3.1.1

Bugfix

• Taxonomy.consensus now correctly handles list of taxids as int

3.1.0

Improvements

• Taxonomy.consensus and Taxonomy.lca can now ignore missing taxa instead of raising an error

3.0.0

Deprecation

• Taxonomy.from_json, load, Taxonomy.from_taxdump and load_ncbi are deprecated. See v2.4.0 notes for replacements

New features

• It is now possible to create Newick tree with Taxonomy.toNewick (Experimental)

2.5.2

• Update docstrings
• Rework documentation
• Taxonomy.getXXX methods now behave like dict.get: allow default return value if key is not found, never raises an error

2.5.1

Improvements

• taxidTools.InvalidNodeError now ihnerits from KeyError as well, this might be more intuitive for some users

2.5.0

New features

• It is now possible to provide merged nodes, either form the taxdump file merged.dmp or directly via instances of the class MergedNode
• Attempting to retrieve a MergedNode from a Taxonomy instance will return the node it was merged with.

Bug Fix

• Instanciating a Lineage from a DummyNode doesn't raise an Error anymore

2.4.0

New features

• Added a Taxonomy.copy() method as a shorthand for copy.deepcopy(Taxonomy)
• Added an inplace argument to Taxonomy methods filterRanks() and prune(), allowing chose whether to return a modified deepcopy of the instance od modifiy it in place

Improvements

• Unit tests now use temporary directories to test IO methods
• The Taxonomy.filter() method will now return a ValueError when attempting to use root rank in the filtering instead of creating new root Nodes

Pending deprecation

• Taxonomy.from_json will be removed in 3.0.0, it is replaced by read_json, a module level constructor.
• load will be removed in 3.0.0, it is replaced by read_json, a module level constructor.
• Taxonomy.from_taxdump will be removed in 3.0.0, it is replaced by read_taxdump, a module level constructor.
• load_ncbi will be removed in 3.0.0, it is replaced by read_ncbi, a better-named module level constructor.

Bug Fix

• Taxonomy.listDescendant now does filter output based on the ranks parameter
• Repaired Node.node_info output to actually use newlines instead of printing '\n'

2.3.1

Distribution

• It is now possible to install taxidTools from DockerHub:

docker pull gregdenay/taxidtools

• conda-forge release should now auomatically find the last release from Github/Pypi

2.3.0

New features

• Attempting to access an invalid Node with the Taxonomy getitem method (Taxonomy["node_id"]) now returns a specifc InvalidNodeError
• Added the load_ncbi function as a shorthand for the constructor Taxonomy.from_taxdump.

2.2.3

Bug fix and perf improvements