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AlexsLemonade / OpenScPCA-analysis

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
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Remove defaults channel from all modules and templates #714

Closed jashapiro closed 3 months ago

jashapiro commented 3 months ago

Closes #710

Here I updated the environment.yml files and associated conda-lock files to remove the defaults channel as an option.

I also made a small change to the detect-doublets environments to remove the last section of version number specs from packages in the environment.yml as we probably want to allow for bugfixes when rebuilding the conda-lock file. If that was going too far, I can revert those changes!

jashapiro commented 3 months ago

This all looks fine to me, but I do want to note that the conda-lock.yml files have ended up with some slightly different versions and new packages. For example, looking through the cell-type-ewings lock file, I see new cuda dependencies that weren't there before and various version bumps (mostly patch but some minor). I'm not concerned/surprised by these kinds of changes given the channel change, but seemed worth pointing out.

I don't think this is the just the channel change, as much as just the passage of time.

The cuda thing is interesting though, and I am not quite sure what to make of it. I don't think having cuda packages installed when there is no GPU available will cause trouble, but this is probably something we will want to keep track of in the future, as we may need to be mindful of cuda versions based on what underlying drivers are available: https://docs.nvidia.com/deploy/cuda-compatibility/ But that is for your other explorations, not here, I think...