Run doctests in pytest. Add linters to pre-commit. Add a pre-commit w…

…orkflow. (#96)

- Adds doctests for pyi and md files.
- Pulls pytest arguments used in build / test workflows into
pyproject.toml.
- Adds [ruff](https://docs.astral.sh/ruff/) and
[rustfmt](https://github.com/rust-lang/rustfmt) checks to pre-commit.
- Adds a pre-commit check workflow that runs on PRs into main.

.github/workflows/pre-commit.yml

@@ -0,0 +1,27 @@
+name: Run pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [ main ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install
+        run: |
+          pip install --upgrade pip
+          pip install -e '.[testing]'
+
+      - name: Run pre-commit
+        uses: pre-commit/[email protected]

.github/workflows/release.yml

@@ -110,8 +110,8 @@ jobs:
 
       - name: Test artifact
         run: |
-          python -m pytest -k test_basic --color=yes --cov-report=xml --cov=acquire --maxfail=5 --log-cli-level=0
-          python -m pytest -k test_zarr --color=yes --cov-report=xml --cov=acquire --maxfail=5 --log-cli-level=0
+          python -m pytest -k test_basic
+          python -m pytest -k test_zarr
 
       - name: Upload wheels
         uses: actions/upload-artifact@v3

.github/workflows/test_pr.yml

@@ -55,8 +55,8 @@ jobs:
           ZARR_V3_EXPERIMENTAL_API: "1"
           ZARR_V3_SHARDING: "1"
         run: |
-          python -m pytest -k test_basic --color=yes --cov-report=xml --cov=acquire --maxfail=5 --log-cli-level=0
-          python -m pytest -k test_zarr --color=yes --cov-report=xml --cov=acquire --maxfail=5 --log-cli-level=0
+          python -m pytest -k test_basic
+          python -m pytest -k test_zarr
 
   dcam:
     name: Python ${{ matrix.python }} (DCAM)
@@ -102,7 +102,7 @@ jobs:
 
       - name: Test
         run: |
-          python -m pytest -k test_dcam --color=yes --cov-report=xml --cov=acquire --maxfail=5 --log-cli-level=0
+          python -m pytest -k test_dcam
 
   egrabber:
     name: Python ${{ matrix.python }} (eGrabber)
@@ -148,7 +148,7 @@ jobs:
 
       - name: Test
         run: |
-          python -m pytest -k test_egrabber --color=yes --cov-report=xml --cov=acquire --maxfail=5 --log-cli-level=0
+          python -m pytest -k test_egrabber
 
 
   spinnaker:
@@ -196,7 +196,7 @@ jobs:
 
       - name: Test
         run: |
-          python -m pytest -k test_spinnaker --color=yes --cov-report=xml --cov=acquire --maxfail=5 --log-cli-level=0
+          python -m pytest -k test_spinnaker
 
 
   typing:

.pre-commit-config.yaml

@@ -1,23 +1,37 @@
 repos:
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 22.6.0
     hooks:
-    - id: black
-      pass_filenames: true
--   repo: https://github.com/PyCQA/flake8
+      - id: black
+        pass_filenames: true
+  - repo: https://github.com/PyCQA/flake8
     rev: 5.0.4
     hooks:
-    - id: flake8
-      additional_dependencies: [flake8-typing-imports]
-      pass_filenames: true
-      exclude: __init__.py
--   repo: https://github.com/asottile/pyupgrade
+      - id: flake8
+        additional_dependencies: [ flake8-typing-imports ]
+        pass_filenames: true
+        exclude: __init__.py
+  - repo: https://github.com/asottile/pyupgrade
     rev: v2.37.3
     hooks:
-    - id: pyupgrade
-      args: ["--py38-plus", "--keep-runtime-typing"]
--   repo: https://github.com/seddonym/import-linter
+      - id: pyupgrade
+        args: [ "--py38-plus", "--keep-runtime-typing" ]
+  - repo: https://github.com/seddonym/import-linter
     rev: v1.2.7
     hooks:
-    - id: import-linter
-      stages: [manual]
+      - id: import-linter
+        stages: [ manual ]
+  - repo: local
+    hooks:
+      - id: ruff
+        name: Lint Python files
+        entry: python -m ruff check .
+        language: system
+        types: [ file ]
+        files: \.py$
+      - id: cargo-fmt
+        name: Format Rust files
+        entry: cargo fmt --all -- --check
+        language: system
+        types: [ file ]
+        files: \.rs$

pyproject.toml

@@ -23,6 +23,7 @@ testing = [
     "zarr",
     "dask",
     "ome-zarr",
+    "ruff",
 ]
 
 [project.entry-points."napari.manifest"]
@@ -57,7 +58,17 @@ profile = "black"
 
 [tool.pytest.ini_options]
 minversion = "7.0"
-addopts = "--tb=short -s"
+addopts = '--tb=short -s --color=yes --cov-report=xml --cov=acquire --maxfail=5 --log-cli-level=0 --doctest-glob="*.pyi" --doctest-glob="*.md"'
 # log_format = "%(asctime)s %(levelname)s %(message)s"
 # log_date_format = "%Y-%m-%d %H:%M:%S"
 log_cli = true # when true, messages are printed immediately
+
+[tool.ruff]
+exclude = [
+    "__init__.py"
+]
+
+ignore = [
+    "F403",
+    "F405",
+]

python/acquire/__init__.pyi

@@ -2,7 +2,7 @@ from typing import List, Optional, Union
 
 import napari  # type: ignore
 
-from .acquire import *
+from .acquire import Runtime, Properties
 
 def setup(
     runtime: Runtime,

python/acquire/acquire.pyi

@@ -91,11 +91,11 @@ class DeviceIdentifier:
 
 @final
 class DeviceKind:
-    Camera: ClassVar[DeviceKind] = DeviceKind.Camera
-    NONE: ClassVar[DeviceKind] = DeviceKind.NONE
-    Signals: ClassVar[DeviceKind] = DeviceKind.Signals
-    StageAxis: ClassVar[DeviceKind] = DeviceKind.StageAxis
-    Storage: ClassVar[DeviceKind] = DeviceKind.Storage
+    Camera: ClassVar[DeviceKind]
+    NONE: ClassVar[DeviceKind]
+    Signals: ClassVar[DeviceKind]
+    StageAxis: ClassVar[DeviceKind]
+    Storage: ClassVar[DeviceKind]
     def __init__(self, *args: None, **kwargs: Any) -> None: ...
     def __eq__(self, other: object) -> bool: ...
     def __ge__(self, other: object) -> bool: ...
@@ -120,12 +120,10 @@ class DeviceManager:
 
 @final
 class DeviceState:
-    Closed: ClassVar[DeviceState] = DeviceState.Closed
-    AwaitingConfiguration: ClassVar[
-        DeviceState
-    ] = DeviceState.AwaitingConfiguration
-    Armed: ClassVar[DeviceState] = DeviceState.Armed
-    Running: ClassVar[DeviceState] = DeviceState.Running
+    Closed: ClassVar[DeviceState]
+    AwaitingConfiguration: ClassVar[DeviceState]
+    Armed: ClassVar[DeviceState]
+    Running: ClassVar[DeviceState]
     def __eq__(self, other: object) -> bool: ...
     def __ge__(self, other: object) -> bool: ...
     def __gt__(self, other: object) -> bool: ...
@@ -142,8 +140,8 @@ class DigitalLineCapabilities:
 
 @final
 class Direction:
-    Backward: ClassVar[Direction] = Direction.Backward
-    Forward: ClassVar[Direction] = Direction.Forward
+    Backward: ClassVar[Direction]
+    Forward: ClassVar[Direction]
     def __eq__(self, other: object) -> bool: ...
     def __ge__(self, other: object) -> bool: ...
     def __gt__(self, other: object) -> bool: ...
@@ -196,10 +194,10 @@ class Property:
 
 @final
 class PropertyType:
-    FixedPrecision: ClassVar[PropertyType] = PropertyType.FixedPrecision
-    FloatingPrecision: ClassVar[PropertyType] = PropertyType.FloatingPrecision
-    Enum: ClassVar[PropertyType] = PropertyType.Enum
-    String: ClassVar[PropertyType] = PropertyType.String
+    FixedPrecision: ClassVar[PropertyType]
+    FloatingPrecision: ClassVar[PropertyType]
+    Enum: ClassVar[PropertyType]
+    String: ClassVar[PropertyType]
     def __eq__(self, other: object) -> bool: ...
     def __ge__(self, other: object) -> bool: ...
     def __gt__(self, other: object) -> bool: ...
@@ -237,14 +235,14 @@ class SampleRateHz:
 
 @final
 class SampleType:
-    F32: ClassVar[SampleType] = SampleType.F32
-    I16: ClassVar[SampleType] = SampleType.I16
-    I8: ClassVar[SampleType] = SampleType.I8
-    U16: ClassVar[SampleType] = SampleType.U16
-    U8: ClassVar[SampleType] = SampleType.U8
-    U10: ClassVar[SampleType] = SampleType.U10
-    U12: ClassVar[SampleType] = SampleType.U12
-    U14: ClassVar[SampleType] = SampleType.U14
+    F32: ClassVar[SampleType]
+    I16: ClassVar[SampleType]
+    I8: ClassVar[SampleType]
+    U16: ClassVar[SampleType]
+    U8: ClassVar[SampleType]
+    U10: ClassVar[SampleType]
+    U12: ClassVar[SampleType]
+    U14: ClassVar[SampleType]
     def __eq__(self, other: object) -> bool: ...
     def __ge__(self, other: object) -> bool: ...
     def __gt__(self, other: object) -> bool: ...
@@ -270,8 +268,8 @@ class ShardingCapabilities:
 
 @final
 class SignalIOKind:
-    Input: ClassVar[SignalIOKind] = SignalIOKind.Input
-    Output: ClassVar[SignalIOKind] = SignalIOKind.Output
+    Input: ClassVar[SignalIOKind]
+    Output: ClassVar[SignalIOKind]
     def __eq__(self, other: object) -> bool: ...
     def __ge__(self, other: object) -> bool: ...
     def __gt__(self, other: object) -> bool: ...
@@ -282,8 +280,8 @@ class SignalIOKind:
 
 @final
 class SignalType:
-    Analog: ClassVar[SignalType] = SignalType.Analog
-    Digital: ClassVar[SignalType] = SignalType.Digital
+    Analog: ClassVar[SignalType]
+    Digital: ClassVar[SignalType]
     def __eq__(self, other: object) -> bool: ...
     def __ge__(self, other: object) -> bool: ...
     def __gt__(self, other: object) -> bool: ...
@@ -334,12 +332,12 @@ class TriggerCapabilities:
 
 @final
 class TriggerEdge:
-    Falling: ClassVar[TriggerEdge] = TriggerEdge.Falling
-    NotApplicable: ClassVar[TriggerEdge] = TriggerEdge.NotApplicable
-    Rising: ClassVar[TriggerEdge] = TriggerEdge.Rising
-    AnyEdge: ClassVar[TriggerEdge] = TriggerEdge.AnyEdge
-    LevelLow: ClassVar[TriggerEdge] = TriggerEdge.LevelLow
-    LevelHigh: ClassVar[TriggerEdge] = TriggerEdge.LevelHigh
+    Falling: ClassVar[TriggerEdge]
+    NotApplicable: ClassVar[TriggerEdge]
+    Rising: ClassVar[TriggerEdge]
+    AnyEdge: ClassVar[TriggerEdge]
+    LevelLow: ClassVar[TriggerEdge]
+    LevelHigh: ClassVar[TriggerEdge]
     def __eq__(self, other: object) -> bool: ...
     def __ge__(self, other: object) -> bool: ...
     def __gt__(self, other: object) -> bool: ...