DEV: rebase windows-support on main #5
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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 <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>
Pull Request Test Coverage Report for Build 14967002457Details
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rmcar17
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May 19, 2025
* 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 <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](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> * 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] <support@github.com> * 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] <support@github.com> * 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] <support@github.com> * 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] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Yapeng Lang <u7181074@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
rmcar17
added a commit
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May 22, 2025
* Bump iqtree2 from `1320c4c` to `39cbee5` Bumps [iqtree2](https://github.com/iqtree/iqtree2) from `1320c4c` to `39cbee5`. - [Release notes](https://github.com/iqtree/iqtree2/releases) - [Commits](iqtree/iqtree2@1320c4c...39cbee5) --- updated-dependencies: - dependency-name: iqtree2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * DEV: ignore dll files * DEV: update libiqtree function signatures and add custom type convertors for structs * DEV: ensure DLLs are included in build on windows * BUG: on windows, change out of tmp directory before cleaning up * TST: skip tests which throw error on IQ-TREE side on windows * ENH: include cstddef for other platforms * MAINT: ignore attr-defined typing error for non-windows * DEV: add windows build scripts * DEV: build windows when building iqtree and cache correct files. * DEV: test build process on windows * DEV: install boost through action on windows, remove non-available choco packages * DEV: set boost env variables * DEV: debug boost env vars * DEV: removed path debugs, manually specify boost dirs * DEV: manually specify toolchain, downgrade llvm * DEV: add lib.exe to path * DEV: debug msvc path * DEV: try running wswhere through cmd * DEV: try configuring MSVC * DEV: use cmd to setup VS env * DEV: use action to setup msvc * DEV: continue build process with found lib * DEV: only brew install on mac * DEV: use different caches on unix/windows * DEV: Install llvm when testing windows ci, make build_iqtree compatible on local windows * DEV: re-enable full CI matrix * DEV: use runner.os for choosing before_all script * DEV: standardise cache names * DEV: use correct input for cache key * DEV: add windows to cibuildwheel * DEV: run before_all_windows script with bash * DEV: debug BOOST env vars * DEV: attempt hardcoding boost paths * DEV: fix BOOST lib path * DEV: remove hardcoding of BOOST paths * DEV: hardcode paths again * DEV: normalise slashes in before_all_windows * MAINT: remove extra space * MAINT: update python version (#4) * MAINT: Add support for Python 3.13, drop for 3.10 * MAINT: Update nox supported python versions * Bump pypa/cibuildwheel from 2.23.0 to 2.23.1 Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23.0 to 2.23.1. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/v2.23.1/docs/changelog.md) - [Commits](pypa/cibuildwheel@v2.23.0...v2.23.1) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * DEV: update iqtree to error handling version * DEV: update return/arg types for calling IQ-TREE * DEV: remove pytest skips on windows * DEV: rebase windows-support on main (#5) * 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 <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](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> * 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] <support@github.com> * 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] <support@github.com> * 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] <support@github.com> * 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] <support@github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Yapeng Lang <u7181074@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * ENH: fix memory leak in `StringResult` * ENH: free error message memory post-check * ENH: simplify memory freeing for StringResult * ENH: reduce memory leaks for `DoubleArrayResult` * MAINT: don't need to use namespace for `free` * ENH: reduce memory leaks from DoubleArray * MAINT: standardise string usage * MAINT: simplify `tmpDoubles` creation * DEV: add `delvewheel` as dev dependency * MAINT: format TOML file * DEV: add scriv fragment for windows support --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Yapeng Lang <u7181074@gmail.com>
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