mx-bluesky 1.4.5__tar.gz → 1.4.7__tar.gz

mx_bluesky-1.4.7/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @DiamondLightSource/developers-mx-daq

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/.github/CONTRIBUTING.md

@@ -17,6 +17,23 @@ Contributions and issues are most welcome! All issues and pull requests are hand
 
 **Work should not be done without an associated ticket describing what the work is**
 
+## Developing mx-bluesky and dodal
+
+Some issues will span the mx-bluesky repo and the dodal repo. When working on both at the same time, follow these instructions:
+1. An issue is created for the work, inside mx-bluesky. This issue should describe in as much detail as possible the work that needs to be done. Anyone is free to make a ticket and/or comment on one.
+2. If a developer is going to do the work they assign themselves to the issue.
+3. The developer makes a new branch in mx-bluesky with the format `issue_short_description` e.g. `122_create_a_contributing_file`. The developer also creates a new branch in dodal, with the format `mx_bluesky_issue_short_description` - the same as the mx-bluesky branch name but with `mx_bluesky_` in front. (External developers are also welcome to make forks)
+4. The developer does the work on these branches, adding their work in small commits. Commit messages should be informative and prefixed with the issue number e.g. `(#122) Added contributing file`.
+5. Once the developer has done the final commit in both repos, they find the latest commit SHA in the dodal repo using `git log`. In `mx-bluesky/pyproject.toml`, the developer changes `dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@{dodal_commmit_SHA}` using the SHA they just found.
+6. The developer commits and pushes this final change on mx-bluesky.
+7. The developer submits a dodal PR for the work they have done in the dodal repo. The pull request should start with `Fixes #issue_num` e.g. `Fixes #122`, and should link to the issue created in mx-bluesky. The developer should also add some background on how the reviewer might test the change.
+8. The developer submits a mx-bluesky PR for the work they have done in the mx-bluesky repo. The pull request should start with `Fixes #issue_num` e.g. `Fixes #122`. This PR should link to the dodal PR just created with something like "Also needs #456". Again, the developer should add some background on how the reviewer might test the change.
+9. If the developer has a particular person in mind to review the work they should assign that person to the PRs as a reviewer.
+10. The reviewer and developer go back and forth on the code until the reviewer approves it. (See "Reviewing Work" below)
+11. Once the work is approved on both PRs, the original developer merges them. The PRs should be merged at the same time.
+
+**Work should not be done without an associated ticket describing what the work is**
+
 ## Reviewing Work
 
 **Work must be reviewed by another developer before it can be merged**. Remember that work is reviewed for a number of reasons:
@@ -36,6 +53,8 @@ Developers are welcome to ignore **nit** comments if they wish and can choose no
 
 For minor changes to code reviewers are welcome to make the changes themselves but in this case the original developer should then recheck what the reviewer has done.
 
+When beginning to review a PR, it is recommended to assign the PR to yourself on GitHub so that other developers know that this code is already being reviewed. If you decide you cannot complete the review, remember to unassign yourself from this PR to let others know.
+
 ## Issue or Discussion?
 
 Github also offers [discussions](https://github.com/DiamondLightSource/mx-bluesky/discussions) as a place to ask questions and share ideas. If

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/.gitignore

@@ -12,6 +12,7 @@ env/
 # Output
 *.png
 !docs/*.png
+!tests/test_data/**/*.png
 
 # Distribution / packaging
 .Python

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
         args: ["--maxkb=500"]
       - id: check-yaml
         args: ["--allow-multiple-documents"]
-        exclude: ^helmchart/
+        exclude: ^helmcharts/
       - id: check-merge-conflict
       - id: end-of-file-fixer
 

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: mx-bluesky
-Version: 1.4.5
+Version: 1.4.7
 Summary: Bluesky tools for MX Beamlines at DLS
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -238,8 +238,8 @@ Requires-Dist: blueapi>=0.5.0
 Requires-Dist: daq-config-server>=0.1.1
 Requires-Dist: ophyd==1.9.0
 Requires-Dist: ophyd-async>=0.9.0a2
-Requires-Dist: bluesky>=1.13
-Requires-Dist: dls-dodal==1.40.0
+Requires-Dist: bluesky>=1.13.1
+Requires-Dist: dls-dodal==1.44.0
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: build; extra == "dev"
@@ -266,6 +266,7 @@ Requires-Dist: tox-direct; extra == "dev"
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: types-mock; extra == "dev"
 Requires-Dist: types-requests; extra == "dev"
+Dynamic: license-file
 
 mx-bluesky
 ===========================
@@ -284,7 +285,7 @@ Releases       https://github.com/DiamondLightSource/mx-bluesky/releases
 Getting Started
 ===============
 
-To get started with developing this repo at DLS run ``dls_dev_setup.sh``.
+To get started with developing this repo at DLS run ``./utility_scripts/dls_dev_env.sh``.
 
 If you want to develop interactively at the beamline we recommend using jupyter notebooks. You can get started with this by running::
 

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/README.rst

@@ -15,7 +15,7 @@ Releases       https://github.com/DiamondLightSource/mx-bluesky/releases
 Getting Started
 ===============
 
-To get started with developing this repo at DLS run ``dls_dev_setup.sh``.
+To get started with developing this repo at DLS run ``./utility_scripts/dls_dev_env.sh``.
 
 If you want to develop interactively at the beamline we recommend using jupyter notebooks. You can get started with this by running::
 

mx_bluesky-1.4.7/docs/developer/general/explanations/callback_and_run_logic.rst

@@ -0,0 +1,27 @@
+Callbacks and Run Logic
+========================
+
+Callbacks are used to trigger external services:
+
+- Ispyb deposition
+- Nexus writing
+- Zocalo triggering
+
+These are linked in that to trigger zocalo you need to have made an ispyb deposition, written a nexus file and have finished writing raw data to disk. Nexus files and ispyb depositions can be made at anytime, we do not need to have necessarily finished writing raw data. 
+
+Currently, the requirement of needing to have written to ispyb is explicit as the ispyb callback will emit to the zocalo callback. The nexus file is written when the hardware is read during a collection and so its ordering is implied. When instantiated the zocalo callback is told on which plan to trigger and it is up to the plan developer to make sure this plan finishes after data is written to the detector.
+
+In general, the ordering flow of when callbacks are triggered is controlled by emitting documents with the expected plan name and data.
+
+Rotation Scans
+---------------------
+
+There are currently two ways of doing rotation scans. A single scan creates one hdf file, one ispyb deposition and then triggers zocalo once. Multi rotation scans create one hdf file for all rotations but then N nexus files, N ispyb depositions and triggers zocalo N times.
+
+Single scans will be removed in https://github.com/DiamondLightSource/mx-bluesky/issues/847
+
+For multi rotations this is does by starting 1+2*N different runs:
+
+1. ``CONST.PLAN.ROTATION_MULTI``: This is emitted once for the whole multiple rotation. It is used by the nexus callback to get the full number of images and meta_data_run_number so that it knows which hdf file to use. When this is finished zocalo end is triggered.
+2. ``CONST.PLAN.ROTATION_OUTER``: Emitted N times, inside a ``CONST.PLAN.ROTATION_MULTI`` run. This is used to create the initial ispyb deposition and create the nexus writer (but not actually write the file)
+3. ``CONST.PLAN.ROTATION_MAIN``: Emitted N times, inside ``CONST.PLAN.ROTATION_OUTER`` run. Used to finish writing to ispyb (i.e. write success/failure) and to send collection information to zocalo.

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/docs/developer/general/how-to/get-started.rst

@@ -4,8 +4,8 @@ Get Started with mx-bluesky
 Development Environment
 =======================
 
-- Clone this repo: ``git@github.com:DiamondLightSource/mx-bluesky.git``
-- To install a ``dev`` environment run ``./dls_dev_setup.sh``. Note that this will also clone and install a local version of ``dodal``, as the ``mx-bluesky`` package makes use of the devices instantiated there. 
+- Clone this repo using SSH: ``git clone git@github.com:DiamondLightSource/mx-bluesky.git``
+- To install a ``dev`` environment, from the top level ``mx-bluesky`` directory, run ``./utility_scripts/dls_dev_env.sh``. Note that this will also clone and install a local version of ``dodal``, as the ``mx-bluesky`` package makes use of the devices instantiated there. 
 
 The recommended IDE is vscode, and a workspace which includes dodal has been set up in the repo. This can be used on a DLS machine as follows:
 

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/docs/developer/general/index.rst

@@ -41,6 +41,7 @@ Documentation is split into four categories, and each is also accessible from li
             :maxdepth: 1
 
             explanations/decisions
+            explanations/callback_and_run_logic
 
         +++
 

mx_bluesky-1.4.7/docs/developer/hyperion/how-to/update-panda-ioc.rst

@@ -0,0 +1,44 @@
+Update the PandA IOC
+=====================
+
+The IOC for the PandA can sometimes get out of sync with the production version of Ophyd-Async. Here is how to update it
+
+Check if the IOC needs updating
+""""""""""""""""""""""""""""""""
+
+- Check the minimum panda IOC version required in the version of ophyd-async used in Hyperion's release version. This can be found in the ``MINIMUM_PANDA_IOC`` constant in `_hdf_panda.py <https://github.com/bluesky/ophyd-async/blob/main/src/ophyd_async/fastcs/panda/_hdf_panda.py>`_
+
+- In a terminal:
+
+.. code-block:: bash
+
+    cd /dls_sw/work/R3.14.12.7/ioc/BL03I/BL03I-PY-IOC-02
+    source venv/bin/activate
+    pip freeze | grep pandablocks-ioc
+
+Note that the IOC location will soon be moving to ``prod`` instead of ``work``.
+
+- Compare the version from step one
+
+Updating the IOC
+""""""""""""""""""""""""""
+
+- Update the Python IOC repo in the venv:
+
+.. code-block:: bash
+
+    cd /dls_sw/work/R3.14.12.7/ioc/BL03I/BL03I-PY-IOC-02
+    source venv/bin/activate
+    pip install --upgrade pandablocks-ioc=={desired version}
+
+
+- After making sure the beamline isn't in use, restart the IOC:
+
+.. code-block:: bash
+
+    module load controls-tools
+
+    console BL03I-PY-IOC-02
+
+- Press ``ctrl+x``
+- Disconnect by pressing ``ctrl+e``, then press ``c``, then press ``.``

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/docs/developer/hyperion/index.rst

@@ -15,7 +15,20 @@ Documentation specific for the Hyperion module within MX-Bluesky
             reference/param-hierarchy
             reference/readme
             deploying-hyperion
+            system-tests
 
         +++
 
         Technical reference material on standards in use.
+
+    .. grid-item-card:: :material-regular:`task;3em`
+
+        .. toctree::
+            :caption: How-to Guides
+            :maxdepth: 1
+
+            how-to/update-panda-ioc
+
+        +++
+
+        Practical step-by-step guides for day-to-day dev tasks.

mx_bluesky-1.4.7/docs/developer/hyperion/system-tests.rst

@@ -0,0 +1,20 @@
+System Tests
+============
+
+The system tests are run by a project hosted in a GitLab private repository, `Hyperion System Testing`_.
+
+This contains a ``.gitlab-ci`` pipeline that defines a job that runs the tests.
+ 
+System Test Images
+------------------
+
+The system tests require a number of container images to run:
+
+   * The test runner image
+   * An ISPyB MariaDB database server image
+   * An ExpEye image
+
+It is expected that these images should need to change only infrequently and builds are triggered
+manually as needed - see the Hyperion System Testing project for how to rebuild them and how to trigger the tests. 
+
+.. _`Hyperion System Testing`: https://gitlab.diamond.ac.uk/MX-GDA/hyperion-system-testing

{mx_bluesky-1.4.5/helmchart → mx_bluesky-1.4.7/helmcharts/hyperion}/templates/deployment.yaml

@@ -14,13 +14,13 @@ spec:
     spec:
       securityContext:
         # gda2
-        runAsUser: {{  .Values.hyperion.runAsUser }}
-        runAsGroup: {{ .Values.hyperion.runAsGroup }}
-        supplementalGroups: {{ .Values.hyperion.supplementalGroups }}
+        runAsUser: {{  .Values.application.runAsUser }}
+        runAsGroup: {{ .Values.application.runAsGroup }}
+        supplementalGroups: {{ .Values.application.supplementalGroups }}
       volumes:
         - name: dls-sw-bl
           hostPath:
-            path: "/dls_sw/{{ .Values.hyperion.beamline }}"
+            path: "/dls_sw/{{ .Values.application.beamline }}"
             type: Directory
         - name: dls-sw-apps
           hostPath:
@@ -33,15 +33,15 @@ spec:
         # Bind some source folders for easier debugging        
         - name: src
           hostPath:
-            path: "{{ .Values.hyperion.projectDir }}/src"
+            path: "{{ .Values.application.projectDir }}/src"
             type: Directory
         - name: tests
           hostPath:
-            path: "{{ .Values.hyperion.projectDir }}/tests"
+            path: "{{ .Values.application.projectDir }}/tests"
             type: Directory
         - name: utility-scripts
           hostPath:
-            path: "{{ .Values.hyperion.projectDir }}/utility_scripts"
+            path: "{{ .Values.application.projectDir }}/utility_scripts"
             type: Directory
         - name: dodal
           hostPath:
@@ -50,14 +50,14 @@ spec:
         - name: logs
           hostPath:
             type: Directory
-            path: "{{ .Values.hyperion.logDir }}"
+            path: "{{ .Values.application.logDir }}"
         - name: data
           hostPath:
             type: Directory
-            path: "{{ .Values.hyperion.dataDir }}"
+            path: "{{ .Values.application.dataDir }}"
       containers:
       - name: hyperion
-        image: {{ .Values.hyperion.imageRepository}}/mx-bluesky:{{ .Values.hyperion.appVersion }}
+        image: {{ .Values.application.imageRepository}}/mx-bluesky:{{ .Values.application.appVersion }}
         securityContext:
           capabilities:
             # Required for hostNetwork 
@@ -103,29 +103,29 @@ spec:
             memory: "1Gi"
         ports:
           - name: hyperion-api
-            containerPort: {{ .Values.hyperion.containerPort }}
+            containerPort: {{ .Values.application.containerPort }}
             protocol: TCP
         env:
           - name: LOG_DIR
             value: /var/log/bluesky
           - name: BEAMLINE
-            value: "{{ .Values.hyperion.beamline }}"
-          {{- if not .Values.hyperion.dev }}
+            value: "{{ .Values.application.beamline }}"
+          {{- if not .Values.application.dev }}
           - name: ZOCALO_GO_USER
             value: "gda2"
           - name: ZOCALO_GO_HOSTNAME
-            value: "{{ .Values.hyperion.beamline }}-control"
+            value: "{{ .Values.application.beamline }}-control"
           - name: ZOCALO_CONFIG
             value: "/dls_sw/apps/zocalo/live/configuration.yaml"
           - name: ISPYB_CONFIG_PATH
-            value: "/dls_sw/dasc/mariadb/credentials/ispyb-hyperion-{{ .Values.hyperion.beamline }}.cfg"
+            value: "/dls_sw/dasc/mariadb/credentials/ispyb-hyperion-{{ .Values.application.beamline }}.cfg"
           {{- end }}
         readinessProbe:
           exec:
             command: [ "/app/hyperion/utility_scripts/docker/healthcheck.sh" ]
           periodSeconds: 5
         volumeMounts:
-          - mountPath: "/dls_sw/{{ .Values.hyperion.beamline }}"
+          - mountPath: "/dls_sw/{{ .Values.application.beamline }}"
             name: dls-sw-bl
             readOnly: true
             mountPropagation: HostToContainer
@@ -147,6 +147,6 @@ spec:
             name: dodal
           - mountPath: "/var/log/bluesky"
             name: logs
-          - mountPath: "/dls/{{ .Values.hyperion.beamline }}/data"
+          - mountPath: "/dls/{{ .Values.application.beamline }}/data"
             name: data
       hostNetwork: true

{mx_bluesky-1.4.5/helmchart → mx_bluesky-1.4.7/helmcharts/hyperion}/templates/ingress.yaml

@@ -1,4 +1,4 @@
-{{- if not .Values.hyperion.dev }}
+{{- if not .Values.application.dev }}
 apiVersion: networking.k8s.io/v1
 kind: Ingress
 metadata:
@@ -7,9 +7,9 @@ spec:
   ingressClassName: nginx
   tls:
   - hosts:
-    - {{ .Values.hyperion.externalHostname }}
+    - {{ .Values.application.externalHostname }}
   rules:
-  - host: {{ .Values.hyperion.externalHostname }}
+  - host: {{ .Values.application.externalHostname }}
     http:
       paths:
       - path: /
@@ -18,6 +18,6 @@ spec:
           service:
             name: hyperion-svc # this must match the name of the service you want to target
             port:
-              number: {{ .Values.hyperion.containerPort }}
+              number: {{ .Values.application.containerPort }}
   {{- end }}
   

{mx_bluesky-1.4.5/helmchart → mx_bluesky-1.4.7/helmcharts/hyperion}/templates/service.yaml

@@ -3,15 +3,15 @@ kind: Service
 metadata:
   name: hyperion-svc
 spec:
-  {{- if .Values.hyperion.dev }}
+  {{- if .Values.application.dev }}
   type: LoadBalancer
   {{- else }}
   type: ClusterIP
   {{- end }}
   ports:
     - name: hyperion-api
-      port: {{ .Values.hyperion.servicePort }}
+      port: {{ .Values.application.servicePort }}
       protocol: TCP
-      targetPort: {{ .Values.hyperion.containerPort }}
+      targetPort: {{ .Values.application.containerPort }}
   selector:
     app: hyperion

{mx_bluesky-1.4.5/helmchart → mx_bluesky-1.4.7/helmcharts/hyperion}/values.yaml

@@ -1,4 +1,4 @@
-hyperion:
+application:
   containerPort: 5005
   servicePort: 80
   imageRepository: ghcr.io/diamondlightsource

mx_bluesky-1.4.7/helmcharts/redis-to-murko/Chart.yaml

@@ -0,0 +1,6 @@
+apiVersion: v2
+name: redis-to-murko
+description: Redis to murko server
+type: application
+# version of the chart
+version: 0.0.1

mx_bluesky-1.4.7/helmcharts/redis-to-murko/templates/deployment.yaml

@@ -0,0 +1,73 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Values.application.name }}-deployment
+spec:
+  selector:
+    matchLabels:
+      app: {{ .Values.application.name }}
+  replicas: 1
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.application.name }}
+        project: murko
+    spec:
+      securityContext:
+        runAsUser: {{  .Values.application.runAsUser }}
+        runAsGroup: {{ .Values.application.runAsGroup }}
+        supplementalGroups: {{ .Values.application.supplementalGroups }}
+      volumes:
+        - name: dls-sw-bl
+          hostPath:
+            path: "/dls_sw/{{ .Values.application.beamline }}"
+            type: Directory
+        # Bind some source folders for easier debugging        
+        - name: src
+          hostPath:
+            path: "{{ .Values.application.projectDir }}/src"
+            type: Directory
+        - name: tests
+          hostPath:
+            path: "{{ .Values.application.projectDir }}/tests"
+            type: Directory
+        - name: utility-scripts
+          hostPath:
+            path: "{{ .Values.application.projectDir }}/utility_scripts"
+            type: Directory
+        - name: dodal
+          hostPath:
+            path: "{{ .Values.dodal.projectDir | clean }}"
+            type: Directory
+      containers:
+      - name: {{ .Values.application.name }}
+        image: {{ .Values.application.imageRepository}}/mx-bluesky:{{ .Values.application.appVersion }}    
+        command: ["redis_to_murko"]      
+        resources:
+          limits:
+            cpu: "1"
+            memory: "1Gi"
+        env:
+          - name: LOG_DIR
+            value: /var/log/bluesky
+          - name: BEAMLINE
+            value: "{{ .Values.application.beamline }}"
+          - name: VALKEY_PASSWORD
+            valueFrom:
+             secretKeyRef:
+               name: valkey-secret
+               key: requirepass
+        volumeMounts:
+          - mountPath: "/dls_sw/{{ .Values.application.beamline }}"
+            name: dls-sw-bl
+            readOnly: true
+            mountPropagation: HostToContainer
+          - mountPath: "/app/hyperion/src"
+            name: src
+          - mountPath: "/app/hyperion/tests"
+            name: tests
+          - mountPath: "/app/hyperion/utility_scripts"
+            name: utility-scripts
+          - mountPath: "/app/dodal"
+            name: dodal
+      hostNetwork: false

mx_bluesky-1.4.7/helmcharts/redis-to-murko/values.yaml

@@ -0,0 +1,17 @@
+podSecurityContext: {}
+
+application:
+  name: redis-to-murko
+  imageRepository: ghcr.io/diamondlightsource
+  beamline: i04
+  # i03-hyperion user and group
+  runAsUser: 36101
+  runAsGroup: 36101
+  supplementalGroups: []
+  # These should be overridden at install time
+  projectDir: SET_ON_INSTALL
+  appVersion: SET_ON_INSTALL
+dodal:
+  projectDir: SET_ON_INSTALL
+service:
+  type: NodePort

{mx_bluesky-1.4.5/.github/PULL_REQUEST_TEMPLATE → mx_bluesky-1.4.7}/pull_request_template.md

@@ -1,7 +1,7 @@
 Fixes #ISSUE
 
 Link to dodal PR (if required): #XXX
-(remember to update `setup.cfg` with the dodal commit tag if you need it for tests to pass!)
+(remember to update `pyproject.toml` with the dodal commit tag if you need it for tests to pass!)
 
 ### Instructions to reviewer on how to test:
 

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/pyproject.toml

@@ -45,8 +45,8 @@ dependencies = [
     "daq-config-server >= 0.1.1",
     "ophyd == 1.9.0",
     "ophyd-async >= 0.9.0a2",
-    "bluesky >= 1.13",
-    "dls-dodal == 1.40.0",
+    "bluesky >= 1.13.1",
+    "dls-dodal == 1.44.0",
 ]
 
 
@@ -94,6 +94,7 @@ hyperion = "mx_bluesky.hyperion.__main__:main"
 hyperion-callbacks = "mx_bluesky.hyperion.external_interaction.callbacks.__main__:main"
 hyperion-generate-test-nexus = "mx_bluesky.hyperion.utils.validation:generate_test_nexus"
 hyperion-populate-test-and-meta-files = "mx_bluesky.hyperion.utils.validation:copy_test_meta_data_files"
+redis_to_murko = "mx_bluesky.beamlines.i04.redis_to_murko_forwarder:main"
 
 [project.urls]
 GitHub = "https://github.com/DiamondLightSource/mx-bluesky"
@@ -119,6 +120,7 @@ markers = [
     "dlstbx: marks tests as requiring dlstbx (deselect with '-m \"not dlstbx\"')",
     "skip_log_setup: marks tests so that loggers are not setup before the test.",
     "skip_in_pycharm: marks test as not working in pycharm testrunner",
+    "system_test: marks tests as a system test",
 ]
 addopts = """
     --tb=native -vv --doctest-modules --doctest-glob="*.rst" --durations=10
@@ -128,6 +130,8 @@ filterwarnings = [
     "error",
     # Ignore deprecation warning from sqlalchemy
     "ignore::sqlalchemy.exc.MovedIn20Warning",
+    # Remove when there's a fix for https://github.com/DiamondLightSource/ispyb-api/issues/233
+    "ignore::sqlalchemy.exc.SADeprecationWarning",
     # Ignore deprecation warning from setuptools_dso (remove when https://github.com/epics-base/setuptools_dso/issues/36 is released)
     "ignore::DeprecationWarning:wheel",
     # Ophyd status objects in tests
@@ -147,6 +151,11 @@ filterwarnings = [
     "ignore:.*custom tp_new.*:DeprecationWarning",
     # Ignore warning about deprecated throw() call https://github.com/bluesky/bluesky/issues/1817
     "ignore:.*signature of throw\\(\\) is deprecated.*:DeprecationWarning",
+    # Ignore warning about deprecations in python-workflows encountered during system tests
+    # https://github.com/DiamondLightSource/python-workflows/issues/188
+    "ignore:.*`Field` should not be instantiated.*:marshmallow.warnings.ChangedInMarshmallow4Warning",
+    # https://github.com/bluesky/ophyd-async/issues/838 and https://github.com/seperman/deepdiff/issues/536
+    "ignore:Accessing this attribute on the instance is deprecated",
 ]
 # Doctest python code in docs, python code in src docstrings, test functions in tests
 testpaths = "docs src tests/unit_tests"
@@ -165,10 +174,12 @@ legacy_tox_ini = """
 [tox]
 skipsdist=True
 
-[testenv:{pre-commit,type-checking,tests,docs}]
+[testenv:{pre-commit,type-checking,tests,docs,systemtests}]
 # Don't create a virtualenv for the command, requires tox-direct plugin
 direct = True
 passenv = *
+setenv =
+    systemtests: DODAL_TEST_MODE=true
 allowlist_externals =
     pytest
     pre-commit
@@ -180,6 +191,7 @@ commands =
     type-checking: pyright src tests {posargs}
     tests: pytest --cov=mx_bluesky --cov-report term --cov-report xml:cov.xml {posargs}
     docs: sphinx-{posargs:build -EW --keep-going} -T docs build/html
+    systemtests: pytest --junit-xml=systemtests_output.xml -m system_test tests/system_tests
 commands_pre =
     docs: /usr/bin/bash -c "{toxinidir}/utility_scripts/generate_plantuml.py > \
         docs/developer/hyperion/reference/param_hierarchy.puml"
@@ -189,14 +201,17 @@ commands_pre =
 src = ["src", "tests"]
 line-length = 88
 lint.select = [
-    "B",   # flake8-bugbear - https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
-    "C4",  # flake8-comprehensions - https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-    "E",   # pycodestyle errors - https://docs.astral.sh/ruff/rules/#error-e
-    "F",   # pyflakes rules - https://docs.astral.sh/ruff/rules/#pyflakes-f
-    "W",   # pycodestyle warnings - https://docs.astral.sh/ruff/rules/#warning-w
-    "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
+    "B",      # flake8-bugbear - https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+    "C4",     # flake8-comprehensions - https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+    "E",      # pycodestyle errors - https://docs.astral.sh/ruff/rules/#error-e
+    "F",      # pyflakes rules - https://docs.astral.sh/ruff/rules/#pyflakes-f
+    "W",      # pycodestyle warnings - https://docs.astral.sh/ruff/rules/#warning-w
+    "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
+    "PT012",  # flake8-pytest-style rules - https://docs.astral.sh/ruff/rules/pytest-raises-with-multiple-statements/#pytest-raises-with-multiple-statements-pt012
+    "RUF018", # walrus operators in asserts - https://docs.astral.sh/ruff/rules/assignment-in-assert/
+    "TID251", # banned api - https://docs.astral.sh/ruff/rules/banned-api/
 ]
 lint.extend-ignore = [
     "E501", # Line too long
@@ -205,8 +220,11 @@ lint.extend-ignore = [
 [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", "B023"]
+# Remove this line to forbid private member access, walrys operators in asserts, banned api in tests
+"tests/**/*" = ["SLF001", "B023", "RUF018", "TID251"]
+
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
+"time.sleep".msg = "Use bps.sleep instead. # noqa will disable this rule for that line. See https://github.com/DiamondLightSource/mx-bluesky/issues/925"
 
 [tool.mypy]
 plugins = ["pydantic.mypy"]

{mx_bluesky-1.4.5 → mx_bluesky-1.4.7}/src/mx_bluesky/_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 = '1.4.5'
-__version_tuple__ = version_tuple = (1, 4, 5)
+__version__ = version = '1.4.7'
+__version_tuple__ = version_tuple = (1, 4, 7)

mx_bluesky-1.4.7/src/mx_bluesky/beamlines/aithre_lasershaping/__init__.py

@@ -0,0 +1,13 @@
+from mx_bluesky.beamlines.aithre_lasershaping.check_goniometer_performance import (
+    check_omega_performance,
+)
+from mx_bluesky.beamlines.aithre_lasershaping.goniometer_controls import (
+    change_goniometer_turn_speed,
+    rotate_goniometer_relative,
+)
+
+__all__ = [
+    "check_omega_performance",
+    "change_goniometer_turn_speed",
+    "rotate_goniometer_relative",
+]