use Python limited API

.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
@@ -99,7 +54,7 @@ jobs:
  - uses: actions/setup-python@v5
  name: Install Python
  with:
- python-version: '3.10'
+ python-version: '3.11'
  - run: python -m pip install build
  - name: Build sdist
  run: python -m build --sdist

pyproject.toml

@@ -7,7 +7,7 @@ requires = [
  "numpy>=2.0.0rc0; python_version >= '3.9'",
  "nodejs-wheel~=20.9",
  "pyyaml",
- "cython>=0.16",
+ "cython>=3.0.1",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -120,6 +120,17 @@ test-skip = "cp37-*"
 
 [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, l, ib, nb
  cdef C_Stack st
  for i in range(_N):
  visited[i]=0
@@ -52,7 +55,10 @@ 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][nb]
+ l = levels[s][nb]
  b_c = b
  if visited[b_c]==0:
  # bond.append((s, b, l) if i < b else (b, s, l))
@@ -67,6 +73,7 @@ def dps(bonds, levels):
  return molecule, bondlist
 
 
+@cython.binding(False)
 def dps_reaction(reactdict):
  """Find A+B->C+D reactions.
 
@@ -87,8 +94,11 @@ def dps_reaction(reactdict):
  cdef set visited_right = set()
  visited = [visited_left, visited_right]
  cdef C_Stack st
+ cdef int nm, im, nr, ir
 
- for init_mol in reactdict[0]:
+ nm = len(reactdict[0])
+ for im in range(nm):
+ init_mol = reactdict[0][im]
  if init_mol not in visited[0]:
  reaction = [[], []]
  st.push(init_mol)
@@ -100,7 +110,9 @@ def dps_reaction(reactdict):
  elif mol in visited[side]:
  continue
  reaction[side].append(mol)
- for r in reactdict[side][mol]:
+ nr = len(reactdict[side][mol])
+ for ir in range(nr):
+ r = reactdict[side][mol][ir]
  if r < 0:
  if r not in reaction[1-side]:
  reaction[1-side].append(r)

reacnetgenerator/utils_np.pyx

@@ -4,6 +4,7 @@
 # cython: linetrace=True
 # cython: infer_types=True
 
+import cython
 import numpy as np
 
 cimport cython
@@ -15,8 +16,7 @@ DTYPE8 = np.int8
 ctypedef np.int8_t DTYPE8_t
 
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
+@cython.binding(False)
 cpdef idx_to_signal(DTYPE_t[:] idx, int step):
  """Converts an index array to a signal array.
 
@@ -51,8 +51,7 @@ cpdef idx_to_signal(DTYPE_t[:] idx, int step):
  return signal
 
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
+@cython.binding(False)
 cpdef check_zero_signal(DTYPE8_t[:] signal):
  """Check if the given signal contains only zeros.
 

setup.py

@@ -12,6 +12,7 @@
 import setuptools.command.build_ext
 import yaml
 from setuptools import Extension, setup
+from wheel.bdist_wheel import bdist_wheel
 
 log = logging.getLogger(__name__)
 
@@ -64,8 +65,19 @@ def run(self):
  super().run()
 
 
+class bdist_wheel_abi3(bdist_wheel):
+ def get_tag(self):
+ python, abi, plat = super().get_tag()
+
+ if python.startswith("cp"):
+ # on CPython, our wheels are abi3 and compatible back to 3.7
+ return "cp37", "abi3", plat
+
+ return python, abi, plat
+
+
 if __name__ == "__main__":
- define_macros = []
+ define_macros = [("CYTHON_LIMITED_API", "1"), ("Py_LIMITED_API", "0x030b0000")]
  if os.environ.get("DEBUG", 0):
  define_macros.extend((("CYTHON_TRACE", "1"), ("CYTHON_TRACE_NOGIL", "1")))
 
@@ -86,7 +98,5 @@ def run(self):
 
  setup(
  ext_modules=ext_modules,
- cmdclass={
- "build_ext": BuildExtCommand,
- },
+ cmdclass={"build_ext": BuildExtCommand, "bdist_wheel": bdist_wheel_abi3},
  )