rmcar17 / piqtree / 14967231703

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DEV: rebase windows-support on main  (#5)

* ENH: provide piqtree_nj and nj_tree option for positive branch lengths (#165)

* ENH: parameter to restrict negative value of branch length

* TST: allow_negative correctly control the behavior of branch length in nj_tree

* ENH: add parameter allow_negative in piqtree_nj app

* MAINT: fix double return error in merge

* MAINT: ruff formatting

* TST: Use full fasta file for checking `nj_tree` negative branch lengths

* MAINT: move from `ArrayAlignment` to `Alignment` in preparation for `new_type` default

* MAINT: simplify logic for negative branch lengths

* MAINT: Sort fixtures by number of taxa

* MAINT: Remove unused test data file

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Co-authored-by: Robert McArthur <robert.mcarthur@anu.edu.au>

* DEV: Update minimum required `cogent3` version (support cogent3 hooks)

* TST: Remove skip for `quick_tree` `cogent3` hook as `cogent3` min version has updated

* Bump ruff from 0.11.0 to 0.11.5

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.0 to 0.11.5.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/0.11.0...0.11.5)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.11.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump pypa/cibuildwheel from 2.23.1 to 2.23.2

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23.1 to 2.23.2.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](https://github.com/pypa/cibuildwheel/compare/v2.23.1...v2.23.2)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabo... (continued)

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