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CHANGELOG.md

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Changelog

1.6.0

  • create computation argument, encourage approx/use_annoy/use_faiss users to move to it
  • simplify per-batch query logic (C. Xu)
  • add key_added argument to mirror scanpy.pp.neighbors()
  • update setup to flit, add missing pandas dependency
  • update sklearn syntax to match >=1.0.2, require appropriate version (Matchy, R. Williams)
  • update scipy syntax to match >=1.6.0, require appropriate version
  • remove pre-0.7.0 anndata support
  • internal coding consistency improvements and readthedocs modernisation

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

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