CHANGELOG

-- Version history --

Certain updates only apply to the web version, but they should be obvious to
figure out since they are likely modification of the interface.

-> FOCUS 1.6:
- Add `focus_database_utils` to add genoems into the database

-> FOCUS 1.2:
- FOCUS on pip as metagenomics-focus
- README edits

-> FOCUS 1.1:
- Setuptools
- Set FOCUS to be agnostic to the location of the script in relation to where the program is executed

-> FOCUS 1.0:
- Refactor to python3

-> FOCUS 0.31:
- Parameter "-s" for multiple samples is not required anymore. FOCUS identies now if the user is passing
  a directory or file

-> FOCUS 0.3:
- Fixed minor bug in the STAMP input creation.

-> FOCUS 0.29:
- Split the STAMP output in different level for different for multiple samples.

-> FOCUS 0.28:
- FOCUS database was updated on (08/08/2015), and now it has 2785 complete genomes
- Now FOCUS can analyse multiple samples, and it generates an output in a format compatible with STAMP.

-> FOCUS 0.27:
-Updated DB by fixing the "Unknown Genus"
-Regularization was removed after reading (Slawski and Hein, 2013).
 The paper argues that the NNLS may have a better result than using regularization
-minor changes

-> FOCUS 0.26:
-Tabular output
-Error when trying to add new add into the database (Thanks Bob Bowers for the report)
-minor changes

-> FOCUS 0.25:
-Minor changes

-> FOCUS 0.24:
-Fixed error caused by Jellyfish when counting k-mer with Jellyfish 2.XX on FOCUS 0.23. Now FOCUS works with any Jellyfish's version.

-> FOCUS 0.23:
-Minor changes


References:
Slawski,M. and Hein,M. (2013) Non-negative least squares for high-dimensional linear models: Consistency and sparse
recovery without regularization. Electron. J. Stat., 7, 3004–3056.