dls-dodal 1.68.0__tar.gz → 2.0.0__tar.gz

dls_dodal-2.0.0/.copier-answers.yml

@@ -0,0 +1,19 @@
+# Changes here will be overwritten by Copier
+_commit: 5.0.1
+_src_path: https://github.com/DiamondLightSource/python-copier-template
+author_email: dominic.oram@diamond.ac.uk
+author_name: Dominic Oram
+component_lifecycle: production
+component_owner: group:data-acquisition
+component_type: library
+description: Ophyd devices and other utils that could be used across DLS beamlines
+distribution_name: dls-dodal  # Can change to dodal https://github.com/DiamondLightSource/dodal/issues/681
+docker: false
+docs_type: sphinx
+git_platform: github.com
+github_org: DiamondLightSource
+package_name: dodal
+pypi: true
+repo_name: dodal
+strict_typing: false  # Should move to strict typing in future
+type_checker: pyright

dls_dodal-2.0.0/.devcontainer/devcontainer.json

@@ -0,0 +1,72 @@
+// 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": "${localEnv:DISPLAY}",
+        // Put things that allow it in the persistent cache
+        "PRE_COMMIT_HOME": "/cache/pre-commit",
+        "UV_CACHE_DIR": "/cache/uv",
+        "UV_PYTHON_CACHE_DIR": "/cache/uv-python",
+        // Make a venv that is specific for this workspace path as the cache is shared
+        "UV_PROJECT_ENVIRONMENT": "/cache/venv-for${localWorkspaceFolder}",
+        // Do the equivalent of "activate" the venv so we don't have to "uv run" everything
+        "VIRTUAL_ENV": "/cache/venv-for${localWorkspaceFolder}",
+        "PATH": "/cache/venv-for${localWorkspaceFolder}/bin:${containerEnv:PATH}"
+    },
+    "customizations": {
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                // Use the container's python by default
+                "python.defaultInterpreterPath": "/cache/venv-for${localWorkspaceFolder}/bin/python",
+                // Don't activate the venv as it is already in the PATH
+                "python.terminal.activateEnvInCurrentTerminal": false,
+                "python.terminal.activateEnvironment": false,
+                // Workaround to prevent garbled python REPL in the terminal
+                // https://github.com/microsoft/vscode-python/issues/25505
+                "python.terminal.shellIntegration.enabled": false
+            },
+            // 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"
+            ]
+        }
+    },
+    // Create the config folder for the bash-config feature and uv cache
+    "initializeCommand": "mkdir -p ${localEnv:HOME}/.config/terminal-config",
+    "runArgs": [
+        // Allow the container to access the host X11 display and EPICS CA
+        "--net=host",
+        // Make sure SELinux does not disable with access to host filesystems like tmp
+        "--security-opt=label=disable"
+    ],
+    "mounts": [
+        // Mount in the user terminal config folder so it can be edited
+        {
+            "source": "${localEnv:HOME}/.config/terminal-config",
+            "target": "/user-terminal-config",
+            "type": "bind"
+        },
+        // Keep a persistent cross container cache for uv, pre-commit, and the venvs
+        {
+            "source": "devcontainer-shared-cache",
+            "target": "/cache",
+            "type": "volume"
+        }
+    ],
+    // 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, recreate the venv then make pre-commit first run faster
+    "postCreateCommand": "uv venv --clear && uv sync && pre-commit install --install-hooks"
+}

dls_dodal-2.0.0/.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/5.0.1/how-to.html).

dls_dodal-2.0.0/.github/workflows/_dist.yml

@@ -0,0 +1,36 @@
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Build sdist and wheel
+        run: >
+          export SOURCE_DATE_EPOCH=$(git log -1 --pretty=%ct) &&
+          uvx --from build pyproject-build
+
+      - name: Upload sdist and wheel as artifacts
+        uses: actions/upload-artifact@v5
+        with:
+          name: dist
+          path: dist
+
+      - name: Check for packaging errors
+        run: uvx twine check --strict dist/*
+
+      - name: Install produced wheel
+        run: python -m pip install dist/*.whl
+
+      - name: Test module --version works using the installed wheel
+        run: python -m dodal --version

dls_dodal-2.0.0/.github/workflows/_docs.yml

@@ -0,0 +1,58 @@
+on:
+  workflow_call:
+
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Avoid git conflicts when tag and branch pushed at same time
+        if: github.ref_type == 'tag'
+        run: sleep 60
+
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Install system packages
+        run: sudo apt-get install graphviz
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      # - name: Install requirements
+      #   run: uv sync --group dev
+
+      - name: Build docs
+        run: uv run --locked tox -e docs
+
+      - name: Remove environment.pickle
+        run: rm build/html/.doctrees/environment.pickle
+
+      - name: Upload built docs artifact
+        uses: actions/upload-artifact@v5
+        with:
+          name: docs
+          path: build
+
+      - name: Sanitize ref name for docs version
+        run: echo "DOCS_VERSION=${GITHUB_REF_NAME//[^A-Za-z0-9._-]/_}" >> $GITHUB_ENV
+
+      - name: Move to versioned directory
+        run: mv build/html .github/pages/$DOCS_VERSION
+
+      - name: Write switcher.json
+        run: python .github/pages/make_switcher.py --add $DOCS_VERSION ${{ github.repository }} .github/pages/switcher.json
+
+      - name: Publish Docs to gh-pages
+        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@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e # v4.0.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: .github/pages
+          keep_files: true

dls_dodal-2.0.0/.github/workflows/_test.yml

@@ -0,0 +1,62 @@
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        type: string
+        description: The version of python to install, default is from .python-version file
+        default: ""
+      runs-on:
+        type: string
+        description: The runner to run this job on
+        required: true
+
+env:
+  # https://github.com/pytest-dev/pytest/issues/2042
+  PY_IGNORE_IMPORTMISMATCH: "1"
+  UV_PYTHON: ${{ inputs.python-version }}
+
+jobs:
+  run:
+    runs-on: ${{ inputs.runs-on }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Install latest versions of python packages
+        run: uv sync --python ${{ inputs.python-version }} --group dev
+      
+      - name: Run tests
+        run: uv run --locked tox -e tests
+
+      - name: Checkout simulated devices
+        uses: actions/checkout@v5
+        with:
+          repository: epics-containers/example-services
+          path: example-services
+
+      - name: Run docker compose
+        uses: hoverkraft-tech/compose-action@v2.4.1
+        with:
+          compose-file: "./example-services/compose.yaml"
+          services: |
+            bl01t-di-cam-01
+            bl01t-mo-sim-01
+            ca-gateway
+
+      - name: Run system tests
+        run: uv run --locked tox -e system-tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          name: ${{ inputs.python-version }}/${{ inputs.runs-on }}
+          files: ./cov.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

dls_dodal-2.0.0/.github/workflows/_tox.yml

@@ -0,0 +1,25 @@
+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@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Run import linter
+        run: uv run --locked lint-imports
+
+      - name: Run tox
+        run: uv run --locked tox -e ${{ inputs.tox }}

dls_dodal-2.0.0/.github/workflows/ci.yml

@@ -0,0 +1,49 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+
+jobs:
+
+  lint:
+    uses: ./.github/workflows/_tox.yml
+    with:
+      tox: pre-commit,type-checking
+
+  test:
+    strategy:
+      matrix:
+        runs-on: ["ubuntu-latest"] # can add windows-latest, macos-latest
+        python-version: ["3.11", "3.12", "3.13"]
+      fail-fast: false
+    uses: ./.github/workflows/_test.yml
+    with:
+      runs-on: ${{ matrix.runs-on }}
+      python-version: ${{ matrix.python-version }}
+
+  docs:
+    uses: ./.github/workflows/_docs.yml
+    permissions:
+      contents: write
+
+  dist:
+    uses: ./.github/workflows/_dist.yml
+
+  pypi:
+    needs: [dist, test]
+    if: github.ref_type == 'tag'
+    uses: ./.github/workflows/_pypi.yml
+    permissions:
+      id-token: write
+
+  release:
+    needs: [dist, test, docs]
+    if: github.ref_type == 'tag'
+    uses: ./.github/workflows/_release.yml
+    permissions:
+      contents: write

dls_dodal-2.0.0/.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 -- -b linkcheck

dls_dodal-2.0.0/.gitleaks.toml

@@ -0,0 +1,19 @@
+# This allow-list is limited to YAML/YML files to cut down SealedSecrets false positives.
+# All gitleaks default rules still apply everywhere (useDefault = true).
+# To broaden this allow-list to all files, comment out the 'paths' line below.
+
+[extend]
+useDefault = true
+
+[[rules]]
+id = "generic-api-key"
+
+# Pattern-only allowlist for long Ag… tokens in YAML 
+[[rules.allowlists]]
+condition = "AND"
+regexes = [
+  # Boundary-safe Ag… token without lookarounds (RE2-safe)
+  '''(?:^|[^A-Za-z0-9+/=])(Ag[A-Za-z0-9+/]{500,}={0,2})(?:[^A-Za-z0-9+/=]|$)'''
+]
+# Limit to YAML only for now. Comment this out if you want it to apply everywhere.
+paths = ['''(?i).*\.ya?ml$''']

dls_dodal-2.0.0/.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+        exclude: ^uv.lock
+      - id: check-yaml
+      - id: check-merge-conflict
+      - id: end-of-file-fixer
+
+  - repo: local
+    hooks:
+      - id: ruff
+        name: lint with ruff
+        language: system
+        entry: ruff check --force-exclude --fix
+        types: [python]
+        require_serial: true
+
+      - id: ruff-format
+        name: format with ruff
+        language: system
+        entry: ruff format --force-exclude
+        types: [python]
+        require_serial: true
+        
+      - id: import-contracts
+        name: Ensure import directionality
+        pass_filenames: false
+        language: system
+        entry: lint-imports
+        types: [python]
+        require_serial: false
+
+      - id: uv-sync
+        name: update uv.lock and venv
+        pass_filenames: false
+        language: system
+        entry: uv sync
+        files: ^(uv\.lock|pyproject\.toml)$
+
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.28.0
+    hooks:
+      - id: gitleaks

dls_dodal-2.0.0/.python-version

@@ -0,0 +1 @@
+3.11

dls_dodal-2.0.0/Dockerfile

@@ -0,0 +1,8 @@
+# The devcontainer should use the developer target and run as root with podman
+# or docker with user namespaces.
+FROM ghcr.io/diamondlightsource/ubuntu-devcontainer:noble AS developer
+
+# Add any system dependencies for the developer/build environment here
+RUN apt-get update -y && apt-get install -y --no-install-recommends \
+    graphviz \
+    && apt-get dist-clean