Re: [scipion-users] Error with reliontomo tests

[Pablo C. <pc...@cn...>]

Dear all, tomography plugins are still unstable. I have temporarily hide 
them form the plugin manger to avoid installing them.

We are very happy how it is all coming together and most of the basic 
tomography pipeline is being covered with Imod, Dynamo, Eman, Xmipp, 
MC2, gCTF, NovaCTF, pyseg, deepfinder, relion, cryoCARE, jjSoft...

But still not usable under our supervision. I'd say we are somewhere in 
an alpha state....getting closer to a beta. Once we feel is stable 
enough for betatesting, I'll announce it and everyone is very welcome to 
betatest the tomography functionality.


On 24/2/21 8:48, Ana Andreea ARTENI wrote:
> 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
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*