v0.2.3

The previous release (0.2.2) on PyPI had script shebangs that pointed to a local development Python, in the wheel and egg distribution files. It is not possible to replace those files on PyPI, so a new release was made to fix this issue, and the old packages withdrawn.

v0.2.2: NCBI changes and bugfixes

• fix for issue #53 (--maxmatch has no effect)
• fix to genbank_get_genomes_by_taxon.py to account for NCBI FTP location changes
• fixed issue #52 (local variable bug)
• fixed issued #49 (TETRA failure) and #51 (matplotlib bug)
• add several tests and support for codecov.io, landscape.io and Travis-CI
• removed requirement for rpy2
• moved scripts to bin/ subdirectory

v0.2.1

v0.2.1 introduces minor changes with respect to v0.2.0:

• genbank_get_genomes_by_taxon.py uses the new NCBI FTP locations, and will attempt to identify and inform the user about failed downloads.
• seaborn output can now handle larger (>500 genomes) datasets
• better handling of missing class information
• adds a Hadamard product output
• you can now rerender graphics without recalculation of alignments
• alignment output is zipped into an archive by default

There are also several bugfixes (see CHANGES.md for more details)

v0.2.0

Version 0.2.0 introduces a number of changes with respect to the v0.1 series of releases. Notably:

• v0.2.0 is for use with Python 3
• a longstanding bug in the --fragsize option is fixed
• several pull requests for enhancements are merged
• BLAST/nucmer results are now written to a subdirectory of the output folder, and are compressed to save disk space
• a script to download publicly-available genomes from NCBI is provided

v0.1.3.2

This bump fixes some bugs (issues #5 and #11), and updates installation instructions reflecting the upload of this package to PyPI.

v0.1.3.1

Release made solely to obtain a Zenodo DOI (10.5281/zenodo.31812)