Build using scikit-build-core and nanobind (#7)

* remove submodules

* implement nanobind wrapper

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix uninitialized pointer

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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

@@ -4,9 +4,9 @@ on:
   pull_request:
   push:
     tags:
-      - "*"
+    - '*'
     branches:
-      - "main"
+    - main
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -21,44 +21,44 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-14, macos-13]
 
     steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: true
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
 
-      - name: Build wheels
-        uses: pypa/[email protected]
+    - name: Build wheels
+      uses: pypa/[email protected]
 
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pyminiply-wheels-${{ matrix.os }}
-          path: ./wheelhouse/*.whl
+    - uses: actions/upload-artifact@v4
+      with:
+        name: pyminiply-wheels-${{ matrix.os }}
+        path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: true
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
 
-      - name: Build sdist
-        run: pipx run build --sdist
+    - name: Build sdist
+      run: pipx run build --sdist
 
-      - name: Validate wheel
-        run: |
-          pip install twine
-          twine check dist/*
+    - name: Validate wheel
+      run: |
+        pip install twine
+        twine check dist/*
 
-      - name: Validate sdist
-        run: |
-          pip install dist/*
-          pip install pytest pyvista
-          pytest
+    - name: Validate sdist
+      run: |
+        pip install dist/*
+        pip install pytest pyvista
+        pytest
 
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pyminiply-sdist
-          path: dist/*.tar.gz
+    - uses: actions/upload-artifact@v4
+      with:
+        name: pyminiply-sdist
+        path: dist/*.tar.gz
 
   upload_pypi:
     needs: [build_wheels, build_sdist]

.gitignore

@@ -7,3 +7,14 @@ dist/
 pyminiply/_wrapper.cpp
 *.so
 *.pyc
+
+# cmake
+#######
+CMakeCache.txt
+CMakeFiles/
+Makefile
+cmake_install.cmake
+compile_commands.json
+
+# cache
+.cache

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "pyminiply/miniply"]
-	path = pyminiply/miniply
+[submodule "src/miniply"]
+	path = src/miniply
 	url = https://github.com/vilya/miniply

.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
+ ```