Multiple errors when running test data about metage2metabo HOT 7 CLOSED

Hi @DafniGi,

The error message indicates that miscoto did not find answers for the dataset which is strange.

I think the error comes from a new version of clyngor (a dependency of MiSCoTo). Some weeks ago, clyngor has been updated to fix an issue with the new python API of clingo but this new version leads to issue with MiSCoTo and MeneTools. With this issue no answers are returned. A first test is to see if your version of the python package clyngor is superior to 0.4.0.

If this is the case, we are currently working on a fix for this issue. Can you try the branches fix_new_clyngor of MiSCoTo and MeneTools and see if it fixes the issue?

Best Regards,
Arnaud Belcour.

from metage2metabo.

You can install the version of miscoto Arnaud talked about using pip install git+https://github.com/cfrioux/miscoto.git@fix_new_clyngor

from metage2metabo.

Thank you both! I indeed have clyngor 0.4.1. I tried with the branches fix_new_clyngor of MiSCoTo and MeneTools, but I am still getting the same error.

from metage2metabo.

I am able to reproduce the error with Python 3.8, conda on Ubuntu but I do not fully understand it yet.
However, I was able to find a combination of python, miscoto and clyngor version that still work well together. I give you my env so you can use m2m while we keep digging.

Are you using conda? If yes:

conda create -n miscoto3.7 python=3.7.7
conda activate miscoto3.7
# python -m pip install --upgrade pip --user
pip install clyngor==0.3.31
pip install miscoto
pip install metage2metabo
pip install networkx bubbletools ete3

Should do the trick.

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Finally understood what happened. The current fixes on Github still have the same version numbers as the releases so when running the install from the Github branch, nothing actually gets installed (requirement already satisfied).

If you uninstall menetools and miscoto first (pip uninstall miscoto menetools) and then install the fix (pip install git+https://github.com/cfrioux/menetools.git@fix_new_clyngorand pip install git+https://github.com/cfrioux/miscoto.git@fix_new_clyngor), it works properly.

We'll update the version numbers and make the releases very soon.

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Menetools v. 3.2.2 and Miscoto v3.1.2 are released and should fix the problems.

from metage2metabo.

Thank you very much for the prompt responses. Menetools v. 3.2.1 was the latest version I could find, and it worked.
For the record in case it is useful in the future, I was in CentOS and I wasn't using conda.

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