DEV: rebase windows-support on main (#5) #207
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* ENH: provide piqtree_nj and nj_tree option for positive branch lengths (iqtree#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 <[email protected]> * 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](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] <[email protected]> * 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](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] <[email protected]> * Bump ruff from 0.11.5 to 0.11.8 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] <[email protected]> * Bump pypa/cibuildwheel from 2.23.2 to 2.23.3 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] <[email protected]> * MAINT: upgrade min `cogent3` and use new `Table` API * ENH: support use of `str` for model in `build_tree` and `fit_tree` * TST: add tests for string represnetations of models * API: simplify expression of model in apps (match that used by `build_tree` and `fit_tree`) * DEV: add scriv fragment * DEV: bump version to 0.5.0 * DEV: collate scriv fragment * DOC: fix typo in release checklist * DEV: update trove classifiers for supported python versions * DEV: add minimum cmake version * Bump ruff from 0.11.8 to 0.11.9 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Yapeng Lang <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Pull Request Test Coverage Report for Build 14967245984Details
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ENH: provide piqtree_nj and nj_tree option for positive branch lengths (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_treenegative branch lengthsMAINT: move from
ArrayAlignmenttoAlignmentin preparation fornew_typedefaultMAINT: simplify logic for negative branch lengths
MAINT: Sort fixtures by number of taxa
MAINT: Remove unused test data file
DEV: Update minimum required
cogent3version (support cogent3 hooks)TST: Remove skip for
quick_treecogent3hook ascogent3min version has updatedBump ruff from 0.11.0 to 0.11.5
Bumps ruff from 0.11.0 to 0.11.5.
updated-dependencies:
Bumps pypa/cibuildwheel from 2.23.1 to 2.23.2.
updated-dependencies:
Bumps ruff from 0.11.5 to 0.11.8.
updated-dependencies:
Bumps pypa/cibuildwheel from 2.23.2 to 2.23.3.
updated-dependencies:
MAINT: upgrade min
cogent3and use newTableAPIENH: support use of
strfor model inbuild_treeandfit_treeTST: add tests for string represnetations of models
API: simplify expression of model in apps (match that used by
build_treeandfit_tree)DEV: add scriv fragment
DEV: bump version to 0.5.0
DEV: collate scriv fragment
DOC: fix typo in release checklist
DEV: update trove classifiers for supported python versions
DEV: add minimum cmake version
Bump ruff from 0.11.8 to 0.11.9
Bumps ruff from 0.11.8 to 0.11.9.
updated-dependencies: