forbidden"
+source_modules = "mx_bluesky.beamlines.*"
+forbidden_modules = "mx_bluesky.hyperion"

src/mx_bluesky/beamlines/i04/thawing_plan.py

@@ -1,11 +1,13 @@
+from collections.abc import Callable
+
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
 from bluesky.preprocessors import run_decorator, subs_decorator
 from dls_bluesky_core.core import MsgGenerator
 from dodal.beamlines.i04 import MURKO_REDIS_DB, REDIS_HOST, REDIS_PASSWORD
 from dodal.common import inject
 from dodal.devices.oav.oav_detector import OAV
-from dodal.devices.oav.oav_to_redis_forwarder import OAVToRedisForwarder
+from dodal.devices.oav.oav_to_redis_forwarder import OAVToRedisForwarder, Source
 from dodal.devices.robot import BartRobot
 from dodal.devices.smargon import Smargon
 from dodal.devices.thawer import Thawer, ThawerStates
@@ -24,10 +26,16 @@ def thaw_and_stream_to_redis(
 ) -> MsgGenerator:
     zoom_percentage = yield from bps.rd(oav.zoom_controller.percentage)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
     sample_id = yield from bps.rd(robot.sample_id)
+    zoom_level_before_thawing = yield from bps.rd(oav.zoom_controller.level)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
 
     yield from bps.abs_set(oav.zoom_controller.level, "1.0x", wait=True)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
     yield from bps.abs_set(oav_to_redis_forwarder.sample_id, sample_id)
 
+    def switch_forwarder_to_ROI() -> MsgGenerator:
+        yield from bps.complete(oav_to_redis_forwarder)
+        yield from bps.mv(oav_to_redis_forwarder.selected_source, Source.ROI)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
+        yield from bps.kickoff(oav_to_redis_forwarder, wait=True)
+
     @subs_decorator(MurkoCallback(REDIS_HOST, REDIS_PASSWORD, MURKO_REDIS_DB))
     @run_decorator(
         md={
@@ -40,20 +48,36 @@ def thaw_and_stream_to_redis(
         }
     )
     def _thaw_and_stream_to_redis():
+        yield from bps.mv(
+            oav_to_redis_forwarder.sample_id,  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
+            sample_id,
+            oav_to_redis_forwarder.selected_source,  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
+            Source.FULL_SCREEN,  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
+        )
+
         yield from bps.kickoff(oav_to_redis_forwarder, wait=True)
         yield from bps.monitor(smargon.omega.user_readback, name="smargon")
         yield from bps.monitor(oav_to_redis_forwarder.uuid, name="oav")
-        yield from thaw(time_to_thaw, rotation, thawer, smargon)
+        yield from thaw(
+            time_to_thaw, rotation, thawer, smargon, switch_forwarder_to_ROI
+        )
         yield from bps.complete(oav_to_redis_forwarder)
 
-    yield from _thaw_and_stream_to_redis()
+    def cleanup():
+        yield from bps.mv(oav.zoom_controller.level, zoom_level_before_thawing)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
+
+    yield from bpp.contingency_wrapper(
+        _thaw_and_stream_to_redis(),
+        final_plan=cleanup,
+    )
 
 
 def thaw(
     time_to_thaw: float,
     rotation: float = 360,
     thawer: Thawer = inject("thawer"),
     smargon: Smargon = inject("smargon"),
+    plan_between_rotations: Callable[[], MsgGenerator] | None = None,
 ) -> MsgGenerator:
     """Rotates the sample and thaws it at the same time.
 
@@ -64,6 +88,8 @@ def thaw(
         thawer (Thawer, optional): The thawing device. Defaults to inject("thawer").
         smargon (Smargon, optional): The smargon used to rotate.
                                      Defaults to inject("smargon")
+        plan_between_rotations (MsgGenerator, optional): A plan to run between rotations
+                                    of the smargon. Defaults to no plan.
     """
     inital_velocity = yield from bps.rd(smargon.omega.velocity)
     new_velocity = abs(rotation / time_to_thaw) * 2.0
@@ -72,6 +98,8 @@ def do_thaw():
         yield from bps.abs_set(smargon.omega.velocity, new_velocity, wait=True)
         yield from bps.abs_set(thawer.control, ThawerStates.ON, wait=True)
         yield from bps.rel_set(smargon.omega, rotation, wait=True)
+        if plan_between_rotations:
+            yield from plan_between_rotations()
         yield from bps.rel_set(smargon.omega, -rotation, wait=True)
 
     def cleanup():

src/mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_moveonclick.py

@@ -11,7 +11,7 @@
 from bluesky.run_engine import RunEngine
 from dodal.beamlines import i24
 from dodal.devices.i24.pmac import PMAC
-from dodal.devices.oav.oav_detector import OAV
+from dodal.devices.oav.oav_async import OAV
 
 from mx_bluesky.beamlines.i24.serial.fixed_target import (
     i24ssx_Chip_Manager_py3v1 as manager,
@@ -28,7 +28,9 @@ def _get_beam_centre(oav: OAV):
     Args:
         oav (OAV): the OAV device.
     """
-    return oav.parameters.beam_centre_i, oav.parameters.beam_centre_j
+    beam_x = yield from bps.rd(oav.beam_centre_i)
+    beam_y = yield from bps.rd(oav.beam_centre_j)
+    return beam_x, beam_y
 
 
 def _calculate_zoom_calibrator(oav: OAV):
@@ -39,13 +41,15 @@ def _calculate_zoom_calibrator(oav: OAV):
 
 
 def _move_on_mouse_click_plan(
-    oav: OAV, pmac: PMAC, beam_centre: Sequence[int], clicked_position: Sequence[int]
+    oav: OAV,
+    pmac: PMAC,
+    clicked_position: Sequence[int],
 ):
     """A plan that calculates the zoom calibrator and moves to the clicked \
         position coordinates.
     """
     zoomcalibrator = yield from _calculate_zoom_calibrator(oav)
-    beamX, beamY = beam_centre
+    beamX, beamY = yield from _get_beam_centre(oav)
     x, y = clicked_position
     xmove = -1 * (beamX - x) * zoomcalibrator
     ymove = -1 * (beamY - y) * zoomcalibrator
@@ -62,14 +66,13 @@ def onMouse(event, x, y, flags, param):
         RE = param[0]
         pmac = param[1]
         oav = param[2]
-        beamX, beamY = _get_beam_centre(oav)
         logger.info(f"Clicked X and Y {x} {y}")
-        RE(_move_on_mouse_click_plan(oav, pmac, (beamX, beamY), (x, y)))
+        RE(_move_on_mouse_click_plan(oav, pmac, (x, y)))
 
 
-def update_ui(oav, frame):
+def update_ui(oav, frame, RE):
     # Get beam x and y values
-    beamX, beamY = _get_beam_centre(oav)
+    beamX, beamY = RE(_get_beam_centre(oav)).plan_result
 
     # Overlay text and beam centre
     cv.ellipse(
@@ -164,7 +167,7 @@ def start_viewer(oav: OAV, pmac: PMAC, RE: RunEngine, oav1: str = OAV1_CAM):
     while success:
         success, frame = cap.read()
 
-        update_ui(oav, frame)
+        update_ui(oav, frame, RE)
 
         k = cv.waitKey(1)
         if k == 113:  # Q
@@ -212,7 +215,7 @@ def start_viewer(oav: OAV, pmac: PMAC, RE: RunEngine, oav1: str = OAV1_CAM):
 
 
 if __name__ == "__main__":
-    RE = RunEngine()
+    RE = RunEngine(call_returns_result=True)
     # Get devices out of dodal
     oav: OAV = i24.oav()
     pmac: PMAC = i24.pmac()

tests/conftest.py

@@ -356,6 +356,15 @@ def oav(test_config_files):
     parameters.micronsPerXPixel = 2.87
     parameters.micronsPerYPixel = 2.87
     oav = i03.oav(fake_with_ophyd_sim=True, params=parameters)
+
+    oav.zoom_controller.zrst.set("1.0x")
+    oav.zoom_controller.onst.set("2.0x")
+
+    oav.parameters.micronsPerXPixel = 1.58
+    oav.parameters.micronsPerYPixel = 1.58
+    oav.parameters.beam_centre_i = 517
+    oav.parameters.beam_centre_j = 350
+
     oav.snapshot.trigger = MagicMock(return_value=NullStatus())
     oav.zoom_controller.zrst.set("1.0x")
     oav.zoom_controller.onst.set("2.0x")