Warning: updated eman dependencies

[Steve Ludtke]

The "eman-dev" dependencies used by EMAN2 have been having some version incompatibilities recently. They have now been updated, along with a minor adjustment to the installation instructions. For those installing updated EMAN2 versions I strongly suggest creating a new conda environment following the instructions.

https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install:sourceinstall

What happened:

NumPy, used in most scientific software written in Python underwent a major version change from 1.X to 2.X in the summer of 2024. This has led to a bit of chaos, as some packages quickly migrated to NumPy 2 and some stuck with NumPy 1. EMAN2 has adopted JAX for use in deep learning and GPU acceleration moving forward, but historically also made use of a TensorFlow, and there were NumPy conflicts. To complicate this, CUDA, the underlying GPU library on NVidia Linux machines also has very specific versioning requirements.

EMAN2 has been updated so it should work properly with NumPy (tested, but not thoroughly), and the dependencies have been updated so everything should now be based on NumPy 2.X and CUDA 1.2.X.

As always, please report any difficulties here.