v0.3.1

Changes in release "0.3.1"

ENH

• Add support for Lie Markov Models.
• Base frequencies default to None (specified by model).

BUG

• piqtree2 apps are now pickleable (they can now be run with parallel=True in the cogent3 app infrastructure)

v0.3.0

Contributors

• @rmcar17 Added new classes to enhance model specification when calling build_tree and fit_tree.
• @thomaskf fixed a bug in IQ-TREE resulting in segmentation faults on some invalid arguments.

ENH

• build_tree and fit_tree now allow specifying base frequencies, invariable sites and rate heterogeneity options.

BUG

• Fixed a segmentation fault on repetitive calls to IQ-TREE with particular arguments.

What's Changed

• Bump iqtree2 from b73ea6c to 5725858 by @dependabot in #38
• ENH: add freq rate type including rate het by @rmcar17 in #39

Full Changelog: 0.2.0...v0.3.0

0.2.0

Contributors

• Richard Morris

• Robert McArthur

ENH

• build_tree and fit_tree now use enums for the substitution model.

BUG

• Fixed an issue where calling build_tree or fit_tree twice, then another function with invalid input resulted in a segmentation fault.

DOC

• Implement scriv as a tool to manage collection of changes, and automated collation into the changelog

v0.1.0

The first official release of piqtree2!

piqtree2 allows you to use IQ-TREE for phylogenetic analysis directly from python.

Currently, we support phylogenetic reconstruction, fitting branch lengths to a fixed topology, generating random tress, and pairwise RF distance of trees.

piqtree2 is still in early pre-alpha development, please raise an issue if you encounter any problems or have any feature requests.

What's Changed

• Build container workflow by @khiron in #8
• disable container build for now by @khiron in #9
• Python API for piqtree2 by @khiron in #10
• ENH: define cogent3 apps and add test stub by @GavinHuttley in #15
• ENH: added available_models() convenience function by @GavinHuttley in #18
• Bump actions/checkout from 2 to 4 by @dependabot in #20
• Bump pypa/cibuildwheel from 2.19.1 to 2.19.2 by @dependabot in #19

New Contributors

• @khiron made their first contribution in #8
• @GavinHuttley made their first contribution in #15
• @dependabot made their first contribution in #20

Full Changelog: https://github.com/iqtree/piqtree2/commits/v0.1.0