dls-dodal 1.40.0__tar.gz → 1.42.0__tar.gz

dls_dodal-1.42.0/.github/scripts/check_test_durations.py

@@ -0,0 +1,30 @@
+import json
+import sys
+
+# Get report filename and threshold from command-line arguments
+REPORT_FILE = sys.argv[1] if len(sys.argv) > 1 else "report.json"
+THRESHOLD = float(sys.argv[2]) if len(sys.argv) > 2 else 1.0
+
+try:
+    with open(REPORT_FILE) as f:
+        data = json.load(f)
+except FileNotFoundError:
+    print(f"❌ Error: Report file '{REPORT_FILE}' not found.")
+    sys.exit(1)
+except json.JSONDecodeError:
+    print(f"❌ Error: Failed to parse JSON in '{REPORT_FILE}'.")
+    sys.exit(1)
+
+slow_tests = [
+    (t["nodeid"], t["call"]["duration"])
+    for t in data.get("tests", [])
+    if "call" in t and t["call"]["duration"] > THRESHOLD
+]
+
+if slow_tests:
+    print(f"❌ The following tests exceeded the {THRESHOLD:.2f}s threshold:")
+    for test, duration in slow_tests:
+        print(f" - {test}: {duration:.2f}s")
+    sys.exit(1)
+
+print("✅ All tests ran within the acceptable time limit.")

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/.github/workflows/_test.yml

@@ -50,13 +50,24 @@ jobs:
           python-version: ${{ inputs.python-version }}
           pip-install: ".[dev]"
 
-      - name: Run tests
-        run: tox -e tests
+      - name: Run unit tests
+        run: tox -e unit-report
+
+      - name: Check unit test durations
+        run: |
+          python .github/scripts/check_test_durations.py unit-report.json 1
+
+      - name: Run system tests
+        run: tox -e system-report
+
+      - name: Check system test durations
+        run: |
+          python .github/scripts/check_test_durations.py system-report.json 5
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
           name: ${{ inputs.python-version }}/${{ inputs.runs-on }}
-          files: cov.xml
+          files: ./unit_cov.xml,./system_cov.xml
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/.gitignore

@@ -74,3 +74,7 @@ lockfiles/
 
 # pycharm project files
 .idea/
+
+
+# custom CI setup 
+report.json

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dls-dodal
-Version: 1.40.0
+Version: 1.42.0
 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
@@ -217,7 +217,7 @@ License-File: LICENSE
 Requires-Dist: click
 Requires-Dist: ophyd
 Requires-Dist: ophyd-async>=0.9.0a2
-Requires-Dist: bluesky
+Requires-Dist: bluesky==1.13.0
 Requires-Dist: pyepics
 Requires-Dist: dataclasses-json
 Requires-Dist: pillow
@@ -238,6 +238,7 @@ Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: diff-cover; extra == "dev"
 Requires-Dist: import-linter; extra == "dev"
+Requires-Dist: ispyb; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: myst-parser; extra == "dev"
 Requires-Dist: ophyd_async[sim]; extra == "dev"
@@ -249,6 +250,7 @@ Requires-Dist: pyright; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-asyncio; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-json-report; extra == "dev"
 Requires-Dist: pytest-random-order; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: sphinx<7.4.6; extra == "dev"

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/docs/how-to/create-beamline.rst

@@ -7,7 +7,7 @@ They include motors in the experiment hutch, optical components in the optics hu
 Beamline Modules
 ----------------
 
-Each beamline should have its own file in the ``doodal.beamlines`` folder, in which the particular devices for the 
+Each beamline should have its own file in the ``dodal.beamlines`` folder, in which the particular devices for the 
 beamline are instantiated. The file should be named after the colloquial name for the beamline. For example:
 
 * ``i03.py``
@@ -25,55 +25,67 @@ The following example creates a fictitious beamline ``w41``, with a simulated tw
 
 .. code-block:: python
 
-    from dodal.common.beamlines.beamline_utils import device_instantiation
+    from ophyd_async.epics.adaravis import AravisDetector
+
+    from dodal.common.beamlines.beamline_utils import (
+        device_factory,
+        get_path_provider,
+        set_path_provider,
+    )
     from dodal.common.beamlines.beamline_utils import set_beamline as set_utils_beamline
-    from dodal.devices.areadetector.adaravis import AdAravisDetector
+    from dodal.common.beamlines.device_helpers import CAM_SUFFIX, HDF5_SUFFIX
+    from dodal.common.visit import LocalDirectoryServiceClient, StaticVisitPathProvider
     from dodal.devices.synchrotron import Synchrotron
     from dodal.log import set_beamline as set_log_beamline
-    from dodal.utils import get_beamline_name, skip_device
+    from dodal.utils import BeamlinePrefix
 
     BL = get_beamline_name("s41")  # Default used when not on a live beamline
+    PREFIX = BeamlinePrefix(BL)
     set_log_beamline(BL)  # Configure logging and util functions
     set_utils_beamline(BL)
 
+    # Currently we must hard-code the visit, determining the visit is WIP.
+    set_path_provider(
+        StaticVisitPathProvider(
+            BL,
+            # Root directory for all detectors
+            Path("/dls/w41/data/YYYY/cm12345-1"),
+            # Uses an existing GDA server to ensure filename uniqueness
+            client=RemoteDirectoryServiceClient("http://s41-control:8088/api"),
+            # Else if no GDA server use a LocalDirectoryServiceClient(),
+        )
+    )
 
     """
     Define device factory functions below this point.
-    A device factory function is any function that has a return type which conforms 
+    A device factory function is any function that has a return type which conforms
     to one or more Bluesky Protocols.
     """
 
-
     """
-    A valid factory function which is:
-    - instantiated only on the live beamline
-    - a maximum of once
-    - can optionally be faked with ophyd simulated axes
-    - can optionally be connected concurrently by not waiting for connect to complete
-    - if constructor took a prefix, could optionally exclude the BLIXX prefix
+    A valid factory function which:
+    - may be instantiated automatically, selectively on live beamline
+        - caches and re-uses the result for subsequent calls
+    - automatically names the device
+    - may be skipped when make_all_devices is called on this module
+    - must be explicitly connected (may be automated by tools)
+        - when connected may connect to a simulated backend
+        - may be connected concurrently (when automated by tools)
     """"
-    @skip_device(lambda: BL == "s41")  # Conditionally do not instantiate this device
-    def synchrotron(
-        wait_for_connection: bool = True, fake_with_ophyd_sim: bool = False
-    ) -> Synchrotron:
-        """Calls the Synchrotron class's constructor with name="synchrotron", prefix=""
-        If this is called when already instantiated, it will return the existing object.
-        """
-        return device_instantiation(
-            Synchrotron,
-            "synchrotron",
-            "",
-            wait_for_connection,
-            fake_with_ophyd_sim,
-            bl_prefix=False,
+    @device_factory(skip = BL == "s41")
+    def synchrotron() -> Synchrotron:
+        return Synchrotron()
+
+
+    @device_factory()
+    def d11() -> AravisDetector:
+        return AravisDetector(
+            f"{PREFIX.beamline_prefix}-DI-DCAM-01:",
+            path_provider=get_path_provider(),
+            drv_suffix=CAM_SUFFIX,
+            fileio_suffix=HDF5_SUFFIX,
         )
 
-    def d11(name: str = "D11") -> AdAravisDetector:
-        """
-        Also a valid Device factory function, but as multiple calls would instantiate
-        multiple copies of a device, discouraged.
-        """
-        return AdAravisDetector(name=name, prefix=f"{BL}-DI-DCAM-01:")
 
 ``w41`` should also be added to the list of ``ALL_BEAMLINES`` in ``tests/beamlines/test_device_instantiation``.
 This test checks that the function returns a type that conforms to Bluesky protocols, 

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/pyproject.toml

@@ -16,7 +16,7 @@ dependencies = [
     "click",
     "ophyd",
     "ophyd-async >= 0.9.0a2",
-    "bluesky",
+    "bluesky == 1.13.0",
     "pyepics",
     "dataclasses-json",
     "pillow",
@@ -45,6 +45,7 @@ dev = [
     "black",
     "diff-cover",
     "import-linter",
+    "ispyb",
     "mypy",
     # Commented out due to dependency version conflict with pydantic 1.x
     # "copier",
@@ -58,6 +59,7 @@ dev = [
     "pytest",
     "pytest-asyncio",
     "pytest-cov",
+    "pytest-json-report",
     "pytest-random-order",
     "ruff",
     "sphinx<7.4.6",              #  pinned due to https://github.com/sphinx-doc/sphinx/issues/12660
@@ -141,7 +143,7 @@ legacy_tox_ini = """
 [tox]
 skipsdist=True
 
-[testenv:{pre-commit,type-checking,tests,docs}]
+[testenv:{pre-commit,type-checking,tests,docs,unit-report,system-report}]
 # Don't create a virtualenv for the command, requires tox-direct plugin
 direct = True
 passenv = *
@@ -156,6 +158,8 @@ commands =
     type-checking: pyright src tests {posargs}
     pre-commit: pre-commit run --all-files --show-diff-on-failure {posargs}
     docs: sphinx-{posargs:build -E} -T docs build/html
+    unit-report: pytest -m 'not (s03 or adsim)' --cov=dodal --cov-report term --cov-report xml:unit_cov.xml --json-report --json-report-file=unit-report.json tests {posargs}
+    system-report: pytest -m 'not (s03 or adsim)' --cov=dodal --cov-report term --cov-report xml:system_cov.xml --json-report --json-report-file=system-report.json system_tests {posargs}
 """
 
 [tool.ruff]
@@ -174,14 +178,15 @@ lint.select = [
     "I",   # isort - https://docs.astral.sh/ruff/rules/#isort-i
     "UP",  # pyupgrade - https://docs.astral.sh/ruff/rules/#pyupgrade-up
     "SLF", # self - https://docs.astral.sh/ruff/settings/#lintflake8-self
+    "RUF018" # walrus operators in asserts - https://docs.astral.sh/ruff/rules/assignment-in-assert/
 ]
 
 [tool.ruff.lint.per-file-ignores]
 # By default, private member access is allowed in tests
 # See https://github.com/DiamondLightSource/python-copier-template/issues/154
-# Remove this line to forbid private member access in tests
-"tests/**/*" = ["SLF001"]
-"system_tests/**/*" = ["SLF001"]
+# Remove this line to forbid private member access and walrus operators in asserts in tests 
+"tests/**/*" = ["SLF001", "RUF018"]
+"system_tests/**/*" = ["SLF001", "RUF018"]
 
 [tool.importlinter]
 root_package = "dodal"

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/src/dls_dodal.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dls-dodal
-Version: 1.40.0
+Version: 1.42.0
 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
@@ -217,7 +217,7 @@ License-File: LICENSE
 Requires-Dist: click
 Requires-Dist: ophyd
 Requires-Dist: ophyd-async>=0.9.0a2
-Requires-Dist: bluesky
+Requires-Dist: bluesky==1.13.0
 Requires-Dist: pyepics
 Requires-Dist: dataclasses-json
 Requires-Dist: pillow
@@ -238,6 +238,7 @@ Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: diff-cover; extra == "dev"
 Requires-Dist: import-linter; extra == "dev"
+Requires-Dist: ispyb; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: myst-parser; extra == "dev"
 Requires-Dist: ophyd_async[sim]; extra == "dev"
@@ -249,6 +250,7 @@ Requires-Dist: pyright; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-asyncio; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-json-report; extra == "dev"
 Requires-Dist: pytest-random-order; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: sphinx<7.4.6; extra == "dev"

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/src/dls_dodal.egg-info/SOURCES.txt

@@ -16,6 +16,7 @@ pyproject.toml
 .github/actions/install_requirements/action.yml
 .github/pages/index.html
 .github/pages/make_switcher.py
+.github/scripts/check_test_durations.py
 .github/workflows/_check.yml
 .github/workflows/_dist.yml
 .github/workflows/_docs.yml
@@ -89,6 +90,7 @@ src/dodal/beamline_specific_utils/i03.py
 src/dodal/beamlines/README.md
 src/dodal/beamlines/__init__.py
 src/dodal/beamlines/adsim.py
+src/dodal/beamlines/aithre.py
 src/dodal/beamlines/b01_1.py
 src/dodal/beamlines/i02_1.py
 src/dodal/beamlines/i03.py
@@ -98,6 +100,7 @@ src/dodal/beamlines/i13_1.py
 src/dodal/beamlines/i18.py
 src/dodal/beamlines/i19_1.py
 src/dodal/beamlines/i19_2.py
+src/dodal/beamlines/i19_optics.py
 src/dodal/beamlines/i20_1.py
 src/dodal/beamlines/i22.py
 src/dodal/beamlines/i23.py
@@ -160,6 +163,7 @@ src/dodal/devices/undulator_dcm.py
 src/dodal/devices/watsonmarlow323_pump.py
 src/dodal/devices/webcam.py
 src/dodal/devices/xbpm_feedback.py
+src/dodal/devices/aithre_lasershaping/goniometer.py
 src/dodal/devices/areadetector/plugins/CAM.py
 src/dodal/devices/areadetector/plugins/MJPG.py
 src/dodal/devices/attenuator/attenuator.py
@@ -196,6 +200,7 @@ src/dodal/devices/i18/diode.py
 src/dodal/devices/i18/table.py
 src/dodal/devices/i18/thor_labs_stage.py
 src/dodal/devices/i19/__init__.py
+src/dodal/devices/i19/hutch_access.py
 src/dodal/devices/i19/shutter.py
 src/dodal/devices/i20_1/__init__.py
 src/dodal/devices/i22/dcm.py
@@ -254,7 +259,10 @@ src/dodal/plan_stubs/wrapped.py
 src/dodal/plans/__init__.py
 src/dodal/plans/save_panda.py
 src/dodal/plans/scanspec.py
+src/dodal/plans/verify_undulator_gap.py
 src/dodal/plans/wrapped.py
+src/dodal/plans/preprocessors/__init__.py
+src/dodal/plans/preprocessors/verify_undulator_gap.py
 system_tests/__init__.py
 system_tests/test_adsim.py
 system_tests/test_aperturescatterguard_system.py
@@ -271,6 +279,7 @@ system_tests/test_zebra_system.py
 system_tests/test_zocalo_results.py
 tests/__init__.py
 tests/conftest.py
+tests/constants.py
 tests/fake_beamline.py
 tests/fake_beamline_all_devices_raise_exception.py
 tests/fake_beamline_broken_dependency.py
@@ -402,7 +411,9 @@ tests/plan_stubs/test_wrapped_stubs.py
 tests/plans/conftest.py
 tests/plans/test_compliance.py
 tests/plans/test_scanspec.py
+tests/plans/test_verify_undulator_gap_plan.py
 tests/plans/test_wrapped.py
+tests/plans/test_preprocessors/test_verify_undulator_gap.py
 tests/preprocessors/test_filesystem_metadata.py
 tests/test_data/bad_beamlineParameters
 tests/test_data/i04_beamlineParameters

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/src/dls_dodal.egg-info/requires.txt

@@ -1,7 +1,7 @@
 click
 ophyd
 ophyd-async>=0.9.0a2
-bluesky
+bluesky==1.13.0
 pyepics
 dataclasses-json
 pillow
@@ -23,6 +23,7 @@ scanspec>=0.7.3
 black
 diff-cover
 import-linter
+ispyb
 mypy
 myst-parser
 ophyd_async[sim]
@@ -34,6 +35,7 @@ pyright
 pytest
 pytest-asyncio
 pytest-cov
+pytest-json-report
 pytest-random-order
 ruff
 sphinx<7.4.6

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/src/dodal/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.40.0'
-__version_tuple__ = version_tuple = (1, 40, 0)
+__version__ = version = '1.42.0'
+__version_tuple__ = version_tuple = (1, 42, 0)

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/src/dodal/beamlines/__init__.py

@@ -13,6 +13,7 @@ _BEAMLINE_NAME_OVERRIDES = {
     "i20-1": "i20_1",
     "i19-1": "i19_1",
     "i19-2": "i19_2",
+    "i19-optics": "i19_optics",
     "s03": "i03",
     "p46": "training_rig",
     "p47": "training_rig",

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/src/dodal/beamlines/adsim.py

@@ -40,7 +40,7 @@ https://epics-containers.github.io/main/tutorials/launch_example.html
 And ensure that the signals are visible:
 
 ```sh
-export EPICS_CA_ADDR_LIST=127.0.0.1
+export EPICS_CA_ADDR_LIST=127.0.0.1:5094
 ```
 
 How to use the devices in a plan:

dls_dodal-1.42.0/src/dodal/beamlines/aithre.py

@@ -0,0 +1,9 @@
+from dodal.common.beamlines.beamline_utils import device_factory
+from dodal.devices.aithre_lasershaping.goniometer import Goniometer
+
+PREFIX = "LA18L"
+
+
+@device_factory()
+def goniometer() -> Goniometer:
+    return Goniometer(f"{PREFIX}-MO-LSR-01:", "goniometer")

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/src/dodal/beamlines/i04.py

@@ -46,7 +46,7 @@ ZOOM_PARAMS_FILE = (
 DISPLAY_CONFIG = "/dls_sw/i04/software/gda_versions/var/display.configuration"
 DAQ_CONFIGURATION_PATH = "/dls_sw/i04/software/daq_configuration"
 
-REDIS_HOST = os.environ.get("VALKEY_PROD_SVC_SERVICE_HOST", "test_redis")
+REDIS_HOST = "i04-valkey-murko.diamond.ac.uk"
 REDIS_PASSWORD = os.environ.get("VALKEY_PASSWORD", "test_redis_password")
 MURKO_REDIS_DB = 7
 

dls_dodal-1.42.0/src/dodal/beamlines/i19_optics.py

@@ -0,0 +1,34 @@
+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.hutch_shutter import HutchShutter
+from dodal.devices.i19.hutch_access import HutchAccessControl
+from dodal.log import set_beamline as set_log_beamline
+from dodal.utils import BeamlinePrefix
+
+BL = "i19-optics"
+PREFIX = BeamlinePrefix("i19", "I")
+set_log_beamline(BL)
+set_utils_beamline(BL)
+
+
+@device_factory()
+def shutter() -> HutchShutter:
+    """Get the i19 hutch shutter device, instantiate it if it hasn't already been.
+    If this is called when already instantiated, it will return the existing object.
+    """
+    return HutchShutter(
+        f"{PREFIX.beamline_prefix}-PS-SHTR-01:",
+        "shutter",
+    )
+
+
+@device_factory()
+def access_control() -> HutchAccessControl:
+    """Get a device that checks the active hutch for i19, instantiate it if it hasn't already been.
+    If this is called when already instantiated, it will return the existing object.
+    """
+    return HutchAccessControl(f"{PREFIX.beamline_prefix}-OP-STAT-01:", "access_control")

{dls_dodal-1.40.0 → dls_dodal-1.42.0}/src/dodal/beamlines/i23.py

@@ -1,13 +1,15 @@
-from dodal.common.beamlines.beamline_utils import device_instantiation
+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.oav.pin_image_recognition import PinTipDetection
 from dodal.log import set_beamline as set_log_beamline
-from dodal.utils import get_beamline_name, get_hostname, skip_device
+from dodal.utils import BeamlinePrefix, get_beamline_name, get_hostname
 
 BL = get_beamline_name("i23")
 set_log_beamline(BL)
 set_utils_beamline(BL)
 
+PREFIX = BeamlinePrefix(BL)
+
 
 def _is_i23_machine():
     """
@@ -18,16 +20,11 @@ def _is_i23_machine():
     return hostname.startswith("i23-ws") or hostname.startswith("i23-control")
 
 
-@skip_device(lambda: not _is_i23_machine())
-def oav_pin_tip_detection(
-    wait_for_connection: bool = True, fake_with_ophyd_sim: bool = False
-) -> PinTipDetection:
+@device_factory(skip=lambda: not _is_i23_machine())
+def oav_pin_tip_detection() -> PinTipDetection:
     """Get the i23 OAV pin-tip detection device"""
 
-    return device_instantiation(
-        PinTipDetection,
+    return PinTipDetection(
+        f"{PREFIX.beamline_prefix}-DI-OAV-01:",
         "pin_tip_detection",
-        "-DI-OAV-01:",
-        wait_for_connection,
-        fake_with_ophyd_sim,
     )