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

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

You are probably missing xmipp binaries.

scipion3 installb xmippSrc

Should do the installation. In case there is any error send it here and 
some xmipp developer will help you.

El 07/12/2023 a las 11:34, Lugmayr, Wolfgang escribió:
> 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: 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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-- 
Pablo Conesa
*Scipion <http://scipipon.i2pc.es> cryo-em workflow engine developer at 
Madrid, among many others.*
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