Colab notebook not working

[vaclavhanzl]

Colab notebook pointed to from the main page is not working for multiple reasons, throwing quite confusing error messages.
I tried to fix it by PR #285. You can test the fixed notebook here. Testers welcome!

[vaclavhanzl]

Colab notebook was fixed by merging my #285 but at the same day broken again by also merging #287 :)
Now Colab fails on missing modelcif dependency, This should be easy to fix.

[vaclavhanzl]

I fixed it again in #308.

If you want to try my fix before it is merged, it is a bit tricky this time but you can. Open the notebook here and edit the Install OpenFold cell (change GIT_REPO and add branch checkout):

#GIT_REPO='https://github.com/aqlaboratory/openfold'
GIT_REPO='https://github.com/vaclavhanzl/openfold'
...
    %shell git clone "{GIT_REPO}" openfold 2>&1 1> /dev/null
    %shell cd openfold && git checkout colab-add-dep-fix-python-version

[burunduk57]

Colab notebook was fixed by merging my #285 but at the same day broken again by also merging #287 :) Now Colab fails on missing modelcif dependency, This should be easy to fix.

I get missing modelcif problem

[vaclavhanzl]

I get missing modelcif problem

@burunduk57 and you would get more problems down the road (changed parameters of functions and a very cryptic failure due to Python version discrepancy). I proposed a fix but until it gets merged, you can try this:

Open the notebook here and edit the Install OpenFold cell (change GIT_REPO and add branch checkout):

#GIT_REPO='https://github.com/aqlaboratory/openfold'
GIT_REPO='https://github.com/vaclavhanzl/openfold'
...
    %shell git clone "{GIT_REPO}" openfold 2>&1 1> /dev/null
    %shell cd openfold && git checkout colab-add-dep-fix-python-version

Edit: This is no longer enough to make it work but see my next comment for an easier way which works.

[vaclavhanzl]

@burunduk57 to make it easier for you (and for others), I merged all my fixes in my fork of the OpenFold repo and just added one more fix (openmm version). Please try my fixed version of the Colab notebook. It works for me now.

[burunduk57]

@burunduk57 to make it easier for you (and for others), I merged all my fixes in my fork of the OpenFold repo and just added one more fix (openmm version). Please try my fixed version of the Colab notebook. It works for me now.

It works for me, many thanks!

[vaclavhanzl]

This notebook is really cat-n-mouse game :) What worked 5 days ago does not work now. My fix was finally just merged to main now, but now the notebook fails at:

%shell conda install -y -q -c conda-forge pdbfixer

I'll look into it once more, maybe there are more things to be automated (my auto-following of the python version already saved us one breakage).

[vaclavhanzl]

I fixed it in #320.
Until it gets merged, you can again use fixed Colab in my repo fork.

[vaclavhanzl]

Merged (thanks @gahdritz), tested, works! Closing the issue.