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CHANGELOG.md

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Changes

[v1.9.2] - 2023-11-26

  • Fixed bug whereby charstate labels with illegal tokens were incorrectly read.
  • Fixed bug whereby the last charstate label was never detected as duplicate.

[v1.9.1] - 2023-11-25

  • Fixed support for writing comments.

[v1.9.0] - 2023-11-17

  • Support renaming taxa when normalising NEXUS.

[v1.8.0] - 2023-11-16

  • Support writing NEXUS which is "more compatible" with some R packages.
  • Add Python 3.12 to supported versions.

[v1.7.0] - 2023-10-13

Allow adding a comment to blocks created from data.

[v1.6.1] - 2023-10-05

  • Fixed bug whereby the correct precedence of taxa labels was not obeyed when translating trees.

[v1.6.0] - 2023-08-09

  • tools.normalise.normalise now accepts a remove_taxa argument, making it easy to remove taxa from a NEXUS file in a consistent way.

[v1.5.0] - 2023-07-20

  • Make NEXUS content created by commonnexus simpler to parse and thus commonnexus normalise more useful as a tool to prepare NEXUS input for other tools.

[v1.4.0] - 2023-07-18

  • Dropped py3.7 compatibility.
  • Allow unquoted content for SYMBOLS sub-command of FORMAT.
  • Warn (or raise Error) when duplicate character names are specified for a MATRIX.

[v1.3.0] - 2023-05-17

  • Cache translate mappings in TREES block to speedup translation of multiple trees.

[v1.2.0] - 2023-03-15

  • API: Added Tree.newick_string property.

[v1.1.0] - 2023-03-13

  • Fixed bug where the Nexus.cfg was not consulted when reading CHARACTERS MATRIX.
  • Keep state labels when normalising a NEXUS CHARACTERS block.
  • Better support for Morphbank-style references in NOTES.
  • CLI: Support dropping characters by number.
  • CLI: Support batch-renaming taxa via lambda function.
  • CLI: Added split command to split Mesquite's multi-block NEXUS.
  • CLI: Added taxa --describe option, which is particularly useful with Morphobank NEXUS.
  • CLI: Added trees --rename option.
  • CLI Backwards incompatibility: characters --multistatise now requires an argument for the --multistatise option.

[v1.0.0] - 2023-03-08

First, feature-complete release.