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atarashansky / self-assembling-manifold

The Self-Assembling-Manifold (SAM) algorithm.
MIT License
41 stars 11 forks source link

compatibility with h5py #40

Closed galicae closed 2 years ago

galicae commented 2 years ago

Dear Alex!

me and many other people are relying on SAM and SAMap for cross-species comparisons (thanks for that!), and installation is always an issue. Especially in conda environments, SAM and SAMap often cause version clashes. Is there anything you could do for that? Would it be possible to bump their version requirements so that the worst offenders (i.e. h5py) don't cause so many problems, or would that break the workflows?

best Niko

atarashansky commented 2 years ago

Hi Niko,

Thanks for alerting me to this. The h5py pin used to be necessary due to past bugs in AnnData.

I removed the h5py pin in both SAM (pip install sam-algorithm==1.0.1) and SAMap (pip install samap==1.0.7). I haven't tested this change, so keeping my fingers crossed that it doesn't break anything :'D

EDIT: just installed locally and was able to run through the tutorial notebook in SAMap...Seems like nothing exploded.

atarashansky commented 2 years ago

Closing for now, please re-open if there are still issues with the installation!

galicae commented 2 years ago

so far I have usually installed by local forks, where I removed the pin myself >.< seems to be working just fine.