mx-bluesky 1.4.0__tar.gz → 1.4.1a0__tar.gz

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/.github/workflows/_container.yml

@@ -30,12 +30,8 @@ jobs:
           DOCKER_BUILD_RECORD_UPLOAD: false
         with:
           context: .
-          # Need load and tags so we can test it below
+          file: Dockerfile.release
           load: true
-          tags: tag_for_testing
-
-      - name: Test cli works in cached runtime image
-        run: docker run --rm tag_for_testing --version
 
       - name: Create tags for publishing image
         id: meta

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/Dockerfile.release

@@ -33,6 +33,6 @@ RUN git restore .
 RUN rm src/mx_bluesky/_version.py
 RUN pip install --no-cache-dir --no-compile --no-deps -e .
 
-ENTRYPOINT /app/hyperion/utility_scripts/docker/entrypoint.sh
+ENTRYPOINT ["/app/hyperion/utility_scripts/docker/entrypoint.sh"]
 
 EXPOSE 5005

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mx-bluesky
-Version: 1.4.0
+Version: 1.4.1a0
 Summary: Bluesky tools for MX Beamlines at DLS
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -237,9 +237,9 @@ Requires-Dist: matplotlib
 Requires-Dist: blueapi>=0.5.0
 Requires-Dist: daq-config-server>=0.1.1
 Requires-Dist: ophyd==1.9.0
-Requires-Dist: ophyd-async>=0.3a5
+Requires-Dist: ophyd-async>=0.8a5
 Requires-Dist: bluesky>=1.13.0a4
-Requires-Dist: dls-dodal==1.35.0
+Requires-Dist: dls-dodal==1.36.1a
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: build; extra == "dev"

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/docs/conf.py

@@ -136,6 +136,7 @@ rst_epilog = """
 .. _black: https://github.com/psf/black
 .. _mypy: http://mypy-lang.org/
 .. _pre-commit: https://pre-commit.com/
+.. _ruff: https://github.com/astral-sh/ruff
 """
 
 # Ignore localhost links for periodic check that links in docs are valid

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/docs/developer/general/explanations/decisions/0003-python-version-support.rst

@@ -1,4 +1,4 @@
-1. Python version support
+3. Python version support
 =========================
 
 Date: 2024-08-22

mx_bluesky-1.4.1a0/docs/developer/general/how-to/dev-ops/dev-ops.rst

@@ -0,0 +1,8 @@
+Dev-Ops guides
+==============================
+
+.. toctree::
+    :maxdepth: 1
+    :glob:
+
+    ./*

{mx_bluesky-1.4.0/docs/developer/general/how-to → mx_bluesky-1.4.1a0/docs/developer/general/how-to/dev-ops}/lint.rst

@@ -1,7 +1,7 @@
 Run linting using pre-commit
 ============================
 
-Code linting is handled by black_, ruff run under pre-commit_.
+Code linting is handled by ruff_, run under pre-commit_.
 
 Running pre-commit
 ------------------
@@ -18,15 +18,15 @@ commit`` on just the files that have changed::
 Fixing issues
 -------------
 
-If black reports an issue you can tell it to reformat all the files in the
+If ruff reports an issue you can attempt to automatically reformat all the files in the
 repository::
 
-    $ black .
+    $ ruff check --fix .
 
 If you get any ruff issues you will have to fix those manually.
 
 VSCode support
 --------------
 
-The ``.vscode/settings.json`` will run black and isort formatters as well as
-flake8 checking on save. Issues will be highlighted in the editor window.
+The ``.vscode/settings.json`` will run linters and formatters 
+on save. Issues will be highlighted in the editor window.

{mx_bluesky-1.4.0/docs/developer/general/how-to → mx_bluesky-1.4.1a0/docs/developer/general/how-to/dev-ops}/run-tests.rst

@@ -4,7 +4,7 @@ Run the tests using pytest
 Testing is done with pytest_. It will find functions in the project that `look
 like tests`_, and run them to check for errors. You can run it with::
 
-    $ tox -e pytest
+    $ tox -e tests
 
 It will also report coverage to the commandline and to ``cov.xml``.
 

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/docs/developer/general/index.rst

@@ -12,7 +12,7 @@ Documentation is split into four categories, and each is also accessible from li
             :caption: Tutorials
             :maxdepth: 1
 
-            tutorials/dev-install
+            tutorials/profile-tests
 
         +++
 
@@ -26,14 +26,9 @@ Documentation is split into four categories, and each is also accessible from li
 
             how-to/get-started
             how-to/contribute
-            how-to/build-docs
-            how-to/run-tests
-            how-to/static-analysis
-            how-to/lint
-            how-to/update-tools
             how-to/create-a-release
             how-to/deploy-a-release
-            how-to/profile-tests
+            how-to/dev-ops/dev-ops
 
         +++
 

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/docs/developer/general/reference/standards.rst

@@ -15,7 +15,7 @@ The code in this repository conforms to standards set by the following tools:
 
 .. seealso::
 
-    How-to guides `../how-to/lint` and `../how-to/static-analysis`
+    How-to guides `../how-to/dev-ops/lint`
 
 .. _documentation_standards:
 
@@ -60,4 +60,4 @@ Docs follow the underlining convention::
 
 .. seealso::
 
-    How-to guide `../how-to/build-docs`
+    How-to guide `../how-to/dev-ops/build-docs`

{mx_bluesky-1.4.0/docs/developer/general/how-to → mx_bluesky-1.4.1a0/docs/developer/general/tutorials}/profile-tests.rst

@@ -15,7 +15,7 @@ value e.g.
 0.1s
 
 How to profile the unit tests
-=============================
+-----------------------------
 
 Sometimes tests can exhibit slowdowns for unknown reasons, in order to diagnose the cause it can be useful to profile
 the test code.
@@ -35,7 +35,7 @@ You can then often step through in the debugger to find lines which execute slow
 
 
 More detailed profiling
-=======================
+------------------------
 
 Occasionally this is not sufficient. In which case more detailed profiling is necessary
 

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/docs/developer/hyperion/index.rst

@@ -1,7 +1,7 @@
-General MX-Bluesky Developer Guide
+Hyperion Developer Guide
 ==================================
 
-Documentation is split into four categories, and each is also accessible from links in the side-bar.
+Documentation specific for the Hyperion module within MX-Bluesky
 
 .. grid:: 2
     :gutter: 2

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/docs/developer/hyperion/reference/param_hierarchy.puml

@@ -31,7 +31,7 @@ package Experiments {
     class RobotLoadAndEnergyChange
     class RobotLoadThenCentre
     class SpecifiedGridScan
-    class ThreeDGridScan
+    class HyperionThreeDGridScan
 }
 
 class HyperionParameters
@@ -66,9 +66,9 @@ RobotLoadThenCentre *-- RobotLoadAndEnergyChange
 RobotLoadThenCentre *-- PinTipCentreThenXrayCentre
 GridCommon <|-- SpecifiedGridScan
 WithScan <|-- SpecifiedGridScan
-SpecifiedGridScan <|-- ThreeDGridScan
-SplitScan <|-- ThreeDGridScan
-WithOptionalEnergyChange <|-- ThreeDGridScan
+SpecifiedGridScan <|-- HyperionThreeDGridScan
+SplitScan <|-- HyperionThreeDGridScan
+WithOptionalEnergyChange <|-- HyperionThreeDGridScan
 WithOavCentring <|-- GridCommon
 WithScan <|-- RotationScan
 RotationScanPerSweep <|-- RotationScan

mx_bluesky-1.4.1a0/docs/index.rst

@@ -0,0 +1,22 @@
+:html_theme.sidebar_secondary.remove:
+
+.. include:: ../README.rst
+    :end-before: when included in index.rst
+
+How the documentation is structured
+-----------------------------------
+
+The documentation consists of a Developer Guide for MX-Bluesky, which also includes documentation for Hyperion. At its current stage in development, there is no user guide.
+
+.. grid:: 1
+
+    .. grid-item-card:: :material-regular:`code;4em`
+        :link: developer/index
+        :link-type: doc
+
+        The Developer Guide contains documentation on how to install, develop and contribute changes to MX-Bluesky; explanations about the purpose of the software and some of the technical concepts; as well as how-to guides and tutorials.
+
+.. toctree::
+    :hidden:
+
+    developer/index

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/pyproject.toml

@@ -44,9 +44,9 @@ dependencies = [
     "blueapi >= 0.5.0",
     "daq-config-server >= 0.1.1",
     "ophyd == 1.9.0",
-    "ophyd-async >= 0.3a5",
+    "ophyd-async >= 0.8a5",
     "bluesky >= 1.13.0a4",
-    "dls-dodal == 1.35.0",
+    "dls-dodal == 1.36.1a",
 ]
 
 

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/run_hyperion.sh

@@ -99,6 +99,8 @@ if [[ $START == 1 ]]; then
     module unload controls_dev
     module load dials
 
+    RELATIVE_SCRIPT_DIR=$( dirname -- "$0"; )
+    cd ${RELATIVE_SCRIPT_DIR}
 
     if [ -z "$LOG_DIR" ]; then
         if [ $IN_DEV == true ]; then

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/src/mx_bluesky/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.4.0'
-__version_tuple__ = version_tuple = (1, 4, 0)
+__version__ = version = '1.4.1a0'
+__version_tuple__ = version_tuple = (1, 4, 1)

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/src/mx_bluesky/beamlines/i04/thawing_plan.py

@@ -3,7 +3,7 @@ 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 bluesky.utils 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

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/src/mx_bluesky/beamlines/i24/serial/dcid.py

@@ -1,6 +1,5 @@
 import datetime
 import json
-import logging
 import math
 import os
 import re
@@ -10,6 +9,7 @@ from functools import lru_cache
 
 import requests
 
+from mx_bluesky.beamlines.i24.serial.log import SSX_LOGGER
 from mx_bluesky.beamlines.i24.serial.parameters import SSXType
 from mx_bluesky.beamlines.i24.serial.setup_beamline import (
     Detector,
@@ -25,8 +25,6 @@ try:
 except ImportError:
     pass
 
-logger = logging.getLogger("I24ssx.DCID")
-
 
 # Collection start/end script to kick off analysis
 COLLECTION_START_SCRIPT = "/dls_sw/i24/scripts/RunAtStartOfCollect-i24-ssx.sh"
@@ -41,7 +39,7 @@ CREDENTIALS_LOCATION = "/scratch/ssx_dcserver.key"
 def get_auth_header() -> dict:
     """Read the credentials file and build the Authorisation header"""
     if not os.path.isfile(CREDENTIALS_LOCATION):
-        logger.warning(
+        SSX_LOGGER.warning(
             "Could not read %s; attempting to proceed without credentials",
             CREDENTIALS_LOCATION,
         )
@@ -205,12 +203,12 @@ class DCID:
 
             # Log what we are doing here
             try:
-                logger.info(
+                SSX_LOGGER.info(
                     "BRIDGE: POST /dc --data %s",
                     repr(json.dumps(data)),
                 )
             except Exception:
-                logger.info(
+                SSX_LOGGER.info(
                     "Caught exception converting data to JSON. Data:\n%s\nVERBOSE:\n%s",
                     str({k: type(v) for k, v in data.items()}),
                 )
@@ -224,20 +222,20 @@ class DCID:
             )
             resp.raise_for_status()
             self.dcid = resp.json()["dataCollectionId"]
-            logger.info("Generated DCID %s", self.dcid)
+            SSX_LOGGER.info("Generated DCID %s", self.dcid)
         except requests.HTTPError as e:
             self.error = True
-            logger.error(
+            SSX_LOGGER.error(
                 "DCID generation Failed; Reason from server: %s", e.response.text
             )
             if self.emit_errors:
                 raise
-            logger.exception("Error generating DCID: %s", e)
+            SSX_LOGGER.exception("Error generating DCID: %s", e)
         except Exception as e:
             self.error = True
             if self.emit_errors:
                 raise
-            logger.exception("Error generating DCID: %s", e)
+            SSX_LOGGER.exception("Error generating DCID: %s", e)
 
     def __int__(self):
         return self.dcid
@@ -248,13 +246,13 @@ class DCID:
             return None
         try:
             command = [COLLECTION_START_SCRIPT, str(self.dcid)]
-            logger.info("Running %s", " ".join(command))
+            SSX_LOGGER.info("Running %s", " ".join(command))
             subprocess.Popen(command)
         except Exception as e:
             self.error = True
             if self.emit_errors:
                 raise
-            logger.warning("Error starting start of collect script: %s", e)
+            SSX_LOGGER.warning("Error starting start of collect script: %s", e)
 
     def notify_end(self):
         """Send notifications that the collection has now ended"""
@@ -262,13 +260,13 @@ class DCID:
             return
         try:
             command = [COLLECTION_END_SCRIPT, str(self.dcid)]
-            logger.info("Running %s", " ".join(command))
+            SSX_LOGGER.info("Running %s", " ".join(command))
             subprocess.Popen(command)
         except Exception as e:
             self.error = True
             if self.emit_errors:
                 raise
-            logger.warning("Error running end of collect notification: %s", e)
+            SSX_LOGGER.warning("Error running end of collect notification: %s", e)
 
     def collection_complete(
         self, end_time: str | datetime.datetime | None = None, aborted: bool = False
@@ -285,7 +283,7 @@ class DCID:
             # end_time might be a string from time.ctime
             if isinstance(end_time, str):
                 end_time = datetime.datetime.strptime(end_time, "%a %b %d %H:%M:%S %Y")
-                logger.debug("Parsed end time: %s", end_time)
+                SSX_LOGGER.debug("Parsed end time: %s", end_time)
 
             if not end_time:
                 end_time = datetime.datetime.now().astimezone()
@@ -302,13 +300,13 @@ class DCID:
             if self.dcid is None:
                 # Print what we would have sent. This means that if something is failing,
                 # we still have the data to upload in the log files.
-                logger.info(
+                SSX_LOGGER.info(
                     'BRIDGE: No DCID but Would PATCH "/dc/XXXX" --data=%s',
                     repr(json.dumps(data)),
                 )
                 return
 
-            logger.info(
+            SSX_LOGGER.info(
                 'BRIDGE: PATCH "/dc/%s" --data=%s', self.dcid, repr(json.dumps(data))
             )
             response = requests.patch(
@@ -318,7 +316,7 @@ class DCID:
                 headers=get_auth_header(),
             )
             response.raise_for_status()
-            logger.info("Successfully updated end time for DCID %d", self.dcid)
+            SSX_LOGGER.info("Successfully updated end time for DCID %d", self.dcid)
         except Exception as e:
             resp_obj = getattr(e, "response", None)
             try:
@@ -333,7 +331,7 @@ class DCID:
             self.error = True
             if self.emit_errors:
                 raise
-            logger.warning("Error completing DCID: %s (%s)", e, resp_str)
+            SSX_LOGGER.warning("Error completing DCID: %s (%s)", e, resp_str)
 
 
 def get_pilatus_filename_template_from_pvs() -> str:
@@ -385,9 +383,9 @@ def get_beamsize() -> tuple[float | None, float | None]:
     h_mode = caget("BL24I-OP-MFM-01:G1:TARGETAPPLY")
     # Validate these and note an error otherwise
     if not v_mode.startswith("VMFM") or v_mode[4:] not in focus_modes:
-        logger.error("Unrecognised vertical beam mode %s", v_mode)
+        SSX_LOGGER.error("Unrecognised vertical beam mode %s", v_mode)
     if not h_mode.startswith("HMFM") or h_mode[4:] not in focus_modes:
-        logger.error("Unrecognised horizontal beam mode %s", h_mode)
+        SSX_LOGGER.error("Unrecognised horizontal beam mode %s", h_mode)
     _, h, _ = focus_modes.get(h_mode[4:], (None, None, None))
     _, _, v = focus_modes.get(v_mode[4:], (None, None, None))
 

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/src/mx_bluesky/beamlines/i24/serial/extruder/i24ssx_Extruder_Collect_py3v2.py

@@ -16,7 +16,7 @@ from time import sleep
 
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
-from blueapi.core import MsgGenerator
+from bluesky.utils import MsgGenerator
 from dodal.common import inject
 from dodal.devices.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
@@ -262,7 +262,7 @@ def main_extruder_plan(
         SSX_LOGGER.info("Using Eiger detector")
 
         SSX_LOGGER.debug(f"Creating the directory for the collection in {filepath}.")
-        Path(filepath).mkdir(parents=True)
+        Path(filepath).mkdir(parents=True, exist_ok=True)
 
         caput(pv.eiger_seqID, int(caget(pv.eiger_seqID)) + 1)
         SSX_LOGGER.info(f"Eiger quickshot setup: filepath {filepath}")

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/src/mx_bluesky/beamlines/i24/serial/fixed_target/FT-gui-edm/DiamondChipI24-py3v1.edl

@@ -1270,21 +1270,18 @@ topShadowColor index 1
 botShadowColor index 8
 controlPv "ME14E-MO-IOC-01:GP2"
 font "arial-medium-r-18.0"
-numItems 3
+numItems 2
 symbolTag {
   0 "None"
   1 "Mapping Lite"
-  2 "Full Mapping"
 }
 symbol0 {
   0 "NN"
   1 "ML"
-  2 "FM"
 }
 value0 {
   0 "none"
   1 "mappinglite"
-  2 "fullmapping"
 }
 endObjectProperties
 

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/src/mx_bluesky/beamlines/i24/serial/fixed_target/ft_utils.py

@@ -12,7 +12,6 @@ from enum import Enum, IntEnum
 class MappingType(IntEnum):
     NoMap = 0
     Lite = 1
-    Full = 2
 
     def __str__(self) -> str:
         """Returns the mapping."""

{mx_bluesky-1.4.0 → mx_bluesky-1.4.1a0}/src/mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_Chip_Collect_py3v1.py

@@ -10,7 +10,7 @@ from time import sleep
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
 import numpy as np
-from blueapi.core import MsgGenerator
+from bluesky.utils import MsgGenerator
 from dodal.common import inject
 from dodal.devices.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
@@ -77,7 +77,7 @@ def calculate_collection_timeout(parameters: FixedTargetParameters) -> float:
     Returns:
         The estimated collection time, in s.
     """
-    buffer = PMAC_MOVE_TIME * parameters.total_num_images + 2
+    buffer = PMAC_MOVE_TIME * parameters.total_num_images + 600
     pump_setting = parameters.pump_repeat
     collection_time = parameters.total_num_images * parameters.exposure_time_s
     if pump_setting in [
@@ -97,7 +97,7 @@ def calculate_collection_timeout(parameters: FixedTargetParameters) -> float:
         )
         if pump_setting == PumpProbeSetting.Medium1:
             # Long delay between pump and probe, with fast shutter opening and closing.
-            timeout = timeout + SHUTTER_OPEN_TIME
+            timeout = timeout + SHUTTER_OPEN_TIME * parameters.total_num_images
     return timeout
 
 
@@ -234,8 +234,6 @@ def load_motion_program_data(
             SSX_LOGGER.info(f"Map type is None, setting program prefix to {prefix}")
         elif map_type == MappingType.Lite:
             prefix = 12
-        elif map_type == MappingType.Full:
-            prefix = 13
         else:
             SSX_LOGGER.warning(f"Unknown Map Type, map_type = {map_type}")
             return
@@ -301,14 +299,6 @@ def get_prog_num(
         SSX_LOGGER.info(f"Map type: {str(map_type)}")
         SSX_LOGGER.info("Program number: 12")
         return 12
-    if map_type == MappingType.Full:
-        # TODO See https://github.com/DiamondLightSource/mx-bluesky/issues/515
-        SSX_LOGGER.info(f"Map type: {str(map_type)}")
-        SSX_LOGGER.info("Program number: 13")
-        # TODO once reinstated return 13
-        msg = "Full mapping is broken and currently disabled."
-        SSX_LOGGER.error(msg)
-        raise ValueError(msg)
 
 
 @log_on_entry
@@ -352,14 +342,6 @@ def datasetsizei24(
         total_numb_imgs = int(np.prod(chip_format) * block_count * n_exposures)
         SSX_LOGGER.info(f"Calculated number of images: {total_numb_imgs}")
 
-    elif map_type == MappingType.Full:
-        SSX_LOGGER.error("Not Set Up For Full Mapping")
-        raise ValueError("The beamline is currently not set for Full Mapping.")
-
-    else:
-        SSX_LOGGER.warning(f"Unknown Map Type, map_type = {str(map_type)}")
-        raise ValueError("Unknown map type")
-
     SSX_LOGGER.info("Set PV to calculated number of images.")
     caput(pv.me14e_gp10, int(total_numb_imgs))
 
@@ -444,7 +426,11 @@ def start_i24(
         )
 
         SSX_LOGGER.debug("Arm Pilatus. Arm Zebra.")
-        shutter_time_offset = SHUTTER_OPEN_TIME if PumpProbeSetting.Medium1 else 0.0
+        shutter_time_offset = (
+            SHUTTER_OPEN_TIME
+            if parameters.pump_repeat is PumpProbeSetting.Medium1
+            else 0.0
+        )
         yield from setup_zebra_for_fastchip_plan(
             zebra,
             parameters.detector_name,
@@ -467,7 +453,7 @@ def start_i24(
         SSX_LOGGER.info("Using Eiger detector")
 
         SSX_LOGGER.debug(f"Creating the directory for the collection in {filepath}.")
-        Path(filepath).mkdir(parents=True)
+        Path(filepath).mkdir(parents=True, exist_ok=True)
 
         SSX_LOGGER.info(f"Triggered Eiger setup: filepath {filepath}")
         SSX_LOGGER.info(f"Triggered Eiger setup: filename {filename}")
@@ -503,7 +489,11 @@ def start_i24(
         )
 
         SSX_LOGGER.debug("Arm Zebra.")
-        shutter_time_offset = SHUTTER_OPEN_TIME if PumpProbeSetting.Medium1 else 0.0
+        shutter_time_offset = (
+            SHUTTER_OPEN_TIME
+            if parameters.pump_repeat is PumpProbeSetting.Medium1
+            else 0.0
+        )
         yield from setup_zebra_for_fastchip_plan(
             zebra,
             parameters.detector_name,