Open Zethson opened 1 year ago
Opened a draft PR #109 with the working version of the updates. I'm going to use the checklist here to keep track of what I have done there.
Notes on some of the points, mostly for reference but I think some of them need discussion.
Done
"batch"
here I think it makes sense to use that (unless there are other suggestions)Todo
@Zethson I don't think you have decided how to handle datasets yet? I'll leave that until we know what the solution is.
Not finally at least.That's fine with me.
For HVGs I think it makes sense to use scanpy because it has batch-aware functionality (added some text about that). We could change to what is suggested in the pre-processing section but it will be some messing around.
That's fine! Keep it as you have it.
@LuckyMD The main thing left is your intro, I'm pretty happy now with everything else. It would be great to have it for this PR so we can have a complete chapter.
I think my intro is pretty much done... i worked on this last week in another PR (also worked on references).
Ok, cool, I missed that on #87. @Zethson how do you want to handle merging these? Do you want to merge them both separately or do you want me to merge Malte's changes into #109 first (which I think is more up to date with the main branch) so that you only have to deal with one PR? I'm guessing there will be a few conflicts to sort out so I'm happy to do that if it makes things easier for you (also not sure if there is a good way to merge Jupyter notebooks or if it's a copy/paste situation).
Merging notebooks is always hell. I think it would be easiest for me if you merge Malte's text into your notebook and we merge yours.
Cool, let's do it that way then. Because it's just the intro text I'm thinking it will be easier to copy-paste rather than to do an actual git merge.
I did more than only text edits in #87 though... also documentation of code and references throughout.
Taken from @lazappi great list of TODOs in his PR with some additions of mine:
Todo:
Waiting on something else:
Merged in PR #109:
Already merged: