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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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Add software primer page #511

Closed sjspielman closed 3 weeks ago

sjspielman commented 3 weeks ago

Closes #498 Related to #458 See #506 for a little more context

This PR adds a short "primer" page on software dependencies to the analysis page. I added this to mkdocs as well to check formatting since I used buttons! I also did a bit of rearrangement of the conda doc that went in in #507 - two of the headers were the wrong level, and I updated the order so that "using an existing environment" comes after all instructions for creating/managing in the first place.

Noting I indeed would also like for @dvenprasad to have a look here for any feedback on the language as it relates to our goal of making it easier for contributors to find docs on adding dependencies.

Edit: I also want to note that a lot of the language here is very similar (..the same?) as that in this new managing software index file: https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/reproducibility-docs/docs/ensuring-repro/managing-software/index.md. I think this repetition is probably good, do you?

jaclyn-taroni commented 3 weeks ago

Edit: I also want to note that a lot of the language here is very similar (..the same?) as that in this new managing software index file: https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/reproducibility-docs/docs/ensuring-repro/managing-software/index.md. I think this repetition is probably good, do you?

I have not looked at the files changed yet but my sense is yes, repetition is good as long as things do not conflict. So consider how likely it is that conflicting information would pop up as these are maintained over time!

sjspielman commented 3 weeks ago

So consider how likely it is that conflicting information would pop up as these are maintained over time!

Conflicting information would occur in this case if we were move away from using conda and renv in the first place....and if that happens we have bigger "problems"! So, this one seems like good repetition to me.