e2tomogram.py error

[justin zhao]

Hi, 

I am a high schooler attempting to try out cryo et processing, so assume I have very limited knowledge in using Linux. I followed a standard conda installation and installed eman2 using the command provided on the site. 

conda create -n eman2 eman-dev==2.99.47 -c cryoem -c conda-forge

e2speedtest.py and e2version.py worked without issues, outputting the following

e2version.py
EMAN 2.99.47 ( GITHUB: 2023-03-04 19:33 - commit: NOT-INSTALLED-FROM-GIT-REPO )
Your EMAN2 is running on: Linux-5.15.146.1-microsoft-standard-WSL2-x86_64-with-glibc2.35 5.15.146.1-microsoft-standard-WSL2
Your Python version is: 3.9.18

However, performing a tomogram in projectmanager.py resulted in the following error, 

/home/justin/miniconda3/envs/eman2/bin/e2tomogram.py:9: UserWarning: A NumPy version >=1.22.4 and <2.3.0 is required for this version of SciPy (detected version 1.20.3)
  from scipy.optimize import minimize
Traceback (most recent call last):
  File "/home/justin/miniconda3/envs/eman2/bin/e2tomogram.py", line 9, in <module>
    from scipy.optimize import minimize
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/optimize/__init__.py", line 413, in <module>
    from ._optimize import *
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/optimize/_optimize.py", line 35, in <module>
    from scipy.linalg import cholesky, issymmetric, LinAlgError
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/linalg/__init__.py", line 205, in <module>
    from ._basic import *
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/linalg/_basic.py", line 13, in <module>
    from ._decomp import _asarray_validated
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/linalg/_decomp.py", line 26, in <module>
    from scipy._lib._util import _asarray_validated
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/_lib/_util.py", line 18, in <module>
    from scipy._lib._array_api import array_namespace
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/_lib/_array_api.py", line 17, in <module>
    from scipy._lib.array_api_compat import (
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/_lib/array_api_compat/numpy/__init__.py", line 16, in <module>
    __import__(__package__ + '.linalg')
  File "/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/scipy/_lib/array_api_compat/numpy/linalg.py", line 2, in <module>
    from numpy.linalg import __all__ as linalg_all
ImportError: cannot import name '__all__' from 'numpy.linalg' (/home/justin/miniconda3/envs/eman2/lib/python3.9/site-packages/numpy/linalg/__init__.py)

similarly, e2tomogram.py in bash produced the following error. 

What am I doing wrong here? 

could anyone help me please. 

Best regards, 

Justin

[Ludtke, Steven J.]

Every so often when Anaconda updates their versions, a version conflict arises with the EMAN2 dependencies. Suggest following the source installation instructions instead until this problem can be resolved. The instructions aren't really any more difficult.

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

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[shadow walker]

Can you try to install eman-dev without specifying a version?

conda create -n eman2 eman-dev -c cryoem -c conda-forge

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shadow_walker

[Judy Huang]

Hi Justin,

I’ve had this issue before installing into a fresh conda env - what fixed it for me was simply running pip install numpy==1.22.4 within the env to give it a compatible version of numpy. 

Best,

Judy 

P.S. you have the same name as my little cousin! but he’s only starting high school this fall.

[justin zhao]

This appeared to fix the issue, thank you very much