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theislab / zellkonverter

Conversion between scRNA-seq objects
https://theislab.github.io/zellkonverter/
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using mamba solver for conda #107

Open LinearParadox opened 7 months ago

LinearParadox commented 7 months ago

The mamba solver is much faster than the default conda solver and would likely speed up the building environment step. Is it possible to support at least a toggle for this?

lazappi commented 7 months ago

Setting up the environment is handled by {basilisk}, so that would need to be handled there https://github.com/LTLA/basilisk.

I think the latest version of conda now uses mamba by default so it might be enough to update that within {basilisk}.

LTLA commented 7 months ago

Happy to take a PR to update the default miniconda version. Though I tried to do that last time and the BioC build machines kept timing out, so that would have to be resolved.

vjcitn commented 7 months ago

Just seeing this now. I'd like to help move this forward. Using the 3.18 bioconductor_docker container, I see that the miniconda version used by basilisk is

https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh

What is a preferred Miniconda version for use in 3.19? We will try to establish a PR and prepare the build system so that a timeout does not occur.

LTLA commented 7 months ago

I think we'd basically want to go to whatever the latest is - based on https://repo.anaconda.com/miniconda/, it seems to be py311_23.11.0-2. Probably need to discuss this on Slack to notify all maintainers, because there's a non-zero chance that everything breaks, and people would probably want a heads-up.