BUG: Numpy 2.0.0: import error from graph_tool

[WhiteSymmetry]

Describe the issue:

Numpy 2.0.0: (graph-tool: 2.69 & 2.70)
from graph_tool.all import *
File "//lib/python3.11/site-packages/graph_tool/init.py", line 118, in
dl_import("from . import libgraph_tool_core as libcore")
File "//lib/python3.11/site-packages/graph_tool/dl_import.py", line 44, in dl_import
exec(import_expr, local_dict, global_dict)
File "", line 1, in

line 44:
try:
exec(import_expr, local_dict, global_dict)
finally:
sys.setdlopenflags(orig_dlopen_flags) # reset it to normal case to

avoid unnecessary symbol

collision

Executing: from . import libgraph_tool_core as libcore

Numpy:1.x
It doesn’t give an error in numpy 1.x.

Reproduce the code example:

import graph_tool.all as gt
from numpy.random import random

Error message:

from graph_tool.all import *
File "/*/lib/python3.11/site-packages/graph_tool/__init__.py", line 118, in <module>
    dl_import("from . import libgraph_tool_core as libcore")
File "/*/lib/python3.11/site-packages/graph_tool/dl_import.py", line 44, in dl_import
    exec(import_expr, local_dict, global_dict)
File "<string>", line 1, in <module>

Python and NumPy Versions:

Python: 3.11.9
Numpy: 2.0.0

Runtime Environment:

[{'numpy_version': '2.0.0',
'python': '3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:53:30) '
'[GCC 12.3.0]',
'uname': uname_result(system='Linux', node='', release='6.9.3-060903-generic', version='#202405300957 SMP PREEMPT_DYNAMIC Thu May 30 11:39:13 UTC 2024', machine='x86_64')},
{'simd_extensions': {'baseline': ['SSE', 'SSE2', 'SSE3'],
'found': ['POPCNT'],
'not_found': ['SSSE3',
'SSE41',
'SSE42',
'AVX',
'F16C',
'FMA3',
'AVX2',
'AVX512F',
'AVX512CD',
'AVX512_KNL',
'AVX512_KNM',
'AVX512_SKX',
'AVX512_CLX',
'AVX512_CNL',
'AVX512_ICL']}},
{'architecture': 'Prescott',
'filepath': '/home//miniconda3/envs/x11/lib/python3.11/site-packages/numpy.libs/libscipy_openblas64_-99b71e71.so',
'internal_api': 'openblas',
'num_threads': 4,
'prefix': 'libscipy_openblas',
'threading_layer': 'pthreads',
'user_api': 'blas',
'version': '0.3.27'}]

Context for the issue:

Kernel Restarting

[rkern]

Packages that have extension modules that import numpy (like graph-tool) need to be rebuilt against numpy 2.0. You cannot use graph-tool binaries that have been built against numpy 1.x and just install numpy 2.0 alongside. Did you rebuild graph-tool, or are you using older binaries?

[WhiteSymmetry]

I tried it on both the old installation and the new conda and mamba installation. Either way, it fails. But I didn't try it because the graph-tool takes a long time to compile on the system.

[seberg]

A bit unclear how it's failing, but indeed: it presumably needs to be rebuild (and may need smaller code fixes). The easiest fix is maybe to just wait a while for conda-forge to build a compatible version.

Closing, I didn't find a tracking issue for graph-tool and it doesn't look like pypi releases are still done for it. But we could add it to the NumPy tracking issue (26191), especially with a tracking issue.