remove submodules

.gitignore

@@ -7,3 +7,11 @@ dist/
 pyminiply/_wrapper.cpp
 *.so
 *.pyc
+
+# cmake
+#######
+CMakeCache.txt
+CMakeFiles/
+Makefile
+cmake_install.cmake
+compile_commands.json

.pre-commit-config.yaml

@@ -1,72 +1,62 @@
 # See https://pre-commit.ci/
 ci:
-    autofix_prs: true
-    autoupdate_schedule: quarterly
+  autofix_prs: true
+  autoupdate_schedule: quarterly
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.12.1
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.2
   hooks:
-  - id: black
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix]
+    exclude: ^(docs/|tests)
+  - id: ruff-format
 
 - repo: https://github.com/keewis/blackdoc
   rev: v0.3.9
   hooks:
   - id: blackdoc
     exclude: README.rst
 
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-  - id: isort
-    exclude: "setup.py"
-    args: [
-    "--profile", "black",
-    "--force-sort-within-sections",
-    "--skip-glob", "*__init__.py",
-    ]
-
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
-  hooks:
-  - id: flake8
-
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.3.0
   hooks:
   - id: codespell
-    args: ["--skip=*.vt*"]
+    args: [--skip=*.vt*]
 
 - repo: https://github.com/pycqa/pydocstyle
   rev: 6.3.0
   hooks:
   - id: pydocstyle
     additional_dependencies: [tomli==2.0.1]
-    files: ^pyminiply/.*\.py
+    files: ^src/pyminiply/.*\.py
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
   - id: check-merge-conflict
   - id: debug-statements
   - id: trailing-whitespace
-    exclude: .*\.cdb$
+
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.14.0
+  hooks:
+  - id: pretty-format-toml
+    args: [--autofix]
+  - id: pretty-format-yaml
+    args: [--autofix, --indent, '2']
 
 - repo: https://github.com/pre-commit/mirrors-clang-format
   rev: v17.0.6
   hooks:
   - id: clang-format
-    files: |
-      (?x)^(
-        pyminiply/[^_].*\.cpp.*
-      )$
 
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.27.3
+  rev: 0.29.0
   hooks:
-    - id: check-github-workflows
+  - id: check-github-workflows
 
 - repo: https://github.com/dzhu/rstfmt
   rev: v0.0.14
   hooks:
-  - id: rstfmt
+  - id: rstfmt

CMakeLists.txt

@@ -0,0 +1,53 @@
+cmake_minimum_required(VERSION 3.15...3.26)
+
+project(nanobind_project LANGUAGES CXX)
+# find_package(OpenMP REQUIRED)
+
+# Try to import all Python components potentially needed by nanobind
+find_package(Python 3.8
+  REQUIRED COMPONENTS Interpreter Development.Module
+  OPTIONAL_COMPONENTS Development.SABIModule)
+
+# Import nanobind through CMake's find_package mechanism
+find_package(nanobind CONFIG REQUIRED)
+
+nanobind_add_module(
+  # Name of the extension
+  _wrapper
+
+  # Target the stable ABI for Python 3.12+, which reduces
+  # the number of binary wheels that must be built. This
+  # does nothing on older Python versions
+  STABLE_ABI
+
+  # conserve space by reusing a shared libnanobind across libraries
+  NB_STATIC
+
+  src/wrapper.cpp
+  src/miniply/miniply.cpp
+)
+
+# Link OpenMP
+# if(OpenMP_CXX_FOUND)
+#   target_link_libraries(_wrapper PRIVATE OpenMP::OpenMP_CXX)
+# endif()
+
+# Compiler-specific options
+if(MSVC)
+  # Use MSVC optimization levels and OpenMP setup
+  target_compile_options(_wrapper PRIVATE /O2 /std:c++17)
+  # /openmp:llvm
+else()
+  # Assuming GCC or Clang
+  target_compile_options(_wrapper PRIVATE -O3)
+  # -fopenmp
+endif()
+
+# Example debugging
+# set solib-search-path /home/user/python/.venv311/lib/python3.11/site-packages/stl_reader/
+# set breakpoint with b qual.cpp:4872
+# target_compile_options(stl_reader PRIVATE -g -O0)
+# target_compile_options(pfh PRIVATE -g -O0)
+
+# Install directive for scikit-build-core
+install(TARGETS _wrapper LIBRARY DESTINATION pyminiply)

CONTRIBUTING.md

@@ -0,0 +1,57 @@
+### C Extension
+
+This repository interfaces with `miniply/miniply.cpp` via
+[nanobind](https://github.com/wjakob/nanobind) to efficiently generate C++
+extensions.
+
+#### Emacs configuration
+
+If using emacs and helm, generate the project configuration files using `-DCMAKE_EXPORT_COMPILE_COMMANDS=ON`. Here's a sample configuration for C++11 on Linux:
+
+```
+pip install nanobind
+export NANOBIND_INCLUDE=$(python -c "import nanobind, os; print(os.path.join(os.path.dirname(nanobind.__file__), 'cmake'))")
+cmake -Dnanobind_DIR=$NANOBIND_INCLUDE -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_CXX_STANDARD_INCLUDE_DIRECTORIES="/usr/include/c++/11;/usr/include/x86_64-linux-gnu/c++/11/;/usr/lib/gcc/x86_64-linux-gnu/11/include/"
+```
+
+These will be necessary for helm and treesit to determine the locations of the header files.
+
+
+#### Debug Build
+
+This can be helpful when debugging segfaults since this extension often uses raw pointers.
+
+
+Set the cmake build type to debug in `pyproject.toml``
+```
+[tool.scikit-build]
+cmake.build-type = "Debug"
+```
+
+Set the target compile options to build debug symbols with `-g` and `-O0` in `CMakeLists.txt`:
+
+```
+target_compile_options(_utilities PRIVATE -g -O0)
+```
+
+Finally, run using `gdb`. For example:
+
+```
+$ gdb --args python test_ext.py
+(gdb) b qual.cpp:4872
+Make breakpoint pending on future shared library load? (y or [n]) y
+Breakpoint 1 (qual.cpp:4872) pending.
+(gdb) run
+Thread 1 "python" hit Breakpoint 1, ComputeWeights<float> (offset=0x1fe5830, neigh=0x20432e0,
+indices=0x1bb8ec0, points=0x1d6a7a0, n_neigh=108, n_points=27, fac=-0.75, num_threads=4) at /home/user/library-path/src/qual.cpp:4872
+4872      T *weights = new T[n_neigh];
+(gdb)
+```
+
+#### Debugging memory leaks
+
+These can be challenging to find. Use [valgrind](https://valgrind.org/) with the following to identify memory leaks. Be sure to download [valgrind-python.supp](https://github.com/python/cpython/blob/main/Misc/valgrind-python.supp).
+
+```
+ valgrind --leak-check=full --log-file=val.txt --suppressions=valgrind-python.supp pytest -k clus && grep 'new\[\]' val.txt
+ ```

README.rst

@@ -12,7 +12,7 @@
 
 ``pyminiply`` is a Python library for rapidly reading PLY files. It is a
 Python wrapper around the fast C++ PLY reading library provided by
-`miniply <ehttps://github.com/vilya/miniply>`_. Thanks @vilya!
+`miniply <https://github.com/vilya/miniply>`_. Thanks @vilya!
 
 The main advantage of ``pyminiply`` over other PLY reading libraries is
 its performance. See the benchmarks below for more details.
@@ -27,6 +27,12 @@ The recommended way to install ``pyminiply`` is via PyPI:
 
    pip install pyminiply
 
+Optionally with PyVista:
+
+.. code:: sh
+
+   pip install pyminipl[pyvista]
+
 You can also clone the repository and install it from source:
 
 .. code:: sh

pyproject.toml

@@ -1,26 +1,39 @@
 [build-system]
-requires = [
-    "setuptools>=42",
-    "wheel>=0.33.0",
-    "cython>=3",
-    "oldest-supported-numpy"
-]
-
-build-backend = "setuptools.build_meta"
+build-backend = "scikit_build_core.build"
+requires = ["scikit-build-core >=0.4.3", "nanobind >=1.3.2"]
 
-[tool.pytest.ini_options]
-junit_family= "legacy"
-filterwarnings = [
-    # bogus numpy ABI warning (see numpy/#432)
-    "ignore:.*numpy.dtype size changed.*:RuntimeWarning",
-    "ignore:.*numpy.ufunc size changed.*:RuntimeWarning"
+[project]
+authors = [
+  {name = "PyVista Developers", email = "[email protected]"}
 ]
+classifiers = [
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: Microsoft :: Windows",
+  "Operating System :: POSIX",
+  "Intended Audience :: Science/Research",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12"
+]
+dependencies = [
+  "numpy"
+]
+description = "Rapidly read in PLY files using a wrapper over miniply"
+name = "pyminiply"
+readme = "README.rst"
+requires-python = ">=3.8"
+version = "0.2.dev0"
+
+[project.optional-dependencies]
+pyvista = ["pyvista"]
 
 [tool.cibuildwheel]
 archs = ["auto64"]  # 64-bit only
 skip = "cp36-* cp37-* pp* *musllinux*"  # disable PyPy and musl-based wheels
-test-requires = "pytest pyvista"
 test-command = "pytest {project}/tests"
+test-requires = "pytest pyvista"
 
 [tool.cibuildwheel.macos]
 archs = ["native"]
@@ -29,18 +42,25 @@ archs = ["native"]
 MACOSX_DEPLOYMENT_TARGET = "10.14"  # Needed for full C++17 support on MacOS
 
 [tool.codespell]
-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
+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'
 
-[tool.isort]
-profile = "black"
-force_sort_within_sections = true
-default_section = "THIRDPARTY"
-skip_glob = ["__init__.py"]
-src_paths = ["doc", "src", "tests"]
+[tool.pytest.ini_options]
+filterwarnings = [
+  # bogus numpy ABI warning (see numpy/#432)
+  "ignore:.*numpy.dtype size changed.*:RuntimeWarning",
+  "ignore:.*numpy.ufunc size changed.*:RuntimeWarning"
+]
+testpaths = 'tests'
 
-[tool.black]
+[tool.ruff]
 line-length = 100
-skip-string-normalization = true
-target-version = ['py39']
-exclude='\.eggs|\.git|\.mypy_cache|\.tox|\.venv|_build|buck-out|build|dist|node_modules'
+
+[tool.ruff.lint]
+extend-select = ["I"]
+
+[tool.scikit-build]
+# Setuptools-style build caching in a local directory
+build-dir = "build/{wheel_tag}"
+minimum-version = "0.4"
+sdist.exclude = [".github", "*.png", "tests", ".mypy_cache", ".pre-commit-config.yaml", "*_cache", "CONTRIBUTING.md", ".gitignore"]