Fix intersection bug and add Python 3.13 support (v0.7.0)

.github/workflows/cibuildwheel.yml

@@ -21,17 +21,9 @@ jobs:
       matrix:
         include:
           # Window 64 bit
-          # Note: windows-2019 is needed for older Python versions:
-          # https://github.com/scikit-learn/scikit-learn/issues/22530
-          - os: windows-2019
-            python: 36
-            platform_id: win_amd64
-            arch: AMD64
-          - os: windows-2019
-            python: 37
-            platform_id: win_amd64
-            arch: AMD64
-          - os: windows-2019
+          # Note: Python 3.6 and 3.7 dropped due to pybind11 v2.13.6 requiring Python >=3.7
+          # and Python 3.7 being EOL (June 2023). Minimum supported version is now Python 3.8.
+          - os: windows-latest
             python: 38
             platform_id: win_amd64
             arch: AMD64
@@ -51,118 +43,191 @@ jobs:
             python: 312
             platform_id: win_amd64
             arch: AMD64
+          - os: windows-latest
+            python: 313
+            platform_id: win_amd64
+            arch: AMD64
+          - os: windows-latest
+            python: 314
+            platform_id: win_amd64
+            arch: AMD64
 
           # Linux 64 bit manylinux2014
+          # Python 3.6 and 3.7 dropped (see Windows section comment)
           - os: ubuntu-latest
-            python: 36
+            python: 38
             platform_id: manylinux_x86_64
             manylinux_image: manylinux2014
             arch: x86_64
           - os: ubuntu-latest
-            python: 37
+            python: 39
             platform_id: manylinux_x86_64
             manylinux_image: manylinux2014
             arch: x86_64
           - os: ubuntu-latest
-            python: 38
+            python: 310
             platform_id: manylinux_x86_64
             manylinux_image: manylinux2014
             arch: x86_64
           - os: ubuntu-latest
-            python: 39
+            python: 311
             platform_id: manylinux_x86_64
             manylinux_image: manylinux2014
             arch: x86_64
           - os: ubuntu-latest
-            python: 310
+            python: 312
             platform_id: manylinux_x86_64
             manylinux_image: manylinux2014
             arch: x86_64
           - os: ubuntu-latest
-            python: 311
+            python: 313
             platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
+            manylinux_image: manylinux_2_28
             arch: x86_64
           - os: ubuntu-latest
-            python: 312
+            python: 314
             platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
+            manylinux_image: manylinux_2_28
             arch: x86_64
 
           # Linux 64 bit aarch64
+          # Python 3.6 and 3.7 dropped (see Windows section comment)
           - os: ubuntu-latest
-            python: 36
+            python: 38
             platform_id: manylinux_aarch64
             manylinux_image: manylinux2014
             arch: aarch64
           - os: ubuntu-latest
-            python: 37
+            python: 39
             platform_id: manylinux_aarch64
             manylinux_image: manylinux2014
             arch: aarch64
           - os: ubuntu-latest
-            python: 38
+            python: 310
             platform_id: manylinux_aarch64
             manylinux_image: manylinux2014
             arch: aarch64
           - os: ubuntu-latest
-            python: 39
+            python: 311
             platform_id: manylinux_aarch64
             manylinux_image: manylinux2014
             arch: aarch64
           - os: ubuntu-latest
-            python: 310
+            python: 312
             platform_id: manylinux_aarch64
             manylinux_image: manylinux2014
             arch: aarch64
           - os: ubuntu-latest
-            python: 311
+            python: 313
             platform_id: manylinux_aarch64
-            manylinux_image: manylinux2014
+            manylinux_image: manylinux_2_28
             arch: aarch64
           - os: ubuntu-latest
-            python: 312
+            python: 314
             platform_id: manylinux_aarch64
-            manylinux_image: manylinux2014
+            manylinux_image: manylinux_2_28
             arch: aarch64
 
           # MacOS x86_64
+          # Python 3.6 and 3.7 dropped (see Windows section comment)
           - os: macos-13
-            python: 36
+            python: 38
             platform_id: macosx_x86_64
             macosx_deployment_target: 10.14
             arch: x86_64
           - os: macos-13
-            python: 37
+            python: 39
             platform_id: macosx_x86_64
             macosx_deployment_target: 10.14
             arch: x86_64
           - os: macos-13
-            python: 38
+            python: 310
             platform_id: macosx_x86_64
             macosx_deployment_target: 10.14
             arch: x86_64
           - os: macos-13
-            python: 39
+            python: 311
             platform_id: macosx_x86_64
             macosx_deployment_target: 10.14
             arch: x86_64
           - os: macos-13
-            python: 310
+            python: 312
             platform_id: macosx_x86_64
             macosx_deployment_target: 10.14
             arch: x86_64
           - os: macos-13
-            python: 311
+            python: 313
             platform_id: macosx_x86_64
             macosx_deployment_target: 10.14
             arch: x86_64
           - os: macos-13
-            python: 312
+            python: 314
             platform_id: macosx_x86_64
             macosx_deployment_target: 10.14
             arch: x86_64
 
+          # Linux musllinux x86_64 (Alpine Linux)
+          # Note: cibuildwheel 3.x auto-selects appropriate musllinux images
+          - os: ubuntu-latest
+            python: 38
+            platform_id: musllinux_x86_64
+            arch: x86_64
+          - os: ubuntu-latest
+            python: 39
+            platform_id: musllinux_x86_64
+            arch: x86_64
+          - os: ubuntu-latest
+            python: 310
+            platform_id: musllinux_x86_64
+            arch: x86_64
+          - os: ubuntu-latest
+            python: 311
+            platform_id: musllinux_x86_64
+            arch: x86_64
+          - os: ubuntu-latest
+            python: 312
+            platform_id: musllinux_x86_64
+            arch: x86_64
+          - os: ubuntu-latest
+            python: 313
+            platform_id: musllinux_x86_64
+            arch: x86_64
+          - os: ubuntu-latest
+            python: 314
+            platform_id: musllinux_x86_64
+            arch: x86_64
+
+          # Linux musllinux aarch64 (Alpine Linux ARM64)
+          # Note: cibuildwheel 3.x auto-selects appropriate musllinux images
+          - os: ubuntu-latest
+            python: 38
+            platform_id: musllinux_aarch64
+            arch: aarch64
+          - os: ubuntu-latest
+            python: 39
+            platform_id: musllinux_aarch64
+            arch: aarch64
+          - os: ubuntu-latest
+            python: 310
+            platform_id: musllinux_aarch64
+            arch: aarch64
+          - os: ubuntu-latest
+            python: 311
+            platform_id: musllinux_aarch64
+            arch: aarch64
+          - os: ubuntu-latest
+            python: 312
+            platform_id: musllinux_aarch64
+            arch: aarch64
+          - os: ubuntu-latest
+            python: 313
+            platform_id: musllinux_aarch64
+            arch: aarch64
+          - os: ubuntu-latest
+            python: 314
+            platform_id: musllinux_aarch64
+            arch: aarch64
+
           # MacOS arm64
           - os: macos-14
             python: 38
@@ -189,10 +254,20 @@ jobs:
             platform_id: macosx_arm64
             macosx_deployment_target: 11.7
             arch: arm64
+          - os: macos-14
+            python: 313
+            platform_id: macosx_arm64
+            macosx_deployment_target: 11.7
+            arch: arm64
+          - os: macos-14
+            python: 314
+            platform_id: macosx_arm64
+            macosx_deployment_target: 11.7
+            arch: arm64
 
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - uses: actions/setup-python@v5
@@ -201,29 +276,33 @@ jobs:
           python-version: '3.10'
       - name: Set up QEMU
         if: runner.os == 'Linux'
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
         with:
           platforms: all
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.17.0
+        uses: pypa/cibuildwheel@v3.2.1
         env:
           CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.manylinux_image }}
+          CIBW_MANYLINUX_AARCH64_IMAGE: ${{ matrix.manylinux_image }}
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           CIBW_BEFORE_BUILD: pip install pybind11
-          CIBW_TEST_COMMAND: pytest {project}/tests -vv
+          CIBW_TEST_COMMAND: python {project}/tests/_ci_debug_import.py && pytest {project}/tests -vv
+          CIBW_TEST_COMMAND_WINDOWS: python {project}\tests\_ci_debug_import.py && pytest {project}\tests -vv
           CIBW_TEST_REQUIRES: pytest numpy
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: ${{ matrix.arch }}
           MACOSX_DEPLOYMENT_TARGET: ${{ matrix.macosx_deployment_target }}
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.platform_id }}-py${{ matrix.python }}
           path: ./wheelhouse/*.whl
+          overwrite: true
 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - uses: actions/setup-python@v5
@@ -232,20 +311,23 @@ jobs:
           python-version: '3.10'
       - name: Build sdist
         run: python setup.py sdist
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
+          name: sdist
           path: dist/*.tar.gz
+          overwrite: true
 
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     # upload to PyPI on every tag starting with 'v'
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: '*'
           path: dist
+          merge-multiple: true
       - uses: pypa/[email protected]
         with:
           user: __token__

CMakeLists.txt

@@ -1,7 +1,7 @@
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.5)
 
 if(WIN32)
-  set(CMAKE_CXX_FLAGS "/O3 /pthread")
+  set(CMAKE_CXX_FLAGS "/O2 /EHsc")
 elseif(APPLE)
   set(CMAKE_CXX_FLAGS "-O3 -pthread")
 else()
@@ -16,6 +16,11 @@ option(SNAPPY_BUILD_TESTS "" OFF)
 option(SNAPPY_BUILD_BENCHMARKS "" OFF)
 option(SNAPPY_INSTALL "" OFF)
 
+option(SKIP_PERFORMANCE_COMPARISON "" ON)
+option(BUILD_TESTS "" OFF)
+option(BUILD_SANDBOX "" OFF)
+option(BUILD_DOC "" OFF)
+
 add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/third/pybind11/)
 add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/third/cereal/)
 add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/third/snappy/)
@@ -40,4 +45,13 @@ set_target_properties(PRTree PROPERTIES
 	C_VISIBILITY_PRESET hidden
 	CXX_VISIBILITY_PRESET hidden
   INTERPROCEDURAL_OPTIMIZATION TRUE
+  LIBRARY_OUTPUT_DIRECTORY "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}"
+  RUNTIME_OUTPUT_DIRECTORY "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}"
+  ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}"
+  LIBRARY_OUTPUT_DIRECTORY_DEBUG "${CMAKE_LIBRARY_OUTPUT_DIRECTORY_DEBUG}"
+  LIBRARY_OUTPUT_DIRECTORY_RELEASE "${CMAKE_LIBRARY_OUTPUT_DIRECTORY_RELEASE}"
+  RUNTIME_OUTPUT_DIRECTORY_DEBUG "${CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG}"
+  RUNTIME_OUTPUT_DIRECTORY_RELEASE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE}"
+  ARCHIVE_OUTPUT_DIRECTORY_DEBUG "${CMAKE_ARCHIVE_OUTPUT_DIRECTORY_DEBUG}"
+  ARCHIVE_OUTPUT_DIRECTORY_RELEASE "${CMAKE_ARCHIVE_OUTPUT_DIRECTORY_RELEASE}"
 )

README.md

@@ -174,6 +174,21 @@ Note that cross-version compatibility is **NOT** guaranteed, so please reconstru
 
 ## New Features and Changes
 
+### `python-prtree>=0.7.0`
+
+**BREAKING CHANGES:**
+
+- **Fixed critical intersection bug**: Boxes with small gaps (< 1e-5) were incorrectly reported as intersecting due to float32 precision loss. Now uses precision-matching two-stage approach: float32 input → pure float32 performance, float64 input → float32 tree + double-precision refinement for correctness.
+- **Python version requirements**: Minimum Python version is now 3.8 (dropped 3.6 and 3.7 due to pybind11 v2.13.6 compatibility). Added support for Python 3.13 and 3.14.
+- **Serialization format changed**: Binary files saved with previous versions are incompatible with 0.7.0+. You must rebuild and re-save your trees after upgrading.
+- **Updated pybind11**: Upgraded from v2.12.0 to v2.13.6 for Python 3.13+ support.
+- **Input validation**: Added validation to reject NaN/Inf coordinates and enforce min <= max per dimension.
+- **Improved test coverage**: Added comprehensive tests for edge cases including disjoint boxes with small gaps, touching boxes, large magnitude coordinates, and degenerate boxes.
+
+**Bug Fix Details:**
+
+The bug occurred when two bounding boxes were separated by a very small gap (e.g., 5.39e-06). When converted from float64 to float32, the values would collapse to the same float32 value, causing the intersection check to incorrectly report them as intersecting. This has been fixed by implementing a precision-matching approach: float32 input uses pure float32 for speed, while float64 input uses a two-stage filter-then-refine approach (float32 tree + double-precision refinement) for correctness.
+
 ### `python-prtree>=0.5.8`
 
 - The insert method has been improved to select the node with the smallest mbb expansion.