Release/v0.1.0

.github/workflows/docs.yml

@@ -18,7 +18,7 @@ jobs:
         python-version: "3.10"
 
     - name: build napf linux
-      run: pip install -e.
+      run: pip install .
 
     - name: test
       run: python3 tests/test_init_and_query.py

.github/workflows/main.yml

@@ -6,26 +6,33 @@ on:
   pull_request:
 
 jobs:
-  macos_wheel:
-    runs-on: macos-latest
-    strategy:
-      matrix:
-        arch: [x86_64, arm64]
-        cw_build: ["pp*", "cp*"]
-        exclude:
-          - arch: arm64
-            cw_build: "pp*"
+  macos_wheel_m:
+    runs-on: macos-14
 
     steps:
     - uses: actions/checkout@v3
       with:
         submodules: recursive
     - name: build wheels
-      uses: pypa/cibuildwheel@v2.18
+      uses: pypa/cibuildwheel@v2.19
       env:
-        CIBW_ARCHS: ${{ matrix.arch }}
-        CIBW_BUILD: ${{ matrix.cw_build }}
-        CIBW_TEST_SKIP: "*-macosx_x86_64"
+        CIBW_ARCHS: "arm64"
+
+    - uses: actions/upload-artifact@v3
+      with:
+        path: ./wheelhouse/*.whl
+
+  macos_wheel_intel:
+    runs-on: macos-13
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: build wheels
+      uses: pypa/[email protected]
+      env:
+        CIBW_ARCHS: "x86_64"
 
     - uses: actions/upload-artifact@v3
       with:
@@ -34,22 +41,16 @@ jobs:
 
   linux_wheel:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        arch: [x86_64]
-        cw_build: ["cp*manylinux*", "pp*manylinux*", "*musllinux*"]
-
 
     steps:
     - uses: actions/checkout@v3
       with:
         submodules: recursive
     - name: build wheels
-      uses: pypa/cibuildwheel@v2.18
+      uses: pypa/cibuildwheel@v2.19
       env:
-        CIBW_ARCHS: ${{ matrix.arch }}
-        CIBW_BUILD: ${{ matrix.cw_build }}
-        CIBW_SKIP: "pp39-many*"
+        CIBW_ARCHS: x86_64
+        CIBW_BUILD: "cp*manylinux*"
 
     - uses: actions/upload-artifact@v3
       with:
@@ -60,14 +61,7 @@ jobs:
     strategy:
       matrix:
         arch: [aarch64, ppc64le]
-        cw_build: ["cp36*many*", "cp37*many*", "cp38*many*", "cp39*many*", "cp310*many*", "cp311*many*", "cp312*many*", "pp37*many*", "pp38*many*", "pp39*many*"]
-        exclude:
-          - arch: ppc64le
-            cw_build: "pp37*many*"
-          - arch: ppc64le
-            cw_build: "pp38*many*"
-          - arch: ppc64le
-            cw_build: "pp39*many*"
+        cw_build: ["cp37*many*", "cp38*many*", "cp39*many*", "cp310*many*", "cp311*many*", "cp312*many*"]
 
     steps:
     - uses: actions/checkout@v3
@@ -81,11 +75,11 @@ jobs:
         platforms: arm64, ppc64le
 
     - name: build wheels
-      uses: pypa/cibuildwheel@v2.18
+      uses: pypa/cibuildwheel@v2.19
       env:
         CIBW_ARCHS: ${{ matrix.arch }}
         CIBW_BUILD: ${{ matrix.cw_build }}
-        CIBW_TEST_SKIP: "*-*linux_{aarch64,ppc64le,s390x}"
+        CIBW_TEST_SKIP: "*-*linux_{aarch64,ppc64le}"
 
     - uses: actions/upload-artifact@v3
       with:
@@ -104,9 +98,10 @@ jobs:
       with:
         submodules: recursive
     - name: build wheels
-      uses: pypa/cibuildwheel@v2.18
+      uses: pypa/cibuildwheel@v2.19
       env:
         CIBW_ARCHS: ${{ matrix.arch }}
+        CIBW_SKIP: "pp*"
 
 
     - uses: actions/upload-artifact@v3
@@ -129,10 +124,8 @@ jobs:
         path: ./dist/*
 
   upload_pypi:
-    needs: [macos_wheel, linux_wheel, windows_wheel, source_dist]
+    needs: [macos_wheel_m, macos_wheel_intel, linux_wheel, windows_wheel, source_dist]
     runs-on: ubuntu-latest
-    permissions:
-      id-token: write
     # try to publish only if this is a push to stable branch
     if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
     steps:
@@ -143,4 +136,4 @@ jobs:
 
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          skip-existing: true
+          skip_existing: true

.pre-commit-config.yaml

@@ -6,11 +6,9 @@
 
 # use default options for ci
 ci:
-  autoupdate_schedule: "monthly"
+  autoupdate_schedule: "weekly"
   submodules: false
 
-exclude: "third_party/nanoflann.hpp"
-
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: "v4.6.0"
@@ -28,31 +26,31 @@ repos:
   - id: requirements-txt-fixer
   - id: trailing-whitespace
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: "v3.15.2"
-  hooks:
-  - id: pyupgrade
-    args: [--py36-plus]
-
-- repo: https://github.com/PyCQA/isort
-  rev: "5.13.2"
-  hooks:
-  - id: isort
-
 - repo: https://github.com/psf/black
   rev: "24.4.2"
   hooks:
   - id: black
-    args: [--line-length=79]
+    additional_dependencies: [tomli]
 
-- repo: https://github.com/PyCQA/flake8
-  rev: 7.0.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.4
   hooks:
-  - id: flake8
-    args: [--extend-ignore=E203]
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
 
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v18.1.4
+  rev: v18.1.8
   hooks:
   - id: clang-format
     types_or: [c++]
+
+- repo: https://github.com/cheshirekow/cmake-format-precommit
+  rev: "v0.6.13"
+  hooks:
+  - id: cmake-format
+
+- repo: https://github.com/keewis/blackdoc
+  rev: v0.3.9
+  hooks:
+  - id: blackdoc
+    additional_dependencies: [tomli]

CMakeLists.txt

@@ -1,13 +1,15 @@
 cmake_minimum_required(VERSION 3.12)
-project(napf VERSION 0.0.0 LANGUAGES CXX)
+project(
+  napf
+  VERSION 0.1.0
+  LANGUAGES CXX)
 
 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+
 endif()
 
 # options
-option(BUILD_EXAMPLES "build examples" ON)
-option(BUILD_FORTRAN_MODULE "build fortran module" ON)
-option(SPLINEPY_EXT "add splinepy extension" ON)
+option(NAPF_BUILD_PYTHON "build python module" ON)
 
 # config
 set(exe_dest "bin")
@@ -29,68 +31,44 @@ add_library(napf INTERFACE)
 add_library(napf::napf ALIAS napf)
 
 # basic path
-target_include_directories(napf
-    INTERFACE
-        $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src>
-        $<INSTALL_INTERFACE:${incl_dest}>)
+target_include_directories(
+  napf INTERFACE $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src>
+                 $<INSTALL_INTERFACE:${incl_dest}>)
 
-# try to use installed nanoflann.
-# else, include the one in the third_party
+# try to use installed nanoflann. else, include the one in the third_party
 find_package(nanoflann QUIET)
 if(nanoflann_FOUND AND nanoflann_VERSION VERSION_GREATER_EQUAL "1.5.0")
   message("nanoflann found - napf will link to nanoflann found in system.")
   target_link_libraries(napf INTERFACE nanoflann::nanoflann)
 else()
   set(CXX_HEADERS ${CXX_HEADERS} third_party/nanoflann.hpp)
-  target_include_directories(napf
-      INTERFACE
-          $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/third_party>)
+  target_include_directories(
+    napf INTERFACE $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/third_party>)
 endif()
 target_compile_features(napf INTERFACE cxx_std_11)
 
-if(BUILD_FORTRAN_MODULE)
-  message("*** building additional fortran module ***")
-  message("*** ------ NOT IMPLEMENTED ----------- ***")
-endif(BUILD_FORTRAN_MODULE)
-
-if(BUILD_EXAMPLES)
-  message("*** building examples ***")
-  message("*** ------ NOT IMPLEMENTED ----------- ***")
-endif(BUILD_EXAMPLES)
-
-if(SPLINEPY_EXT)
-  target_compile_definitions(napf INTERFACE -DSPLINEPYEXT)
-endif(SPLINEPY_EXT)
+if(NAPF_BUILD_PYTHON)
+  add_subdirectory(src/python)
+endif()
 
 # configure config files
 include(CMakePackageConfigHelpers)
-write_basic_package_version_file(
-    "${version_config}" COMPATIBILITY SameMajorVersion
-)
-configure_package_config_file(
-    "cmake/config.cmake.in"
-    "${project_config}"
-    INSTALL_DESTINATION "${cfg_dest}"
-)
+write_basic_package_version_file("${version_config}"
+                                 COMPATIBILITY SameMajorVersion)
+configure_package_config_file("cmake/config.cmake.in" "${project_config}"
+                              INSTALL_DESTINATION "${cfg_dest}")
 
 install(
-    TARGETS napf
-    EXPORT "${TARGETS_EXPORT_NAME}"
-    LIBRARY DESTINATION ${lib_dest}
-    ARCHIVE DESTINATION ${lib_dest}
-    INCLUDES DESTINATION "${incl_dest}"
-)
-install(
-    FILES "${project_config}" "${version_config}"
-    DESTINATION "${cfg_dest}"
-)
+  TARGETS napf
+  EXPORT "${TARGETS_EXPORT_NAME}"
+  LIBRARY DESTINATION ${lib_dest}
+  ARCHIVE DESTINATION ${lib_dest}
+  INCLUDES
+  DESTINATION "${incl_dest}")
+install(FILES "${project_config}" "${version_config}" DESTINATION "${cfg_dest}")
 
 install(
-    EXPORT "${TARGETS_EXPORT_NAME}"
-    NAMESPACE "${namespace}"
-    DESTINATION "${cfg_dest}"
-)
-install(
-    FILES ${CXX_HEADERS}
-    DESTINATION ${incl_dest}
-)
+  EXPORT "${TARGETS_EXPORT_NAME}"
+  NAMESPACE "${namespace}"
+  DESTINATION "${cfg_dest}")
+install(FILES ${CXX_HEADERS} DESTINATION ${incl_dest})

README.md

@@ -1,8 +1,10 @@
-# napf
+<p align="center"><img src="https://github.com/tataratat/napf/raw/main/docs/source/_static/napf.png" width="50%" title="nurbs"></p>
+
+**napf - [nanoflann](https://github.com/jlblancoc/nanoflann) wrappers for python and maybe fortran**
+
 [![main](https://github.com/tataratat/napf/actions/workflows/main.yml/badge.svg)](https://github.com/tataratat/napf/actions/workflows/main.yml)
 [![PyPI version](https://badge.fury.io/py/napf.svg)](https://badge.fury.io/py/napf)
 
-[nanoflann](https://github.com/jlblancoc/nanoflann) wrappers for python and maybe fortran.
 
 ## python
 As `nanoflann` offers template classes, separate classes are implemented in `napf` for each ___{datatype, distance metric}___. All the search functions are equipped with multi-thread execution. Uses [numpy.ndarray](https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html) for data input and output.

napf/_version.py

@@ -1 +1 @@
-version = "0.0.8"
+version = "0.1.0"

napf/base.py

@@ -252,7 +252,7 @@ def knn_search(self, queries, kneighbors, nthread=None):
 
         Parameters
         -----------
-        queires: (m, d) np.ndarray
+        queries: (m, d) np.ndarray
           Data type will be casted to the same type as `tree_data`.
         kneighbors: int
         nthread: int
@@ -405,7 +405,7 @@ def radii_search(self, queries, radii, return_sorted, nthread=None):
         # input size check
         if len(queries) != len(radii):
             raise ValueError(
-                f"Input size mismatch between queires ({len(queries)}) "
+                f"Input size mismatch between queries ({len(queries)}) "
                 f" and radii ({len(radii)})."
                 "They should be the same."
             )
@@ -447,7 +447,7 @@ def unique_data_and_inverse(
           Same as kdt.tree_data[unique_ids].
         unique_ids: np.ndarray
           Indices of unique entries from tree data.
-          First occurance is considered unique.
+          First occurrence is considered unique.
         inverse_ids: np.ndarray
           Indices to reconstruct original tree_data with
           unique_data. kdt.tree_data == unique_data[inverse_ids]