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Release Notes

The release notes below might be a summarized version of the project CHANGELOG, please, read those if you are looking for the latest changes between versions.

[0.15.2] - 2023-10-23​

Fixed​

  • Fixed broken pixeldataset aggregation for more than two samples.
  • Fixed a bug in graph generation caused by accidentally writing the index to the parquet file. For backwards compatiblity, if there is an column named index in the edgelist, this will be removed and the user will get a warning indicating that this has happened.

[0.15.1] - 2023-10-18​

Fixed​

  • Fixed a bug in filtering pixeldataset causing it to return the wrong types.
  • Fixed a bug in graph layout generation due to incorrect data frame concatenation.

[0.15.0] - 2023-10-16​

Added​

  • Add support for Python 3.11.
  • Add early enablement work for a networkx backend for the graph stage.

Fixed​

  • Fix report color axis in report figures not updating when selecting markers or cell types.
  • Remove placeholder links in report tooltips.
  • Fix a bug where aggregating data did not add the correct sample, and unique component columns.

[0.14.0] - 2023-10-05​

Added​

  • Lazy option for edge list loading (pixeldataset.edgelist_lazy), which returns a polars LazyFrame that can be used to operate on the edge list without reading all of it into memory.
  • Option (ignore_edgelists) to skip the edge lists when aggregating files. This defaults to False.

Changed​

  • Types on the edge list in memory will utilize the pandas category type for string, and uint16 for numeric values to lower the memory consumption when working with the edge list
  • Remove --pbs1 and --pbs2 commandline arguments to pixelator single-cell adapterqc.
  • Restructure report figures.
  • Improve metric names and tooltips in the report.
  • Synchronize zoom level between the scatter plots in cell annotations section of the report.
  • Add report placeholder for missing cell annotation data
  • Add Fraction of discarded UMIs and Avg. Reads per Molecule metrics to the report.

Fixed​

  • Fix an issue where pixelator --version would return 0.0.0 when installing in editable mode.

v0.13.1 - 2023-09-15​

Changed​

  • Unpin igraph dependency to allow for newer versions of igraph to be used.
  • Cleanup README and point to the external documentation site.
  • Change PyPI package name to pixelgen-pixelator.

Fixed​

  • Fix an issue where --keep-workdirs option for pytest was not available when running pytest without restricting the testdir to tests/integration.
  • Fix an issue where pixelator --version would return 0.0.0.

v0.13.0 - 2023-09-13​

  • First public release of pixelator.