Re: [scipion-users] [EXT] Re: scipion 3.3 - xmipp 3.23.11.0 - No module named 'xmipp.constants'; 'xmipp' is not a package

[Lugmayr, W. <w.l...@uk...>]

Hi Grigory, 

yes, this has no problems: 
$ scipion inspect xmipp3 
Scipion v3.3.0 - Eugenius 
Plugin: xmipp3 
>>> constants: loaded 
>>> convert: loaded 
>>> protocols: loaded 
>>> wizards: loaded 
>>> viewers: loaded 
>>> tests: loaded 

but how do i get now rid of the message??? 
>>> WARNING: Image library not found! 
> Please install Xmipp to get full functionality. 

cheers, 
wolfgang 


From: "Grigory Sharov" <sha...@gm...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Thursday, 7 December, 2023 11:18:55 
Subject: [EXT] Re: [scipion-users] scipion 3.3 - xmipp 3.23.11.0 - No module named 'xmipp.constants'; 'xmipp' is not a package 

Hi Wolfgang, 
you should use "scipion3 inspect xmipp3" instead 

Best regards, 
Grigory 

-------------------------------------------------------------------------------- 
Grigory Sharov, Ph.D. 

MRC Laboratory of Molecular Biology, 
Francis Crick Avenue, 
Cambridge Biomedical Campus, 
Cambridge CB2 0QH, UK. 
tel. +44 (0) 1223 267228 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 


On Thu, Dec 7, 2023 at 9:58 AM Lugmayr, Wolfgang < [ mailto:w.l...@uk... | w.l...@uk... ] > wrote: 


hi, 

i made an new fresh installation of scipion 3.3 (incl. new miniconda) with only stable tomo plugins and got the following error: 
>>> WARNING: Image library not found! 
> Please install Xmipp to get full functionality. 
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) 

the plugin manager thinks its installed: 
scipion-em-xmipp 23.11.0.0 [X] 
scipion-em-xmipp2 [ ] 
scipion-em-xmipptomo 3.23.11.0 [X] 

and with inspect i get: 
$ scipion3 inspect xmipp 
Scipion v3.3.0 - Eugenius 

>>> WARNING: 'import xmipp' is deprecated for the xmipp binding. 
Plugin: xmipp 
>>> constants: error -> Traceback (most recent call last): 
File "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/inspect_plugins.py", line 74, in getSubmodule 
m = importlib.import_module('%s.%s' % (name, subname)) 
File "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/importlib/__init__.py", line 127, in import_module 
return _bootstrap._gcd_import(name[level:], package, level) 
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import 
File "<frozen importlib._bootstrap>", line 991, in _find_and_load 
File "<frozen importlib._bootstrap>", line 970, in _find_and_load_unlocked 
ModuleNotFoundError: No module named 'xmipp.constants'; 'xmipp' is not a package 
: 

do i need a development version of the core packages? 
$ scipion3 update 
Scipion v3.3.0 - Eugenius 
The package scipion-pyworkflow is up to date. Your version is 3.3.1 
The package scipion-em is up to date. Your version is 3.4.0 
The package scipion-app is up to date. Your version is 3.3.0 
Scipion is up to date. 

cheers, 
wolfgang 

p.s. 
the last lines of the xmipp install: 
: 
Compiling xmippViz---------------------------------------- 
Done. Visit compileLOG.txt for details 

* Xmipp has been successfully compiled * 
> > > Don't forget to install! < < < 


CC variable found in the environment with this value: /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/gcc. 
CXX variable found in the environment with this value: /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/g++. 

Installing ----------------------------------------------- 
Xmipp installed on /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmippSrc-v3.23.11.0/build 

Linking to Scipion --------------------------------------- 
Xmipp linked to Scipion on /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmipp 
************************************************************ 
* * 
* Xmipp Nereus has been successfully installed, enjoy it! * 
* * 
************************************************************ 



-- 
Universitätsklinikum Hamburg-Eppendorf (UKE) 
@ Centre for Structral Systems Biology (CSSB) 
@ Deutsches Elektronen-Synchrotron (DESY) 
Notkestrasse 85 Gebäude 15 
22607 Hamburg, Germany 
Tel.: +49 40 8998-87652 
Email: [ mailto:wol...@cs... | wol...@cs... ] 
[ http://www.cssb-hamburg.de/ | http://www.cssb-hamburg.de/ ] 


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