Taxtastic

Latest version: v0.11.1

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0.8.2

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* add psycopg2 as a requirement (support for postgresql from a docker image)

0.8.1

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* major speedups (> 30x) for ``new_database`` and ``taxtable``
* sql expressions for calculating lineages require sqlite 3.8.3+;
include script for installing pysqlite and updated sqlite3 library.
* names.is_classified is set to true only for scientific names at rank species
* nodes.is_valid is true for all ranks above species
* remove names.id and ranks.is_below from schema
* ``taxtable`` renames "no rank" intermediate ranks by appending "_"
to parent rank name (instead of prepending "below_")
* intermediate ranks are renamed on the fly when creating the taxtable
rather than on database creation.
* add Taxonomy.get_source()
* add Taxonomy.add_name() and Taxonomy.add_names()
* Taxonomy.add_node() takes a list of dicts representing tax_names
* adding nodes or names occur within a transaction
* removed subcommands merge_taxtables, merge, count_taxids
* remove numpy, pandas, BioPython as dependencies, add Dendropy
* ``taxit add_nodes`` requires input in YAML format (replaces csv) and
can add names as well

0.7.0

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* All commands can read from a specified .conf or .ini configuration file
* ``taxit --ranked`` now takes one of two arguments ``{rows, columns}``
* Records containing the word "group" in taxonomic name are no
longer flagged as unclassified/invalid [GH-93]
* fix missing parent_id column in taxtable
* include docker build

0.6.4

=====

* rank cohort has been added as an official rank
* ``taxit taxtable --taxtable`` has been added back to work from a
pre-built taxtable. This switch used to be called ``--from-table``

0.6.3

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* root is now a valid node

0.6.2

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* bug fixes

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