Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix references #3032

Merged
merged 15 commits into from
Apr 26, 2024
Merged

Fix references #3032

merged 15 commits into from
Apr 26, 2024

Conversation

flying-sheep
Copy link
Member

@flying-sheep flying-sheep commented Apr 26, 2024

That was a lot of work, despite https://www.doi2bib.org/

Copy link

codecov bot commented Apr 26, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 73.90%. Comparing base (a70582e) to head (cf54425).

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3032      +/-   ##
==========================================
- Coverage   76.27%   73.90%   -2.38%     
==========================================
  Files         117      117              
  Lines       12795    12759      -36     
==========================================
- Hits         9760     9430     -330     
- Misses       3035     3329     +294     
Files Coverage Δ
scanpy/datasets/_datasets.py 86.04% <ø> (ø)
scanpy/experimental/pp/_highly_variable_genes.py 63.46% <ø> (ø)
scanpy/experimental/pp/_normalization.py 95.06% <ø> (ø)
scanpy/experimental/pp/_recipes.py 100.00% <ø> (ø)
scanpy/external/exporting.py 13.44% <ø> (ø)
scanpy/external/pp/_bbknn.py 58.33% <ø> (ø)
scanpy/external/pp/_dca.py 58.33% <ø> (ø)
scanpy/external/pp/_harmony_integrate.py 53.33% <ø> (-33.34%) ⬇️
scanpy/external/pp/_hashsolo.py 89.74% <ø> (ø)
scanpy/external/pp/_magic.py 25.00% <ø> (-61.12%) ⬇️
... and 35 more

... and 18 files with indirect coverage changes

@flying-sheep flying-sheep changed the title WIP fix references Fix references Apr 26, 2024
@flying-sheep flying-sheep marked this pull request as ready for review April 26, 2024 13:20
@flying-sheep flying-sheep added this to the 1.10.2 milestone Apr 26, 2024
@flying-sheep flying-sheep enabled auto-merge (squash) April 26, 2024 15:20
@flying-sheep flying-sheep merged commit fd48fa0 into main Apr 26, 2024
13 of 14 checks passed
@flying-sheep flying-sheep deleted the fix-refs branch April 26, 2024 15:48
meeseeksmachine pushed a commit to meeseeksmachine/scanpy that referenced this pull request Apr 26, 2024
flying-sheep added a commit that referenced this pull request Apr 26, 2024
@bio-la
Copy link
Contributor

bio-la commented Apr 27, 2024

has the order of the markers column changed in this PR?

i got a local scanpy version 1.10.1 output with the expected order

markers = sc.get.rank_genes_groups_df(mdata["atac"], group=None)
>>> markers
        group                      names    scores  logfoldchanges         pvals     pvals_adj
0           0    chr21-45639191-45644849  8.696832        1.327774  3.412781e-18  1.838448e-13
1           0         chrX-316242-321327  6.274838        0.534321  3.499977e-10  3.770841e-06
2           0  chr12-119988038-119991086  6.187730        0.806758  6.103680e-10  5.978221e-06
3           0   chr6-111086859-111088937  6.162030        2.258481  7.181815e-10  6.448013e-06
4           0    chr11-66311251-66319124  6.112362        0.588367  9.816710e-10  7.675946e-06
...       ...                        ...       ...             ...           ...           ...
1077385     9  chr10-132415335-132424369 -2.942694       -3.170910  3.253696e-03  5.058441e-01
1077386     9  chr10-126040813-126043736 -3.092387      -29.032339  1.985538e-03  3.968830e-01
1077387     9    chr22-44023051-44027851 -3.237911      -28.983782  1.204083e-03  3.101063e-01
1077388     9   chr9-127395571-127399337 -3.403331       -1.821466  6.656958e-04  2.238189e-01
1077389     9       chr3-4975833-4984808 -3.997460       -1.672931  6.402590e-05  6.457136e-02

but pulling the latest merged branch has the old order of scanpy<1.7.0 with flipped score and names columns - ( group, scores,names, logfoldchanges,pvals,pvals_adj) ?

@flying-sheep
Copy link
Member Author

flying-sheep commented Apr 27, 2024

I very much doubt that this PR changed any behavior. It only touched the documentation.

This PR isn't in 1.10.1 in any case

@flying-sheep flying-sheep self-assigned this Apr 29, 2024
flying-sheep added a commit that referenced this pull request Apr 29, 2024
flying-sheep added a commit to mumichae/scanpy that referenced this pull request Apr 29, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants