Add Python 3.11 to workflows and apply ruff linting (#51)

* Add Python 3.11 to workflows

* Add ruff to dependencies

* Update makefile clean commands

* Apply ruff linting suggestions

.github/workflows/build.yml

@@ -8,14 +8,15 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
 
     - name: Checkout the repo
       uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
+      id: setup-python
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
@@ -31,7 +32,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: .venv
-        key: ${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        key: ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
 
     - name: Install dependencies
       if: steps.cached-dependencies.outputs.cache-hit != 'true'

.github/workflows/documentation.yml

@@ -15,6 +15,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python 3.9
+      id: setup-python
       uses: actions/setup-python@v5
       with:
         python-version: 3.9
@@ -30,7 +31,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: .venv
-        key: ${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        key: ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
 
     - name: Install dependencies
       if: steps.cached-dependencies.outputs.cache-hit != 'true'

.github/workflows/lint.yml

@@ -12,6 +12,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python 3.9
+      id: setup-python
       uses: actions/setup-python@v5
       with:
         python-version: 3.9
@@ -27,7 +28,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: .venv
-        key: ${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        key: ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
 
     - name: Install dependencies
       if: steps.cached-dependencies.outputs.cache-hit != 'true'

Makefile

@@ -1,21 +1,22 @@
 .PHONY: clean build docs
 
 clean: # clean all build, python, and testing files
-	rm -fr build/
-	rm -fr dist/
-	rm -fr .eggs/
-	find . -name '*.egg-info' -exec rm -fr {} +
-	find . -name '*.egg' -exec rm -f {} +
+	rm -rf build/
+	rm -rf dist/
+	rm -rf .eggs/
+	find . -name '*.egg-info' -exec rm -rf {} +
+	find . -name '*.egg' -exec rm -rf {} +
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
 	find . -name '*~' -exec rm -f {} +
 	find . -name '__pycache__' -exec rm -fr {} +
-	rm -fr .tox/
-	rm -fr .coverage
-	rm -fr coverage.xml
-	rm -fr htmlcov/
-	rm -fr .pytest_cache
-	rm -fr .mypy_cache
+	rm -rf .tox/
+	rm -rf .coverage
+	rm -rf coverage.xml
+	rm -rf htmlcov/
+	rm -rf .pytest_cache
+	rm -rf .mypy_cache
+	rm -rf .ruff_cache
 
 build: # run tox tests and lint
 	tox

pyproject.toml

@@ -13,9 +13,10 @@ python = "^3.9"
 prefect = "^2.8.2"
 numpy = "^1.24.2"
 pandas = "^1.5.3"
-aicsshparam = "^0.1.7"
+aicsshparam = "^0.1.10"
 vtk = "^9.2.5"
 trimesh = "^3.18.3"
+scikit-image = "^0.21.0"
 
 [tool.poetry.group.dev.dependencies]
 black = "^24.3.0"
@@ -30,6 +31,7 @@ furo = "^2023.5.20"
 myst-parser = "^2.0.0"
 sphinx-copybutton = "^0.5.2"
 tox = "^4.5.1"
+ruff = "^0.6.3"
 
 [tool.isort]
 profile = "black"
@@ -67,11 +69,51 @@ module = [
 ]
 ignore_missing_imports = true
 
+[tool.ruff]
+line-length = 100
+target-version = "py39"
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "COM812", # missing-trailing-comma
+    "D100",   # undocumented-public-module
+    "D105",   # undocumented-magic-method
+    "D107",   # undocumented-public-init
+    "D202",   # no-blank-line-after-function
+    "D203",   # one-blank-line-before-class
+    "D212",   # multi-line-summary-first-line
+    "D413",   # blank-line-after-last-section
+    "D416",   # section-name-ends-in-colon
+]
+
+[tool.ruff.lint.pylint]
+max-args = 10
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = [
+    "D",      # pydocstyle
+    "PT009",  # pytest-unittest-assertion
+    "PT027",  # pytest-unittest-raises-assertion
+    "INP001", # implicit-namespace-package
+    "ANN201", # missing-return-type-undocumented-public-function
+    "S311",   # suspicious-non-cryptographic-random-usage
+    "ANN001", # missing-type-function-argument
+    "ANN003", # missing-type-kwargs
+    "ANN202", # missing-type-args
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+]
+
 [tool.tox]
 legacy_tox_ini = """
 [tox]
 isolated_build = True
-envlist = py{39,310}, format, lint, typecheck
+envlist = py{39,310,311}, format, lint, typecheck
 skipsdist=True
 
 [testenv]
@@ -87,6 +129,7 @@ commands =
 [testenv:lint]
 commands =
     poetry run pylint --ignore-patterns=test.*?py src/ tests/ --fail-under=9.0
+    poetry run ruff check src/ tests/
 
 [testenv:typecheck]
 commands =

src/abm_shape_collection/__init__.py

@@ -1,4 +1,4 @@
-"""Tasks for analyzing cell shapes including spherical harmonics and shape modes."""
+"""Collection of tasks for analyzing cell shapes."""
 
 from prefect import task
 

src/abm_shape_collection/calculate_feature_statistics.py

@@ -29,10 +29,10 @@ def calculate_feature_statistics(
 
     for feature in features:
         # Extract values for specific component.
-        ref_values = ref_data[feature].values
-        values = data[feature].values
+        ref_values = ref_data[feature].to_numpy()
+        values = data[feature].to_numpy()
 
-        # Calculate Kolmogorov–Smirnov statistic.
+        # Calculate Kolmogorov-Smirnov statistic.
         ks_result = ks_2samp(values, ref_values, mode="asymp")
 
         statistics.append(

src/abm_shape_collection/calculate_shape_statistics.py

@@ -11,8 +11,7 @@ def calculate_shape_statistics(
     label: str = "shcoeffs",
 ) -> pd.DataFrame:
     """
-    Perform two-sample Kolmogorov-Smirnov test for goodness of fit on shape
-    components.
+    Perform two-sample Kolmogorov-Smirnov test for goodness of fit on shapes.
 
     Parameters
     ----------
@@ -45,7 +44,7 @@ def calculate_shape_statistics(
         ref_values = ref_transform[:, component]
         values = transform[:, component]
 
-        # Calculate Kolmogorov–Smirnov statistic.
+        # Calculate Kolmogorov-Smirnov statistic.
         ks_result = ks_2samp(values, ref_values, mode="asymp")
 
         statistics.append(

src/abm_shape_collection/construct_mesh_from_array.py

@@ -6,7 +6,7 @@
 
 def construct_mesh_from_array(array: np.ndarray, reference: np.ndarray) -> vtkPolyData:
     """
-    Constructs a mesh from binary image array.
+    Construct a mesh from binary image array.
 
     Parameters
     ----------

src/abm_shape_collection/construct_mesh_from_coeffs.py

@@ -16,7 +16,7 @@ def construct_mesh_from_coeffs(
     scale: float = 1.0,
 ) -> vtkPolyData:
     """
-    Constructs a mesh from spherical harmonic coefficients.
+    Construct a mesh from spherical harmonic coefficients.
 
     Parameters
     ----------

src/abm_shape_collection/construct_mesh_from_points.py

@@ -15,7 +15,7 @@ def construct_mesh_from_points(
     suffix: str = "",
 ) -> vtkPolyData:
     """
-    Constructs mesh given PCA transformation points.
+    Construct mesh given PCA transformation points.
 
     Parameters
     ----------

src/abm_shape_collection/extract_mesh_projections.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 import tempfile
-from typing import Optional, Union
+from enum import Enum
 
 import numpy as np
 import trimesh
@@ -13,11 +15,20 @@
 """Mesh projection names, normals, and extent axes."""
 
 
+class ProjectionType(Enum):
+    """Projection slice types."""
+
+    SLICE = 1
+    """Slice projection type."""
+
+    EXTENT = 2
+    """Extent projection type."""
+
+
 def extract_mesh_projections(
-    mesh: Union[vtkPolyData, trimesh.Trimesh],
-    slices: bool = True,
-    extents: bool = True,
-    offset: Optional[tuple[float, float, float]] = None,
+    mesh: vtkPolyData | trimesh.Trimesh,
+    projection_types: list[ProjectionType],
+    offset: tuple[float, float, float] | None = None,
 ) -> dict:
     """
     Extract slices and/or extents from mesh.
@@ -31,10 +42,8 @@ def extract_mesh_projections(
     ----------
     mesh
         Mesh object.
-    slices
-        True to extract slices, False otherwise.
-    extents : bool, optional
-        True to extract extents, False otherwise.
+    projection_types
+        Mesh projection types.
     offset
         Mesh translation applied before extracting slices and/or meshes.
 
@@ -50,15 +59,13 @@ def extract_mesh_projections(
     if offset is not None:
         mesh.apply_translation(offset)
 
-    projections: dict[str, Union[list[list[list[float]]], dict[float, list[list[list[float]]]]]] = (
-        {}
-    )
+    projections: dict[str, list[list[list[float]]] | dict[float, list[list[list[float]]]]] = {}
 
-    if slices:
+    if ProjectionType.SLICE in projection_types:
         for projection, normal, _ in PROJECTIONS:
             projections[f"{projection}_slice"] = get_mesh_slice(mesh, normal)
 
-    if extents:
+    if ProjectionType.EXTENT in projection_types:
         for projection, normal, index in PROJECTIONS:
             projections[f"{projection}_extent"] = get_mesh_extent(mesh, normal, index)
 
@@ -67,7 +74,7 @@ def extract_mesh_projections(
 
 def convert_vtk_to_trimesh(mesh: vtkPolyData) -> trimesh.Trimesh:
     """
-    Converts VTK polydata to trimesh object.
+    Convert VTK polydata to trimesh object.
 
     Parameters
     ----------
@@ -85,9 +92,7 @@ def convert_vtk_to_trimesh(mesh: vtkPolyData) -> trimesh.Trimesh:
         writer.SetFileTypeToASCII()
         writer.SetFileName(f"{temp.name}.ply")
         _ = writer.Write()
-        mesh = trimesh.load(f"{temp.name}.ply")
-
-    return mesh
+        return trimesh.load(f"{temp.name}.ply")
 
 
 def get_mesh_slice(mesh: trimesh.Trimesh, normal: tuple[int, int, int]) -> list[list[list[float]]]:
@@ -108,8 +113,7 @@ def get_mesh_slice(mesh: trimesh.Trimesh, normal: tuple[int, int, int]) -> list[
     """
 
     mesh_slice = mesh.section_multiplane((0, 0, 0), normal, [0])
-    points = [[list(point) for point in entity] for entity in mesh_slice[0].discrete]
-    return points
+    return [[list(point) for point in entity] for entity in mesh_slice[0].discrete]
 
 
 def get_mesh_extent(
@@ -136,9 +140,8 @@ def get_mesh_extent(
     layers = int(mesh.extents[index] + 2)
     plane_indices = list(np.arange(-layers, layers + 1, 0.5))
     mesh_extents = mesh.section_multiplane((0, 0, 0), normal, plane_indices)
-    points = {
+    return {
         index: [[list(point) for point in entity] for entity in mesh_extent.discrete]
         for mesh_extent, index in zip(mesh_extents, plane_indices)
         if mesh_extent is not None
     }
-    return points

src/abm_shape_collection/extract_mesh_wireframe.py

@@ -1,13 +1,17 @@
-from typing import Optional, Union
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
 
-import trimesh
 from vtk import vtkPolyData  # pylint: disable=no-name-in-module
 
 from abm_shape_collection.extract_mesh_projections import convert_vtk_to_trimesh
 
+if TYPE_CHECKING:
+    import trimesh
+
 
 def extract_mesh_wireframe(
-    mesh: Union[vtkPolyData, trimesh.Trimesh], offset: Optional[tuple[float, float, float]] = None
+    mesh: vtkPolyData | trimesh.Trimesh, offset: tuple[float, float, float] | None = None
 ) -> list[list[tuple[float, float, float]]]:
     """
     Extract wireframe edges from mesh.
@@ -32,9 +36,7 @@ def extract_mesh_wireframe(
         mesh.apply_translation(offset)
 
     all_edges = [[tuple(mesh.vertices[a]), tuple(mesh.vertices[b])] for a, b in mesh.edges]
-    wireframe = [
+    return [
         [(x1, y1, z1), (x2, y2, z2)]
         for (x1, y1, z1), (x2, y2, z2) in {frozenset(edge) for edge in all_edges}
     ]
-
-    return wireframe