v0.5.0

Contributors

• @GavinHuttley added nj_tree as a hook for cogent3.Alignment.quick_tree.
• @YapengLang handled negative branch lengths from the rapidNJ tree.
• @rmcar17, @thomaskf general maintanence on the piqtree/IQ-TREE sides including work on windows behind the scenes.

ENH

• Add support for Python 3.13, remove support for 3.10
• IQ-TREE's rapidNJ implementation can be used as a hook for quick_tree on cogent3 alignment objects. Try Alignment.quick_tree(use_hook="piqtree").
• nj_tree now by default does not allow negative branch lengths. Set allow_negative=True if this behaviour is desired.
• Allow str to be used for model in build_tree and fit_tree. The value is automatically coerced into the Model class.

API

• Simplify API for piqtree_phylo and piqtree_fit apps. Both now take a single parameter for the model, matching the parameter for model in build_tree and fit_tree.

What's Changed

• Bump ruff from 0.8.2 to 0.8.3 by @dependabot in #140
• Bump mypy from 1.13.0 to 1.14.1 by @dependabot in #149
• Bump ruff from 0.8.3 to 0.9.1 by @dependabot in #150
• DOC: add documentation for developers by @rmcar17 in #151
• ENH: RtD Error Handling + Backup Token Name by @rmcar17 in #152
• ENH: use get for when status isn't in GitHub API return by @rmcar17 in #153
• DOC: add contributing guide to README by @rmcar17 in #154
• ENH: Create CODE_OF_CONDUCT.md by @rmcar17 in #155
• Bump ruff from 0.9.1 to 0.9.2 by @dependabot in #156
• Bump ruff from 0.9.2 to 0.9.3 by @dependabot in #157
• Bump ruff from 0.9.3 to 0.9.4 by @dependabot in #158
• Bump ruff from 0.9.4 to 0.9.7 by @dependabot in #162
• Bump mypy from 1.14.1 to 1.15.0 by @dependabot in #159
• Bump pypa/cibuildwheel from 2.22.0 to 2.23.0 by @dependabot in #164
• Bump ruff from 0.9.7 to 0.9.10 by @dependabot in #166
• Bump iqtree2 from ccf68f4 to 39c2ea4 by @dependabot in #167
• Bump iqtree2 from 39c2ea4 to 92725d3 by @dependabot in #169
• ENH: add piqtree_nj as a cogent3 quick_tree hook by @GavinHuttley in #170
• Bump ruff from 0.9.10 to 0.11.0 by @dependabot in #172
• Bump iqtree2 from 92725d3 to 4da7093 by @dependabot in #174
• Bump iqtree2 from 4da7093 to 1320c4c by @dependabot in #175
• MAINT: Add support for Python 3.13, drop for 3.10 by @rmcar17 in #180
• Bump pypa/cibuildwheel from 2.23.0 to 2.23.1 by @dependabot in #173
• ENH: provide piqtree_nj and nj_tree option for positive branch lengths by @YapengLang in #165
• DEV: Update minimum cogent3 version by @rmcar17 in #186
• Bump ruff from 0.11.0 to 0.11.5 by @dependabot in #193
• Bump pypa/cibuildwheel from 2.23.1 to 2.23.2 by @dependabot in #191
• Bump ruff from 0.11.5 to 0.11.8 by @dependabot in #199
• Bump pypa/cibuildwheel from 2.23.2 to 2.23.3 by @dependabot in #196
• MAINT/API: Fix Table references in latest version of cogent3, simplify API of model for build and fit tree apps by @rmcar17 in #201
• REL: Prepare for 0.5.0 release by @rmcar17 in #202
• DEV: update trove classifiers for supported python versions by @rmcar17 in #203
• DEV: add minimum cmake version by @rmcar17 in #204

Full Changelog: v0.4.0...v0.5.0