ENH: Add windows support #184
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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] <[email protected]>
…le on local windows
* 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] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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A note that the windows-latest status checks should be added to the ruleset for merging to main |
Pull Request Test Coverage Report for Build 14968114796Details
💛 - Coveralls |
tests/test_iqtree/test_build_tree.py
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suggest making this an xfail, rather than skipif, since the intent is to fix this. actually, nix that because the whole thing will probably crash if this is not blocked
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Yep that's right, unfortunately crashes the tests if not skipped. Though @thomaskf is working on a different way of propogating error messages to the python side.
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This now processes error messages from IQ-TREE on windows. All that remains is the question of memory leaks from heap allocated struct members. |
* 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 --------- 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>
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#43
Adds windows support to piqtree including in release workflow.
Limitation with relying with error handling on IQ-TREE side - errors which would be thrown as an IqTreeError on mac/linux instead cause an ungraceful exit. See skipped tests for examples. Could potentially handle common cases on Python side, though preference would be handling on IQ-TREE side in the long-term so new errors can be freely added/removed without duplication on Python side.
Phew!