Release History

2.3.0 (2024-05-13)

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 (2021-10-08)

Bug Fix

  • Fixed an error in the listDescendant method that affected the prune and filterRanks methods.

Performance

  • Node.children attribute is now a set, considerably speeding up file loading.

2.2.2 (2021-09-21)

Bug Fix

  • Fixed some bugged references to Node class

2.2.0(2021-09-21)

Bug Fix

  • Fixed broken implementation of Taxonomy.filterRanks

Implementation changes

  • Node and Dummy Node classes now ihnerit from the new _BaseNode classe. No impact on methods and properties.

2.1.2 (2021-08-18)

Bug Fix

  • Fix a bug resulting in the deletion of the children attribute of Nodes after writing to a JSON file (#2)

  • Fix an issue with the creation of DummyNdoes from JSON files (#3)

2.1.1 (2021-07-15)

Bug fix

  • Fixed unlinking of removed branches in Taxonomy.prune

Other

  • Linting code, still ignoring W293 and W291 =)

2.1.0 (2021-07-14)

Bug fix

  • Taxonomy.filterRanks now correctly handles rerooted trees

  • Fixed and bug to Taxonomy.consensus where search would only be in range of the shortest lineage

Changes

  • Implementation of Taxonomy.reroot was changed to conserve the ancestry of the input taxid.

  • Taxonomy.reroot was renamed to Taxonomy.prune

Additions

  • Added taxid search by name Taxonomy.getTaxid

2.0.0 (2021-07-13)

  • Released version 2. Implementation reworked from scraps.

  • NOT backwards compatible