mx-bluesky 0.0.2__tar.gz → 1.1.0__tar.gz

mx_bluesky-1.1.0/.copier-answers.yml

@@ -0,0 +1,16 @@
+# Changes here will be overwritten by Copier
+_commit: 2.2.0
+_src_path: gh:DiamondLightSource/python-copier-template
+author_email: dominic.oram@diamond.ac.uk
+author_name: Dominic Oram
+component_owner: group:data-acquisition
+description: Bluesky tools for MX Beamlines at DLS
+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
+type_checker: pyright

mx_bluesky-1.1.0/.coveragerc

@@ -0,0 +1,18 @@
+[run]
+omit = 
+    */test_*
+    **/conftest.py
+data_file = /tmp/hyperion.coverage
+
+[report]
+exclude_also = 
+    if TYPE_CHECKING:
+    def __repr__
+    raise NotImplementedError
+    @(abc\.)?abstractmethod
+
+[paths]
+# Tests are run from installed location, map back to the src directory
+source =
+    src
+    **/site-packages/

{mx_bluesky-0.0.2 → mx_bluesky-1.1.0}/.devcontainer/Dockerfile

@@ -3,7 +3,7 @@
 # The devcontainer should use the build target and run as root with podman
 # or docker with user namespaces.
 #
-FROM python:3.11 as build
+FROM python:3.11 AS build
 
 ARG PIP_OPTIONS
 
@@ -24,7 +24,7 @@ WORKDIR /context
 # install python package into /venv
 RUN pip install ${PIP_OPTIONS}
 
-FROM python:3.11-slim as runtime
+FROM python:3.11-slim AS runtime
 
 # Add apt-get system dependecies for runtime here if needed
 
@@ -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"]

mx_bluesky-1.1.0/.devcontainer/devcontainer.json

@@ -0,0 +1,46 @@
+// For format details, see https://containers.dev/implementors/json_reference/
+{
+    "name": "Python 3 Developer Container",
+    "build": {
+        "dockerfile": "../Dockerfile",
+        "target": "developer"
+    },
+    "remoteEnv": {
+        // Allow X11 apps to run inside the container
+        "DISPLAY": "${localEnv:DISPLAY}"
+    },
+    "customizations": {
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/venv/bin/python"
+            },
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": [
+                "ms-python.python",
+                "github.vscode-github-actions",
+                "tamasfe.even-better-toml",
+                "redhat.vscode-yaml",
+                "ryanluker.vscode-coverage-gutters",
+                "charliermarsh.ruff",
+                "ms-azuretools.vscode-docker"
+            ]
+        }
+    },
+    "features": {
+        // Some default things like git config
+        "ghcr.io/devcontainers/features/common-utils:2": {
+            "upgradePackages": false
+        }
+    },
+    "runArgs": [
+        // Allow the container to access the host X11 display and EPICS CA
+        "--net=host",
+        // Make sure SELinux does not disable with access to host filesystems like tmp
+        "--security-opt=label=disable"
+    ],
+    // Mount the parent as /workspaces so we can pip install peers as editable
+    "workspaceMount": "source=${localWorkspaceFolder}/..,target=/workspaces,type=bind",
+    // After the container is created, install the python project in editable form
+    "postCreateCommand": "pip install $([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e '.[dev]' && pre-commit install"
+}

mx_bluesky-1.1.0/.dockerignore

@@ -0,0 +1,12 @@
+# List of folders and files to be excluded from the docker image
+.devcontainer
+.github
+.pytest_cache
+.ruff_cache
+**/__pycache__/
+
+# virtualenv stuff - this gets built by the docker script
+.venv
+activate
+
+tmp

mx_bluesky-1.1.0/.github/CONTRIBUTING.md

@@ -0,0 +1,57 @@
+# How to contribute to mx-bluesky
+
+We should prioritise working, agile code over strict standards, particularly for contributors that are not full time developers. The standards below are thus guidelines that developers should try to follow as much as possible (apart from when something is specified in bold, which is required).
+
+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 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.
+
+## General Workflow
+
+1. An issue is created for the work. 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 with the format `issue_short_description` e.g. `122_create_a_contributing_file`. (External developers are also welcome to make forks)
+4. The developer does the work on this branch, adding their work in small commits. Commit messages should be informative and prefixed with the issue number e.g. `(#122) Added contributing file`.
+5. The developer submits a PR for the work. In the pull request should start with `Fixes #issue_num` e.g. `Fixes #122`, this will ensure the issue is automatically closed when the PR is merged. The developer should also add some background on how the reviewer might test the change.
+6. If the developer has a particular person in mind to review the work they should assign that person to the PR as a reviewer.
+7. The reviewer and developer go back and forth on the code until the reviewer approves it. (See "Reviewing Work" below)
+8. Once the work is approved the original developer merges it.
+
+**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:
+
+- In order to maintain quality and avoid errors
+- Help people learn
+
+It is not a judgement on someone's technical abilities so be kind.
+
+It is suggested that the reviewer prefixes comments with something like the following:
+
+- **must**: A change that must be made before merging e.g. it will break something if not made
+- **should/sugg**: A change that should be made e.g. definitely improves code quality but does not neccessarily break anything
+- **nit**: A minor suggestion that the reviewer would like to see but is happy to leave as is e.g. rename a variable to something
+
+Developers are welcome to ignore **nit** comments if they wish and can choose not to do **should** comments but the must give a reason as to why they disagree with the change.
+
+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.
+
+## Issue or Discussion?
+
+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.
+
+## Code Coverage
+
+While 100% code coverage does not make a library bug-free, it significantly
+reduces the number of easily caught bugs! Please make sure coverage remains the
+same or is improved by a pull request!
+
+## Developer Information
+
+It is recommended that developers use a [vscode devcontainer](https://code.visualstudio.com/docs/devcontainers/containers). This repository contains configuration to set up a containerized development environment that suits its own needs.
+
+This project was created using the [Diamond Light Source Copier Template](https://github.com/DiamondLightSource/python-copier-template) for Python projects.
+
+For more information on common tasks like setting up a developer environment, running the tests, and setting a pre-commit hook, see the template's [How-to guides](https://diamondlightsource.github.io/python-copier-template/2.2.0/how-to.html).

mx_bluesky-1.1.0/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,21 @@
+---
+name: Bug Report
+about: The template to use for reporting bugs and usability issues
+title: " "
+labels: 'bug'
+assignees: ''
+
+---
+
+Describe the bug, including a clear and concise description of the expected behavior, the actual behavior and the context in which you encountered it (ideally include details of your environment).
+
+## Steps To Reproduce
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+
+## Acceptance Criteria
+- Specific criteria that will be used to judge if the issue is fixed

mx_bluesky-1.1.0/.github/ISSUE_TEMPLATE/issue.md

@@ -0,0 +1,13 @@
+---
+name: Issue
+about: The standard template to use for feature requests, design discussions and tasks
+title: " "
+labels: ''
+assignees: ''
+
+---
+
+A brief description of the issue, including specific stakeholders and the business case where appropriate
+
+## Acceptance Criteria
+- Specific criteria that will be used to judge if the issue is fixed

mx_bluesky-1.1.0/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,13 @@
+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!)
+
+### Instructions to reviewer on how to test:
+
+1. Do thing x
+2. Confirm thing y happens
+
+### Checks for reviewer
+
+- [ ] Would the PR title make sense to a user on a set of release notes

mx_bluesky-1.1.0/.github/actions/install_requirements/action.yml

@@ -0,0 +1,34 @@
+name: Install requirements
+description: Install a version of python then call pip install and report what was installed
+inputs:
+  python-version:
+    description: Python version to install, default is from Dockerfile
+    default: "dev"
+  pip-install:
+    description: Parameters to pass to pip install
+    default: "$([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e .[dev]"
+
+runs:
+  using: composite
+  steps:
+    - name: Get version of python
+      run: |
+        PYTHON_VERSION="${{ inputs.python-version }}"
+        if [ $PYTHON_VERSION == "dev" ]; then
+          PYTHON_VERSION=$(sed -n "s/ARG PYTHON_VERSION=//p" Dockerfile)
+        fi
+        echo "PYTHON_VERSION=$PYTHON_VERSION" >> "$GITHUB_ENV"
+      shell: bash
+
+    - name: Setup python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
+
+    - name: Install packages
+      run: pip install ${{ inputs.pip-install }}
+      shell: bash
+
+    - name: Report what was installed
+      run: pip freeze
+      shell: bash

mx_bluesky-1.1.0/.github/actions/verify-nexus/Dockerfile

@@ -0,0 +1,3 @@
+FROM ghcr.io/githubgphl/imginfo:main
+COPY entrypoint.sh /entrypoint.sh
+ENTRYPOINT ["/entrypoint.sh"]

mx_bluesky-1.1.0/.github/actions/verify-nexus/action.yml

@@ -0,0 +1,18 @@
+name: "Verify nexus"
+description: "Verify nexus files against imginfo"
+inputs:
+  filename:
+    description: "nexus file to verify"
+    required: true
+outputs:
+  imginfo_stdout:
+    description: "imginfo output"
+  imginfo_stderr:
+    description: "imginfo error output"
+  imginfo_exit_code:
+    description: "imginfo exit code"
+runs:
+  using: "docker"
+  image: "Dockerfile"
+  args:
+    - ${{ inputs.filename }}

mx_bluesky-1.1.0/.github/actions/verify-nexus/entrypoint.sh

@@ -0,0 +1,25 @@
+#!/bin/sh -l
+echo "Contents of /github/workspace:"
+ls /github/workspace
+echo "current dir: $(pwd)"
+echo "Running imginfo on $1"
+/imginfo/imginfo  $1 >> imginfo_out_file 2>> imginfo_err_file
+{ echo "imginfo_output<<EOF"
+  cat imginfo_out_file
+  echo EOF
+} >> "$GITHUB_OUTPUT"
+{ echo "imginfo_output<<EOF"
+  cat imginfo_err_file
+  echo EOF
+} >> "$GITHUB_OUTPUT"
+echo "imginfo_exit_code=$?" >> "$GITHUB_OUTPUT"
+echo "------------- IMGINFO STDOUT -------------"
+cat imginfo_out_file
+echo "------------- IMGINFO STDERR -------------"
+cat imginfo_err_file
+echo "------------------------------------------"
+if [ -s imginfo_err_file ]; then
+  echo "ERRORS IN IMGINFO PROCESSING!"
+  exit 1
+fi
+echo "VALIDATED SUCCESSFULLY!"

{mx_bluesky-0.0.2 → mx_bluesky-1.1.0}/.github/dependabot.yml

@@ -9,8 +9,16 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
 
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      dev-dependencies:
+        patterns:
+          - "*"

{mx_bluesky-0.0.2 → mx_bluesky-1.1.0}/.github/pages/index.html

@@ -8,4 +8,4 @@
     <link rel="canonical" href="main/index.html">
 </head>
 
-</html>
+</html>

{mx_bluesky-0.0.2 → mx_bluesky-1.1.0}/.github/pages/make_switcher.py

@@ -3,28 +3,27 @@ import logging
 from argparse import ArgumentParser
 from pathlib import Path
 from subprocess import CalledProcessError, check_output
-from typing import List, Optional
 
 
-def report_output(stdout: bytes, label: str) -> List[str]:
+def report_output(stdout: bytes, label: str) -> list[str]:
     ret = stdout.decode().strip().split("\n")
     print(f"{label}: {ret}")
     return ret
 
 
-def get_branch_contents(ref: str) -> List[str]:
+def get_branch_contents(ref: str) -> list[str]:
     """Get the list of directories in a branch."""
     stdout = check_output(["git", "ls-tree", "-d", "--name-only", ref])
     return report_output(stdout, "Branch contents")
 
 
-def get_sorted_tags_list() -> List[str]:
+def get_sorted_tags_list() -> list[str]:
     """Get a list of sorted tags in descending order from the repository."""
     stdout = check_output(["git", "tag", "-l", "--sort=-v:refname"])
     return report_output(stdout, "Tags list")
 
 
-def get_versions(ref: str, add: Optional[str], remove: Optional[str]) -> List[str]:
+def get_versions(ref: str, add: str | None) -> list[str]:
     """Generate the file containing the list of all GitHub Pages builds."""
     # Get the directories (i.e. builds) from the GitHub Pages branch
     try:
@@ -36,15 +35,12 @@ def get_versions(ref: str, add: Optional[str], remove: Optional[str]) -> List[st
     # Add and remove from the list of builds
     if add:
         builds.add(add)
-    if remove:
-        assert remove in builds, f"Build '{remove}' not in {sorted(builds)}"
-        builds.remove(remove)
 
     # Get a sorted list of tags
     tags = get_sorted_tags_list()
 
     # Make the sorted versions list from main branches and tags
-    versions: List[str] = []
+    versions: list[str] = []
     for version in ["master", "main"] + tags:
         if version in builds:
             versions.append(version)
@@ -58,27 +54,26 @@ def get_versions(ref: str, add: Optional[str], remove: Optional[str]) -> List[st
 
 def write_json(path: Path, repository: str, versions: str):
     org, repo_name = repository.split("/")
+    pages_url = f"https://{org}.github.io"
+    if repo_name != f"{org}.github.io":
+        # Only add the repo name if it isn't the source for the org pages site
+        pages_url += f"/{repo_name}"
     struct = [
-        {"version": version, "url": f"https://{org}.github.io/{repo_name}/{version}/"}
-        for version in versions
+        {"version": version, "url": f"{pages_url}/{version}/"} for version in versions
     ]
     text = json.dumps(struct, indent=2)
     print(f"JSON switcher:\n{text}")
-    path.write_text(text)
+    path.write_text(text, encoding="utf-8")
 
 
 def main(args=None):
     parser = ArgumentParser(
-        description="Make a versions.txt file from gh-pages directories"
+        description="Make a versions.json file from gh-pages directories"
     )
     parser.add_argument(
         "--add",
         help="Add this directory to the list of existing directories",
     )
-    parser.add_argument(
-        "--remove",
-        help="Remove this directory from the list of existing directories",
-    )
     parser.add_argument(
         "repository",
         help="The GitHub org and repository name: ORG/REPO",
@@ -91,7 +86,7 @@ def main(args=None):
     args = parser.parse_args(args)
 
     # Write the versions file
-    versions = get_versions("origin/gh-pages", args.add, args.remove)
+    versions = get_versions("origin/gh-pages", args.add)
     write_json(args.output, args.repository, versions)
 
 

mx_bluesky-1.1.0/.github/workflows/_check.yml

@@ -0,0 +1,27 @@
+on:
+  workflow_call:
+    outputs:
+      branch-pr:
+        description: The PR number if the branch is in one
+        value: ${{ jobs.pr.outputs.branch-pr }}
+
+jobs:
+  pr:
+    runs-on: "ubuntu-latest"
+    outputs:
+      branch-pr: ${{ steps.script.outputs.result }}
+    steps:
+      - uses: actions/github-script@v7
+        id: script
+        if: github.event_name == 'push'
+        with:
+          script: |
+            const prs = await github.rest.pulls.list({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              head: context.repo.owner + ':${{ github.ref_name }}'
+            })
+            if (prs.data.length) {
+              console.log(`::notice ::Skipping CI on branch push as it is already run in PR #${prs.data[0]["number"]}`)
+              return prs.data[0]["number"]
+            }

mx_bluesky-1.1.0/.github/workflows/_container.yml

@@ -0,0 +1,60 @@
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GitHub Docker Registry
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and export to Docker local cache
+        uses: docker/build-push-action@v6
+        env:
+          DOCKER_BUILD_RECORD_UPLOAD: false
+        with:
+          context: .
+          # Need load and tags so we can test it below
+          load: true
+          tags: tag_for_testing
+
+      - name: Test cli works in cached runtime image
+        run: docker run --rm tag_for_testing --version
+
+      - name: Create tags for publishing image
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            type=ref,event=tag
+            type=raw,value=latest
+
+      - name: Push cached image to container registry
+        if: github.ref_type == 'tag'
+        uses: docker/build-push-action@v6
+        env:
+          DOCKER_BUILD_RECORD_UPLOAD: false
+        # This does not build the image again, it will find the image in the
+        # Docker cache and publish it
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

mx_bluesky-1.1.0/.github/workflows/_dist.yml

@@ -0,0 +1,36 @@
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Build sdist and wheel
+        run: >
+          export SOURCE_DATE_EPOCH=$(git log -1 --pretty=%ct) &&
+          pipx run build
+
+      - name: Upload sdist and wheel as artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Check for packaging errors
+        run: pipx run twine check --strict dist/*
+
+      - name: Install produced wheel
+        uses: ./.github/actions/install_requirements
+        with:
+          pip-install: dist/*.whl
+
+      - name: Test module --version works using the installed wheel
+        # If more than one module in src/ replace with module name to test
+        run: python -m $(ls --hide='*.egg-info' src | head -1) --version

mx_bluesky-0.0.2/.github/workflows/docs.yml → mx_bluesky-1.1.0/.github/workflows/_docs.yml

@@ -1,39 +1,39 @@
-name: Docs CI
-
 on:
-  push:
-  pull_request:
+  workflow_call:
 
 jobs:
-  docs:
-    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+  build:
     runs-on: ubuntu-latest
 
     steps:
       - name: Avoid git conflicts when tag and branch pushed at same time
-        if: startsWith(github.ref, 'refs/tags')
+        if: github.ref_type == 'tag'
         run: sleep 60
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           # Need this to get version number from last tag
           fetch-depth: 0
 
       - name: Install system packages
-        # Can delete this if you don't use graphviz in your docs
         run: sudo apt-get install graphviz
 
       - name: Install python packages
         uses: ./.github/actions/install_requirements
-        with:
-          requirements_file: requirements-dev-3.x.txt
-          install_options: -e .[dev]
-          python_version: "3.11"
 
       - name: Build docs
         run: tox -e docs
 
+      - name: Remove environment.pickle
+        run: rm build/html/.doctrees/environment.pickle
+
+      - name: Upload built docs artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs
+          path: build
+
       - name: Sanitize ref name for docs version
         run: echo "DOCS_VERSION=${GITHUB_REF_NAME//[^A-Za-z0-9._-]/_}" >> $GITHUB_ENV
 
@@ -44,10 +44,10 @@ jobs:
         run: python .github/pages/make_switcher.py --add $DOCS_VERSION ${{ github.repository }} .github/pages/switcher.json
 
       - name: Publish Docs to gh-pages
-        if: github.event_name == 'push' && github.actor != 'dependabot[bot]'
+        if: github.ref_type == 'tag' || github.ref_name == 'main'
         # We pin to the SHA, not the tag, for security reasons.
         # https://docs.github.com/en/actions/learn-github-actions/security-hardening-for-github-actions#using-third-party-actions
-        uses: peaceiris/actions-gh-pages@de7ea6f8efb354206b205ef54722213d99067935 # v3.9.0
+        uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e # v4.0.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: .github/pages

mx_bluesky-1.1.0/.github/workflows/_pypi.yml

@@ -0,0 +1,17 @@
+on:
+  workflow_call:
+
+jobs:
+  upload:
+    runs-on: ubuntu-latest
+    environment: release
+
+    steps:
+      - name: Download dist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI using trusted publishing
+        uses: pypa/gh-action-pypi-publish@release/v1