Working in `pyani` v0.2 vs v0.3

For the time being, we are maintaining two distinct codebases for pyani. These are v0.2 and v0.3.

• v0.2 will be deprecated after a grace period, once v0.3 is released

v0.2

• This is the "original" version of pyani, and will be deprecated
• The package is called using average_nucleotide_identity.py with various options
• This version is the one that is currently packaged on pip and bioconda
• The base branch for v0.2 is version_0_2

v0.3

• This is "modern" pyani
• The program is called using pyani [SUBCOMMAND] with various options
• The base branch for v0.3 is the default, master branch

It is important to git rebase, git merge and to issue pull requests against the correct base branch.