Changes in release "0.4.0"

Contributors

• @rmcar17 integrated new functions from IQ-TREE in Python, added multithreading support, and wrote the API refererence and quickstart.
• @thomaskf exposed all new functions from IQ-TREE to be available from Python, and worked on multithreading support.
• @GavinHuttley worked on setting up and writing the documentation and associated devtools, ModelFinder, and integration with cogent3 apps.
• @YapengLang worked on bootstrapping support and extracting model parameters
• @KatherineCaley worked on processing the ModelFinder results.

ENH

• piqtree2 renamed piqtree to support future major releases of IQ-TREE.
• piqtree now supports multithreading!
• New function nj_tree constructs a rapid neighbour-joining tree from a pairwise distance matrix.
• New function model_finder finds the best model for a given alignment.
• New function jc_distances constructs a pairwise JC distance matrix from an alignment.
• New function make_model allows converting an IQ-TREE string representation of a model to a Model class.
• API for random_trees has changed - new order (num_trees, num_taxa, tree_mode, then rand_seed).
• API for robinson_foulds has changed - now accepts a Sequence of trees.
• Model parameters are now extracted from IQ-TREE where for now possible.
• build_tree now supports ultrafast bootstrapping.
• Model creation is now more robust.
• Use piqtree.__iqtree_version__ to see what version of piqtree is being used.
• See what can now be done in our new documentation!

DOC

• Documentation is now on readthedocs!

What's Changed

• DEV: remove ssh mounts (use ssh-agent instead) by @rmcar17 in #64
• Bump iqtree2 from 9ee7f6c to cf47d36 by @dependabot in #63
• DEV: remove ssh mount (use ssh-agent instead) by @rmcar17 in #65
• Bump iqtree2 from cf47d36 to 07aa4b3 by @dependabot in #70
• ENH: attached rate and motif parameters to cogent3 tree object by @YapengLang in #49
• Bump pypa/cibuildwheel from 2.20.0 to 2.21.1 by @dependabot in #71
• Bump iqtree2 from 07aa4b3 to 70152d2 by @dependabot in #74
• ENH: add support for nj tree, jc distances, and raw results of model finder by @rmcar17 in #79
• Bump pypa/cibuildwheel from 2.21.1 to 2.21.3 by @dependabot in #80
• TST: added tests for branch lengths by @YapengLang in #82
• Bump iqtree2 from 70152d2 to f04b6f2 by @dependabot in #81
• ENH: parse parameters in Lie Markov model and rate model by @YapengLang in #88
• DEV: Drop support for Python 3.9 by @rmcar17 in #86
• MAINT: ensure unix line endings (artefact from initial windows development) by @rmcar17 in #89
• ENH: modifications in prep for the documentation by @GavinHuttley in #85
• ENH: add bootstrapping parameter in build_tree, and update _process_tree_yaml to handle inconsistent newick by @YapengLang in #91
• ENH: Add JC Distance App by @rmcar17 in #92
• ENH: Model can be imported from top level by @rmcar17 in #93
• DOC: Use new Model API in README by @rmcar17 in #94
• DEV: Add Type Checking With mypy by @rmcar17 in #95
• MAINT: fix piqtree_fit app help by @rmcar17 in #100
• Misc changes by @GavinHuttley in #101
• API and DOC by @GavinHuttley in #103
• DEV: add ruff linting to CI by @rmcar17 in #104
• Prepping for rtd by @GavinHuttley in #105
• Support serialisation of ModelFinderResult by @GavinHuttley in #106
• DEV: git submodule update by @GavinHuttley in #107
• DEV: bump version to trigger doc build by @GavinHuttley in #108
• Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 by @dependabot in #109
• MAINT: Fix linting, pin ruff by @rmcar17 in #110
• DEV: added scripts for building and uploading docs by @GavinHuttley in #111
• DEV: Simplify Workflows by @rmcar17 in #112
• Bump iqtree2 from f04b6f2 to 18fa5a3 by @dependabot in #113
• Bump iqtree2 from 18fa5a3 to ea7a080 by @dependabot in #114
• DOC: infrastructure by @GavinHuttley in #115
• DOC: case matters by @GavinHuttley in #117
• DOC: fixes to docs by @GavinHuttley in #118
• DEV: added link to documentation to pyproject.toml by @GavinHuttley in #119
• Bump iqtree2 from ea7a080 to da38244 by @dependabot in #120
• Bump ruff from 0.8.0 to 0.8.1 by @dependabot in #122
• DOC: point README to documentation website by @rmcar17 in #121
• Bump iqtree2 from da38244 to 839f3f1 by @dependabot in #123
• DEV: Support building all mac/linux wheels by @rmcar17 in #124
• ENH: refactor ModelFinderResult to use new ModelResultValue class, fixes #102 by @KatherineCaley in #125
• Bump ruff from 0.8.1 to 0.8.2 by @dependabot in #126
• Bump iqtree2 from 839f3f1 to ccf68f4 by @dependabot in #127
• ENH: export iqtree version to piqtree2 module by @rmcar17 in #128
• DEV: fix typo in linting ci job by @rmcar17 in #129
• DOC: add quickstart and API reference by @rmcar17 in #130
• DEV: make dockerfile setup dev environment by @rmcar17 in #131
• DEV: push to iqtree ghcr by @rmcar17 in #132
• DEV: fix build for dockerfile by @rmcar17 in #133
• DEV: revert docker editting by @rmcar17 in #134
• MAINT: rename piqtree2 to piqtree by @rmcar17 in #135
• DEV: store devcontainer in iqtree org, include btop and rename env to piq-dev by @rmcar17 in #136
• ENH: add make_model by @rmcar17 in #137
• DOC: Add documentation for model_finder by @rmcar17 in #138
• REL: release 0.4.0 by @rmcar17 in #139

New Contributors

• @YapengLang made their first contribution in #49
• @KatherineCaley made their first contribution in #125

Full Changelog: v0.3.1...v0.4.0

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)

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

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

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