search

RasmussenLab / MOVE

MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations
https://move-dl.readthedocs.io/
MIT License
64 stars 25 forks source link

numpy 2.0 update #97

Open enryH opened 4 months ago

enryH commented 4 months ago

It looks like currently the installation uses numpy 2.* - which leads to errors:

Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.9/x64/bin/move-dl", line 5, in <module>
    from move.__main__ import main
  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/move/__init__.py", line 5, in <module>
    from move import conf, data, models  # noqa:E402
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/move/conf/__init__.py", line 3, in <module>
    from move.conf.schema import MOVEConfig
  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/move/conf/schema.py", line 18, in <module>
    from move.models.vae import VAE
  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/move/models/__init__.py", line 3, in <module>
    from move.models.vae import VAE
  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/move/models/vae.py", line 10, in <module>
    from move.core.typing import FloatArray, IntArray
  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/move/core/__init__.py", line 3, in <module>
    from move.core import logging, typing
  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/move/core/typing.py", line 13, in <module>
    FloatArray = NDArray[np.float_]
                         ^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/numpy/__init__.py", line 397, in __getattr__
    raise AttributeError(
AttributeError: `np.float_` was removed in the NumPy 2.0 release. Use `np.float64` instead.. Did you mean: 'float[16](https://github.com/RasmussenLab/MOVE/actions/runs/9566168242/job/26370771716?pr=95#step:5:17)'?

@ri-heme Should we switch to np.float64 in the type annotations?