Re: [scipion-users] Error with reliontomo tests

[Ana A. A. <ana...@i2...>]

Morning,
I also have errors for reliontomo:

Scipion v3.0.7 - Eugenius
WARNING FOR DEVELOPERS:  phenix/bibtex._bibtex unnecessarily declared. Just the doc string is enough.
 > error when importing from reliontomo.protocols: cannot import name 'pwem' from 'relion.convert' (/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/convert/__init__.py)
   File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/reliontomo/protocols/protocol_refine_3d_tomo.py", line 34, in <module>
   Check the plugin manager (Configuration->Plugins in Scipion manager window)
   or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
   it could be a versions compatibility issue.

My kind regards,
           ana arteni.

----- Original Message -----
From: "scipion-users" <sci...@li...>
To: "scipion-users" <sci...@li...>
Cc: "Hoover, David (NIH/CIT) [E]" <hoo...@hp...>
Sent: Wednesday, 24 February, 2021 03:02:43
Subject: [scipion-users] Error with reliontomo tests

Hi,

I've managed to install scipion3 (3.0.7) and am trying to run tests.  The reliontomo test doesn't seem to work at all:

================================================================================================================

$ scipion3 tests --show

...
>>>> reliontomo
Error loading the test. Please, run the test for more information: reliontomo.tests.test_workflow_reliontomo
...

$ scipion3 tests reliontomo.tests.test_workflow_reliontomo
Scipion v3.0.7 - Eugenius
Running tests....
WARNING FOR DEVELOPERS:  phenix/bibtex._bibtex unnecessarily declared. Just the doc string is enough.
[   FAILED ] _FailedTest.test_workflow_reliontomo

Traceback (most recent call last):
   File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
     yield
   File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run
     self._callTestMethod(testMethod)
   File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
     method()
   File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/loader.py", line 34, in testFailure
     raise self._exception
ImportError: Failed to import test module: test_workflow_reliontomo
Traceback (most recent call last):
   File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/loader.py", line 154, in loadTestsFromName
     module = __import__(module_name)
   File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/tests/test_workflow_reliontomo.py", line 35, in <module>
     from reliontomo.protocols.protocol_ctf_3d_estimation import CTF3D_PER_SUBVOLUME
   File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/protocols/__init__.py", line 28, in <module>
     from .protocol_refine_3d_tomo import ProtRelionSubtomoRefine3D
   File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/protocols/protocol_refine_3d_tomo.py", line 34, in <module>
     from relion.convert import Table, pwem, convert31
ImportError: cannot import name 'pwem' from 'relion.convert' (/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/__init__.py)


[==========] run 1 tests (0.001 secs)
[  FAILED  ] 1 tests
[  PASSED  ] 0 tests

================================================================================================================

Is there something I am missing?

David
-- 
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoo...@hp...


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