ENH: Add windows support #184
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
|
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 15152165805Details
💛 - Coveralls |
|
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>
Closed
|
Memory leaks for the struct types have now been resolved |
|
Squashing to only keep working states |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
#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!