Poppunk

The main feature added is `--generate-viz` mode.

New features:
* Allow visualisation to be generated independently 44
* Add extra output to STDERR for GMM fits 45

Bug fixes:
* Fix in plot of DBSCAN introduced in previous version 45
* Fix README rendering in PyPI
* Fix readthedocs build ([details](http://www.johnlees.me/blog/2019/04/26/readthedocs-failing-to-build-module-setuptools-build_meta-has-no-attribute-__legacy__/))
* Fix to genome length check when inputs not present

This release is mostly to create a function to assign samples, usable by an API for pathogenwatch.

Other changes

New features:
* Added script to generate the microreact output (yet to be fully exported)

Bug fixes
* Fixes to `--use-model` mode
* Guard against huge memory use in making plots of refined fits with very large datasets
* Correct error message when fit fails 41

Adding some changes and fixes that have arisen from more people testing out on their data!

New features:
* Add basic quality control for assemblies input (37, 42).
* Generate a network and cluster assignment by applying a fitted model to a distance database (`--use-model`).
* Added script to calculate Rand distances between cluster assignments (`calculate_rand_indices.py`)
* Added script to extract `.graphml` files for all clusters (`extract_components.py`).

Bug fixes:
* More general parsing of epiData for `--microreact` (35).
* Correct paths in output prefix with mash sketch.
* Removed the zero level contour in distance plots (38).

Other:
* Updated docs (troubleshooting, installation, README.md)
* Removed n subscript on pi on x-axis of plots.
* Updated `networkx` version for `pip` (39).
* Catch errors when curve fit fails (41).
* Travis-CI uses conda rather than pip to install dependencies.

This release contains an important bug fix and some changes to the output files

New features:
* Available as a conda package (31)
* Plots are now plotted in terms of pi_n and a, rather than in the arbitrary scaled space (32)
* Easy run mode now uses HDBSCAN and fit refinement, a more intuitive default (34)
* Min and max k-mer sizes set as noted in paper

Bug fixes:
* Clusters are output in reverse frequency order, in every mode (33)
* Use of databases with reference only (i.e. without `--full-db`) work with future `--assign-query` commands (35)
* Parsing of CSV column headers for microreact output fixed for some cases

Small change to `setup.py` for compatibility with bioconda

This release contains features and fixes in response to review comments in the manuscript, as well as other raised issue fixes.

New features:
* Arbitrary cluster definitions can be merged with the clusters found using `--external-clustering` (30)
* A new, simpler, example has been added to the documentation
* All plots are clearer and show the unscaled distances a and pi_n (32)

Bug fixes:
* Check distance file provided when using `--assign-query` (29)
* Ensure python3 is being used (v2.7 unsupported)
* General tidying of code from pylint errors and warnings