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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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ImportError: cannot import name 'SCIPSolver' from 'reframed.solvers' #191

Closed yqq-79 closed 10 months ago

yqq-79 commented 12 months ago

Hi! I am trying to reconstruct the metabolic network of a bacteria wiht carveme. I installed the carveme(version 1.6.0) successfully, but I met a problem when I run the comment "carve ./S13-cb23Y1/goldbacteria.faa". The problem is as follows. Traceback (most recent call last): File "/mnt/raid5/Softwares/mambaforge/bin/carve", line 5, in from carveme.cli.carve import main File "/mnt/raid5/Softwares/mambaforge/lib/python3.10/site-packages/carveme/cli/carve.py", line 3, in from carveme.reconstruction.carving import carve_model, build_ensemble File "/mnt/raid5/Softwares/mambaforge/lib/python3.10/site-packages/carveme/reconstruction/carving.py", line 8, in from reframed.solvers import solver_instance, SCIPSolver ImportError: cannot import name 'SCIPSolver' from 'reframed.solvers' (/mnt/raid5/Softwares/mambaforge/lib/python3.10/site-packages/reframed/solvers/init.py)

louis-pare commented 12 months ago

Hi,

I had the same issue and fixed it by installing SCIP solver with conda:

conda install -c conda-forge pyscipopt

cf. see: https://carveme.readthedocs.io/en/latest/installation.html

It seems that the SCIP solver is mandatory to make carveme work even if you do not intend in using it.

I hope this fix your issue.

yqq-79 commented 12 months ago

Hi,

I had the same issue and fixed it by installing SCIP solver with conda:

conda install -c conda-forge pyscipopt

cf. see: https://carveme.readthedocs.io/en/latest/installation.html

It seems that the SCIP solver is mandatory to make carveme work even if you do not intend in using it.

I hope this fix your issue.

Hi! Are you using version 1.6.0? I tried this method but it didn't work for version 1.6.0. When I was on version 1.5.2, I didn't have such a problem again.

louis-pare commented 12 months ago

Hi! Are you using version 1.6.0? I tried this method but it didn't work for version 1.6.0. When I was on version 1.5.2, I didn't have such a problem again.

Hi,

Yes, I do use the 1.6.0 version. What happens if you try to import SCIPSolver in a python session?

from reframed.solvers import SCIPSolver

yqq-79 commented 11 months ago

Hi! Are you using version 1.6.0? I tried this method but it didn't work for version 1.6.0. When I was on version 1.5.2, I didn't have such a problem again.

Hi,

Yes, I do use the 1.6.0 version. What happens if you try to import SCIPSolver in a python session?

from reframed.solvers import SCIPSolver

Hi, I installed version 1.6.0 of carveme and SCIPSolver via conda, but when I run carveme I still get the same error(ImportError: cannot import name 'SCIPSolver' from 'reframed.solvers' ). After that, I uninstalled version 1.6.0 and reinstalled version 1.5.2 and I didn't have this issue again.

Fedorov113 commented 11 months ago

I am also facing the same issue with version 1.6.0.

kuzmpa commented 11 months ago

I am also facing the same issue with version 1.6.0

jrcasey commented 11 months ago

Same issue here. After installing scip, the new error is:

RuntimeError: Solver cplex not available.

Cplex is working fine in the same environment

YahyaFarooqi commented 11 months ago

Same issue here, and i need to run on 1.6.0, @cdanielmachado any resolution to this?

cdanielmachado commented 10 months ago

Apologies for the long delay during holiday season... :)

I think it should be fixed now. Can you please uninstall carveme 1.6.0 and install 1.6.1 ?