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Re: [scipion-users] scipion 3.3 - xmipp 3.23.11.0 - No module named 'xmipp.constants'; 'xmipp' is not a package
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From: Grigory S. <sha...@gm...> - 2023-12-07 10:19:15
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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 <+44%201223%20267228>
e-mail: gs...@mr...
On Thu, Dec 7, 2023 at 9:58 AM Lugmayr, Wolfgang <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: wol...@cs...
> http://www.cssb-hamburg.de/
>
>
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> scipion-users mailing list
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