use ruff; build python3.12

.github/workflows/build-and-deploy.yml

@@ -17,30 +17,42 @@ jobs:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.3
+        uses: pypa/cibuildwheel@v2.16.5
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: pymeshfix-wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build sdist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - name: Install package from sdist
+        run: pip install dist/*.tar.gz
+
+      - name: Install test requirements
+        run: pip install -r requirements_test.txt
+
+      - name: Run tests
+        run: pytest
+
+      - uses: actions/upload-artifact@v4
         with:
+          name: pymeshfix-sdist
           path: dist/*.tar.gz
 
   upload_pypi:
@@ -51,12 +63,12 @@ jobs:
     # alternatively, to publish when a GitHub Release is created, use the following rule:
     # if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
 
-      - uses: pypa/[email protected].6
+      - uses: pypa/[email protected].11
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

.pre-commit-config.yaml

@@ -5,32 +5,27 @@ ci:
     autoupdate_schedule: quarterly
 
 repos:
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-
-- repo: https://github.com/psf/black
-  rev: 23.7.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.1.11
   hooks:
-  - id: black
-    args:
-      - --line-length=100
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+      exclude: ^(docs/|tests)
+    - id: ruff-format
 
 - repo: https://github.com/keewis/blackdoc
-  rev: v0.3.8
+  rev: v0.3.9
   hooks:
   - id: blackdoc
     files: '\.py$'
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 7.0.0
   hooks:
   - id: flake8
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.5
+  rev: v2.2.6
   hooks:
   - id: codespell
     args: ["--toml", "pyproject.toml"]
@@ -44,13 +39,13 @@ repos:
     exclude: "examples/"
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-merge-conflict
   - id: debug-statements
 
 # this validates our github workflow files
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.23.3
+  rev: 0.28.0
   hooks:
     - id: check-github-workflows

MANIFEST.in

@@ -1,2 +1,3 @@
+include pymeshfix/cython/*.pyx
 include pymeshfix/cython/*.h
 include tests/*

doc/conf.py

@@ -1,20 +1,20 @@
 """Configuration for the documentation generation of pymeshfix."""
+
 import datetime
 import os
 
-import numpy as np
-import pymeshfix
-
-# -- pyvista configuration ---------------------------------------------------
 import pyvista
+from sphinx_gallery.sorting import FileNameSortKey
+
+import pymeshfix
 
 # Manage errors
 pyvista.set_error_output_file("errors.txt")
 # Ensure that offscreen rendering is used for docs generation
 pyvista.OFF_SCREEN = True  # Not necessary - simply an insurance policy
 # Preferred plotting style for documentation
 pyvista.set_plot_theme("document")
-pyvista.rcParams["window_size"] = np.array([1024, 768]) * 2
+pyvista.global_theme.window_size = [1024, 768]
 # Save figures in specified directory
 pyvista.FIGURE_PATH = os.path.abspath("./images/")
 if not os.path.exists(pyvista.FIGURE_PATH):
@@ -99,7 +99,9 @@
     # Enable the "Edit in GitHub link within the header of each page.
     "display_github": True,
     # Set the following variables to generate the resulting github URL for each page.
-    # Format Template: https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }}
+    # Format Template: https://{{ github_host|default("github.com") }}/{{
+    # github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path
+    # }}{{ pagename }}{{ suffix }}
     "github_user": "pyvista",
     "github_repo": "pymeshfix",
     "github_version": "master/doc/",
@@ -184,8 +186,6 @@
 
 
 # -- Sphinx Gallery Options
-from sphinx_gallery.sorting import FileNameSortKey
-
 sphinx_gallery_conf = {
     # path to your examples scripts
     "examples_dirs": [

examples/bunny.py

@@ -5,12 +5,12 @@
 Repair the holes in the bunny mesh.
 """
 
-import pymeshfix as mf
-
 # sphinx_gallery_thumbnail_number = 2
 import pyvista as pv
 from pyvista import examples
 
+import pymeshfix as mf
+
 ################################################################################
 bunny = examples.download_bunny()
 

examples/cow.py

@@ -6,12 +6,13 @@
 """
 
 import numpy as np
-import pymeshfix as mf
 
 # sphinx_gallery_thumbnail_number = 1
 import pyvista as pv
 from pyvista import examples
 
+import pymeshfix as mf
+
 ################################################################################
 cow = examples.download_cow()
 

examples/repair_planar.py

@@ -7,10 +7,11 @@
 
 # sphinx_gallery_thumbnail_number = 1
 import numpy as np
+import pyvista as pv
+
 from pymeshfix import MeshFix
 from pymeshfix._meshfix import PyTMesh
 from pymeshfix.examples import planar_mesh
-import pyvista as pv
 
 ###############################################################################
 # plot the holes on the original mesh

examples/torso.py

@@ -6,12 +6,12 @@
 parts of the mesh
 """
 
-import pymeshfix as mf
-
 # sphinx_gallery_thumbnail_number = 2
 import pyvista as pv
 from pyvista import examples
 
+import pymeshfix as mf
+
 mesh = examples.download_torso()
 print(mesh)
 

pymeshfix/__init__.py

@@ -1,5 +1,5 @@
 """PyMeshFix module."""
-from pymeshfix import _meshfix
-from pymeshfix._meshfix import PyTMesh, clean_from_arrays, clean_from_file
-from pymeshfix._version import __version__
-from pymeshfix.meshfix import *
+from pymeshfix import _meshfix  # noqa: F401
+from pymeshfix._meshfix import PyTMesh, clean_from_arrays, clean_from_file  # noqa: F401
+from pymeshfix._version import __version__  # noqa: F401
+from pymeshfix.meshfix import MeshFix  # noqa: F401

pymeshfix/_version.py

@@ -6,5 +6,6 @@
 version_info = 0, 27, 'dev0'
 
 """
+
 version_info = 0, 17, "dev0"
 __version__ = ".".join(map(str, version_info))

pymeshfix/examples/__init__.py

@@ -1,9 +1,10 @@
 """Built-in examples."""
+
 # get location of the example meshes
 from os.path import dirname, join, realpath
 
 pth = dirname(realpath(__file__))
 bunny_scan = join(pth, "StanfordBunny.ply")
 planar_mesh = join(pth, "planar_mesh.ply")
 
-from pymeshfix.examples.fix import *
+from pymeshfix.examples.fix import native, with_vtk  # noqa: F401, E402

pymeshfix/examples/fix.py

@@ -1,11 +1,13 @@
 """Demonstrate mesh repair on the standford bunny mesh."""
+
 import os
 import time
 
 import numpy as np
+import pyvista as pv
+
 import pymeshfix
 from pymeshfix.examples import bunny_scan
-import pyvista as pv
 
 
 def native(outfile="repaired.ply"):

pymeshfix/meshfix.py

@@ -1,7 +1,9 @@
 """Python module to interface with wrapped meshfix."""
+
 import ctypes
 
 import numpy as np
+
 from pymeshfix import _meshfix
 
 try:
@@ -12,7 +14,7 @@
     PV_INSTALLED = False
 
 
-class MeshFix(object):
+class MeshFix:
     """Clean and tetrahedralize surface meshes using MeshFix.
 
     Parameters

pyproject.toml

@@ -2,7 +2,7 @@
 requires = [
     "setuptools>=42",
     "wheel>=0.33.0",
-    "cython>=0.29.32",
+    "cython>=3.0.0",
     "oldest-supported-numpy"
 ]
 
@@ -18,7 +18,7 @@ filterwarnings = [
 
 [tool.cibuildwheel]
 archs = ["auto64"]  # 64-bit only
-skip = "pp* *musllinux*"  # disable PyPy and musl-based wheels
+skip = "pp* *musllinux* cp37-*"  # disable PyPy and musl-based wheels and Python<3.8
 test-requires = "pytest"
 test-command = "pytest {project}/tests"
 
@@ -31,9 +31,7 @@ test-skip = ["*_arm64", "*_universal2:arm64"]
 skip = '*.cxx,*.h,*.gif,*.png,*.jpg,*.js,*.html,*.doctree,*.ttf,*.woff,*.woff2,*.eot,*.mp4,*.inv,*.pickle,*.ipynb,flycheck*,./.git/*,./.hypothesis/*,*.yml,./doc/build/*,./doc/images/*,./dist/*,*~,.hypothesis*,*.cpp,*.c'
 quiet-level = 3
 
-[tool.isort]
-profile = "black"
-force_sort_within_sections = true
-default_section = "THIRDPARTY"
-skip_glob = ["__init__.py"]
-src_paths = ["doc", "src", "tests"]
+[tool.ruff]
+line-length = 100
+# pyflakes, pycodestyle, isort
+select = ["F", "E", "W", "I001"]

setup.py

@@ -1,10 +1,11 @@
 """Setup for pymeshfix."""
-from io import open as io_open
+
 import os
 import sys
+from io import open as io_open
 
-from Cython.Build import cythonize
 import numpy as np
+from Cython.Build import cythonize
 from setuptools import Extension, setup
 
 filepath = os.path.dirname(__file__)