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Release History

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

Improvements

  • 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 Lineagefrom 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 (2024-06-04)

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 (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