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Changelog

CellTypist 1.6.3 (June 6, 2024)

  • GPU support based on rapids-singlecell during the over-clustering step #110
  • Load custom model directly #60

CellTypist 1.6.2 (November 1, 2023)

  • Reformat error and warning messages during prediction #89
  • Fix cuml import during model training
  • Fix categorical output from new versions of pandas during majority voting #96

CellTypist 1.6.1 (September 25, 2023)

  • Add cuML-based GPU support for model training #80
  • Detect data input format only for the first 1000 cells
  • Fix KeyError in to_adata when setting mode = 'prob match' in celltypist.annotate
  • Add gene symbol to ID conversion file and expand README #87

CellTypist 1.6.0 (August 5, 2023)

  • Separate CellHint from CellTypist
  • Keep strict one-to-one orthologs during species model conversion
  • Auto-fetch feature transfer files for model conversion
  • Adapt code to sklearn>=1.3.0 #75

CellTypist 1.5.3 (July 10, 2023)

  • Fix DistanceMetric import for sklearn >= 1.3.0 #73
  • Detect input format for celltypist.dotplot
  • Require leidenalg >= 0.9.0

CellTypist 1.5.2 (June 8, 2023)

  • Patch log1p serialization issue and model download error

CellTypist 1.5.1 (May 26, 2023)

  • Fix error in not importing spmatrix in pct

CellTypist 1.5.0 (May 16, 2023)

A more mature release before the formal CellTypist v2

CellTypist 1.4.0 (May 2, 2023)

  • Add modules of cell type harmonisation and integration (a release before the formal CellTypist v2)

CellTypist 1.3.0 (December 14, 2022)

  • Transfer numpy matrix to array during prediction for compatibility with sklearn >= 1.0 #50

CellTypist 1.2.0 (August 22, 2022)

  • Report all model url request errors (including timeout error) #28
  • Add with_mean parameter in celltypist.train to optimize RAM usage by not subtracting the mean #29
  • Raise warning instead of error during prediction when the input expression matrix contains only a subset of genes
  • Reformat docs with independent pages for main functions
  • Support dot plot when the prediction comes from the 'prob match' mode #33
  • Disable hard-coded max_iter in celltypist.train with default values varying according to dataset sizes

CellTypist 1.1.0 (June 09, 2022)

  • Add citation (PMID: 35549406)
  • Add Docker/Singularity container
  • Fix the error of celltypist.dotplot when reference cluster is type of int #22
  • Relax the criteria of detecting the plain file format
  • Expand the docstring of convert to explicitly support gene name transfer #26
  • Automatically transpose (with warning) the input gene-by-cell matrix instead of raising an error

CellTypist 1.0.0 (May 12, 2022)

CellTypist 1.0.0

CellTypist 0.2.1 (Apr 24, 2022)

Final beta version

CellTypist 0.2.0 (Feb 12, 2022)

Closer-to-mature version

CellTypist 0.1.9 (Dec 14, 2021)

Close-to-mature version