build: enable Python limited API (#2215)

Closes #1997. Closes #2202.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
  - Added support for Python 3.9 on macOS and Windows platforms.
- Introduced new build configurations for better integration and
compatibility.

- **Bug Fixes**
- Removed unsupported Python 3.8 configurations for certain platforms to
ensure compatibility.

- **Refactor**
- Updated minimum required CMake version to improve build stability and
performance.
- Streamlined Python API settings in build configurations for enhanced
functionality.

- **Documentation**
- Updated build and wheel repair commands in documentation to reflect
current support and configurations.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <[email protected]>

.github/workflows/wheel.yml

@@ -22,62 +22,17 @@ jobs:
  matrix:
  include:
  # linux-64
- - os: ubuntu-latest
- python: 37
- platform_id: manylinux_x86_64
  - os: ubuntu-latest
  python: 38
  platform_id: manylinux_x86_64
- - os: ubuntu-latest
- python: 39
- platform_id: manylinux_x86_64
- - os: ubuntu-latest
- python: 310
- platform_id: manylinux_x86_64
- - os: ubuntu-latest
- python: 311
- platform_id: manylinux_x86_64
- - os: ubuntu-latest
- python: 312
- platform_id: manylinux_x86_64
  # macos-x86-64
- - os: macos-latest
- python: 37
- platform_id: macosx_x86_64
- - os: macos-latest
- python: 38
- platform_id: macosx_universal2
  - os: macos-latest
  python: 39
  platform_id: macosx_universal2
- - os: macos-latest
- python: 310
- platform_id: macosx_universal2
- - os: macos-latest
- python: 311
- platform_id: macosx_universal2
- - os: macos-latest
- python: 312
- platform_id: macosx_universal2
  # win-64
- - os: windows-2019
- python: 37
- platform_id: win_amd64
  - os: windows-2019
  python: 38
  platform_id: win_amd64
- - os: windows-2019
- python: 39
- platform_id: win_amd64
- - os: windows-2019
- python: 310
- platform_id: win_amd64
- - os: windows-2019
- python: 311
- platform_id: win_amd64
- - os: windows-2019
- python: 312
- platform_id: win_amd64
  steps:
  - uses: actions/checkout@v4
  - name: Build wheels

CMakeLists.txt

@@ -1,9 +1,9 @@
-cmake_minimum_required(VERSION 3.18...3.28)
+cmake_minimum_required(VERSION 3.26...3.28)
 project(${SKBUILD_PROJECT_NAME} LANGUAGES C CXX)
 
 find_package(
  Python
- COMPONENTS Interpreter Development.Module
+ COMPONENTS Interpreter Development.SABIModule
  # NumPy
  REQUIRED)
 
@@ -52,10 +52,16 @@ add_custom_command(
  VERBATIM)
 
 python_add_library(
- dps MODULE ${CMAKE_CURRENT_BINARY_DIR}/dps.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/c_stack.cpp WITH_SOABI)
+ dps
+ MODULE
+ USE_SABI
+ 3.7
+ ${CMAKE_CURRENT_BINARY_DIR}/dps.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/c_stack.cpp
+ WITH_SOABI)
 target_include_directories(dps
  PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator)
+target_compile_definitions(dps PRIVATE CYTHON_LIMITED_API=1)
 if(CMAKE_BUILD_TYPE STREQUAL "Debug")
  target_compile_definitions(dps PRIVATE CYTHON_TRACE=1 CYTHON_TRACE_NOGIL=1)
 endif()
@@ -73,9 +79,10 @@ if(FALSE)
  DEPENDS reacnetgenerator/utils_np.pyx
  VERBATIM)
 
- python_add_library(utils_np MODULE ${CMAKE_CURRENT_BINARY_DIR}/utils_np.c
- WITH_SOABI)
+ python_add_library(utils_np MODULE USE_SABI 3.11
+ ${CMAKE_CURRENT_BINARY_DIR}/utils_np.c WITH_SOABI)
  target_link_libraries(utils_np PRIVATE Python::NumPy)
+ target_compile_definitions(utils_np PRIVATE CYTHON_LIMITED_API=1)
  if(CMAKE_BUILD_TYPE STREQUAL "Debug")
  target_compile_definitions(utils_np PRIVATE CYTHON_TRACE=1
  CYTHON_TRACE_NOGIL=1)

pyproject.toml

@@ -2,10 +2,10 @@
 requires = [
  "scikit-build-core>=0.9.0",
  # "oldest-supported-numpy; python_version < '3.9'",
- "numpy>=2.0.0rc0; python_version >= '3.9'",
+ # "numpy>=2.0.0rc0; python_version >= '3.9'",
  "nodejs-wheel~=20.9",
  "pyyaml",
- "cython>=0.16",
+ "cython>=3.0.1",
 ]
 build-backend = "scikit_build_core.build"
 
@@ -100,10 +100,11 @@ docs = [
 
 [tool.scikit-build]
 minimum-version = "0.9"
+wheel.py-api = "cp37"
 metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
 sdist.include = ["reacnetgenerator/_version.py"]
 sdist.exclude = ["reacnetgenerator/static/webpack/"]
-cmake.version = ">=3.18"
+cmake.version = ">=3.26"
 
 [tool.setuptools_scm]
 write_to = "reacnetgenerator/_version2.py"
@@ -118,6 +119,17 @@ before-test = ["python -m pip install replace-pip-with-uv-pip"]
 
 [tool.cibuildwheel.linux]
 environment-pass = ["CIBW_BUILD"]
+# Use abi3audit to catch issues with Limited API wheels
+repair-wheel-command = [
+ "auditwheel repair -w {dest_dir} {wheel}",
+ "pipx run abi3audit --strict --report {wheel}",
+]
+
+[tool.cibuildwheel.macos]
+repair-wheel-command = [
+ "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
+ "pipx run abi3audit --strict --report {wheel}",
+]
 
 [tool.pyright]
 include = [

reacnetgenerator/dps.pyx

@@ -6,6 +6,8 @@
 """Connect molecule with Depth-First Search."""
 from libc.stdlib cimport free, malloc
 
+import cython
+
 
 cdef extern from "c_stack.h":
  # This function is copied from https://zhuanlan.zhihu.com/p/38212302
@@ -14,6 +16,7 @@ cdef extern from "c_stack.h":
  int pop()
 
 
+@cython.binding(False)
 def dps(bonds, levels):
  """Connect molecule with Depth-First Search.
 
@@ -35,7 +38,7 @@ def dps(bonds, levels):
  bondlist = []
  cdef int _N = len(bonds)
  cdef int *visited = <int *> malloc(_N * sizeof(int))
- cdef int i, s, b_c, l
+ cdef int i, s, b_c, ll, ib, nb
  cdef C_Stack st
  for i in range(_N):
  visited[i]=0
@@ -52,11 +55,13 @@ def dps(bonds, levels):
  elif visited[s]==1:
  continue
  mol.append(s)
- for b, l in zip(bonds[s], levels[s]):
+ nb = len(bonds[s])
+ for ib in range(nb):
+ b = bonds[s][ib]
+ ll = levels[s][ib]
  b_c = b
  if visited[b_c]==0:
- # bond.append((s, b, l) if i < b else (b, s, l))
- bond.append((s, b, l) if s < b else (b, s, l))
+ bond.append((s, b, ll) if s < b else (b, s, ll))
  st.push(b_c)
  visited[s]=1
  mol.sort()
@@ -67,6 +72,7 @@ def dps(bonds, levels):
  return molecule, bondlist
 
 
+@cython.binding(False)
 def dps_reaction(reactdict):
  """Find A+B->C+D reactions.
 

reacnetgenerator/utils_np.pyx

@@ -15,6 +15,7 @@ DTYPE8 = np.int8
 ctypedef np.int8_t DTYPE8_t
 
 
+@cython.binding(False)
 @cython.boundscheck(False)
 @cython.wraparound(False)
 cpdef idx_to_signal(DTYPE_t[:] idx, int step):