0.19.4

CHANGELOG

Improvements
run_marker_search now uses updated find_markers_by_rank that has better runtimes when using precached data
Updated requirements

0.19.3

CHANGELOG

Improvements
make_graph takes an additional parameter (ann_index_save_path) to read and write ANN index to/from custom path

0.19.2

CHANGELOG

Bug fixes
Fixed issues from UMAP version 0.5.2
Exposed heatmap kwargs plot_heatmap

Improvements
Improved support for prenormalized values in find_markers_by_rank
show_zarr_tree now has a maximum depth of 2

0.19.1

CHANGELOG

Changelog of 0.19.0 is also included here

Critical bug fix
Fixed critical bug in iter_normed_feature_wise that caused usage of the wrong parameter in the normed method call.

New features
Added save_normed_for_query which will create a new slot in the assay and save all the normalized values for the quick lookup. get_cells_vals was improved to utilize these calculated normalized values when available.

Improvements
iter_normed_feature_wise now features any selection of features.
Added title parameter to plot_layout and plot_unified_layout that allows using custom titles in the plots.
create_zarr_obj_array now supports compression and disabling of chunking.

Documentation changes
API page now included class init level docstrings.

0.18.2

CHANGELOG

Critical bug fix
ZarrMerge bug which led to +1 counts for all the features was fixed
Fixed a bug in DataStore.mark_hvgs that caused the failure of ANN search when reusing 0 dims.

Improvements
Improved handling for groups with no markers in DataStore.export_markers_to_csv and DataStore.get_markers
hide_title and title_size parameters included in plot_scatter and shade_scatter and exposed in DataStore.plot_layout and DataStore.plot_unified_layout

Documentation changes
Improved instructions for installation on Windows
API page now includes classes from readers, writers and metadata modules

Dev notes
Dask requirement pinned >=2020.8.1
Reblackened code

0.18.1

CHANGELOG

Improvements
Bug fixes in find_markers_by_regression and find_markers_by_rank causing unnecessary dataframe (gene-wise chunk) renaming on the wrong axis
Bugfix in handle_download causing wrong tar extraction target
Bugfix in _scatter_make_colors causing wrong cmap choice
plot_marker_heatmap raises error now when no marker gene is found

Documentation changes
Removed Dask warning from homepage
code style made black-like on all the vignettes

Dev notes
Dask requirement pinned >=2020.8.1
Reblackened code

0.18.0

CHANGELOG

New features
Rewrote meld_assay module and exposed functionality of coordinate_melding through add_melded_assay method of DataStore. Coordinate intersections are done using binary_search function that employs a Numba accelerated implementation of binary search algorithm. This means that we don't need to use Bedtools anymore, which is hard to install on windows. create_counts_mat function modified to used normalized data and perform sparse write operations. meld_assay function renamed to coordinate_melding

Added tutorials
Added GeneScores section to scATAC-Seq basic workflow

Improvements
Added lsi_skip_first parameter to make_graph and AnnStream. The first LSI dimension usually captures sequencing depth so this parameter helps users control if they want to keep or discard this dimension.

Documentation changes
Changed order of vignettes in the TOC tree.
Added pseudotime vignette to colab list
Improved installation instructions for Windows

0.17.1

CHANGELOG

Logged changes since 0.16.3

Improvements
Removed MtxReader and MtxToZarr classes. Their functionality folded into CrDirReader and CrToZarr.
CrDirReader now supports multiassay data and CrToZarr avoids data densification
_load_assays supports assays named HTO and GeneScores

Dev notes
Added issues templates for bug reports and feature inclusions
Multiple tests added using a toy MTX matrix

0.16.3

CHANGELOG

Improvements
Fixes in get_markers in DataStore to allow backward compatibility with marker search results.

0.16.2

CHANGELOG

Logged changes since 0.12.0

New features
datastore module: Added run_pseudotime_marker_search, plot_pseudotime_heatmap, add_grouped_assay, and run_pseudotime_aggregation
assay module: Added iter_normed_feature_wise and save_aggregated_ordering
markers module: Added knn_clusteringand find_markers_by_regression
plots module: Added plot_annotated_heatmap

Added tutorials
Cell-cycle vignette

Improvements
Bug fixes in smart_label to work with non-integer labels
markers module overhauled.
Major memory improvements to run_pseudotime_scoring along with ability to add sources and sinks
CrToZarr now does not densify the data and uses fancy indexing.
assay_names in DataStore is now a property
Minor bug fix in ann module which cause wrong number of threads in ann index
Paris clustering now uses reorder=False argument

Documentation changes
Fixed bugs in CSS causing scrolling issue on left bar
Switched to myst-nb from nbsphinx
Reduced fontsize of tables in notebooks using CSS

Dev notes
Added tests for all new methods added.
Tests for Dens-UMAP needed!