Use ruff as formatter and linter

.pre-commit-config.yaml

@@ -1,9 +1,12 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 24.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.2
     hooks:
-      - id: black
-        args: [--check]
+      - id: ruff # linter
+        name: Run ruff (linter for Python)
+        args: ["--fix", "--select", "I,TID252,F401"] # "I => sort imports, TID252 => ban relative imports, F401 => unused imports"
+      - id: ruff-format # formatter
+        name: Run ruff (formatter for Python)
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "biomesh"
-version = "0.5.0"
+version = "0.5.1"
 authors = [
   { name="The biomesh Authors" },
 ]
@@ -40,3 +40,6 @@ dependencies = [
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/biomesh"]
+
+[tool.ruff.lint.per-file-ignores]
+"src/biomesh/__init__.py" = ["F401"]

src/biomesh/__init__.py

@@ -6,23 +6,22 @@
 """Biomesh is a Python package for working with 3D meshes, providing tools for
 mesh generation, manipulation, and analysis tailored for finite element
 simulations of biomechanical applications."""
-from . import run_gmsh
+
 import pathlib
-from . import mesh
-import lnmmeshio
 import tempfile
+
+import lnmmeshio
 import meshio
-from .reorder import reorder
+
+from . import laplace, mesh, run_gmsh, utils
 from .adapt import lin_to_quad
-from .merge import merge
 from .filter import (
-    filter_by_cellblock,
     filter_by_block_ids,
+    filter_by_cellblock,
     filter_by_cellblock_point_mapping,
 )
-
-from . import utils
-from . import laplace
+from .merge import merge
+from .reorder import reorder
 
 
 def combine_colored_stl_files(*stl_files: pathlib.Path) -> meshio.Mesh:

src/biomesh/fe.py

@@ -4,9 +4,11 @@
 #
 # SPDX-License-Identifier: MIT
 """Small utilities for finite elements."""
-import numpy as np
+
 import math
+
 import meshio
+import numpy as np
 import symfem
 import sympy as sp
 

src/biomesh/filter.py

@@ -5,9 +5,10 @@
 # SPDX-License-Identifier: MIT
 """Filter for meshes to extract a subset."""
 
+from typing import Callable
+
 import meshio
 import numpy as np
-from typing import Callable
 
 
 def filter_by_cellblock_point_mapping(

src/biomesh/laplace.py

@@ -4,10 +4,11 @@
 #
 # SPDX-License-Identifier: MIT
 """A simple dummy Laplace-solver."""
-import numpy as np
-import math
+
 import meshio
+import numpy as np
 import scipy.sparse
+
 from . import fe
 
 _OPTIMAL_NUMBER_OF_INTEGRATION_POINTS = {

src/biomesh/merge.py

@@ -4,6 +4,7 @@
 #
 # SPDX-License-Identifier: MIT
 """A module to merge multuple meshes into one larger mesh."""
+
 import meshio
 import numpy as np
 

src/biomesh/mesh.py

@@ -5,10 +5,11 @@
 # SPDX-License-Identifier: MIT
 """A module for utils for generating meshes."""
 
-import lnmmeshio
 import pathlib
-import numpy as np
+
+import lnmmeshio
 import meshio
+import numpy as np
 import scipy.spatial as sp
 
 
@@ -90,7 +91,6 @@ def merge_colored_stl(
 
         # append cells
         for cell_id, cell in enumerate(mesh.cells[0].data):
-
             key = _sort_cell_node_ids([node_mapping[i] for i in cell])
 
             if key not in cell_surface_ids:

src/biomesh/reorder.py

@@ -5,11 +5,12 @@
 # SPDX-License-Identifier: MIT
 """A module for reordering nodes in a finite element mesh."""
 
+import copy
+from collections import defaultdict
+
 import meshio
-import scipy.sparse as sp
 import numpy as np
-from collections import defaultdict
-import copy
+import scipy.sparse as sp
 
 
 def reverse_permutation(perm: np.ndarray) -> np.ndarray:

src/biomesh/run_gmsh.py

@@ -6,9 +6,10 @@
 """A module controlling running the gmsh api if installed."""
 
 import pathlib
-import meshio
 import tempfile
-from types import TracebackType, ModuleType
+from types import TracebackType
+
+import meshio
 
 
 class GmshApi:

src/biomesh/utils.py

@@ -4,6 +4,7 @@
 #
 # SPDX-License-Identifier: MIT
 """Some small utilities."""
+
 import numpy as np
 import scipy.spatial as sp
 

tests/test_adapt.py

@@ -4,11 +4,14 @@
 #
 # SPDX-License-Identifier: MIT
 """Testing mesh adaptation utilities."""
+
 import pathlib
+
 import meshio
-import biomesh
 import numpy as np
 
+import biomesh
+
 
 def test_lin_to_quad():
     """Testing converting linear cells to quadratic cells."""

tests/test_fe.py

@@ -4,11 +4,14 @@
 #
 # SPDX-License-Identifier: MIT
 """Tests for small finite element ulitities."""
-import pytest
+
 import pathlib
+
 import meshio
-import biomesh
 import numpy as np
+import pytest
+
+import biomesh
 
 
 @pytest.mark.parametrize("shape", ["tetra", "tetra10"])

tests/test_filter.py

@@ -4,11 +4,14 @@
 #
 # SPDX-License-Identifier: MIT
 """Testing filtering meshes."""
-import biomesh
+
 import pathlib
+
 import meshio
 import numpy as np
 
+import biomesh
+
 
 def test_filter_by_cellblock():
     """Test the filter by a specific cellblock filter."""

tests/test_laplace.py

@@ -4,11 +4,14 @@
 #
 # SPDX-License-Identifier: MIT
 """A test suite for the dummy Laplace solver."""
-import pytest
-import biomesh
-import numpy as np
+
 import pathlib
+
 import meshio
+import numpy as np
+import pytest
+
+import biomesh
 
 
 def test_cell_stiffness_hex():

tests/test_merge.py

@@ -5,11 +5,13 @@
 # SPDX-License-Identifier: MIT
 """Test merge meshes."""
 
-import meshio
-import biomesh
 import pathlib
+
+import meshio
 import numpy as np
 
+import biomesh
+
 
 def test_merge():
     """Test merging multiple meshes."""

tests/test_mesh_stl.py

@@ -5,11 +5,11 @@
 # SPDX-License-Identifier: MIT
 """Tests for meshing stl-files."""
 
-import biomesh
 import pathlib
-import meshio
+
 import pytest
-import numpy as np
+
+import biomesh
 
 _my_script_dir = pathlib.Path(__file__).parent
 

tests/test_reorder.py

@@ -6,10 +6,12 @@
 """Tests for reordering nodes/elements in a finite element mesh."""
 
 import pathlib
+
 import meshio
-import biomesh
 import numpy as np
 
+import biomesh
+
 
 def test_reorder():
     """Tests reordering the nodes in a finite element mesh."""

tests/test_utils.py

@@ -4,10 +4,12 @@
 #
 # SPDX-License-Identifier: MIT
 """Test small utilities."""
+
 import numpy as np
-import biomesh
 import scipy.spatial as sp
 
+import biomesh
+
 
 def test_bislerp():
     """Test bislerp operation for rotations."""