v0.6.0

Contributors

• @rmcar17 and @thomaskf enabled windows support for piqtree!
• @rmcar17 ensured nj_tree raises an appropriate error on NaN input.
• @rmcar17 reworked random_trees and the related app to become random_tree, returning a single tree.
• @rmcar17 and @thomaskf integrated IQ-TREE 3 into piqtree.
• @rmcar17 added support for Lie Markov Model prefixes.
• @rmcar17 added the STRSYM and UNREST models.
• @rmcar17 added source tracking for the inputs of apps.
• @rmcar17 and @thomaskf integrated consensus tree construction into piqtree.
• @rmcar17 added support for the parameterisation of currently supported models, base frequencies, and rate heterogeneity.
• @GavinHuttley improved the docs and performed some deprecation maintanence for a dependency.

ENH

• Added windows support!
• Add random_tree and piqtree_random_tree. The function and app have the same parameters as the random_trees and piqtree_random_trees versions, except the num_trees argument has been removed.
• piqtree now uses IQ-TREE 3 for its internal library.
• Add support for Lie Markov Model prefixes.
• Add the STRSYM and UNREST models.
• piqtree apps now track the sources of their inputs.
• Add a method for building consensus trees with specifiable support parameters.
• Add a consensus tree app.
• Substitution models, base frequencies, and models for rateheterogeneity can now be parameterised.

BUG

• An error is now raised when calling nj_tree with NaN distances instead of failing silently.

API

• Split Lie Markov Models out of the standard dna enum.
• Remove unused rand_seed from fit_tree.
• All apps have been renamed to take the form piq_<func_name>.
• random_trees and piqtree_random_trees have been removed in favour of random_tree and piq_random_tree. Looping can be used if multiple trees are needed.

What's Changed

• Bump ruff from 0.11.8 to 0.11.9 by @dependabot[bot] in #205
• Bump ruff from 0.11.9 to 0.11.10 by @dependabot[bot] in #210
• ENH: Add windows support by @rmcar17 in #184
• Bump iqtree2 from 1320c4c to c401ac4 by @dependabot[bot] in #198
• ENH: Handle when distance matrix contains NaN values (raise exception) by @rmcar17 in #213
• TST: only check for piqtree provenance on quick tree hook when piqtree explicitly selected by @rmcar17 in #214
• Bump MarkusJx/install-boost from 2.4.5 to 2.5.0 in /.github/actions/build-iqtree by @dependabot[bot] in #217
• Bump MarkusJx/install-boost from 2.4.5 to 2.5.0 by @dependabot[bot] in #216
• Bump ruff from 0.11.10 to 0.11.11 by @dependabot[bot] in #215
• DEV: Add action to upload full sdist (including submodules) to releases by @rmcar17 in #218
• ENH: Build docs filters by workflow to avoid runs getting buried. Also ensures actual latest is used by @rmcar17 in #219
• MAINT: Reduce readthedocs polling interval by @rmcar17 in #220
• MAINT: Standarise actions and prepare for IQ-TREE 3 by @rmcar17 in #221
• DEV: specify minimum permissions for github actions to work by @rmcar17 in #222
• ENH: Add SHA256 Checksum to Release by @rmcar17 in #223
• DEV: Cancel old CI runs when new run on same target starts by @rmcar17 in #225
• MAINT: Remove references to IQ-TREE 2 in favour of simply IQ-TREE by @rmcar17 in #226
• DOC: Modernise Examples in README, and Ruff Badge by @rmcar17 in #228
• Bump mypy from 1.15.0 to 1.16.0 by @dependabot[bot] in #230
• Bump ruff from 0.11.11 to 0.11.12 by @dependabot[bot] in #229
• Bump ruff from 0.11.12 to 0.11.13 by @dependabot[bot] in #231
• DEV: update cogent3 by @rmcar17 in #233
• API: Discontinue random_trees and related app in favour of random_tree by @rmcar17 in #232
• Bump softprops/action-gh-release from 2.2.2 to 2.3.2 by @dependabot[bot] in #234
• Bump pypa/cibuildwheel from 2.23.3 to 3.0.0 by @dependabot[bot] in #235
• DEV: Move to IQ-TREE 3 by @rmcar17 in #236
• DEV: add scriv fragment for IQ-TREE 3 by @rmcar17 in #238
• Bump iqtree3 from f7660f4 to 1357e36 by @dependabot[bot] in #239
• MAINT: Split out Lie Markov Model Class by @rmcar17 in #240
• ENH: add UNREST and STRSYM models by @rmcar17 in #241
• ENH: Track sources of objects on apps by @rmcar17 in #242
• MAINT: address cogent3 tree .traverse() deprecation by @GavinHuttley in #244
• Bump iqtree3 from 1357e36 to d9bc0a6 by @dependabot[bot] in #246
• ENH: Add consensus tree merger by @rmcar17 in #245
• Bump iqtree3 from d9bc0a6 to ce5b6ce by @dependabot[bot] in #247
• DOC: Modernise docs by @rmcar17 in #250
• Bump mypy from 1.16.0 to 1.16.1 by @dependabot[bot] in #249
• DEV: Use main repo for iqtree3 by @rmcar17 in #251
• API: Remove rand_seed from fit_tree by @rmcar17 in #252
• Bump ruff from 0.11.13 to 0.12.0 by @dependabot[bot] in #248
• DEV: ignore dependabot push ci jobs (already triggered by pull_request) by @rmcar17 in #254
• DEV: Improve testing speed by @rmcar17 in #255
• Bump iqtree3 from ce5b6ce to 993275d by @dependabot[bot] in #253
• DEV: Update license in toml to use SPDX license expression by @rmcar17 in #256
• ENH: Add consensus tree app by @rmcar17 in #257
• MAINT: Ensure testing compatability with new cogent3 version (new get_distances) by @rmcar17 in #258
• Mods to documentation structure and assorted tweaks by @GavinHuttley in #259
• DEV: Downgrade cibuildwheel as broken with Python 3.13.4 (numba) by @rmcar17 in #260
• MAINT: Reduce size of wheels (>90% reduction on linux) by @rmcar17 in #261
• DOC: Test .py files in docs by @rmcar17 in #262
• MAINT: exclude scripts folder from docs building by @rmcar17 in #263
• DEV: Fix IQ-TREE building on CI by @rmcar17 in #268
• Bump ruff from 0.12.0 to 0.12.1 by @dependabot[bot] in #267
• Bump iqtree3 from 993275d to 7cded0c by @dependabot[bot] in #264
• API: Rename apps by @rmcar17 in #271
• ENH: Parameterise models by @rmcar17 in #275
• DEV: Upgrade cibuildwheel dependency by @rmcar17 in #277
• Bump ruff from 0.12.1 to 0.12.2 by @dependabot[bot] in #272
• DEV: Update cogent3 by @rmcar17 in #278
• DEV: Prepare for 0.6.0 release by @rmcar17 in #279

Full Changelog: v0.5.0...v0.6.0