dls-dodal 1.67.0__tar.gz → 1.69.0__tar.gz

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: 4.0.1
+_commit: 5.0.1
 _src_path: https://github.com/DiamondLightSource/python-copier-template
 author_email: dominic.oram@diamond.ac.uk
 author_name: Dominic Oram
@@ -7,7 +7,7 @@ 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
+distribution_name: dls-dodal  # Can change to dodal https://github.com/DiamondLightSource/dodal/issues/681
 docker: false
 docs_type: sphinx
 git_platform: github.com
@@ -15,5 +15,5 @@ github_org: DiamondLightSource
 package_name: dodal
 pypi: true
 repo_name: dodal
-strict_typing: false
+strict_typing: false  # Should move to strict typing in future
 type_checker: pyright

dls_dodal-1.69.0/.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-1.67.0 → dls_dodal-1.69.0}/.github/CONTRIBUTING.md

@@ -24,4 +24,4 @@ It is recommended that developers use a [vscode devcontainer](https://code.visua
 
 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/4.0.1/how-to.html).
+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-1.67.0 → dls_dodal-1.69.0}/.github/workflows/_dist.yml

@@ -12,10 +12,13 @@ jobs:
           # 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) &&
-          pipx run build
+          uvx --from build pyproject-build
 
       - name: Upload sdist and wheel as artifacts
         uses: actions/upload-artifact@v5
@@ -24,12 +27,10 @@ jobs:
           path: dist
 
       - name: Check for packaging errors
-        run: pipx run twine check --strict dist/*
+        run: uvx twine check --strict dist/*
 
       - name: Install produced wheel
-        uses: ./.github/actions/install_requirements
-        with:
-          pip-install: dist/*.whl
+        run: python -m pip install dist/*.whl
 
       - name: Test module --version works using the installed wheel
         run: python -m dodal --version

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/.github/workflows/_docs.yml

@@ -20,11 +20,14 @@ jobs:
       - name: Install system packages
         run: sudo apt-get install graphviz
 
-      - name: Install python packages
-        uses: ./.github/actions/install_requirements
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      # - name: Install requirements
+      #   run: uv sync --group dev
 
       - name: Build docs
-        run: tox -e docs
+        run: uv run --locked tox -e docs
 
       - name: Remove environment.pickle
         run: rm build/html/.doctrees/environment.pickle

dls_dodal-1.69.0/.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-1.67.0 → dls_dodal-1.69.0}/.github/workflows/_tox.yml

@@ -14,14 +14,12 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v5
-        with:
-          fetch-depth: 0
 
-      - name: Install python packages
-        uses: ./.github/actions/install_requirements
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
 
       - name: Run import linter
-        run: lint-imports
+        run: uv run --locked lint-imports
 
       - name: Run tox
-        run: tox -e ${{ inputs.tox }}
+        run: uv run --locked tox -e ${{ inputs.tox }}

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/.github/workflows/ci.yml

@@ -20,21 +20,16 @@ jobs:
       matrix:
         runs-on: ["ubuntu-latest"] # can add windows-latest, macos-latest
         python-version: ["3.11", "3.12", "3.13"]
-        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:
     uses: ./.github/workflows/_docs.yml
-
+    permissions:
+      contents: write
 
   dist:
     uses: ./.github/workflows/_dist.yml

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/.github/workflows/periodic.yml

@@ -10,4 +10,4 @@ jobs:
   linkcheck:
     uses: ./.github/workflows/_tox.yml
     with:
-      tox: docs build -- -b linkcheck
+      tox: docs -- -b linkcheck

dls_dodal-1.69.0/.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-1.67.0 → dls_dodal-1.69.0}/.pre-commit-config.yaml

@@ -3,6 +3,7 @@ repos:
     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
@@ -31,6 +32,13 @@ repos:
         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:

dls_dodal-1.69.0/.python-version

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

dls_dodal-1.69.0/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

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dls-dodal
-Version: 1.67.0
+Version: 1.69.0
 Summary: Ophyd devices and other utils that could be used across DLS beamlines
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>, Joseph Ware <joseph.ware@diamond.ac.uk>, Oliver Silvester <Oliver.Silvester@diamond.ac.uk>, Noemi Frisina <noemi.frisina@diamond.ac.uk>
 License:                                  Apache License
@@ -231,37 +231,7 @@ Requires-Dist: redis
 Requires-Dist: scanspec>=0.7.3
 Requires-Dist: pyzmq==26.3.0
 Requires-Dist: deepdiff
-Requires-Dist: daq-config-server>=v1.0.0-rc.2
-Provides-Extra: dev
-Requires-Dist: black; extra == "dev"
-Requires-Dist: diff-cover; extra == "dev"
-Requires-Dist: import-linter; extra == "dev"
-Requires-Dist: ispyb; extra == "dev"
-Requires-Dist: mypy; extra == "dev"
-Requires-Dist: myst-parser; extra == "dev"
-Requires-Dist: ophyd_async[sim]>=v0.14.0; extra == "dev"
-Requires-Dist: pipdeptree; extra == "dev"
-Requires-Dist: pre-commit; extra == "dev"
-Requires-Dist: psutil; extra == "dev"
-Requires-Dist: pydata-sphinx-theme>=0.12; extra == "dev"
-Requires-Dist: pyright==1.1.406; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
-Requires-Dist: pytest-asyncio; extra == "dev"
-Requires-Dist: pytest-cov; extra == "dev"
-Requires-Dist: pytest-json-report; extra == "dev"
-Requires-Dist: pytest-random-order; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: sphinx<7.4.6; extra == "dev"
-Requires-Dist: sphinx-autobuild; extra == "dev"
-Requires-Dist: sphinx-copybutton; extra == "dev"
-Requires-Dist: sphinxcontrib-mermaid; extra == "dev"
-Requires-Dist: sphinx-design; extra == "dev"
-Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
-Requires-Dist: tox-direct; extra == "dev"
-Requires-Dist: types-requests; extra == "dev"
-Requires-Dist: types-mock; extra == "dev"
-Requires-Dist: types-PyYAML; extra == "dev"
-Requires-Dist: types-aiofiles; extra == "dev"
+Requires-Dist: daq-config-server>=v1.0.0
 Dynamic: license-file
 
 [![CI](https://github.com/DiamondLightSource/dodal/actions/workflows/ci.yml/badge.svg)](https://github.com/DiamondLightSource/dodal/actions/workflows/ci.yml)

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/docs/how-to/coverage.md

@@ -1,7 +1,7 @@
 
 # How to check code coverage
 
-Code coverage is reported to the command line and to a `cov.xml` file by the command `tox -e tests`. The file is uploaded to the Codecov service in CI.
+Code coverage is reported to the command line and to a `cov.xml` file by the command `uv run tox -e tests`. The file is uploaded to the Codecov service in CI.
 
 If you are using VSCode IDE, you can also check code coverage by right-clicking on the test icon and selecting `Run with coverage`. This will re-run the test and highlight line numbers in your file:
 - Green = covered by tests

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/docs/how-to/dev-install.md

@@ -19,17 +19,16 @@ in a container under [VSCode](https://code.visualstudio.com/)
 If on a DLS machine make sure you have python >3.11 running by doing `module load python/3.11`
 
 ```
-python3 -m venv venv
-source venv/bin/activate
-pip install --upgrade pip
-pip install -e '.[dev]'
+module load uv
+uv sync --group dev
+source .venv/bin/activate
 ```
 
 ## See what was installed
 
 To see a graph of the python package dependency tree type:
 
-    $ pipdeptree
+    $ uv tree
 
 :::
 
@@ -49,7 +48,7 @@ code .
 Now you have a development environment you can run the tests in a terminal:
 
 ```
-tox -p
+uv run tox -p
 ```
 
 This will run in parallel the following checks:

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/docs/how-to/lint.md

@@ -7,7 +7,7 @@ Code linting is handled by [ruff](https://docs.astral.sh/ruff) run under [pre-co
 You can run the above checks on all files with this command:
 
 ```
-$ tox -e pre-commit
+$ uv run tox -e pre-commit
 ```
 
 Or you can install a pre-commit hook that will run each time you do a `git commit` on just the files that have changed:

dls_dodal-1.69.0/docs/how-to/lock-requirements.md

@@ -0,0 +1,43 @@
+# Lock requirements
+
+## Introduction
+
+Since the move to `uv`, this project natively supports a lockfile. This is a set of "known good" dependencies that the tests are run against, and will be used to create a container if one is built.
+
+## Specifying dependencies
+
+The source of dependencies is the project's `pyproject.toml`. They can come from:
+- Project dependencies (from `[project]` `dependencies =`)
+- Dev dependencies (from `[dependency-groups]` `dev =`)
+- Transitive dependencies (child dependencies of the above)
+
+Dependencies are loosely specified in `pyproject.toml`, like `sphinx-autobuild` or `pydata-sphinx-theme>=0.12`. They should state a minimum version if you are using features that are added in a specific version. There should be no upper bound by default, only insert one if an upstream release of a dependency breaks your code, and you don't have time to fix it immediately.
+
+## Updating the lockfile
+
+When you have updated `pyproject.toml` then run:
+```
+$ uv sync
+```
+
+This will ensure that any new dependencies you add will be placed in the lockfile, and your venv updated to match. It will *not* update any existing dependencies, unless `pyproject.toml` requires a later version.
+
+This command will be run by [pre-commit](./lint) during a `git commit` and by CI.
+
+To update all dependencies to their latest versions run:
+```
+uv sync --upgrade
+```
+This command will be run by [renovate](./renovate) once a week in CI.
+
+```{seealso}
+[The uv docs on locking and syncing](https://docs.astral.sh/uv/concepts/projects/sync)
+```
+
+## Modifying the venv to add other projects
+
+Peer projects (those checked out next to the project) are visible in the devcontainer, and can be added into the venv by running `uv pip install -e ../other_project`. This will allow live changes made in this other project to be immediately reflected in the venv.
+
+```{note}
+This venv is activated by default, and global to the container, so if you `uv sync` from `other_project` then it will **replace** the contents of the venv with `other_project`'s dependencies.
+```

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/docs/how-to/run-tests.md

@@ -28,7 +28,7 @@ If you find that your tests are being skipped or not recognised by `pytest`, che
 When you have some fully working tests then you can run it with coverage:
 
 ```
-$ tox -e tests
+$ uv run tox -e tests
 ```
 
 It will also report coverage to the command line and to `cov.xml`.
@@ -54,8 +54,11 @@ cd example-services
 podman compose up -d bl01t-di-cam-01 bl01t-mo-sim-01 ca-gateway
 ```
 
+**Note:** Do not run the system tests from the same shell as the above `environment.sh` script interferes with the 
+ability to run the tests due to also setting EPICS_ environment variables.
+
 Once this is done, then the system tests can be run:
 
 ```commandline
-tox -e system-report
+uv run tox -e system-tests
 ```

{dls_dodal-1.67.0 → dls_dodal-1.69.0}/docs/how-to/static-analysis.md

@@ -3,5 +3,5 @@
 Static type analysis is done with [pyright](https://microsoft.github.io/pyright) or [mypy](https://www.mypy-lang.org) dependent on the settings in `pyproject.toml`. It checks type definition in source files without running them, and highlights potential issues where types do not match. You can run it with:
 
 ```
-$ tox -e type-checking
+$ uv run tox -e type-checking
 ```