Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

0.0.2#

ds.read_imaginary_metrics: samples one row per unique benchmark configuration from the metrics table and relabels it as 'ImaginaryMethod', useful for baseline comparisons or testing visualizations.
get_terms: retrieves the filtering terms for a given dataset as a dictionary mapping evaluation database names to lists of terms.
tl.cre_to_tss_distance: computes the distance from each CRE in a GRN to the promoter window of its target gene, using the Promoters database. Accepts a single GRN DataFrame or a dictionary of GRNs.
pl.cre_to_tss_distance: plots CRE-to-TSS distance distributions as horizontal boxplots, with an optional vertical threshold line (default 250,000 bp).
Tutorial notebooks.
Added scanpy and xgboost as explicit dependencies; removed the [full] extra from decoupler.

Dataset filtering terms moved from inline Python dicts in config.py into bundled YAML files (src/gretapy/data/), loaded at import time. This reduces config.py from ~2,600 lines to ~260 lines with no change to the public API.
pl.links: legend is now displayed once on the middle TF panel (with multi-column layout for many GRNs) instead of being repeated on every subplot.
mt.correlation now filters for promoters first and then computes correlations, reducing the number of compute.