Version at bioRxiv submission

Bug fixes:

• Use the relative and not absolute path, allowing --assign-query to work with inputs from non-writable directories, or directories in other locations.
• Corrected model copying with poppunk_references

Code:

• Move many functions from mash.py to utils.py

Reference selection

Added features:

• Added program poppunk_references to perform clique-based reference selection, if --full-db was run first time round.
• If core or accessory refined models have been created, also write out their networks when using --cytoscape.

Bug fixes:

• When picking references, remove the non-reference isolates from the distance file

Adding output types

Added features:

• Ability to write output for GrapeTree
• Ability to write output for Phandango
• Ability to re-run t-SNE with different perplexity without rerunning everything (poppunk_tsne)

Bug fixes:

• Pasting epi information into Microreact output (#24)
• Storing accessory distances with --assign-query

Initial release

First public version

First PyPI package

Code almost complete, but a few final features and tests remain before first release.
This is the same as v0.1 on PyPI