Import Error in "Calculate the electrostatic potential of a protein from its atomic structure" use case

alex4200 commented 4 years ago

Usecase will be excluded from automated tests.

Expected behavior

Notebook runs fine

Actual Behavior (please include screenshot if possible)

After the package 'multipipsa' has been installed (version 4.0.3) it's import will fail in the next cell.

from multipipsa.multipipsa import ApbsRun

ImportErrorTraceback (most recent call last)
<ipython-input-2-9efe82e59be5> in <module>()
----> 1 from multipipsa.multipipsa import ApbsRun

/opt/conda/envs/python2/lib/python2.7/site-packages/multipipsa/multipipsa.py in <module>()
     21 import warnings
     22 from pprint import pformat
---> 23 from multipipsa.clusterpipsa import ClusterPipsa
     24 from multipipsa.pipsatypes import ScoreType
     25 from multipipsa.pipsatypes import SimilarityType

ImportError: No module named clusterpipsa

Steps to reproduce the problem

! pip install --extra-index-url https://projects.h-its.org/pypi multipipsa
from multipipsa.multipipsa import ApbsRun

Optional infrastructural data (user, platform, browser, environment, ...)

PROD

StefanGIT commented 4 years ago

The notebook was fixed by upgrading the multipipsa package from 4.0.2 to 4.0.3. However it looks like if 4.0.2 is already installed on the Collab it thinks the requirement is already satisfied.

I have now made the 4.0.3 in the notebook explicit: pip install --extra-index-url https://projects.h-its.org/pypi multipipsa==4.0.3 and copied the modified notebook to the MolecularUsecase Collab.

alex4200 commented 4 years ago

@StefanGIT I see no change in the DEV location https://collab.humanbrainproject.eu/#/collab/50197/nav/350840 Are you sure you have updated the notebook and saved it?

StefanGIT commented 4 years ago

@alex4200 ok, i copied it now to MolecularUseCases_pub, but now there are two notebooks. The one with multipipsa==4.0.3 is correct. Can/Should i delete the other one?

alex4200 commented 4 years ago

@StefanGIT Please proceed with the following procedure:

Delete the new notebook you created. It contains a header that is added to that notebook when you clone it. This is not what we want.
Edit/correct your ORIGINAL notebook in that Collab, do not create a new notebook. This will make things only more complicated (for you and me).
If you have corrected your ORIGINAL notebook let me know. Then I will test it and - if everything works fine - update the PRODUCTION notebook which are stored in a safe place in a github repository.

StefanGIT commented 4 years ago

Hi Alex,

i have now edited the original, set the kernel to python 3 and the multipipsa version to 4.0.3. See:

https://collab.humanbrainproject.eu/#/collab/50197/nav/350840

I hope this is ok now.

Best,

Stefan?

?

Von: alex4200 notifications@github.com Gesendet: Freitag, 7. Februar 2020 07:08 An: cnr-ibf-pa/hbp-bsp-issues Cc: Richter, Stefan; Mention Betreff: Re: [cnr-ibf-pa/hbp-bsp-issues] Import Error in "Calculate the electrostatic potential of a protein from its atomic structure" use case (#523)

@StefanGIThttps://github.com/StefanGIT Please proceed with the following procedure:

Delete the new notebook you created. It contains a header that is added to that notebook when you clone it. This is not what we want.
Edit/correct your ORIGINAL notebook in that Collab, do not create a new notebook. This will make things only more complicated (for you and me).
If you have corrected your ORIGINAL notebook let me know. Then I will test it and - if everything works fine - update the PRODUCTION notebook which are stored in a safe place in a github repository.

- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/cnr-ibf-pa/hbp-bsp-issues/issues/523?email_source=notifications&email_token=ABRB7RSUSO3WIGHC7UAGO5TRBT3GJA5CNFSM4KQ2VWEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELB2Y4Q#issuecomment-583249010, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABRB7RWFDLV6IIWNFZU2YGLRBT3GJANCNFSM4KQ2VWEA.

alex4200 commented 4 years ago

@StefanGIT Thank you for the update. The notebook seems to work.

However, I have one request: Can you please remove the try-except clause in the second cell? Because in the case something is wrong with the setup, you only get a note saying that something is wrong with the setup, but not what. I think it is best to let the cell fail with the appropriate error.

Thank you

StefanGIT commented 4 years ago

I have removed the try except in the second cell and saved it again. Best,

alex4200 commented 4 years ago

@StefanGIT Thanks a lot - that is all that is required from your side.

I will update the notebook in production and close this ticket once it is in production.

DKokh commented 4 years ago

Alex, as the notebook is in production, may I close this ticket?

alex4200 commented 4 years ago

@DKokh I will do a quick check first.

alex4200 commented 4 years ago

Notebook seems to wotk in prod. closing ticket

cnr-ibf-pa / hbp-bsp-issues