installation mismatch in versions of numpy #118
Description
Importing the package gives errors concerning the numpy versions. I give details about the installation below.
(env_bnlearn) mymac[test_bnlearn/]% python
Python 3.10.19 | packaged by conda-forge | (main, Oct 22 2025, 22:46:36) [Clang 19.1.7 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import bnlearn
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "<stdin>", line 1, in <module>
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/bnlearn/__init__.py", line 1, in <module>
from bnlearn.bnlearn import (
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/bnlearn/bnlearn.py", line 27, in <module>
from pgmpy.models import BayesianNetwork, NaiveBayes, MarkovNetwork
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/pgmpy/__init__.py", line 1, in <module>
from .global_vars import config
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/pgmpy/global_vars.py", line 4, in <module>
import torch
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/torch/__init__.py", line 1477, in <module>
from .functional import * # noqa: F403
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/torch/functional.py", line 9, in <module>
import torch.nn.functional as F
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/torch/nn/__init__.py", line 1, in <module>
from .modules import * # noqa: F403
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/torch/nn/modules/__init__.py", line 35, in <module>
from .transformer import TransformerEncoder, TransformerDecoder, \
File "/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/torch/nn/modules/transformer.py", line 20, in <module>
device: torch.device = torch.device(torch._C._get_default_device()), # torch.device('cpu'),
/Users/an/opt/anaconda3/envs/env_bnlearn/lib/python3.10/site-packages/torch/nn/modules/transformer.py:20: UserWarning: Failed to initialize NumPy: _ARRAY_API not found (Triggered internally at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:84.)
device: torch.device = torch.device(torch._C._get_default_device()), # torch.device('cpu'),
>>>
FYI, I am giving here more infomation on my installation:
(dd) mymac[~/]% conda create -n env_bnlearn python=3.10
Retrieving notices: done
Channels:
- nvidia
- conda-forge
- defaults
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 25.7.0
latest version: 25.11.0
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/an/opt/anaconda3/envs/env_bnlearn
added / updated specs:
- python=3.10
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | h500dc9f_8 129 KB conda-forge
ca-certificates-2025.11.12 | hbd8a1cb_0 149 KB conda-forge
libexpat-2.7.3 | heffb93a_0 72 KB conda-forge
libffi-3.5.2 | h750e83c_0 51 KB conda-forge
liblzma-5.8.1 | hd471939_2 102 KB conda-forge
libsqlite-3.51.1 | h6cc646a_0 968 KB conda-forge
openssl-3.6.0 | h230baf5_0 2.7 MB conda-forge
pip-25.3 | pyh8b19718_0 1.1 MB conda-forge
python-3.10.19 |h988dfef_2_cpython 12.5 MB conda-forge
setuptools-80.9.0 | pyhff2d567_0 731 KB conda-forge
tk-8.6.13 | hf689a15_3 3.1 MB conda-forge
wheel-0.45.1 | pyhd8ed1ab_1 61 KB conda-forge
------------------------------------------------------------
Total: 21.6 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h500dc9f_8
ca-certificates conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0
icu conda-forge/osx-64::icu-75.1-h120a0e1_0
libexpat conda-forge/osx-64::libexpat-2.7.3-heffb93a_0
libffi conda-forge/osx-64::libffi-3.5.2-h750e83c_0
liblzma conda-forge/osx-64::liblzma-5.8.1-hd471939_2
libsqlite conda-forge/osx-64::libsqlite-3.51.1-h6cc646a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2
ncurses conda-forge/osx-64::ncurses-6.5-h0622a9a_3
openssl conda-forge/osx-64::openssl-3.6.0-h230baf5_0
pip conda-forge/noarch::pip-25.3-pyh8b19718_0
python conda-forge/osx-64::python-3.10.19-h988dfef_2_cpython
readline conda-forge/osx-64::readline-8.2-h7cca4af_2
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
tk conda-forge/osx-64::tk-8.6.13-hf689a15_3
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate env_bnlearn
#
# To deactivate an active environment, use
#
# $ conda deactivate
(dd) mymac[~/]% conda activate env_bnlearn
(env_bnlearn) mymac[test_bnlearn/]% pip install bnlearn
Collecting bnlearn
Downloading bnlearn-0.12.0-py3-none-any.whl.metadata (15 kB)
Collecting pgmpy==0.1.25 (from bnlearn)
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Collecting pandas (from bnlearn)
Downloading pandas-2.3.3-cp310-cp310-macosx_10_9_x86_64.whl.metadata (91 kB)
Collecting tqdm (from bnlearn)
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
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Collecting python-louvain (from bnlearn)
Downloading python-louvain-0.16.tar.gz (204 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting packaging (from bnlearn)
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting df2onehot (from bnlearn)
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Downloading semopy-2.3.11.tar.gz (1.6 MB)
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Collecting patsy>=0.5.6 (from statsmodels->bnlearn)
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Building wheels for collected packages: python-louvain, semopy
Building wheel for python-louvain (pyproject.toml) ... done
Created wheel for python-louvain: filename=python_louvain-0.16-py3-none-any.whl size=9460 sha256=dc4e7e21e26a795a658f1382271b4cc1bf17dfd32dda6f175bd13ba932c07025
Stored in directory: /Users/an/Library/Caches/pip/wheels/d0/b0/d7/6dd26c3817810fa379088eaeb755a01d9a2a411c37632079d1
Building wheel for semopy (pyproject.toml) ... done
Created wheel for semopy: filename=semopy-2.3.11-py3-none-any.whl size=1659769 sha256=ec870228036f9b8600b069f2d967e75ca1ec0281014c1a4ff007c02ff82ee244
Stored in directory: /Users/an/Library/Caches/pip/wheels/53/ec/0d/0b294c02d8c4e9e80afea58839f2c1b4706770594bc99ec045
Successfully built python-louvain semopy
Installing collected packages: pytz, pure-eval, ptyprocess, mpmath, funcsigs, widgetsnbextension, wcwidth, urllib3, tzdata, typing_extensions, traitlets, tqdm, threadpoolctl, tabulate, sympy, six, pypickle, pyparsing, pygments, pyarrow, pillow, pexpect, parso, packaging, opt-einsum, numpy, networkx, MarkupSafe, kiwisolver, jupyterlab_widgets, joblib, idna, graphviz, fsspec, fonttools, filelock, executing, decorator, cycler, comm, charset_normalizer, certifi, asttokens, stack_data, scipy, requests, python-utils, python-louvain, python-dateutil, prompt_toolkit, patsy, matplotlib-inline, jinja2, jedi, ismember, exceptiongroup, contourpy, autograd, torch, setgraphviz, scikit-learn, progressbar2, pandas, numdifftools, matplotlib, ipython, statsmodels, pygam, psy, ipywidgets, datazets, semopy, pgmpy, df2onehot, lingam, bnlearn
Successfully installed MarkupSafe-3.0.3 asttokens-3.0.1 autograd-1.8.0 bnlearn-0.12.0 certifi-2025.11.12 charset_normalizer-3.4.4 comm-0.2.3 contourpy-1.3.2 cycler-0.12.1 datazets-1.1.3 decorator-5.2.1 df2onehot-1.0.8 exceptiongroup-1.3.1 executing-2.2.1 filelock-3.20.0 fonttools-4.61.0 fsspec-2025.10.0 funcsigs-1.0.2 graphviz-0.21 idna-3.11 ipython-8.37.0 ipywidgets-8.1.8 ismember-1.1.0 jedi-0.19.2 jinja2-3.1.6 joblib-1.5.2 jupyterlab_widgets-3.0.16 kiwisolver-1.4.9 lingam-1.12.1 matplotlib-3.10.7 matplotlib-inline-0.2.1 mpmath-1.3.0 networkx-3.4.2 numdifftools-0.9.41 numpy-2.2.6 opt-einsum-3.4.0 packaging-25.0 pandas-2.3.3 parso-0.8.5 patsy-1.0.2 pexpect-4.9.0 pgmpy-0.1.25 pillow-12.0.0 progressbar2-4.5.0 prompt_toolkit-3.0.52 psy-0.0.1 ptyprocess-0.7.0 pure-eval-0.2.3 pyarrow-19.0.1 pygam-0.11.0 pygments-2.19.2 pyparsing-3.2.5 pypickle-2.0.1 python-dateutil-2.9.0.post0 python-louvain-0.16 python-utils-3.9.1 pytz-2025.2 requests-2.32.5 scikit-learn-1.7.2 scipy-1.15.3 semopy-2.3.11 setgraphviz-1.0.3 six-1.17.0 stack_data-0.6.3 statsmodels-0.14.5 sympy-1.14.0 tabulate-0.9.0 threadpoolctl-3.6.0 torch-2.2.2 tqdm-4.67.1 traitlets-5.14.3 typing_extensions-4.15.0 tzdata-2025.2 urllib3-2.5.0 wcwidth-0.2.14 widgetsnbextension-4.0.15