Merge branch 'main' into feat/add-delaunay-class

pyvista · Aug 11, 2024 · 8870735 · 8870735
2 parents 8643b93 + de5b189
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -1,6 +1,6 @@
 {
   "files": [
-    "README.md"
+    "CONTRIBUTORS.md"
   ],
   "imageSize": 100,
   "commit": false,
@@ -42,6 +42,15 @@
       "contributions": [
         "maintenance"
       ]
+    },
+    {
+      "login": "dependabot",
+      "name": "Dependabot",
+      "avatar_url": "https://avatars.githubusercontent.com/u/27347476?v=4",
+      "profile": "https://github.com/features/security",
+      "contributions": [
+        "maintenance"
+      ]
     }
   ],
   "contributorsPerLine": 7,

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,10 +3,6 @@ ci:
   autofix_prs: true
   autoupdate_schedule: weekly
 repos:
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
-    hooks:
-      - id: black
   - repo: https://github.com/adamchainz/blacken-docs
     rev: 1.18.0
     hooks:
@@ -16,10 +12,6 @@ repos:
     rev: 0.29.1
     hooks:
       - id: check-github-workflows
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
@@ -57,11 +49,6 @@ repos:
     hooks:
       - id: prettier
         types_or: [yaml, markdown, html, css, scss, javascript, json, toml]
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
-    hooks:
-      - id: pyupgrade
-        args: [--py39-plus, --keep-runtime-typing]
   - repo: https://github.com/DanielNoord/pydocstringformatter
     rev: v0.7.3
     hooks:
@@ -83,6 +70,7 @@ repos:
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
+      - id: ruff-format
   - repo: https://github.com/scientific-python/cookie
     rev: 2024.04.23
     hooks:

diff --git a/AUTHORS.md b/AUTHORS.md
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -39,7 +39,7 @@ question, concern, feature request, or desire to contribute.
 ## Being Respectful
 
 [![Contributor
-Covenant](https://img.shields.io/badge/contributor%20covenant-2.1-4baaaa.svg?style=for-the-badge)](CODE_OF_CONDUCT.md)
+Covenant](https://img.shields.io/badge/contributor%20covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
 
 Please demonstrate empathy and kindness toward other people, other
 software, and the communities who have worked diligently to build
@@ -140,7 +140,7 @@ original author to relicense the code.
 
 ## Development Practices
 
-[![Nox](https://img.shields.io/badge/%F0%9F%A6%8A-Nox-D85E00.svg?style=for-the-badge)](https://github.com/wntrblm/nox)
+[![Nox](https://img.shields.io/badge/%F0%9F%A6%8A-Nox-D85E00.svg)](https://github.com/wntrblm/nox)
 
 This section provides a guide to how we conduct development in the
 scikit-gmsh repository. Please follow the practices outlined here when
@@ -202,19 +202,15 @@ section](#creating-a-new-pull-request).
 
 #### Coding Style
 
-[![Code style:
-black](https://img.shields.io/badge/code%20style-black-000000.svg?style=for-the-badge)](https://github.com/psf/black)
-[![Imports:
-isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=for-the-badge&labelColor=ef8336)](https://pycqa.github.io/isort/)
-[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json&style=for-the-badge)](https://github.com/astral-sh/ruff)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![code style:
-prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg?style=for-the-badge)](https://github.com/prettier/prettier)
+prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg)](https://github.com/prettier/prettier)
 
 We adhere to [PEP 8](https://www.python.org/dev/peps/pep-0008/) wherever
 possible, except that line widths are permitted to go beyond 79
 characters to a max of 99 characters for code. This should tend to be
 the exception rather than the norm. A uniform code style is enforced by
-[black](https://github.com/psf/black) to prevent energy wasted on style
+[Ruff](https://github.com/astral-sh/ruff) to prevent energy wasted on style
 disagreements.
 
 As for docstrings, scikit-gmsh follows the `numpydoc` style for its
@@ -555,9 +551,7 @@ style requirements:
 
     $ pre-commit install
     $ git commit -m "added my cool feature"
-    black....................................................................Passed
-    isort....................................................................Passed
-    flake8...................................................................Passed
+    ruff.....................................................................Passed
     codespell................................................................Passed
 
 The actual installation of the environment happens before the first

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
@@ -0,0 +1,22 @@
+Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+<table>
+  <tbody>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://allcontributors.org"><img src="https://avatars.githubusercontent.com/u/46410174?v=4?s=100" width="100px;" alt="All Contributors"/><br /><sub><b>All Contributors</b></sub></a><br /><a href="https://github.com/pyvista/scikit-gmsh/commits?author=all-contributors" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/features/security"><img src="https://avatars.githubusercontent.com/u/27347476?v=4?s=100" width="100px;" alt="Dependabot"/><br /><sub><b>Dependabot</b></sub></a><br /><a href="#maintenance-dependabot" title="Maintenance">🚧</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/tkoyama010"><img src="https://avatars.githubusercontent.com/u/7513610?v=4?s=100" width="100px;" alt="Tetsuo Koyama"/><br /><sub><b>Tetsuo Koyama</b></sub></a><br /><a href="#infra-tkoyama010" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pyvista/scikit-gmsh/commits?author=tkoyama010" title="Tests">⚠️</a> <a href="https://github.com/pyvista/scikit-gmsh/commits?author=tkoyama010" title="Code">💻</a> <a href="#ideas-tkoyama010" title="Ideas, Planning, & Feedback">🤔</a> <a href="#maintenance-tkoyama010" title="Maintenance">🚧</a> <a href="https://github.com/pyvista/scikit-gmsh/issues?q=author%3Atkoyama010" title="Bug reports">🐛</a> <a href="https://github.com/pyvista/scikit-gmsh/commits?author=tkoyama010" title="Documentation">📖</a> <a href="#design-tkoyama010" title="Design">🎨</a> <a href="https://github.com/pyvista/scikit-gmsh/pulls?q=is%3Apr+reviewed-by%3Atkoyama010" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://pre-commit.ci"><img src="https://avatars.githubusercontent.com/u/64617429?v=4?s=100" width="100px;" alt="pre-commit.ci"/><br /><sub><b>pre-commit.ci</b></sub></a><br /><a href="#maintenance-pre-commit-ci" title="Maintenance">🚧</a></td>
+    </tr>
+  </tbody>
+</table>
+
+<!-- markdownlint-restore -->
+<!-- prettier-ignore-end -->
+
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
diff --git a/README.md b/README.md
@@ -7,14 +7,9 @@
 
 > Scikit for Gmsh to generate 3D finite element mesh.
 
-<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-
-[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
-
-<!-- ALL-CONTRIBUTORS-BADGE:END -->
-
-[![Contributing](https://img.shields.io/badge/PR-Welcome-%23FF8300.svg?style=flat-square)](https://github.com/pyvista/scikit-gmsh/issues)
-[![GitHub Repo stars](https://img.shields.io/github/stars/pyvista/scikit-gmsh?style=flat-square)](https://github.com/pyvista/scikit-gmsh/stargazers)
+[![All Contributors](https://img.shields.io/github/all-contributors/pyvista/scikit-gmsh?color=ee8449)](https://scikit-gmsh.readthedocs.io/en/latest/reference/about.html#contributors)
+[![Contributing](https://img.shields.io/badge/PR-Welcome-%23FF8300.svg)](https://github.com/pyvista/scikit-gmsh/issues)
+[![GitHub Repo stars](https://img.shields.io/github/stars/pyvista/scikit-gmsh)](https://github.com/pyvista/scikit-gmsh/stargazers)
 
 Contributions are _very welcome_ .
 This project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md).
@@ -28,22 +23,21 @@ Enjoying scikit-gmsh? Show your support with a [GitHub star](https://github.com/
 
 ## Table of Contents
 
-[![Documentation Status](https://readthedocs.org/projects/scikit-gmsh/badge/?version=latest&style=flat-square)](https://scikit-gmsh.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/scikit-gmsh/badge/?version=latest)](https://scikit-gmsh.readthedocs.io/en/latest/?badge=latest)
 
 <!-- START doctoc generated TOC please keep comment here to allow auto update -->
 <!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
 
 - [Installation](#installation)
 - [Usage](#usage)
 - [License](#license)
-- [Contributors ✨](#contributors-)
 - [Star History](#star-history)
 
 <!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 ## Installation
 
-[![pypi](https://img.shields.io/pypi/v/scikit-gmsh?style=flat-square&label=pypi&logo=python&logoColor=white)](https://pypi.org/project/scikit-gmsh/)
+[![pypi](https://img.shields.io/pypi/v/scikit-gmsh?label=pypi&logo=python&logoColor=white)](https://pypi.org/project/scikit-gmsh/)
 
 ```shell
 pip install scikit-gmsh
@@ -127,34 +121,10 @@ clipped = mesh.clip(origin=(0.0, 0.0, 0.0), normal=(0.0, 0.0, 1.0), crinkle=True
 
 ## License
 
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg?style=flat-square)](https://www.gnu.org/licenses/gpl-3.0)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 This software is published under the [GPLv3 license](https://www.gnu.org/licenses/gpl-3.0.en.html).
 
-## Contributors ✨
-
-Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
-
-<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
-<!-- prettier-ignore-start -->
-<!-- markdownlint-disable -->
-<table>
-  <tbody>
-    <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/tkoyama010"><img src="https://avatars.githubusercontent.com/u/7513610?v=4?s=100" width="100px;" alt="Tetsuo Koyama"/><br /><sub><b>Tetsuo Koyama</b></sub></a><br /><a href="#infra-tkoyama010" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pyvista/scikit-gmsh/commits?author=tkoyama010" title="Tests">⚠️</a> <a href="https://github.com/pyvista/scikit-gmsh/commits?author=tkoyama010" title="Code">💻</a> <a href="#ideas-tkoyama010" title="Ideas, Planning, & Feedback">🤔</a> <a href="#maintenance-tkoyama010" title="Maintenance">🚧</a> <a href="https://github.com/pyvista/scikit-gmsh/issues?q=author%3Atkoyama010" title="Bug reports">🐛</a> <a href="https://github.com/pyvista/scikit-gmsh/commits?author=tkoyama010" title="Documentation">📖</a> <a href="#design-tkoyama010" title="Design">🎨</a> <a href="https://github.com/pyvista/scikit-gmsh/pulls?q=is%3Apr+reviewed-by%3Atkoyama010" title="Reviewed Pull Requests">👀</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://allcontributors.org"><img src="https://avatars.githubusercontent.com/u/46410174?v=4?s=100" width="100px;" alt="All Contributors"/><br /><sub><b>All Contributors</b></sub></a><br /><a href="https://github.com/pyvista/scikit-gmsh/commits?author=all-contributors" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://pre-commit.ci"><img src="https://avatars.githubusercontent.com/u/64617429?v=4?s=100" width="100px;" alt="pre-commit.ci"/><br /><sub><b>pre-commit.ci</b></sub></a><br /><a href="#maintenance-pre-commit-ci" title="Maintenance">🚧</a></td>
-    </tr>
-  </tbody>
-</table>
-
-<!-- markdownlint-restore -->
-<!-- prettier-ignore-end -->
-
-<!-- ALL-CONTRIBUTORS-LIST:END -->
-
-This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
-
 ## Star History
 
 [![Star History Chart](https://api.star-history.com/svg?repos=pyvista/scikit-gmsh&type=Date)](https://star-history.com/#pyvista/scikit-gmsh&Date)
diff --git a/docs/conf.py b/docs/conf.py
@@ -8,8 +8,8 @@
 from __future__ import annotations
 
 import datetime
-import os
 from importlib.metadata import version as get_version
+import os
 from pathlib import Path
 
 # -- Project information -----------------------------------------------------

diff --git a/docs/index.md b/docs/index.md
@@ -7,3 +7,8 @@ We've marked content with a 🚧 to indicate that it's still under construction.
 ## 🚧 Overview
 
 The `sikit-gmsh` package provides a simple interface to the `gmsh` library.
+
+## Contributors
+
+:::{include} ../CONTRIBUTORS.md
+:parser: myst_parser.sphinx
diff --git a/noxfile.py b/noxfile.py
@@ -1,11 +1,12 @@
 """Automation using nox."""
 
+from __future__ import annotations
+
 import nox
 
 
-@nox.session(python=["3.8", "3.9", "3.10", "3.11", "3.12"])
+@nox.session(python=["3.9", "3.10", "3.11", "3.12"])
 def tests(session: nox.Session) -> None:
     """Run the unit and regular tests."""
     session.install(".[test]")
-    session.run("pip", "install", "-r", "requirements_test.txt", *session.posargs)
     session.run("pytest", *session.posargs)
diff --git a/pyproject.toml b/pyproject.toml
@@ -69,12 +69,21 @@ ignore = [
 ]
 
 [tool.ruff.lint.isort]
+# Sort by name, don't cluster "from" vs "import"
+force-sort-within-sections = true
+# Combines "as" imports on the same line
+combine-as-imports = true
+required-imports = ["from __future__ import annotations"]
 force-single-line = true
 
 [tool.ruff.lint.per-file-ignores]
 "docs/**" = ["INP001"]
 "tests/**" = ["INP001", "S101"]
 
+[tool.ruff.lint.pyupgrade]
+# Preserve types, even if a file imports `from __future__ import annotations`.
+keep-runtime-typing = true
+
 [tool.setuptools.dynamic]
 version = {attr = 'skgmsh.__version__'}
 readme = {file = "README.md", content-type = "text/markdown"}
diff --git a/setup.py b/setup.py
@@ -1,5 +1,7 @@
 """scikit-gmsh setuptools packaging."""
 
+from __future__ import annotations
+
 from pathlib import Path
 
 from setuptools import setup

diff --git a/src/skgmsh/__init__.py b/src/skgmsh/__init__.py
@@ -6,9 +6,9 @@
 from typing import TYPE_CHECKING
 
 import gmsh
+from pygmsh.helpers import extract_to_meshio
 import pyvista as pv
 import scooby
-from pygmsh.helpers import extract_to_meshio
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
@@ -45,9 +45,7 @@ class Report(scooby.Report):  # type: ignore[misc]
 
     """
 
-    def __init__(
-        self: Report, ncol: int = 3, text_width: int = 80
-    ) -> None:  # numpydoc ignore=PR01
+    def __init__(self: Report, ncol: int = 3, text_width: int = 80) -> None:  # numpydoc ignore=PR01
         """Generate a :class:`scooby.Report` instance."""
         # mandatory packages
         core: list[str] = [
@@ -148,9 +146,7 @@ def delaunay_3d(
         gmsh.model.geo.add_line(face[1] + 1, face[2] + 1, i * 4 + 1)
         gmsh.model.geo.add_line(face[2] + 1, face[3] + 1, i * 4 + 2)
         gmsh.model.geo.add_line(face[3] + 1, face[0] + 1, i * 4 + 3)
-        gmsh.model.geo.add_curve_loop(
-            [i * 4 + 0, i * 4 + 1, i * 4 + 2, i * 4 + 3], i + 1
-        )
+        gmsh.model.geo.add_curve_loop([i * 4 + 0, i * 4 + 1, i * 4 + 2, i * 4 + 3], i + 1)
         gmsh.model.geo.add_plane_surface([i + 1], i + 1)
         gmsh.model.geo.remove_all_duplicates()
         gmsh.model.geo.synchronize()
@@ -231,10 +227,8 @@ def frontal_delaunay_2d(
         target_sizes = [target_sizes] * edge_source.number_of_points
 
     embedded_points = []
-    for i, (target_size, point) in enumerate(zip(target_sizes, points)):
-        id_ = i + 1
-        gmsh.model.geo.add_point(point[0], point[1], point[2], target_size, id_)
-        embedded_points.append(id_)
+    for target_size, point in zip(target_sizes, points):
+        embedded_points.append(gmsh.model.geo.add_point(point[0], point[1], point[2], target_size))
 
     for i in range(lines[0] - 1):
         id_ = i + 1

diff --git a/tests/test_skgmsh.py b/tests/test_skgmsh.py
@@ -45,9 +45,7 @@ def test_frontal_delaunay_2d_recombine() -> None:
 
 @pytest.mark.parametrize("edge_source", EDGE_SOURCES)
 @pytest.mark.parametrize("target_sizes", [2.0, [1.0, 2.0, 3.0, 4.0]])
-def test_frontal_delaunay_2d(
-    edge_source: pv.Polygon, target_sizes: float | Sequence[float]
-) -> None:
+def test_frontal_delaunay_2d(edge_source: pv.Polygon, target_sizes: float | Sequence[float]) -> None:
     """Frontal-Delaunay 2D mesh algorithm test code."""
     mesh = sg.frontal_delaunay_2d(edge_source, target_sizes=target_sizes)
     assert mesh.number_of_points > edge_source.number_of_points
@@ -57,9 +55,7 @@ def test_frontal_delaunay_2d(
     # https://github.com/pyvista/scikit-gmsh/pull/125
 
 
-@pytest.mark.parametrize(
-    "target_sizes", [0.5, [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8]]
-)
+@pytest.mark.parametrize("target_sizes", [0.5, [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8]])
 def test_delaunay_3d(target_sizes: float | Sequence[float]) -> None:
     """Delaunay 3D mesh algorithm test code."""
     edge_source = pv.Cube()