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update env-reporting.yml version pins #226

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ctb opened this issue Aug 23, 2022 · 3 comments
Open

update env-reporting.yml version pins #226

ctb opened this issue Aug 23, 2022 · 3 comments

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@ctb
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ctb commented Aug 23, 2022

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 and it's pretty out of date.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
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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
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ctb commented Aug 23, 2022

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

@ctb
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ctb commented Sep 11, 2022

related: #221

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

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