v0.16.1

[0.16.1] - 2024-01-12

Fixed

• Bug in README shield formatting

v0.16.0

[0.16.0] - 2024-01-12

This release introduces two major change in pixelator:

1. the Graph backend has been switched from using igraph to using networkx
2. the license has been changed from GLP2.0 to MIT

Added

• Experimental 3D heatmap plotting feature.
• Optional caching of layouts to speed up computations in some scenarios.
• experimental mark that can be added to functions that are not yet production ready.
• The underlying graph instance e.g. a networkx Graph instance is exposed as a property called raw from the pixelator Graph class.
• Monte Carlo permutations supported when calculating Moran's I (morans_z_sim) in polarization_scores.

Changed

• The default (and only) graph backend in pixelator is now based on networkx.
• mean_reads and median_reads in adata.obs to mean_reads_per_molecule and median_reads_per_molecule respectively.
• Drop support for python 3.8 and 3.9.
• Change output format of collapse from csv to parquet.
• Change input and output format of graph from csv to parquet.
• Change input format of annotate from csv to parquet.
• Rename the report to "qc report"
• Add a Reads per Molecule frequency figure to the sequencing section of the qc report.
• Remove placeholder warning of missing data for not yet implemented features.
• Change "Median antibody molecules per cell" to "Average antibody molecules per cell" in the qc report.
• Refactoring of the graph backend implementations module.
• Speeding up the amplicon step by roughly 3x.

Fixed

• Nicer error messages when there are no components valid for computing colocalization.
• A bunch of warnings.

Removed

• graph no longer outputs the raw edge list.
• igraph has been dropped as a graph backend for pixelator.

v0.15.2

[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.

v0.15.1

[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.

v0.15.0

[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.

v0.14.0

[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

[0.13.1] - 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

[0.13.0] - 2023-09-13

• First public release of pixelator