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Numpy 2 issue #79

Description

@e-osipov

Standard installation pulls numpy 2, which causes some errors:

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.4 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 "/usr/local/xray/conda/mamba/envs/omegafold/bin/omegafold", line 5, in <module>
    from omegafold.__main__ import main
  File "/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/__init__.py", line 24, in <module>
    from omegafold.model import OmegaFold
  File "/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/model.py", line 29, in <module>
    from omegafold import (
  File "/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/confidence.py", line 29, in <module>
    from omegafold import modules, utils
  File "/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/modules.py", line 30, in <module>
    from omegafold import utils
  File "/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/utils/__init__.py", line 27, in <module>
    from omegafold.utils.protein_utils import residue_constants
  File "/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/utils/protein_utils/__init__.py", line 23, in <module>
    from omegafold.utils.protein_utils.aaframe import AAFrame
  File "/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/utils/protein_utils/aaframe.py", line 34, in <module>
    from omegafold.utils.protein_utils import (
  File "/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/utils/protein_utils/residue_constants.py", line 62, in <module>
    chi_angles_mask = torch.tensor(
/usr/local/xray/conda/mamba/envs/omegafold/lib/python3.10/site-packages/omegafold/utils/protein_utils/residue_constants.py:62: UserWarning: Failed to initialize NumPy: _ARRAY_API not found (Triggered internally at  ../torch/csrc/utils/tensor_numpy.cpp:68.)
  chi_angles_mask = torch.tensor(

Could be solved by forced installation of Numpy v1.X: pip install "numpy<2.0"

May be the correct way to do this is to adjust requirements.txt to install correct Numpy?

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