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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
102 stars 40 forks source link

`scanpy` docs bug still not resolved #264

Closed alam-shahul closed 9 months ago

alam-shahul commented 9 months ago

Hi,

I was looking at the forked repo (that seems to be more up-to-date) and it seems to have a fix for this problematic Scanpy loading code, but it seems like the updated docs are not up yet in the actual Cell Browser. Can that be fixed?

import scanpy as sc
import pandas as pd
ad = sc.read_text("exprMatrix.tsv.gz")
meta = pd.read_csv("meta.tsv", sep="\t")
ad.var = meta

I'm referring to this webpage.

alam-shahul commented 9 months ago

Also, I left this issue here because issues are disabled for the other repo, I think?

maximilianh commented 9 months ago

Thank you thank you! The readthedocs build was broken, readthedocs upgraded and so nothing updated automatically anymore. I added the new config files.

Should be all good now: https://cellbrowser.readthedocs.io/en/develop/load.html

Thanks for letting us know.

How did you find this old repo? It shouldn't be linked from anywhere anymore. I've added a link to the main repo now to the repo description. I guess I should also modify the README? How do other projects point people to the right repo?

Oops, you're right, I had issues switch off. They're active now on https://github.com/ucscGenomeBrowser/cellBrowser/

On Tue, Oct 10, 2023 at 1:04 AM alam-shahul @.***> wrote:

Also, I left this issue here because issues are disabled for the other repo, I think?

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/264#issuecomment-1754034456, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TLGJKH54AQICZGSK4LX6R7HZAVCNFSM6AAAAAA5ZOG7SKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJUGAZTINBVGY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

alam-shahul commented 9 months ago

Thanks for fixing it!

Ah, no, I think all your documentation links point to the new repo, but when I noticed that I couldn't leave an issue in the new one, I clicked the "forked from maximilianh/CellBrowser" in the top left corner. Apparently if you want to remove the forking relationship with the old repo, you have to submit a request (although it's pretty straightforward): https://ralphjsmit.com/unfork-github-repo

alam-shahul commented 9 months ago

Well, I will note that the link to leave an issue here is to this repo, not the new one...

maximilianh commented 9 months ago

Ohhh! I totally forgot about this link! Many thanks. Fixed now on https://cells-test.gi.ucsc.edu/ and will make out to the public site with the next push. Many thanks again and don't hesitate to tell us about other things you notice that we do not see anymore!

On Tue, Oct 10, 2023 at 11:14 PM alam-shahul @.***> wrote:

Well, I will note that the link to leave an issue here http://cells.ucsc.edu is to this repo, not the new one...

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