Migrate to copier

.copier-answers.yml

@@ -5,12 +5,12 @@ author_email: [email protected]
 author_name: Dominic Oram
 component_owner: group:data-acquisition
 description: Bluesky tools for MX Beamlines at DLS
-distribution_name: mx_bluesky
+distribution_name: mx-bluesky
 docker: true
 docs_type: sphinx
 git_platform: github.com
 github_org: DiamondLightSource
 package_name: mx_bluesky
 pypi: true
-repo_name: mx_bluesky
+repo_name: mx-bluesky
 type_checker: pyright

.devcontainer/Dockerfile

@@ -33,5 +33,5 @@ COPY --from=build /venv/ /venv/
 ENV PATH=/venv/bin:$PATH
 
 # change this entrypoint if it is not the same as the repo
-ENTRYPOINT ["mx_bluesky"]
+ENTRYPOINT ["mx-bluesky"]
 CMD ["--version"]

.github/CONTRIBUTING.md

@@ -1,14 +1,14 @@
 # Contribute to the project
 
 Contributions and issues are most welcome! All issues and pull requests are
-handled through [GitHub](https://github.com/DiamondLightSource/mx_bluesky/issues). Also, please check for any existing issues before
+handled through [GitHub](https://github.com/DiamondLightSource/mx-bluesky/issues). Also, please check for any existing issues before
 filing a new one. If you have a great idea but it involves big changes, please
 file a ticket before making a pull request! We want to make sure you don't spend
 your time coding something that might not fit the scope of the project.
 
 ## Issue or Discussion?
 
-Github also offers [discussions](https://github.com/DiamondLightSource/mx_bluesky/discussions) as a place to ask questions and share ideas. If
+Github also offers [discussions](https://github.com/DiamondLightSource/mx-bluesky/discussions) as a place to ask questions and share ideas. If
 your issue is open ended and it is not obvious when it can be "closed", please
 raise it as a discussion instead.
 

.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       matrix:
         runs-on: ["ubuntu-latest"] # can add windows-latest, macos-latest
-        python-version: ["3.10", "3.11"] # , "3.12"] # when the dependency thing is resolved
+        python-version: ["3.10", "3.11"] # , "3.12"] # add 3.12 when p4p #145 is fixed
         include:
           # Include one that runs in the dev environment
           - runs-on: "ubuntu-latest"

Dockerfile

@@ -1,7 +1,7 @@
 # The devcontainer should use the developer target and run as root with podman
 # or docker with user namespaces.
 ARG PYTHON_VERSION=3.11
 FROM python:${PYTHON_VERSION} as developer
 
 # Add any system dependencies for the developer/build environment here
 RUN apt-get update && apt-get install -y --no-install-recommends \
@@ -13,17 +13,17 @@
 ENV PATH=/venv/bin:$PATH
 
 # The build stage installs the context into the venv
 FROM developer as build
 COPY . /context
 WORKDIR /context
 RUN touch dev-requirements.txt && pip install -c dev-requirements.txt .
 
 # The runtime stage copies the built venv into a slim runtime container
 FROM python:${PYTHON_VERSION}-slim as runtime
 # Add apt-get system dependecies for runtime here if needed
 COPY --from=build /venv/ /venv/
 ENV PATH=/venv/bin:$PATH
 
 # change this entrypoint if it is not the same as the repo
-ENTRYPOINT ["mx_bluesky"]
+ENTRYPOINT ["mx-bluesky"]
 CMD ["--version"]

README.rst

@@ -1,15 +1,15 @@
-mx_bluesky
+mx-bluesky
 ===========================
 
 |code_ci| |docs_ci| |coverage| |pypi_version| |license|
 
 Contains code for working with Bluesky on MX beamlines at Diamond
 
 ============== ==============================================================
-PyPI           ``pip install mx_bluesky``
-Source code    https://github.com/DiamondLightSource/mx_bluesky
-Documentation  https://DiamondLightSource.github.io/mx_bluesky
-Releases       https://github.com/DiamondLightSource/mx_bluesky/releases
+PyPI           ``pip install mx-bluesky``
+Source code    https://github.com/DiamondLightSource/mx-bluesky
+Documentation  https://DiamondLightSource.github.io/mx-bluesky
+Releases       https://github.com/DiamondLightSource/mx-bluesky/releases
 ============== ==============================================================
 
 Getting Started
@@ -26,20 +26,20 @@ If you're doing more in-depth development we recommend developing with VSCode. Y
     $ module load vscode
     $ code .vscode/mx-bluesky.code-workspace
 
-.. |code_ci| image:: https://github.com/DiamondLightSource/mx_bluesky/actions/workflows/code.yml/badge.svg?branch=main
-    :target: https://github.com/DiamondLightSource/mx_bluesky/actions/workflows/code.yml
+.. |code_ci| image:: https://github.com/DiamondLightSource/mx-bluesky/actions/workflows/code.yml/badge.svg?branch=main
+    :target: https://github.com/DiamondLightSource/mx-bluesky/actions/workflows/code.yml
     :alt: Code CI
 
-.. |docs_ci| image:: https://github.com/DiamondLightSource/mx_bluesky/actions/workflows/docs.yml/badge.svg?branch=main
-    :target: https://github.com/DiamondLightSource/mx_bluesky/actions/workflows/docs.yml
+.. |docs_ci| image:: https://github.com/DiamondLightSource/mx-bluesky/actions/workflows/docs.yml/badge.svg?branch=main
+    :target: https://github.com/DiamondLightSource/mx-bluesky/actions/workflows/docs.yml
     :alt: Docs CI
 
-.. |coverage| image:: https://codecov.io/gh/DiamondLightSource/mx_bluesky/branch/main/graph/badge.svg
-    :target: https://codecov.io/gh/DiamondLightSource/mx_bluesky
+.. |coverage| image:: https://codecov.io/gh/DiamondLightSource/mx-bluesky/branch/main/graph/badge.svg
+    :target: https://codecov.io/gh/DiamondLightSource/mx-bluesky
     :alt: Test Coverage
 
-.. |pypi_version| image:: https://img.shields.io/pypi/v/mx_bluesky.svg
-    :target: https://pypi.org/project/mx_bluesky
+.. |pypi_version| image:: https://img.shields.io/pypi/v/mx-bluesky.svg
+    :target: https://pypi.org/project/mx-bluesky
     :alt: Latest PyPI version
 
 .. |license| image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
@@ -50,4 +50,4 @@ If you're doing more in-depth development we recommend developing with VSCode. Y
     Anything below this line is used when viewing README.rst and will be replaced
     when included in index.rst
 
-See https://DiamondLightSource.github.io/mx_bluesky for more detailed documentation.
+See https://DiamondLightSource.github.io/mx-bluesky for more detailed documentation.

catalog-info.yaml

@@ -1,12 +1,12 @@
 apiVersion: backstage.io/v1alpha1
 kind: Component
 metadata:
-  name: mx_bluesky
-  title: mx_bluesky
+  name: mx-bluesky
+  title: mx-bluesky
   description: Bluesky tools for MX Beamlines at DLS
   annotations:
     backstage.io/techdocs-ref: dir:.
-    github.com/project-slug: DiamondLightSource/mx_bluesky
+    github.com/project-slug: DiamondLightSource/mx-bluesky
   tags:
     - python
     - bluesky

docs/conf.py

@@ -15,7 +15,7 @@
 # -- General configuration ------------------------------------------------
 
 # General information about the project.
-project = "mx_bluesky"
+project = "mx-bluesky"
 
 # The full version, including alpha/beta/rc tags.
 release = mx_bluesky.__version__
@@ -83,7 +83,7 @@
 default_role = "any"
 
 # The suffix of source filenames.
-source_suffix = ".rst"
+source_suffix = [".rst", ".md"]
 
 # The master toctree document.
 master_doc = "index"

docs/developer/general/how-to/create-a-release.rst

@@ -11,7 +11,7 @@ Release
 
 1. Create a new branch from main named pre followed by the release version e.g. pre_v0.1.0. The release versions should look like ``v{major}.{minor}.{patch}``.
 2. On this branch pin the up-to-date version of dodal and the latest release of nexgen if necessary.
-3. Go `here <https://github.com/DiamondLightSource/mx_bluesky/releases/new>`_.
+3. Go `here <https://github.com/DiamondLightSource/mx-bluesky/releases/new>`_.
 4. Select Choose a new tag and type the version of the release, then select the branch created in step 1 as the target.
 5. Click on Generate release notes. This will create a starting set of release notes based on PR titles since the last release.
 6. You should now manually go through each line on the release notes and read it from the perspective of a beamline scientist. It should be clear from each what the change means to the beamline and should have links to easily find further info.

docs/developer/general/how-to/deploy-a-release.rst

@@ -3,7 +3,7 @@ Deploy a New Release
 
 **Remember to discuss any new deployments with the appropriate beamline scientist.**
 
-The ``/deploy/deploy_mxbluesky.py`` script will deploy the latest Hyperion version to a specified beamline. Deployments live in ``/dls_sw/ixx/software/bluesky/mx_bluesky_vXXX``. To do a new deployment you should run the deploy script from your mx_bluesky dev environment with e.g.
+The ``/deploy/deploy_mxbluesky.py`` script will deploy the latest Hyperion version to a specified beamline. Deployments live in ``/dls_sw/ixx/software/bluesky/mx-bluesky_vXXX``. To do a new deployment you should run the deploy script from your mx-bluesky dev environment with e.g.
 
 ``python ./deploy/deploy_mxbluesky.py --beamline i24``
 
@@ -21,5 +21,5 @@ If you need a specific beamline test deployment you can also run:
 which will create the beamline deployment (eg. I24) in the specified test directory ``/your-path/mxbluesky_release_test``.
 
 
-**Note:** When deploying on I24, the edm screens for serial crystallography will be deployed automatically along with the mx_bluesky release. 
-When running a ``dev`` deployment instead, `this script <https://github.com/DiamondLightSource/mx_bluesky/wiki/Serial-Crystallography-on-I24#deploying-a-local-version-of-the-edm-screens>`_ will also need to be run to get the latest version of the screens.
+**Note:** When deploying on I24, the edm screens for serial crystallography will be deployed automatically along with the mx-bluesky release. 
+When running a ``dev`` deployment instead, `this script <https://github.com/DiamondLightSource/mx-bluesky/wiki/Serial-Crystallography-on-I24#deploying-a-local-version-of-the-edm-screens>`_ will also need to be run to get the latest version of the screens.

docs/developer/general/how-to/get-started.rst

@@ -1,19 +1,19 @@
-Get Started with mx_bluesky
+Get Started with mx-bluesky
 ---------------------------
 =======================
 Development Environment
 =======================
 
-- Clone this repo: ``[email protected]: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: ``[email protected]: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. 
 
 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:
 
 .. code-block:: bash
 
-    cd /path/to/mx_bluesky  
+    cd /path/to/mx-bluesky  
     module load vscode  
-    code ./.vscode/mx_bluesky.code-workspace  
+    code ./.vscode/mx-bluesky.code-workspace  
 
 - If you use vs code, you may need to set the python interpreter for both repositories to the one from the virtual environment created in ``.venv``
 

docs/developer/general/tutorials/dev-install.rst

@@ -10,7 +10,7 @@ Clone the repository
 First clone the repository locally using `Git
 <https://git-scm.com/downloads>`_::
 
-    $ git clone git://github.com/DiamondLightSource/mx_bluesky.git
+    $ git clone git://github.com/DiamondLightSource/mx-bluesky.git
 
 Install dependencies
 --------------------
@@ -25,7 +25,7 @@ requires python 3.9 or later) or to run in a container under `VSCode
 
         .. code::
 
-            $ cd mx_bluesky
+            $ cd mx-bluesky
             $ python3 -m venv venv
             $ source venv/bin/activate
             $ pip install -e .[dev]
@@ -34,7 +34,7 @@ requires python 3.9 or later) or to run in a container under `VSCode
 
         .. code::
 
-            $ vscode mx_bluesky
+            $ vscode mx-bluesky
             # Click on 'Reopen in Container' when prompted
             # Open a new terminal
 

docs/developer/index.rst

@@ -16,7 +16,7 @@ Documentation is split general and topic-specific sections. Each section is spli
 
         +++
 
-        General information for working on mx_bluesky
+        General information for working on mx-bluesky
 
     .. grid-item-card:: :material-regular:`apps;3em`
 

docs/developer/murko-integration/explanations/architecture.rst

@@ -5,14 +5,14 @@ The architecture of how Murko is integrated is still in flux but as of 07/08 the
 
 .. image:: ../images/murko_setup.drawio.png
 
-The mx_bluesky code is deployed into the `beamline kubernetes cluster <https://k8s-i04.diamond.ac.uk/>`_ behind a `blueAPI <https://github.com/DiamondLightSource/blueapi>`_ REST interface. Alongside this an instance of murko is also deployed to the k8s cluster.
+The mx-bluesky code is deployed into the `beamline kubernetes cluster <https://k8s-i04.diamond.ac.uk/>`_ behind a `blueAPI <https://github.com/DiamondLightSource/blueapi>`_ REST interface. Alongside this an instance of murko is also deployed to the k8s cluster.
 
-When GDA reaches a point where it will thaw the pin (usually just after robot load), if the ``gda.mx.bluesky.thaw`` property has been set to True it will instead call out to the thaw_and_center plan inside mx_bluesky.
+When GDA reaches a point where it will thaw the pin (usually just after robot load), if the ``gda.mx.bluesky.thaw`` property has been set to True it will instead call out to the thaw_and_center plan inside mx-bluesky.
 
-The thawing plan will first create a ``MurkoCallback`` callback, this will stream metadata into a key in a redis database running on i04-control (this should be moved in `#145 <https://github.com/DiamondLightSource/mx_bluesky/issues/145>`_).
+The thawing plan will first create a ``MurkoCallback`` callback, this will stream metadata into a key in a redis database running on i04-control (this should be moved in `#145 <https://github.com/DiamondLightSource/mx-bluesky/issues/145>`_).
 
 It will then trigger the ``OAVToRedisForwarder`` device in ``dodal`` that will stream image data to redis in the form of pickled RGB numpy arrays. Each image is given a uuid by this device, which is used to correlate the images with the other metadata, which could be streamed with a different frequency.
 
 The image streaming must be done with an ophyd device as there is too much data for it all to be emitted in bluesky documents.
 
-When the data is entered into redis it will publish a message to the redis ``murko`` channel. This will get picked up by the `socket_handler <https://github.com/DiamondLightSource/mx_auto_mjpeg_capture/tree/main/socket_handler>`_, which will forward the data to murko. Currently, during testing the socket_handler is just manually run on a workstation, `#146 <https://github.com/DiamondLightSource/mx_bluesky/issues/146>`_ should fix this.
+When the data is entered into redis it will publish a message to the redis ``murko`` channel. This will get picked up by the `socket_handler <https://github.com/DiamondLightSource/mx_auto_mjpeg_capture/tree/main/socket_handler>`_, which will forward the data to murko. Currently, during testing the socket_handler is just manually run on a workstation, `#146 <https://github.com/DiamondLightSource/mx-bluesky/issues/146>`_ should fix this.

docs/developer/serial-crystallography-on-i24/how-to/environment-setup.rst

@@ -7,7 +7,7 @@ Once this is done, the environment can be started by running:
 
 .. code:: bash
 
-   cd /path/to/mx_bluesky
+   cd /path/to/mx-bluesky
    source .venv/bin/activate
 
 On beamline I24, the package will be saved in
@@ -25,7 +25,7 @@ shell commands pointing to the correct scripts/edm locations.
 
 .. code:: bash
 
-   ./path/to/mx_bluesky/deploy/deploy_edm_for_ssx.sh
+   ./path/to/mx-bluesky/deploy/deploy_edm_for_ssx.sh
 
 Setting the current visit directory
 ===================================
@@ -37,7 +37,7 @@ point to the current visit and then running the command:
 
 .. code:: bash
 
-   ./path/to/mx_bluesky/src/mx_bluesky/i24/serial/set_visit_directory.sh
+   ./path/to/mx-bluesky/src/mx-bluesky/i24/serial/set_visit_directory.sh
 
 Note that the default experiment type for the script setting the
 directory will be ``fixed-target``. In case of an extruder collection,
@@ -46,4 +46,4 @@ the command line.
 
 .. code:: bash
 
-   ./path/to/mx_bluesky/src/mx_bluesky/i24/serial/set_visit_directory.sh extruder
+   ./path/to/mx-bluesky/src/mx-bluesky/i24/serial/set_visit_directory.sh extruder

docs/developer/serial-crystallography-on-i24/how-to/run-a-collection.rst

@@ -12,7 +12,7 @@ A couple of entry points have been set up so that:
 
 Before opening the experiment specific edm, each of these entry points
 will start a ``BlueAPI`` server. The configuration used by ``BlueAPI``
-is saved in ``src/mx_bluesky/i24/serial/blueapi_config.yaml``.
+is saved in ``src/mx-bluesky/i24/serial/blueapi_config.yaml``.
 
 Detector choice
 ===============
@@ -75,7 +75,7 @@ set up the coordinate system.
 
 Before this step remember to reset the scale and skew factors as well as
 the motor directions as needed. Current values are saved in
-``src/mx_bluesky/i24/serial/parameters/fixed_target`` in the
+``src/mx-bluesky/i24/serial/parameters/fixed_target`` in the
 ``cs_maker.json`` and ``motor_direction.txt`` files.
 
 1. From the main edm screen open the ``viewer`` and ``moveonclick``.

docs/developer/serial-crystallography-on-i24/how-to/stage-pmac-moves.rst

@@ -47,7 +47,7 @@ in a couple of different ways.
 
    .. code:: python
 
-      yield from bps.mv(pmac.x, 0, pmac.y, 1)https://github.com/DiamondLightSource/mx_bluesky/wiki/Serial-Crystallography-on-I24#cs_reset-custom-chips
+      yield from bps.mv(pmac.x, 0, pmac.y, 1)https://github.com/DiamondLightSource/mx-bluesky/wiki/Serial-Crystallography-on-I24#cs_reset-custom-chips
 
 Notes on the coordinate system for a fixed-target collection
 ============================================================
@@ -81,8 +81,8 @@ Theory for this computation
 
 The plan needs information stored in a few files:
 
-* The motor directions are stored in ``src/mx_bluesky/i24/serial/parameters/fixed_target/cs/motor_directions.txt.`` The motor number multiplied by the motor direction should give the positive chip direction. 
-* The scale values for x,y,z, the skew value and the sign of Sx, Sy, Sz are all stored in ``src/mx_bluesky/i24/serial/parameters/fixed_target/cs/cs_maker.json``
+* The motor directions are stored in ``src/mx-bluesky/i24/serial/parameters/fixed_target/cs/motor_directions.txt.`` The motor number multiplied by the motor direction should give the positive chip direction. 
+* The scale values for x,y,z, the skew value and the sign of Sx, Sy, Sz are all stored in ``src/mx-bluesky/i24/serial/parameters/fixed_target/cs/cs_maker.json``
 * The fiducials 1 and 2 positions are written to file when selecting the fiducials (Setting fiducial 0 instead sends a homing command directly to the pmac_string PV)
 
 NOTE. The ``motor_direction.txt`` and ``cs_maker.json`` files should

docs/developer/serial-crystallography-on-i24/project-planning/roadmap.rst

@@ -6,7 +6,7 @@ board <https://github.com/orgs/DiamondLightSource/projects/10/views/2>`__
 
 Ongoing list of things needed:
 
-1. Solution for enabling users to run mx_bluesky instead of old scripts:
+1. Solution for enabling users to run mx-bluesky instead of old scripts:
    blocked by permission issues. Preferred solution would be run on
    beamline kubernetes cluster - in the meantime also loooking into
    procserv as a possibility. (Fixing this should also allow us to stop
@@ -59,7 +59,7 @@ Ongoing list of things needed:
 +---------------------------------------+----------------+---------------------------------+
 | Permissions issues - run as a service | Dec. 23        | :material-regular:`check;2em`   |
 +---------------------------------------+----------------+---------------------------------+
-| Deploy a first version of MX_BLUESKY  | Nov. 23        |                                 |
+| Deploy a first version of mx-bluesky  | Nov. 23        |                                 |
 | with the current iteration - tested   |                | :material-regular:`check;2em`   |
 | on the beamline - of the serial       |                |                                 |
 | tools. Set up a ``module load`` that  |                |                                 |

docs/index.rst

@@ -14,13 +14,13 @@ The documentation is split into 2 sections:
         :link: user/index
         :link-type: doc
 
-        The User Guide contains documentation on how to install and use mx_bluesky.
+        The User Guide contains documentation on how to install and use mx-bluesky.
 
     .. grid-item-card:: :material-regular:`code;4em`
         :link: developer/index
         :link-type: doc
 
-        The Developer Guide contains documentation on how to develop and contribute changes back to mx_bluesky.
+        The Developer Guide contains documentation on how to develop and contribute changes back to mx-bluesky.
 
 .. toctree::
     :hidden:

docs/user/how-to/run-container.rst

@@ -1,15 +1,15 @@
 Run in a container
 ==================
 
-Pre-built containers with mx_bluesky and its dependencies already
+Pre-built containers with mx-bluesky and its dependencies already
 installed are available on `Github Container Registry
-<https://ghcr.io/DiamondLightSource/mx_bluesky>`_.
+<https://ghcr.io/DiamondLightSource/mx-bluesky>`_.
 
 Starting the container
 ----------------------
 
 To pull the container from github container registry and run::
 
-    $ docker run ghcr.io/DiamondLightSource/mx_bluesky:main --version
+    $ docker run ghcr.io/DiamondLightSource/mx-bluesky:main --version
 
 To get a released version, use a numbered release instead of ``main``.