CHANGELOG.md

Changelog

1.5.1

• correctly check for pynndescent metric space in bbknn.bbknn()

1.5.0

• pynndescent support (suggested by G. Palla)
• default metric set to Euclidean
• code refactoring; impactful changes:
  • innards relocated to bbknn.matrix, bbknn.bbknn_pca_matrix() is now bbknn.matrix.bbknn()
  • n_trees is now annoy_n_trees

1.4.1

• remove trimming bug which would lead to an asymmetric matrix for cells with a neighbour count very near the threshold (spotted by E. Dann)
• clarify docstring, neighbour counts are there for the initial KNN computation

1.4.0

• add ridge regression preprocessing like in [https://science.sciencemag.org/content/367/6480/eaay3224.abstract](Park, 2020)
• require batches to feature a minimum of neighbors_within_batch cells each
• rework demo notebook, remove old preprint notebooks to separate repository

1.3.12

• add packaging as a dependency in setup.py

1.3.11

• fix version parsing for newer versions of anndata and packaging

1.3.10

• store the computed graphs in .obsp if anndata is 0.7 or newer
• include additional parameter information in .uns['neighbors']
• return .uns['neighbor']-style parameter dictionary as third tuple element from bbknn_pca_matrix

1.3.9

• sklearn is actually scikit-learn for dependency purposes (D. DeTomaso)

1.3.8

• support umap-learn 0.4 connectivity output in a backward compatible manner (I. Driver)

1.3.7

• support for non-PCA dimensionality reductions on input (brought to attention by D. Cittaro)

1.3.6

• further updated scanpy logging compatibility tweak (F. Rost)

1.3.5

• update logging to match scanpy 1.4.4 standards

1.3.4

• rework .obsm['X_pca'] check to be compatible with new structure (I. Virshup)

1.3.3

• add MANIFEST.in for conda purposes (J. Preußner)

1.3.2

• run trimming by default at 10 times the neighbour count for each cell
• remove scanpy dependency from bbknn_pca_matrix; rework setup dependencies as a result
• removal of save_knn option
• creation of diagnostic extract_cell_connectivity function for plotting connectivities

1.3.1

• metric sanity check typo fix

1.3.0

• optional faiss support
• default swap to annoy neighbours with angular as the metric, add annoy's n_trees parameter
• removal of distance scaling
• removal of n_jobs parameter - automatically parallelise cKDTree
• metric sanity checks

1.2.0

• bbknn_pca_matrix function
• code refactoring

1.1.0

• annoy support

1.0.0

• initial release