Version 0.3.1

• Garnet integration test case using FOXA1 ChIP-seq
• Correct formatting problems in example data wgEncodeRegDnaseClusteredV2.fasta.gz
• Fix bug when reading Garnet results in Forest
• Use relative paths for motif gifs in Garnet HTML output file
• Update sort order in Garnet output table
• Garnet uses balanced binary search tree to speed up the search for genes within peaks
• Change default values of arguments in Garnet's map_peaks_to_known_genes.py

Version 0.3.0

Bug fixes:

• Remove conflicts between Forest edge noise and garnetBeta parameters
• Correctly query for whether prize nodes are in a directed network
• Use correct p-value or q-value to filter Garnet output
• Switch to msgsteiner-1.3 to fix bugs with directed edges and suboptimal forests

New features:

• BSD license
• Forest unit tests to assess the effects of w, beta, mu, and D
• Continuous integration testing with Travis CI
• Option to save plots from Garnet motif regression
• Write Forest objective function value of optimal forest to info file

Version 0.2.0

• Add a Forest integration test
• Correct nondeterministic msgsteiner behavior
• Add additional example data sets and scripts
• Switch to Creative Commons Attribution-NonCommercial 4.0 International Public License
• Rename Forest configuration file parameter n to garnetBeta
• Add Forest configuration file parameter processes
• Correct error in negative prize score calculation
• Improve Garnet output file format
• Add Forest option to exclude terminals