support python 3.11 (#48)

Author: akaszynski

.flake8

@@ -0,0 +1,8 @@
+[flake8]
+exclude = venv, __init__.py, build, doc/source/examples
+# To be added after refactoring code to be compliant: E501 
+select = W191, W291, W293, W391, E115, E117, E122, E124, E125, E225, E231, E301, E303, F401, F403
+count = True
+max-complexity = 10
+max-line-length = 100
+statistics = True

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

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Build wheels
-        uses: pypa/[email protected].0
+        uses: pypa/[email protected].1
 
       - uses: actions/upload-artifact@v3
         with:
@@ -46,7 +46,7 @@ jobs:
           name: artifact
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@v1.5.0
+      - uses: pypa/gh-action-pypi-publish@v1.6.4
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+repos:
+
+- repo: https://github.com/pycqa/isort
+  rev: 5.11.2
+  hooks:
+  - id: isort
+
+- repo: https://github.com/psf/black
+  rev: 22.12.0
+  hooks:
+  - id: black
+    args:
+      - --line-length=100
+
+- repo: https://github.com/PyCQA/flake8
+  rev: 6.0.0
+  hooks:
+  - id: flake8
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.2
+  hooks:
+  - id: codespell
+    args: ["--toml", "pyproject.toml"]
+    additional_dependencies: ["tomli"]
+
+# - repo: https://github.com/pycqa/pydocstyle
+#   rev: 6.1.1
+#   hooks:
+#   - id: pydocstyle
+#     additional_dependencies: [toml]
+#     exclude: "tests/"
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-merge-conflict
+  - id: debug-statements
+
+# this validates our github workflow files
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.19.2
+  hooks:
+    - id: check-github-workflows

doc/conf.py

@@ -1,32 +1,32 @@
-import os
-import sys
 import datetime
+import os
 
+import numpy as np
 import pymeshfix
 
 # -- pyvista configuration ---------------------------------------------------
 import pyvista
-import numpy as np
+
 # Manage errors
-pyvista.set_error_output_file('errors.txt')
+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
+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.set_plot_theme("document")
+pyvista.rcParams["window_size"] = np.array([1024, 768]) * 2
 # Save figures in specified directory
-pyvista.FIGURE_PATH = os.path.abspath('./images/')
+pyvista.FIGURE_PATH = os.path.abspath("./images/")
 if not os.path.exists(pyvista.FIGURE_PATH):
     os.makedirs(pyvista.FIGURE_PATH)
 
 pyvista.BUILDING_GALLERY = True
 
 # -- Project information -----------------------------------------------------
 
-project = 'pymeshfix'
+project = "pymeshfix"
 year = datetime.date.today().year
 copyright = f"2017-{year}, The PyVista Developers"
-author = 'Alex Kaszynski'
+author = "Alex Kaszynski"
 
 # The short X.Y version
 version = release = pymeshfix.__version__
@@ -42,29 +42,30 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.napoleon',
-              'sphinx.ext.doctest',
-              'sphinx.ext.autosummary',
-              'notfound.extension',
-              'sphinx_copybutton',
-              'sphinx_gallery.gen_gallery',
-              'sphinx.ext.extlinks',
-             ]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autosummary",
+    "notfound.extension",
+    "sphinx_copybutton",
+    "sphinx_gallery.gen_gallery",
+    "sphinx.ext.extlinks",
+]
 
 html_static_path = ["_static"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -79,11 +80,11 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # Copy button customization ---------------------------------------------------
 # exclude traditional Python prompts from the copied code
-copybutton_prompt_text = r'>>> ?|\.\.\. '
+copybutton_prompt_text = r">>> ?|\.\.\. "
 copybutton_prompt_is_regexp = True
 
 
@@ -95,17 +96,20 @@
 html_theme = "pydata_sphinx_theme"
 html_context = {
     # Enable the "Edit in GitHub link within the header of each page.
-    'display_github': True,
+    "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 }}
-    'github_user': 'pyvista',
-    'github_repo': 'pymeshfix',
-    'github_version': 'master/doc/',
-    'menu_links_name': 'Getting Connected',
-    'menu_links': [
-        ('<i class="fa fa-slack fa-fw"></i> Slack Community', 'http://slack.pyvista.org'),
-        ('<i class="fa fa-comment fa-fw"></i> Support', 'https://github.com/pyvista/pyvista-support'),
-        ('<i class="fa fa-github fa-fw"></i> Source Code', 'https://github.com/pyvista/pymeshfix'),
+    "github_user": "pyvista",
+    "github_repo": "pymeshfix",
+    "github_version": "master/doc/",
+    "menu_links_name": "Getting Connected",
+    "menu_links": [
+        ('<i class="fa fa-slack fa-fw"></i> Slack Community', "http://slack.pyvista.org"),
+        (
+            '<i class="fa fa-comment fa-fw"></i> Support',
+            "https://github.com/pyvista/pyvista-support",
+        ),
+        ('<i class="fa fa-github fa-fw"></i> Source Code', "https://github.com/pyvista/pymeshfix"),
     ],
 }
 
@@ -118,7 +122,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'PyMeshFix'
+htmlhelp_basename = "PyMeshFix"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -129,19 +133,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'pymeshfix.tex', 'PyMeshFix Documentation',
-     'Alex Kaszynski', 'manual'),
+    (master_doc, "pymeshfix.tex", "PyMeshFix Documentation", "Alex Kaszynski", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'PyMeshFix', 'PyMeshFix Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "PyMeshFix", "PyMeshFix Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -150,9 +150,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'PyMeshFix', 'PyMeshFix Documentation',
-     author, 'PyMeshFix', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "PyMeshFix",
+        "PyMeshFix Documentation",
+        author,
+        "PyMeshFix",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 
@@ -161,9 +167,10 @@
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None,
-                       'https://docs.pyvista.org': None,
-                      }
+intersphinx_mapping = {
+    "https://docs.python.org/": None,
+    "https://docs.pyvista.org": None,
+}
 
 # -- Options for todo extension ----------------------------------------------
 
@@ -181,7 +188,7 @@
     ],
     # path where to save gallery generated examples
     "gallery_dirs": ["examples"],
-    # Patter to search for example files
+    # Pattern to search for example files
     "filename_pattern": r"\.py",
     # Remove the "Download all examples" button from the top level gallery
     "download_all_examples": False,
@@ -191,7 +198,7 @@
     "backreferences_dir": None,
     # Modules for which function level galleries are created.  In
     "doc_module": "pymeshfix",
-    "image_scrapers": (pyvista.Scraper(), 'matplotlib'),
+    "image_scrapers": (pyvista.Scraper(), "matplotlib"),
     "thumbnail_size": (350, 350),
 }
 

examples/bunny.py

@@ -2,37 +2,36 @@
 Bunny
 -----
 
-Repair the holes in the bunny mesh
+Repair the holes in the bunny mesh.
 """
 
+import pymeshfix as mf
+
 # sphinx_gallery_thumbnail_number = 2
 import pyvista as pv
-import pymeshfix as mf
 from pyvista import examples
 
 ################################################################################
 bunny = examples.download_bunny()
 
 # Define a camera position that shows the holes in the mesh
-cpos = [(-0.2, -0.13, 0.12),
-        (-0.015, 0.10, -0.0),
-        (0.28, 0.26, 0.9)]
+cpos = [(-0.2, -0.13, 0.12), (-0.015, 0.10, -0.0), (0.28, 0.26, 0.9)]
 
 # Show mesh
 bunny.plot(cpos=cpos)
 
 ################################################################################
-# Genereate a meshfix mesh ready for fixing and extract the holes
+# Generate a meshfix mesh ready for fixing and extract the holes
 meshfix = mf.MeshFix(bunny)
 holes = meshfix.extract_holes()
 
 ################################################################################
 # Render the mesh and outline the holes
 p = pv.Plotter()
 p.add_mesh(bunny, color=True)
-p.add_mesh(holes, color='r', line_width=8)
+p.add_mesh(holes, color="r", line_width=8)
 p.camera_position = cpos
-p.enable_eye_dome_lighting() # helps depth perception
+p.enable_eye_dome_lighting()  # helps depth perception
 p.show()
 
 ################################################################################

examples/cow.py

@@ -5,36 +5,35 @@
 Repair a holey cow
 """
 
+import numpy as np
+import pymeshfix as mf
+
 # sphinx_gallery_thumbnail_number = 1
 import pyvista as pv
-import pymeshfix as mf
 from pyvista import examples
-import numpy as np
 
 ################################################################################
 cow = examples.download_cow()
 
 # Add holes and cast to triangulated PolyData
-cow['random'] = np.random.rand(cow.n_cells)
+cow["random"] = np.random.rand(cow.n_cells)
 holy_cow = cow.threshold(0.9, invert=True).extract_geometry().triangulate()
 print(holy_cow)
 
 ################################################################################
 
 # A nice camera location of the cow
-cpos= [(6.56, 8.73, 22.03),
-       (0.77, -0.44, 0.0),
-       (-0.13, 0.93, -0.35)]
+cpos = [(6.56, 8.73, 22.03), (0.77, -0.44, 0.0), (-0.13, 0.93, -0.35)]
 
 meshfix = mf.MeshFix(holy_cow)
 holes = meshfix.extract_holes()
 
 # Render the mesh and outline the holes
 p = pv.Plotter()
 p.add_mesh(holy_cow, color=True)
-p.add_mesh(holes, color='r', line_width=8)
+p.add_mesh(holes, color="r", line_width=8)
 p.camera_position = cpos
-p.enable_eye_dome_lighting() # helps depth perception
+p.enable_eye_dome_lighting()  # helps depth perception
 p.show()