create_individual_features.py issue

[KrFrandsen]

Hi
I try create_individual_features.py, but I get the error below.
What do you recommend ?

home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/Bio/Data/SCOPData.py:18: BiopythonDeprecationWarning: The 'Bio.Data.SCOPData' module will be deprecated in a future release of Biopython in favor of 'Bio.Data.PDBData.
warnings.warn(

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.1 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 "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/alphapulldown/scripts/create_individual_features.py", line 19, in
from alphapulldown.utils.create_custom_template_db import create_db
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/alphapulldown/utils/create_custom_template_db.py", line 17, in
from alphapulldown.utils.remove_clashes_low_plddt import MmcifChainFiltered
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/alphapulldown/utils/remove_clashes_low_plddt.py", line 9, in
from colabfold.batch import convert_pdb_to_mmcif
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/colabfold/batch.py", line 76, in
import jax
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/jax/init.py", line 37, in
import jax.core as _core
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/jax/core.py", line 18, in
from jax._src.core import (
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/jax/_src/core.py", line 39, in
from jax._src import dtypes
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/jax/_src/dtypes.py", line 30, in
import ml_dtypes
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/ml_dtypes/init.py", line 32, in
from ml_dtypes._custom_floats import bfloat16
AttributeError: _ARRAY_API not found
ImportError: numpy.core._multiarray_umath failed to import
Traceback (most recent call last):
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/alphapulldown/scripts/create_individual_features.py", line 19, in
from alphapulldown.utils.create_custom_template_db import create_db
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/alphapulldown/utils/create_custom_template_db.py", line 17, in
from alphapulldown.utils.remove_clashes_low_plddt import MmcifChainFiltered
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/alphapulldown/utils/remove_clashes_low_plddt.py", line 9, in
from colabfold.batch import convert_pdb_to_mmcif
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/colabfold/batch.py", line 76, in
import jax
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/jax/init.py", line 37, in
import jax.core as _core
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/jax/core.py", line 18, in
from jax._src.core import (
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/jax/_src/core.py", line 39, in
from jax._src import dtypes
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/jax/_src/dtypes.py", line 30, in
import ml_dtypes
File "/home/kristian/miniconda3/envs/AlphaPulldown/lib/python3.10/site-packages/ml_dtypes/init.py", line 32, in
from ml_dtypes._custom_floats import bfloat16
ImportError: numpy.core.umath failed to import

[DimaMolod]

Hi @KrFrandsen
it seems like your jax version was compiled with numpy version 1 but you have numpy version 2.
The easiest solution would be to downgrade your numpy to version 1
pip install "numpy<2"
Please let me know if this helps,
Dima