Taxtastic

=====

* Add ``.drop()`` ``.collapse()`` methods to ``taxtastic.taxtable.TaxNode``
* Change ``is_classified`` column in taxonomy database: now does not mark
below species as unclassified if the species-level classification is valid. [GH-59]
* Add ``taxit composition`` - shows the taxonomic composition of a reference package at a given rank
* Fix broken ``taxit lonelynodes``
* Add ``taxit merge`` - Identifies tax_ids which have been merged, suggests new tax_ids.
* Add ``taxit add_to_taxtable`` - adds nodes to a taxonomy [GH-60]
* Fix support for newer versions of PhyML [GH-61]
* Updates for compatibility with RAxML 7.7.2

===

* 'names' table in the taxonomy database has a new column
'is_classified' indicating whether 'tax_name' should be considered
"classified".
* Bugfix in ``taxit findcompany``
* Support stdin as a source for ``taxit findcompany``
* Taxonomy objects use NCBI ranks by default
* Reference packages are created optionally (fixes creation of empty reference
packages for commands like ``taxit info nonexisting.refpkg``)
* Support zipped reference packages
* Add a taxtable API: ``taxtastic.taxtable``
* Remove some tests requiring a full taxonomy database
* Rerooting reference packages on creation [GH-57]
* More intelligent file name generation on clash
* Deprecate the default ``create=True`` in ``taxtastic.refpkg.Refpkg``
* Some PEP8 fixes

=====

* version number contains abbreviated git sha identifying the commit.
* Initial release to PyPI
* Add findcompany subcommand
* Add refpkg_intersection subcommand
* Remove some obsolete components
* Check required fields in seqinfo file [GH-46]
* Add option to build taxtable from seqinfo file [GH-55]
* Add subcommand to update taxids [GH-56]
* Support FastTree AA and DNA log files
* Fix rank order bug (infraorder was below parvorder)
* Documentation updates