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Umap Learn dependency issue #37
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@GemmaTuron, Did you get an error for umap like?
Actually I had setup zairachem a few months ago. But to reproduce this, I have installed afresh. I have realized we need to use atleast python3.8 instead of 3.7(the step of creating the zairachem env in install_linux.sh) But still, we might need to pin versions of some packages. I can be on top of this if you want me to. |
awesome @HellenNamulinda thanks for checking, that is the error I was having as well |
I will work on this. |
With Python3.10, Umap Learn version 0.5.5 works well. But autogluon V0.5.2 isn't supported. So, changing the version for autogluon.tabular, from 0.5.2 to 0.7.0 helps. |
I get the following error with the installation:
when I try to run it, it requires: After pip installing dask, we still hit the click dependency The dependencies currently installed are this ones |
Yes, there is that issue of conflicting versions of pandas and click for different packages. forexample Why click 8.0.4 is being installed: FLAML requires Though I didn't except click versions to have significant impact, And pinning its version will break installation of major dependencies. In my environment, dask isn't installed zairachem_requirements.txt. I had removed it from the requirements and zairachem works without it. Just that it is slow at fitting where fetching the hub models takes long. Is there a specific command run that is leading to Let me reinstall and see. |
Sorry, I have reinstalled, same requirements.txt and install_linux.sh files as on github; zairachem_installation.txt The CLI commands(zairachem) are working. |
Hi @HellenNamulinda ! Does it work for you? On my end, if I use the current bash script to install ZairaChem, I am missing Dask. If we want to keep click at v8.0.4, we need to use dask==2023.10.1 But when doing so, we still run into the following dependency conflicts
An option here is to move the eosce descriptors to use the Ersilia Model Hub implementation, as the rest of the descriptors do, as we have it as a model - this would be convenient but still leave us with the issue with Ersilia. And get this error when trying to fit a model (actually, zairachem --help does not crash, which might be the command you have tried.) It seems mellody is not working properly?
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Hi @GemmaTuron, On my end, the split command works(split_zairachem.log), as well as fit command. While fitting, there are these 2 models(
But during fitting, the descriptors were calculated, and models were trained, except for the molmap estimator whose models weren't fetched prior. Unfortunately, I can't reproduce the error with mellody. While the pip dependency conflicts(pandas and click) aren't causing any issues on my end, let me look more into this to resolve and harmonize the versions. |
mm thanks @HellenNamulinda , I can't understand why we get different errors with the same install. I am on an Ubuntu 22.04 machine btw |
Ok, I have worked on the issue and made the following changes:
I hope these changes work for all systems, I am on an Ubuntu 22.04. Note that we still have some dependency issues that do not break the code, so solution #30 would be cleaner
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Please have a look and let me know if these changes also work for you. I'd like to ping Success here as well but I don't have his github handle. Once we can confirm this works, and whether we want to pin the versions indicated above, I will create the new stable release of ZairaChem |
I get the same set of conflicts as you do above. However, please note that the Ersilia Compound Embedding Lite version should be pinned to 'v.0.2.0' instead of 'v0.2.0' (or perhaps rather re-tag the compound embedding number to be consistent with its first version number format?) I am having also having an issue with the mordred fingerprints, but that occurred before these changes and when I disable it, the rest of the code works just fine. I'm going to do another build on my workstation later tonight to test it all again. |
Thanks @GemmaTuron. I got an installation error for ersilia-compound-embedding.
I decided to test by removing the v0.2.0 and it installed the latest esoce version. Aside correcting the tag for eosce, the rest(such as split and fit commands) work. Am also using Ubuntu 22.04. |
No worries - I think the new ZairaChem build is good to go then. 👍 Thanks for the info and update on mordred - that is indeed the issue I saw. |
I'll wait for Success confirmation that the installation works for him and then close this issue |
@sucksido please confirm that the installation is working in your system so we can close this issue |
Describe the bug
I think we might need to pin Umap Learn version 0.5.3, as it now automatically installs version 0.5.5 and it gives an error.
Have not had time to look into it in detail so I might be wrong... but definitely something we should revise
To Reproduce
Steps to reproduce the behavior:
Desktop (please complete the following information):
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