DEV: rebase windows-support on main #206
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#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 --------- Co-authored-by: Robert McArthur <robert.mcarthur@anu.edu.au>
…sion has updated
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](astral-sh/ruff@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>
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](pypa/cibuildwheel@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: dependabot[bot] <support@github.com>
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.5 to 0.11.8. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.11.5...0.11.8) --- updated-dependencies: - dependency-name: ruff dependency-version: 0.11.8 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23.2 to 2.23.3. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](pypa/cibuildwheel@v2.23.2...v2.23.3) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-version: 2.23.3 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
…tree` and `fit_tree`)
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.8 to 0.11.9. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.11.8...0.11.9) --- updated-dependencies: - dependency-name: ruff dependency-version: 0.11.9 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
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