Code

Overhaul to use the new libscran#83

Code

Merged

LTLA merged 85 commits intomasterlibscran/scranpy:masterfrom overhaullibscran/scranpy:overhaulCopy head branch name to clipboardJan 3, 2025

+8,167-11,084

Commits

Commits on Dec 18, 2024

• Begin the slow haul over to pybind11.

  LTLA

  committed
  bf7e81b

• Bring the ADT QC tests online.

  LTLA

  committed
  2a6ac65

• Removed unnecessary checks.

  LTLA

  committed
  bf60398

• Transferred the RNA functions over to the new world.

  LTLA

  committed
  1733ac9

• Forgot to commit the header.

  LTLA

  committed
  c49388b

• Got rid of a bunch of unnecessary files.

  LTLA

  committed
  27fd227

Commits on Dec 19, 2024

• Got tests working for the RNA QC.

  LTLA

  committed
  ef4b1c5

• Migrated the CRISPR code to the new world.

  LTLA

  committed
  5e51949

• Got rid of a whole bunch of unnecessary tests.

  LTLA

  committed
  64090a1

• Removed the old QC functions.

  LTLA

  committed
  9713c48

• Migrated the normalize_counts function.

  LTLA

  committed
  3553e28

Commits on Dec 20, 2024

• Migrate center_size_factors over to the new world.

  LTLA

  committed
  6effce3

• Added bindings for sanitize_size_factors.

  LTLA

  committed
  5209cf1

• Added bindings for CLRm1 normalization.

  LTLA

  committed
  3117392

Commits on Dec 21, 2024

• Make some progress migrating model_gene_variances.

  LTLA

  committed
  5bdd844

• Got the tests working.

  LTLA

  committed
  35ffbe3

• Added bindings for fit_variance_trend.

  LTLA

  committed
  9575b2f

• Added bindings for choosing HVGs.

  LTLA

  committed
  9a4c6a1

• Added bindings for the pseudo-count chooser.

  LTLA

  committed
  9e72584

• Removed unnecessary files.

  LTLA

  committed
  866113d

• Added bindings for PCA.

  LTLA

  committed
  a3dad33

Commits on Dec 22, 2024

• Added bindings for t-SNE and UMAP.

  LTLA

  committed
  9c0a5ce

• Added bindings for build_snn_graph.

  LTLA

  committed
  76a62bc

• Removed some unnecessary files.

  LTLA

  committed
  3cf34d8

Commits on Dec 23, 2024

• Added bindings for igraph-based methods.

  LTLA

  committed
  731c138

• Fixed warnings for precedence.

  LTLA

  committed
  8729c15

• Added bindings for k-means.

  LTLA

  committed
  82b4796

• Set copy=None to allow copying if it must.

  LTLA

  committed
  0e7c2d1

Commits on Dec 24, 2024

• Converted the run_all_neighbor_steps to the new world.

  LTLA

  committed
  d7d20c4

Commits on Dec 26, 2024

• Migrated most of the marker machinery.

  LTLA

  committed
  60d1792

Commits on Dec 27, 2024

• Added all the marker-related tests.

  LTLA

  committed
  644751e

• Began flipping over the aggregate code.

  LTLA

  committed
  fa554b4

Commits on Dec 28, 2024

• Inch closer towards getting this done.

  LTLA

  committed
  0fea5d2

• Added the tests for the various new aggregate functions.

  LTLA

  committed
  9ab8a9a

• Removed the old test files.

  LTLA

  committed
  d7339a0

• Removed some TODOs given that the C++ libs have been updated.

  LTLA

  committed
  d579239

Commits on Dec 29, 2024

• Flipped over MNN correction.

  LTLA

  committed
  b0d7f0b

• Shifted tests for ordering over to C++.

  LTLA

  committed
  352bc32

Commits on Dec 30, 2024

• Flipped over the subsampling by neighbors.

  LTLA

  committed
  ae58901

• Got rid of a whole bunch of obsolete files.

  LTLA

  committed
  654bee5

• Migrated scale_by_neighbors to the new world.

  LTLA

  committed
  0a2572e

• Converted the feature set scoring machinery.

  LTLA

  committed
  df40d5f

• Added bindings for the enrichment testing function.

  LTLA

  committed
  b107af0

• Removed vestiges of the old world.

  LTLA

  committed
  5a17198

Commits on Dec 31, 2024

• Completed the first half of the final grind.

  LTLA

  committed
  a3f461f

• Removed some unnecessary scripts.

  LTLA

  committed
  b8706b7

• Removed the manifest file, we don't need that.

  LTLA

  committed
  9c18b4b

• Mention that CLRm1 factors need to be centered.

  LTLA

  committed
  25d6f86

• Added a test suite for the new analyze function.

  LTLA

  committed
  f68f79c

Commits on Jan 1, 2025

• Shift igraph configuration into the setup.py.

  Show description for af43b65
  LTLA

  committed
  af43b65

• chore: remove Python 3.8 support (#82)

  Show description for 458983c
  jkanche

  authored
  458983c

• Update actions

  jkanche

  committed
  d68346b

• add pubind11

  jkanche

  committed
  2cc678c

• add knncolle to build level deps

  jkanche

  committed
  b966d98

• add scrnaseq as optional dep; version build level deps

  jkanche

  committed
  5aa33dc

Commits on Jan 2, 2025

• Slowly haul ass into cleaning up the docstrings, adding back Bioc classes.

  LTLA

  committed
  e3263b7

• Convert the variance modelling results.

  LTLA

  committed
  44ff11f

• More control in the ADT QC metrics conversion.

  LTLA

  committed
  cc0641d

• Added BiocFrame conversion for RNA, CRISPR QC functions.

  LTLA

  committed
  22bd132

• Added BiocFrame conversions for the marker functions.

  LTLA

  committed
  6540460

• Added capability to create an igraph.Graph from build_snn_graph.

  LTLA

  committed
  2dae506

• Forgot to add our new dependencies.

  LTLA

  committed
  1d12472

• Forgot to stress that this si not a directed graph.

  LTLA

  committed
  048ad59

• Removed unnecessary tests.

  LTLA

  committed
  18bdb6f

• Added SCE converters for analyze().

  LTLA

  committed
  4dc4ca9

• Use igraph's vendored dependencies to avoid delocate problems.

  LTLA

  committed
  c5a2389

• Fixed a compile warning.

  LTLA

  committed
  fffe54d

• Added tests and docs for the analyze() to SCE conversion.

  LTLA

  committed
  c2fc88a

• bump versions of biocframe and scrnaseq. optionally include scipy in tests

  jkanche

  committed
  a086d35

• you don't need scipy

  jkanche

  committed
  39c6329

• stop generating wheels; seems like it works

  jkanche

  committed
  7367488

• add version for scrnaseq

  jkanche

  committed
  fd71430

• Support SE inputs to analyze and respect the dimnames.

  LTLA

  committed
  5040ef5

• I guess you do need scipy

  jkanche

  committed
  7e5df9e

• Add scipy as optional dep

  jkanche

  committed
  1770e34

• Fix rnames and cnames for cripsr, change not ... to is not

  jkanche

  committed
  878c1da

• mostly not .. to is not ...

  jkanche

  committed
  edcfe3a

• Bump the version requirement for biocutils.

  LTLA

  committed
  f393bee

• Cleaned up the docstrings.

  LTLA

  committed
  f248f84

• Avoid redundant crap in the index.md.

  LTLA

  committed
  531ca1c

Commits on Jan 3, 2025

• Made some progress in updating the README.

  LTLA

  committed
  3b80a0e

• Cap the number of PCs to the maximum available.

  LTLA

  committed
  052af3d

• Greatly fleshed out the README.

  LTLA

  committed
  549dabc

• Switch to the latest knncolle with observations in the rows.

  LTLA

  committed
  c369536

• Mention the CHANGELOG.

  LTLA

  committed
  5731e45