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CHANGELOG.md

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Changelog

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