Overview

The master branch of MABE2 currently depends on the MABE_devel branch of Empirical.
This pull request is to merge changes into MABE_devel; it does not touch the master branch of Empirical.

We are supporting the following branches of MABE2:

• avida_merge: https://github.com/FergusonAJ/MABE2/tree/avida_merge
• systematics: https://github.com/emilydolson/MABE2/tree/systematics

These mostly rely on the following branches of Empirical, which have been merged into this one branch:

• virtual_cpu_merge (this one) : https://github.com/FergusonAJ/Empirical/tree/virtual_cpu_merge
• mabe-systematics : https://github.com/emilydolson/Empirical/tree/mabe-systematics

Details

• Changes to systematics to allow it to work with MABE2
  • Modifications mostly in include/emp/Evolve/Systematics.hpp and include/emp/Evolve/SystematicsAnalysis.hpp
  • See Fix bug in systematics #419 and Changes to Systematics manager to support MABE #451 for more details
• Add VirtualCPU (include/emp/hardware/VirtualCPU.hpp and include/emp/hardware/VirtualCPU_InstLib.hpp)
  • Implementation of an Avidian as in Avida 2
  • Required minor changes to include/emp/hardware/InstLib.hpp and the files that depend on it
• Small tweaks to files supporting Avida in MABE2 (e.g., include/emp/functional/AnyFunction.hpp, include/emp/meta/TypeID)
• A new file, include/emp/math/CombinedBinomialDistribution.hpp that stores multiple instances of emp::Binomial to pull random numbers from a binomial distribution with arbitrary N