update `env-reporting.yml` version pins

dib-lab / charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.

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update `env-reporting.yml` version pins #226

Open ctb opened 2 years ago

ctb commented 2 years ago

env-reporting.yml is the largest and most complex conda environment we have in charcoal, and it pins a lot of things... and it's pretty out of date. this is causing trouble in #225 where we need to upgrade the minimum python version which changed to > 3.7 for the latest sourmash.

taylorreiter commented 2 years ago

ya that environment has been a pain for me too. @bluegenes seemed to think it would be a light lift to use the snakemake jupyter notebooks run feature instead of papermill, but I think we decided not to go for it because it was like 5 minutes before this was due to be presented at ISMB.

ctb commented 2 years ago

I don't think the problem is papermill - I'd guess that matplotlib and plotly together are bringing in a lot of dependencies.

ctb commented 2 years ago

I wonder if we could speed this up with better versions 🤔