Open pitmanme opened 1 year ago
@pitmanme I am having the same error but running within a .coordinantes.tica in my Jupyter notebook. I have tried uninstalling and reinstalling early version of numpy, with no success. Your solution worked for me! Thank you.
@acadiaconnor if you end up having other issues (I'm not using many of the functions from pyemma) you might double check which numpy loads into your Jupyter notebook.
Depending on what you try to do, you can also have a look at deeptime. That one is still being somewhat maintained and should be compatible to newest bumpy versions :)
Just came here to report the same issue.
In my case it was related to vamp, and I solve it downgrading to numpy 1.23.5 version (vs the 1.24 I was originaly using)
If you have a working version you could also make a PR, i'm happy to review and merge it, just don't have the time right now to do any active development (new job and all...)
PyEMMA appears to not be compatible with the most recent NumPy version. I detail the version related bug I ran into below and a quick fix I implemented on my installation of PyEMMA so that I didn't have to backtrack my NumPy installation.
Here is the Traceback :
This is with the newest numpy version
>>> numpy.__version__ '1.24.1'
The environment file is attached (env.txt) for pyemma version 2.5.12 ran on OS X v. 11.4 (Big Sur).
Minimal example
Get the trj file and structure file:
Produce error:
Potential solution:
I edited my installation of covartools.py to replace numpy.bool with numpy.bool_ and that resolved the issue. I believe you can use the standard python bool as well. Alternatively, you could pin the numpy version in the conda install to not allow more recent numpy versions.
env.txt