error with numpy 2.0.0

[laurentijn]

I tried to install the latest version of Medaka (1.12.0) and got this error when I downloaded the models
medaka tools download_models

Traceback (most recent call last):
  File "/usr/local/bin/medaka", line 5, in <module>
    from medaka.medaka import main
  File "/usr/local/lib/python3.10/dist-packages/medaka/medaka.py", line 8, in <module>
    import medaka.datastore
  File "/usr/local/lib/python3.10/dist-packages/medaka/datastore.py", line 20, in <module>
    import h5py
  File "/usr/local/lib/python3.10/dist-packages/h5py/__init__.py", line 25, in <module>
    from . import _errors
  File "h5py/_errors.pyx", line 1, in init h5py._errors
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

Installing version 1.26.4 of numpy solved the problem:

pip uninstall numpy -y
pip install numpy==1.26.4

[cjw85]

We've just released a v1.12.1 package that pins numpy to <2.0.0.