将基于 f2py 的 Python 模块从 numpy.distutils 移动到 scikit-build-core 时出现问题

Question

我维护一个名为 Tsyganenko 的 Python 模块，当前有一个 setup.py

 文件，如下所示：

from numpy.distutils.core import Extension, setup

ext = Extension('geopack',
                sources=['src/tsyganenko/geopack_py.pyf',
                         'src/tsyganenko/geopack_py.f',
                         'src/tsyganenko/T96.f',
                         'src/tsyganenko/T02.f'])

with open("README.md", "r", encoding="utf-8") as f:
    long_description = f.read()

setup(author="John Coxon and Sebastien de Larquier",
      author_email="[email protected]",
      classifiers=[
          "Development Status :: 4 - Beta",
          "Intended Audience :: Science/Research",
          "Natural Language :: English",
          "Programming Language :: Python/Fortran"
      ],
      description="A wrapper to call GEOPACK routines in Python.",
      ext_modules=[ext],
      install_requires=[
          "numpy",
          "matplotlib",
          "pandas"
      ],
      keywords=['Scientific/Space'],
      long_description=long_description,
      long_description_content_type="text/markdown",
      name="Tsyganenko",
      package_dir={"": "src"},
      packages=setuptools.find_packages(where="src"),
      python_requires=">=3.9",
      url="https://github.com/johncoxon/tsyganenko",
      version="2020.1",
      )

由于

scikit-build-core

 已被弃用，我正在尝试将其移至使用 

numpy.distutils

。我正在尝试按照 

scikit-build-core

 文档

来执行此操作，并得到如下所示的 pyproject.toml

：

[build-system]
requires = ["scikit-build-core", "numpy"]
build-backend = "scikit_build_core.build"

[project]
name = "Tsyganenko"
version = "2020.2"
dependencies = ["numpy"]

[tool.scikit-build]
ninja.version = ">=1.10"
cmake.version = ">=3.17.2"

[tool.setuptools.packages.find]
where = ["src"]

和一个

CMakeLists.txt

文件，如下所示：

cmake_minimum_required(VERSION 3.17.2...3.29)
project(${SKBUILD_PROJECT_NAME} LANGUAGES C Fortran)

find_package(
  Python
  COMPONENTS Interpreter Development.Module NumPy
  REQUIRED)

# F2PY headers
execute_process(
  COMMAND "${PYTHON_EXECUTABLE}" -c
          "import numpy.f2py; print(numpy.f2py.get_include())"
  OUTPUT_VARIABLE F2PY_INCLUDE_DIR
  OUTPUT_STRIP_TRAILING_WHITESPACE)

add_library(fortranobject OBJECT "${F2PY_INCLUDE_DIR}/fortranobject.c")
target_link_libraries(fortranobject PUBLIC Python::NumPy)
target_include_directories(fortranobject PUBLIC "${F2PY_INCLUDE_DIR}")
set_property(TARGET fortranobject PROPERTY POSITION_INDEPENDENT_CODE ON)

add_custom_command(
  OUTPUT geopack_pymodule.c geopack_py-f2pywrappers.f
  DEPENDS src/tsyganenko/geopack_py.f
  VERBATIM
  COMMAND "${Python_EXECUTABLE}" -m numpy.f2py
          "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack_py.f" -m geopack_py --lower)

python_add_library(
  geopack_py MODULE "${CMAKE_CURRENT_BINARY_DIR}/geopack_pymodule.c"
  "${CMAKE_CURRENT_BINARY_DIR}/geopack_py-f2pywrappers.f"
  "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack_py.f" WITH_SOABI)
target_link_libraries(geopack_py PRIVATE fortranobject)

install(TARGETS geopack_py DESTINATION .)

据称，它已成功安装，但在尝试导入模块时出现以下错误。我不太了解 

scikit-build-core

文档，无法调试它。我相当确定这是一个问题，

T96.f

和

T02.f

在

CMakeLists.txt

中的任何地方都没有提到，但我不知道如何添加它们，而且我不确定是否需要包括

geopack_py.pyf 

。有人可以帮忙吗？

如果你想直接访问代码，都在GitHub上模块的change-setup分支中。

In [1]: import geopack_py
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[1], line 1
----> 1 import geopack_py

ImportError: dlopen(/opt/homebrew/Caskroom/mambaforge/base/envs/test/lib/python3.12/site-packages/geopack_py.cpython-312-darwin.so, 0x0002): symbol not found in flat namespace '_t01_01_'

Answer 1

add_custom_command

以包含此 .pyf 文件和其他 Fortran 文件：

add_custom_command(
  OUTPUT geopack_pymodule.c geopack_py-f2pywrappers.f
  DEPENDS
    src/tsyganenko/geopack_py.pyf
    src/tsyganenko/geopack_py.f
    src/tsyganenko/T96.f
    src/tsyganenko/T02.f
  COMMAND "${Python_EXECUTABLE}" -m numpy.f2py
    -m geopack_py
    --lower
    "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack_py.pyf"
    "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack_py.f"
    "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/T96.f"
    "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/T02.f"
)

您也可以尝试将所有 Fortran 文件包含在

python_add_library

命令中

python_add_library(
  geopack_py MODULE
  "${CMAKE_CURRENT_BINARY_DIR}/geopack_pymodule.c"
  "${CMAKE_CURRENT_BINARY_DIR}/geopack_py-f2pywrappers.f"
  "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack_py.f"
  "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/T96.f"
  "${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/T02.f"
  WITH_SOABI
)

在此之后使用 scikit-build-core 重建一切：

pip install .

并尝试

import geopack_py