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scipion-em / scipion-pyworkflow

Underlying pyworkflow module for the Scipion framework
GNU General Public License v3.0
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Is Xmipp installed #495

Closed davidhoover closed 2 weeks ago

davidhoover commented 5 months ago

Why do I keep seeing this warning:

 >>> WARNING: Image library not found!
  > Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)

Xmipp is installed:

Installing scipion-em-xmipp ...
/usr/local/apps/scipion/3.4.0/mamba/envs/scipion3/bin/python -m pip install scipion-em-xmipp==23.11.0.0
Requirement already satisfied: scipion-em-xmipp==23.11.0.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (23.11.0.0)
Requirement already satisfied: scipion-pyworkflow>=3.0.31 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (3.3.1)
Requirement already satisfied: scikit-learn==0.22 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (0.22)
Requirement already satisfied: scipion-em in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (3.4.0)
Requirement already satisfied: scipy<=1.10.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (1.8.1)
Requirement already satisfied: joblib in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (1.3.2)
Requirement already satisfied: peppercorn in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (0.6)
Requirement already satisfied: plotter in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (1.3.20)
Requirement already satisfied: scons in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (4.6.0.post1)
Requirement already satisfied: PyWavelets in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em-xmipp==23.11.0.0) (1.4.1)
Requirement already satisfied: numpy>=1.11.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scikit-learn==0.22->scipion-em-xmipp==23.11.0.0) (1.23.0)
Requirement already satisfied: bibtexparser<=1.2.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (1.2.0)
Requirement already satisfied: psutil<=5.9.1 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (5.9.1)
Requirement already satisfied: configparser<=5.2.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (5.2.0)
Requirement already satisfied: requests<=2.28.1 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (2.28.1)
Requirement already satisfied: tkcolorpicker in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (2.1.3)
Requirement already satisfied: distro<=1.8 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (1.8.0)
Requirement already satisfied: matplotlib==3.5.2 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (3.5.2)
Requirement already satisfied: pillow==9.2.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (9.2.0)
Requirement already satisfied: cycler>=0.10 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.5.2->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.5.2->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (4.47.2)
Requirement already satisfied: kiwisolver>=1.0.1 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.5.2->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (1.4.5)
Requirement already satisfied: packaging>=20.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.5.2->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (23.2)
Requirement already satisfied: pyparsing>=2.2.1 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.5.2->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (3.1.1)
Requirement already satisfied: python-dateutil>=2.7 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.5.2->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (2.8.2)
Requirement already satisfied: biopython==1.79 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-xmipp==23.11.0.0) (1.79)
Requirement already satisfied: tifffile<=2021.11.2 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-xmipp==23.11.0.0) (2021.11.2)
Requirement already satisfied: emtable in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-xmipp==23.11.0.0) (0.0.14)
Requirement already satisfied: mrcfile<=1.4.3 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-xmipp==23.11.0.0) (1.4.3)
Requirement already satisfied: setuptools in ./mamba/envs/scipion3/lib/python3.8/site-packages (from scons->scipion-em-xmipp==23.11.0.0) (69.0.3)
Requirement already satisfied: future>=0.16.0 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (0.18.3)
Requirement already satisfied: charset-normalizer<3,>=2 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from requests<=2.28.1->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (2.1.1)
Requirement already satisfied: idna<4,>=2.5 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from requests<=2.28.1->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (3.6)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from requests<=2.28.1->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (1.26.18)
Requirement already satisfied: certifi>=2017.4.17 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from requests<=2.28.1->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (2023.11.17)
Requirement already satisfied: six>=1.5 in ./mamba/envs/scipion3/lib/python3.8/site-packages (from python-dateutil>=2.7->matplotlib==3.5.2->scipion-pyworkflow>=3.0.31->scipion-em-xmipp==23.11.0.0) (1.16.0)
Done (1.73 seconds)
azazellochg commented 5 months ago

scipion-em-xmipp is a python package, xmipp Image library is a c++ package. The error indicates that either binary compilation has failed or your xmipp is not connected to Scipion Xmipp docs are here: https://i2pc.github.io/docs/index.html