dls-dodal 1.29.4__tar.gz → 1.30.0__tar.gz

dls_dodal-1.30.0/.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: Ophyd devices and other utils that could be used across DLS beamlines
+distribution_name: dls-dodal
+docker: false
+docs_type: sphinx
+git_platform: github.com
+github_org: DiamondLightSource
+package_name: dodal
+pypi: true
+repo_name: dodal
+type_checker: pyright

dls_dodal-1.30.0/.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"
+}

dls_dodal-1.30.0/.github/CONTRIBUTING.md

@@ -0,0 +1,27 @@
+# Contribute to the project
+
+Contributions and issues are most welcome! All issues and pull requests are
+handled through [GitHub](https://github.com/DiamondLightSource/dodal/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/dodal/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).

dls_dodal-1.30.0/.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

{dls_dodal-1.29.4 → dls_dodal-1.30.0}/.github/dependabot.yml

@@ -10,11 +10,15 @@ updates:
     schedule:
       interval: "weekly"
     groups:
-      github-artifacts:
+      actions:
         patterns:
-          - actions/*-artifact
+          - "*"
 
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      dev-dependencies:
+        patterns:
+          - "*"

{dls_dodal-1.29.4 → dls_dodal-1.30.0}/.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
 
 
-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: str | None, remove: str | None) -> 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: str | None, remove: str | None) -> List[str]:
     # 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)
@@ -58,9 +54,12 @@ def get_versions(ref: str, add: str | None, remove: str | None) -> List[str]:
 
 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}")
@@ -69,16 +68,12 @@ def write_json(path: Path, repository: str, versions: str):
 
 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)
 
 

dls_dodal-1.30.0/.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"]
+            }

dls_dodal-1.30.0/.github/workflows/_dist.yml

@@ -0,0 +1,35 @@
+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
+        run: python -m dodal --version

dls_dodal-1.29.4/.github/workflows/docs.yml → dls_dodal-1.30.0/.github/workflows/_docs.yml

@@ -1,17 +1,13 @@
-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
@@ -21,20 +17,23 @@ jobs:
           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"
-          artifact_name: docs
 
       - 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
 
@@ -45,10 +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@64b46b4226a4a12da2239ba3ea5aa73e3163c75b # v3.9.1
+        uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e # v4.0.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: .github/pages

dls_dodal-1.30.0/.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

dls_dodal-1.30.0/.github/workflows/_release.yml

@@ -0,0 +1,32 @@
+on:
+  workflow_call:
+
+jobs:
+  artifacts:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+
+      - name: Zip up docs
+        run: |
+          set -vxeuo pipefail
+          if [ -d html ]; then
+            mv html $GITHUB_REF_NAME
+            zip -r docs.zip $GITHUB_REF_NAME
+            rm -rf $GITHUB_REF_NAME
+          fi
+
+      - name: Create GitHub Release
+        # 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: softprops/action-gh-release@c062e08bd532815e2082a85e87e3ef29c3e6d191 # v2.0.8
+        with:
+          prerelease: ${{ contains(github.ref_name, 'a') || contains(github.ref_name, 'b') || contains(github.ref_name, 'rc') }}
+          files: "*"
+          generate_release_notes: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

dls_dodal-1.30.0/.github/workflows/_test.yml

@@ -0,0 +1,62 @@
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        type: string
+        description: The version of python to install
+        required: true
+      runs-on:
+        type: string
+        description: The runner to run this job on
+        required: true
+    secrets:
+      CODECOV_TOKEN:
+        required: true
+
+env:
+  # https://github.com/pytest-dev/pytest/issues/2042
+  PY_IGNORE_IMPORTMISMATCH: "1"
+
+jobs:
+  run:
+    runs-on: ${{ inputs.runs-on }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - if: inputs.python-version == 'dev'
+        name: Install dev versions of python packages
+        uses: ./.github/actions/install_requirements
+
+      - if: inputs.python-version == 'dev'
+        name: Write the requirements as an artifact
+        run: pip freeze --exclude-editable > /tmp/dev-requirements.txt
+
+      - if: inputs.python-version == 'dev'
+        name: Upload dev-requirements.txt
+        uses: actions/upload-artifact@v4
+        with:
+          name: dev-requirements
+          path: /tmp/dev-requirements.txt
+
+      - if: inputs.python-version != 'dev'
+        name: Install latest versions of python packages
+        uses: ./.github/actions/install_requirements
+        with:
+          python-version: ${{ inputs.python-version }}
+          pip-install: ".[dev]"
+
+      - name: Run tests
+        run: tox -e tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          name: ${{ inputs.python-version }}/${{ inputs.runs-on }}
+          files: cov.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

dls_dodal-1.30.0/.github/workflows/_tox.yml

@@ -0,0 +1,24 @@
+on:
+  workflow_call:
+    inputs:
+      tox:
+        type: string
+        description: What to run under tox
+        required: true
+
+
+jobs:
+  run:
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install python packages
+        uses: ./.github/actions/install_requirements
+
+      - name: Run tox
+        run: tox -e ${{ inputs.tox }}

dls_dodal-1.30.0/.github/workflows/ci.yml

@@ -0,0 +1,59 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  check:
+    uses: ./.github/workflows/_check.yml
+
+  lint:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    uses: ./.github/workflows/_tox.yml
+    with:
+      tox: pre-commit,type-checking
+
+  test:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    strategy:
+      matrix:
+        runs-on: ["ubuntu-latest"] # can add windows-latest, macos-latest
+        python-version: ["3.10", "3.11"] # add 3.12 when p4p #145 is fixed
+        include:
+          # Include one that runs in the dev environment
+          - runs-on: "ubuntu-latest"
+            python-version: "dev"
+      fail-fast: false
+    uses: ./.github/workflows/_test.yml
+    with:
+      runs-on: ${{ matrix.runs-on }}
+      python-version: ${{ matrix.python-version }}
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  docs:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    uses: ./.github/workflows/_docs.yml
+
+  dist:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    uses: ./.github/workflows/_dist.yml
+
+  pypi:
+    if: github.ref_type == 'tag'
+    needs: dist
+    uses: ./.github/workflows/_pypi.yml
+    permissions:
+      id-token: write
+
+  release:
+    if: github.ref_type == 'tag'
+    needs: [dist, docs]
+    uses: ./.github/workflows/_release.yml
+    permissions:
+      contents: write

dls_dodal-1.30.0/.github/workflows/periodic.yml

@@ -0,0 +1,13 @@
+name: Periodic
+
+on:
+  workflow_dispatch:
+  schedule:
+    # Run weekly to check URL links still resolve
+    - cron: "0 8 * * WED"
+
+jobs:
+  linkcheck:
+    uses: ./.github/workflows/_tox.yml
+    with:
+      tox: docs build -- -b linkcheck

{dls_dodal-1.29.4 → dls_dodal-1.30.0}/.gitignore

@@ -8,7 +8,6 @@ __pycache__/
 # Distribution / packaging
 .Python
 env/
-.venv
 build/
 develop-eggs/
 dist/
@@ -57,7 +56,7 @@ tmp/
 
 # Sphinx documentation
 docs/_build/
-docs/user/reference/generated/
+docs/reference/generated/
 
 # PyBuilder
 target/
@@ -71,3 +70,6 @@ lockfiles/
 
 # ruff cache
 .ruff_cache/
+
+# pycharm project files
+.idea/

{dls_dodal-1.29.4 → dls_dodal-1.30.0}/.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
       - id: check-added-large-files
       - id: check-yaml
       - id: check-merge-conflict
+      - id: end-of-file-fixer
 
   - repo: local
     hooks:

dls_dodal-1.30.0/.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "ms-vscode-remote.remote-containers",
+    ]
+}

{dls_dodal-1.29.4 → dls_dodal-1.30.0}/.vscode/launch.json

@@ -6,7 +6,7 @@
     "configurations": [
         {
             "name": "Debug Unit Test",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "justMyCode": false,
             "program": "${file}",
@@ -16,10 +16,9 @@
             "console": "integratedTerminal",
             "preLaunchTask": "load_dials_env",
             "env": {
-                // The default config in setup.cfg's "[tool:pytest]" adds coverage.
-                // Cannot have coverage and debugging at the same time.
-                // https://github.com/microsoft/vscode-python/issues/693
-                "PYTEST_ADDOPTS": "--no-cov"
+                // Enable break on exception when debugging tests (see: tests/conftest.py)
+                "PYTEST_RAISE": "1",
+                "PYTEST_ADDOPTS": "--no-cov -vv"
             },
         }
     ]

{dls_dodal-1.29.4 → dls_dodal-1.30.0}/.vscode/settings.json

@@ -1,9 +1,13 @@
 {
-    "python.testing.pytestArgs": [],
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
     "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+        "source.organizeImports": "explicit"
+    },
+    "files.insertFinalNewline": true,
     "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
         "editor.rulers": [
             88
         ],
@@ -15,5 +19,5 @@
     "python.analysis.extraPaths": [
         "./src"
     ],
-    "python.analysis.typeCheckingMode": "basic",
-}
+    "python.analysis.typeCheckingMode": "basic"
+}