I maintain a Python module called Tsyganenko which currently has a setup.py file as below:
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",
)
I am trying to move this over to use scikit-build-core due to numpy.distutils being deprecated. I am trying to follow the scikit-build-core documentation to do this, and have arrived at a pyproject.toml that looks like this:
[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"]
and a CMakeLists.txt file which looks like this:
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"
"${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack_py.f" WITH_SOABI)
target_link_libraries(geopack_py PRIVATE fortranobject)
install(TARGETS geopack_py DESTINATION .)
It successfully installs, allegedly, but when trying to import the module I get the following error. I don't understand the scikit-build-core documentation well enough to be able to debug it. I'm fairly certain that it's a problem that T96.f and T02.f aren't mentioned anywhere in CMakeLists.txt but I'm not sure how to add them, and I'm not sure whether I need to include geopack_py.pyf. Can anyone assist? If you want to access the code directly, it's all in the change-setup branch of the module on GitHub.
In [1]: import geopack_py
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[1], line 1
----> 1 import geopack_py
ImportError: dlopen(/opt/homebrew/Caskroom/mambaforge/base/envs/test/lib/python3.12/site-packages/geopack_py.cpython-312-darwin.so, 0x0002): symbol not found in flat namespace '_t01_01_'
Your stumbling block is that for some reason numpy.f2py doesn't like the name geopack_py -- specifically, it doesn't like the _py. So, renaming the relevant files to geopack.f and geopack.pyf, and modifying your CMakeLists.txt to:
add_custom_command(
OUTPUT geopackmodule.c geopack-f2pywrappers.f
DEPENDS
src/tsyganenko/geopack.pyf
src/tsyganenko/geopack.f
src/tsyganenko/T96.f
src/tsyganenko/T02.f
COMMAND "${Python_EXECUTABLE}" -m numpy.f2py
-m geopack
--lower
"${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack.pyf"
"${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack.f"
"${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/T96.f"
"${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/T02.f"
)
python_add_library(
geopack MODULE "${CMAKE_CURRENT_BINARY_DIR}/geopackmodule.c"
"${CMAKE_CURRENT_BINARY_DIR}/geopack-f2pywrappers.f"
"${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/geopack.f"
"${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/T96.f"
"${CMAKE_CURRENT_SOURCE_DIR}/src/tsyganenko/T02.f"
WITH_SOABI)
target_link_libraries(geopack PRIVATE fortranobject)
install(TARGETS geopack DESTINATION .)
we now have something that builds and can be imported.