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Overhaul to use the new libscran #83

Merged
merged 85 commits into from
Jan 3, 2025
Merged

Overhaul to use the new libscran #83

merged 85 commits into from
Jan 3, 2025

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LTLA
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@LTLA LTLA commented Jan 1, 2025

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LTLA added 30 commits December 17, 2024 18:02
@LTLA
Begin the slow haul over to pybind11.
bf7e81b
@LTLA
Bring the ADT QC tests online.
2a6ac65
@LTLA
Removed unnecessary checks.
bf60398
@LTLA
Transferred the RNA functions over to the new world.
1733ac9
@LTLA
Forgot to commit the header.
c49388b
@LTLA
Got rid of a bunch of unnecessary files.
27fd227
@LTLA
Got tests working for the RNA QC.
ef4b1c5
@LTLA
Migrated the CRISPR code to the new world.
5e51949
@LTLA
Got rid of a whole bunch of unnecessary tests.
64090a1
@LTLA
Removed the old QC functions.
9713c48
@LTLA
Migrated the normalize_counts function.
3553e28
@LTLA
Migrate center_size_factors over to the new world.
6effce3
@LTLA
Added bindings for sanitize_size_factors.
5209cf1
@LTLA
Added bindings for CLRm1 normalization.
3117392
@LTLA
Make some progress migrating model_gene_variances.
5bdd844
@LTLA
Got the tests working.
35ffbe3
@LTLA
Added bindings for fit_variance_trend.
9575b2f
@LTLA
Added bindings for choosing HVGs.
9a4c6a1
@LTLA
Added bindings for the pseudo-count chooser.
9e72584
@LTLA
Removed unnecessary files.
866113d
@LTLA
Added bindings for PCA.
a3dad33
@LTLA
Added bindings for t-SNE and UMAP.
9c0a5ce
@LTLA
Added bindings for build_snn_graph.
76a62bc
@LTLA
Removed some unnecessary files.
3cf34d8
@LTLA
Added bindings for igraph-based methods.
731c138
@LTLA
Fixed warnings for precedence.
8729c15
@LTLA
Added bindings for k-means.
82b4796
@LTLA
Set copy=None to allow copying if it must.
0e7c2d1
@LTLA
Converted the run_all_neighbor_steps to the new world.
d7d20c4
@LTLA
Migrated most of the marker machinery.
60d1792
@LTLA
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LTLA commented Jan 2, 2025

@jkanche remaining CI error is because scipy is somehow required by scrnaseq but that import should really be conditional on whether it's already installed.

LTLA and others added 19 commits January 2, 2025 08:58
@LTLA
Fixed a compile warning.
fffe54d
@LTLA
Added tests and docs for the analyze() to SCE conversion.
c2fc88a
@jkanche
bump versions of biocframe and scrnaseq. optionally include scipy in …
a086d35 
…tests
@jkanche
you don't need scipy
39c6329
@jkanche
stop generating wheels; seems like it works
7367488
@jkanche
add version for scrnaseq
fd71430
@LTLA
Support SE inputs to analyze and respect the dimnames.
5040ef5
@jkanche
I guess you do need scipy
7e5df9e
@jkanche
Add scipy as optional dep
1770e34
@jkanche
Fix rnames and cnames for cripsr, change not ... to is not
878c1da
@jkanche
mostly not .. to is not ...
edcfe3a
@LTLA
Bump the version requirement for biocutils.
f393bee
@LTLA
Cleaned up the docstrings.
f248f84
@LTLA
Avoid redundant crap in the index.md.
531ca1c
@LTLA
Made some progress in updating the README.
3b80a0e
@LTLA
Cap the number of PCs to the maximum available.
052af3d
@LTLA
Greatly fleshed out the README.
549dabc
@LTLA
Switch to the latest knncolle with observations in the rows.
c369536
@LTLA
Mention the CHANGELOG.
5731e45
@LTLA LTLA merged commit 25905ce into master Jan 3, 2025
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@LTLA LTLA deleted the overhaul branch January 3, 2025 18:51
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@LTLA @jkanche