mx-bluesky 1.5.16__tar.gz → 1.6.3__tar.gz

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/.github/workflows/_helm.yml

@@ -19,7 +19,7 @@ jobs:
       - name: Helm login to GHCR
         if: ${{ github.event_name == 'push' && github.ref_type == 'tag' }}
         run: |
-          echo ${{ secrets.GITHUB_TOKEN }} | helm registry login ghcr.io/${{ github.repository }} --username ${{ github.repository_owner }} --password-stdin
+          echo ${{ secrets.GITHUB_TOKEN }} | helm registry login ghcr.io --username DiamondLightSource --password-stdin
 
       - name: Get version from Git tag
         id: meta

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/.github/workflows/_test.yml

@@ -28,15 +28,12 @@ jobs:
 
       - name: Install uv
         uses: astral-sh/setup-uv@v7
-      
-      - name: Update dodal
-        run: uv add --upgrade dls-dodal
-      
+
       - name: Run tests
         # Longer timeout for CI due to likelihood of cold caches,
         # cloud infra hw contention etc.
         run: uv run --locked tox -e tests -- -m "not dlstbx" --timeout=2 --cov=mx_bluesky --cov-report term --cov-report xml:cov.xml
-      
+
       - name: Print dependency versions
         if: always()
         run: uv pip list

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/.github/workflows/_tox.yml

@@ -5,7 +5,11 @@ on:
         type: string
         description: What to run under tox
         required: true
-
+      skip_hooks:
+        description: "Comma-separated pre-commit hook IDs to skip"
+        required: false
+        type: string
+        default: "" # important so the context always exists
 
 jobs:
   run:
@@ -18,8 +22,7 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v7
 
-      - name: Update dodal
-        run: uv add --upgrade dls-dodal
-
       - name: Run tox
+        env:
+          SKIP: ${{ inputs.skip_hooks }}
         run: uv run --locked tox -e ${{ inputs.tox }}

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/.github/workflows/ci.yml

@@ -5,11 +5,10 @@ on:
     branches:
       - main
     tags:
-      - '*'
+      - "*"
   pull_request:
 
 jobs:
-
   require-label:
     if: github.event_name == 'pull_request'
     uses: ./.github/workflows/_label.yml
@@ -18,6 +17,7 @@ jobs:
     uses: ./.github/workflows/_tox.yml
     with:
       tox: pre-commit,type-checking
+      skip_hooks: local-install-dodal
 
   test:
     strategy:
@@ -64,14 +64,14 @@ jobs:
 
   dist:
     uses: ./.github/workflows/_dist.yml
-  
+
   pypi:
     needs: [dist, test]
     if: github.ref_type == 'tag'
     uses: ./.github/workflows/_pypi.yml
     permissions:
       id-token: write
-  
+
   release:
     needs: [dist, test, docs]
     if: github.ref_type == 'tag'

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/.pre-commit-config.yaml

@@ -35,6 +35,12 @@ repos:
         types: [python]
         require_serial: false
 
+      - id: lock dodal
+        name: keep dodal up to date in lockfile
+        pass_filenames: false
+        language: system
+        entry: uv lock --upgrade-package dls-dodal
+
       - id: uv-sync
         name: update uv.lock and venv
         pass_filenames: false
@@ -42,9 +48,16 @@ repos:
         entry: uv sync
         files: ^(uv\.lock|pyproject\.toml)$
 
+      - id: local-install-dodal
+        name: editable install of dodal
+        language: system
+        pass_filenames: false
+        entry: uv pip install -e ../dodal
+        files: ^(uv\.lock|pyproject\.toml)$
+
   # Type checking
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.19.1
     hooks:
       - id: mypy
         files: 'src/.*\.py$'

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/Dockerfile

@@ -2,6 +2,8 @@
 # or docker with user namespaces.
 FROM ghcr.io/diamondlightsource/ubuntu-devcontainer:noble AS developer
 
+ENV CMAKE_POLICY_VERSION_MINIMUM=3.5
+
 # Add any system dependencies for the developer/build environment here
 RUN apt-get update -y && apt-get install -y --no-install-recommends \
     graphviz \
@@ -10,10 +12,6 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \
     libxext6 \
     && apt-get dist-clean
 
-# Set up a virtual environment and put it in PATH
-RUN python -m venv /venv
-ENV PATH=/venv/bin:$PATH
-
 # The build stage installs the context into the venv
 FROM developer AS build
 

mx_bluesky-1.6.3/Dockerfile.blueapi

@@ -0,0 +1,24 @@
+# Before changing this BlueAPI version number, you should check that 
+# the BlueAPI pin in pyproject.toml is compatible, else the version will
+# be overridden
+FROM ghcr.io/diamondlightsource/blueapi:latest
+USER root
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Need:
+# libgl, libglib2.0 for python cv2 dependency 
+RUN apt update -y && \
+    apt upgrade -y && \
+    apt install -y libgl1 libglib2.0-0
+
+RUN uv pip install --no-cache-dir --no-compile mx-bluesky
+
+# Create and set permissions for uv venv, root cache
+# and user cache. Allows Blueapi's setup-scratch
+# to change dependencies without permission errors
+RUN mkdir -p /app/.venv /root/.cache/uv /home/app/.cache/uv \
+    && chmod -R 777 /app/.venv /root/.cache/uv /home/app/.cache/uv
+
+
+USER ubuntu

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mx-bluesky
-Version: 1.5.16
+Version: 1.6.3
 Summary: Bluesky tools for MX Beamlines at DLS
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -242,7 +242,7 @@ Requires-Dist: blueapi>=1.8.0
 Requires-Dist: ophyd>=1.10.5
 Requires-Dist: ophyd-async>=0.14.0
 Requires-Dist: bluesky>=1.14.6
-Requires-Dist: dls-dodal==1.69.0
+Requires-Dist: dls-dodal==2.0.0
 Dynamic: license-file
 
 mx-bluesky

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/docs/developer/serial-crystallography-on-i24/how-to/pmac-docs.rst

@@ -12,7 +12,7 @@ Among these:
 - Laser control
 
 
-For reference, see also the PMAC device implementation in dodal: `PMAC docs <https://diamondlightsource.github.io/dodal/main/reference/generated/dodal.devices.i24.pmac.html>`_
+For reference, see also the PMAC device implementation in dodal: `PMAC docs <https://diamondlightsource.github.io/dodal/main/reference/generated/dodal.devices.beamlines.i24.pmac.html>`_
 
 
 Stage motor moves using the PMAC device

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/helm/hyperion/templates/zocalo-config.yaml

@@ -30,7 +30,6 @@ data:
     environments:
 
       bluesky:
-        logging: graylog
         plugins:
           - default-transport
         {{- if .Values.zocalo.secrets }}

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/helm/mx-bluesky-blueapi/templates/zocalo-config.yaml

@@ -28,7 +28,6 @@ data:
     environments:
 
       bluesky:
-        logging: graylog
         plugins:
           - default-transport
         {{- if .Values.zocalo.secrets }}

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/pyproject.toml

@@ -2,6 +2,10 @@
 requires = ["setuptools>=64", "setuptools_scm[toml]>=8"]
 build-backend = "setuptools.build_meta"
 
+[tool.uv]
+# Restrict lockfile to a sane subset of platforms
+environments = ["sys_platform == 'linux' and platform_machine == 'x86_64'"]
+
 [project]
 name = "mx-bluesky"
 classifiers = [
@@ -50,7 +54,7 @@ dependencies = [
     "ophyd >= 1.10.5",
     "ophyd-async >= 0.14.0",
     "bluesky >= 1.14.6",
-    "dls-dodal == 1.69.0",
+    "dls-dodal == 2.0.0",
 ]
 
 
@@ -90,6 +94,7 @@ dev = [
     "tox-uv",
     "types-mock",
     "types-requests",
+    "sphinxcontrib.mermaid", # To build dodal docs
 ]
 
 [project.scripts]
@@ -208,7 +213,7 @@ commands = [
 description = "Run tests with coverage"
 commands = [
     [
-        "pytest", 
+        "pytest",
         "--cov=mx_bluesky",
         "--cov-report",
         "term",
@@ -225,27 +230,23 @@ description = "Run tests with coverage"
 commands = [
     [
         "pytest",
+        "--junit-xml=systemtests_output.xml",
         "-m",
         "system_test",
-        "tests/system_test",
+        "tests/system_tests",
         "--timeout=60",
         { replace = "posargs", default = [
         ], extend = true },
     ],
 ]
+set_env = { DODAL_TEST_MODE = "true" }
 
 
 # Runs the system tests locally
 [tool.tox.env.localsystemtests]
-setenv = [
-    "DOCKER=podman",
-    "DODAL_TEST_MODE=true",
-    "ISPYB_CONFIG_PATH={toxinidir}/tests/test_data/ispyb-test-credentials.cfg",
-    "ZOCALO_CONFIG={toxinidir}/tests/test_data/zocalo-test-configuration.yaml",
-]
 commands = [
     [
-        "pytest", 
+        "pytest",
         "-m",
         "system_test",
         "--timeout=60",
@@ -255,8 +256,23 @@ commands = [
     ],
 ]
 
+[tool.tox.env.localsystemtests.set_env]
+DOCKER = "podman"
+DODAL_TEST_MODE = "true"
+ISPYB_CONFIG_PATH = "{toxinidir}/tests/test_data/ispyb-test-credentials.cfg"
+ZOCALO_CONFIG = "{toxinidir}/tests/test_data/zocalo-test-configuration.yaml"
+
 [tool.tox.env.docs]
 description = "Run docs build with clean environment"
+env_dir = ".venv"
+skip_install = true
+commands_pre = [
+    [
+        "python",
+        "{toxinidir}/utility_scripts/generate_plantuml.py",
+        "docs/developer/hyperion/reference/param_hierarchy.puml",
+    ],
+]
 commands = [
     [
         "sphinx-build",
@@ -278,7 +294,7 @@ commands = [
         "sphinx-autobuild",
         "--show-traceback",
         "--watch",
-        "README.md",
+        "README.rst",
         "docs",
         "build/html",
         { replace = "posargs", default = [

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/run_hyperion.sh

@@ -119,18 +119,16 @@ if [[ $START == 1 ]]; then
     if [ $IN_DEV == false ]; then
         check_user
         ISPYB_CONFIG_PATH="/dls_sw/dasc/mariadb/credentials/ispyb-hyperion-${BEAMLINE}.cfg"
+        ZOCALO_CONFIG=/dls_sw/apps/zocalo/live/configuration.yaml 
     else
         ISPYB_CONFIG_PATH="$RELATIVE_SCRIPT_DIR/tests/test_data/ispyb-test-credentials.cfg"
         ZOCALO_CONFIG="$RELATIVE_SCRIPT_DIR/tests/test_data/zocalo-test-configuration.yaml"
-        export ZOCALO_CONFIG
     fi
+    export ZOCALO_CONFIG
     export ISPYB_CONFIG_PATH
 
     kill_active_apps
 
-    module unload controls_dev
-    module load dials
-
     cd ${RELATIVE_SCRIPT_DIR}
 
     if [ -z "$LOG_DIR" ]; then

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/src/mx_bluesky/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.5.16'
-__version_tuple__ = version_tuple = (1, 5, 16)
+__version__ = version = '1.6.3'
+__version_tuple__ = version_tuple = (1, 6, 3)
 
-__commit_id__ = commit_id = 'g9274f2ea3'
+__commit_id__ = commit_id = 'ge6527680e'

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/src/mx_bluesky/beamlines/i02_1/parameters/gridscan.py

@@ -1,4 +1,4 @@
-from dodal.devices.i02_1.fast_grid_scan import ZebraGridScanParamsTwoD
+from dodal.devices.beamlines.i02_1.fast_grid_scan import ZebraGridScanParamsTwoD
 from scanspec.specs import Product
 
 from mx_bluesky.common.parameters.components import SplitScan, WithOptionalEnergyChange

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/src/mx_bluesky/beamlines/i04/__init__.py

@@ -2,6 +2,8 @@ from mx_bluesky.beamlines.i04.experiment_plans.i04_grid_detect_then_xray_centre_
     i04_default_grid_detect_and_xray_centre,
 )
 from mx_bluesky.beamlines.i04.oav_centering_plans.oav_imaging import (
+    find_beam_centres,
+    optimise_transmission_with_oav,
     take_oav_image_with_scintillator_in,
 )
 from mx_bluesky.beamlines.i04.thawing_plan import (
@@ -16,4 +18,6 @@ __all__ = [
     "i04_default_grid_detect_and_xray_centre",
     "thaw_and_murko_centre",
     "take_oav_image_with_scintillator_in",
+    "optimise_transmission_with_oav",
+    "find_beam_centres",
 ]

{mx_bluesky-1.5.16 → mx_bluesky-1.6.3}/src/mx_bluesky/beamlines/i04/experiment_plans/i04_grid_detect_then_xray_centre_plan.py

@@ -9,6 +9,8 @@ from dodal.common import inject
 from dodal.devices.aperturescatterguard import ApertureScatterguard, ApertureValue
 from dodal.devices.attenuator.attenuator import BinaryFilterAttenuator
 from dodal.devices.backlight import Backlight
+from dodal.devices.beamlines.i04.beamsize import Beamsize
+from dodal.devices.beamlines.i04.transfocator import Transfocator
 from dodal.devices.common_dcm import DoubleCrystalMonochromator
 from dodal.devices.detector.detector_motion import DetectorMotion
 from dodal.devices.eiger import EigerDetector
@@ -17,8 +19,6 @@ from dodal.devices.fast_grid_scan import (
     set_fast_grid_scan_params,
 )
 from dodal.devices.flux import Flux
-from dodal.devices.i04.beamsize import Beamsize
-from dodal.devices.i04.transfocator import Transfocator
 from dodal.devices.mx_phase1.beamstop import Beamstop
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.pin_image_recognition import PinTipDetection