FAVITES 1.1.1

• Terminate VirusTreeSimulator if it fails to coalesce after a user-specified maximum number of attempts
  • Normally, it just runs infinitely, resulting in an infinitely-growing log file
  • This adds the vts_max_attempts parameter to the NodeEvolution_VirusTreeSimulator module

FAVITES 1.1.0

• Most output files are now gzipped with -9 compression (instead of being written as plaintext)
• GEXF transmission network is no longer output to save space in the case of dense contact networks
  • A conversion script has been added to the helper scripts directory
• Added tester config files in .travis_tests
  • Can be used as examples for each module implementation's usage
• Fixed many bugs and added safety checks across multiple module implementations
• Initial attempts to allow for using a user-specified random number generator seed
  • Seems to work for contact network and transmission network generation, but not yet for downstream things

FAVITES 1.0.3

• Fixed PANGEA module
  • Docker image might not work until PANGEA.HIV.sim merge my pull request (they use print print "STRING" syntax instead of print("STRING") syntax, so their code is incompatible with Python 3)
• Added tester for PANGEA module

FAVITES 1.0.2

• Removed unnecessary nw_rename requirement from NodeEvolution_VirusTreeSimulator
• Updated NodeEvolution_DualBirth and NodeEvolution_Yule to use the linear-time C++ dual-birth simulator instead of the prior O(n log n) Python simulator

FAVITES 1.0.1

Fixed bugs in Sequencing_DWGSIM and added error checks in NodeEvolution_VirusTreeSimulator

Initial Official Release

This is the initial official versioned release of FAVITES