search

weecology / EvergladesTools

Computational tools for working with Everglades image data
MIT License
0 stars 2 forks source link

Update conda environment #161

Closed bw4sz closed 1 year ago

bw4sz commented 1 year ago

The goal of this PR is to create a single .yml file for the snakemake. I tested out if the pinned packages from previous versions could be unpinned. I added snakemake from bioconda::. Its a little hard to test these things, since you have to build it iteratively as you encounter errors. I did my best by not using command line, but each time running

mamba env update -f=environment.yml

test against 

(EvergladesTools) [b.weinstein@c0909a-s23 Zooniverse]$ snakemake --printshellcmds --keep-going --cores 10 --rerun-incomplete --resources --unlock gpu=2
bw4sz commented 1 year ago

I tested all the imports from

pwd
/home/b.weinstein/EvergladesTools/Zooniverse
cat *.py | grep import

and confirmed we work on 

srundev --partition=gpu --gpus=1
>>> import torch
>>> torch.cuda.is_available()
True