Stochastic Tree Builder Class #60
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Test Results540 tests +29 539 ✅ +29 27m 32s ⏱️ - 18m 3s Results for commit 5fbb6ba. ± Comparison against base commit 4103bde. This pull request removes 13 and adds 42 tests. Note that renamed tests count towards both.♻️ This comment has been updated with latest results. |
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #60 +/- ##
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+ Coverage 96.32% 97.18% +0.86%
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Files 32 41 +9
Lines 4355 5048 +693
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+ Hits 4195 4906 +711
+ Misses 160 142 -18 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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MattesMrzik
reviewed
May 27, 2025
MattesMrzik
reviewed
May 27, 2025
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Yeah I actually have code changes that fix some of what you said, just have the issue using TextSlices from bio package for distance function. Might remove that for now and commit the private tests |
…acg-team/rust-phylo into feature/stochastic-tree-builder * 'feature/stochastic-tree-builder' of https://github.com/acg-team/rust-phylo: Format Rust code using rustfmt
… feature/stochastic-tree-builder
…pass, unwrap needed may change return type of NJBuilder new.
…stic functionality
…acg-team/rust-phylo into feature/stochastic-tree-builder
MattesMrzik
reviewed
Jul 18, 2025
…Builder parameter implemented with default. NJBuilder::new not used as of now.
…dded and function can be broken down further. Good for initial review.
… feature/stochastic-tree-builder
Added a test case with the original distance matrix and final tree from the original paper to check NJBuilder against.
kalxed
commented
Aug 5, 2025
…ic over types implementing EvolutionaryDistance trait, created evolutionary_distances module
…acg-team/rust-phylo into feature/stochastic-tree-builder
Removed mut self from tree builder interface, now rng should be provided to the build method instead
…/rust-phylo into feature/stochastic-tree-builder
Simplified JC96-style evolutionary distance computations and clarified comments
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The rust version was bumped from 1.82.0 to 1.84.0 because the |
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Pull Request Overview
Copilot reviewed 13 out of 13 changed files in this pull request and generated 5 comments.
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Refactored starting tree creation into a method to remove duplicate code
Fixed `nj_builder_fake_softmax` test to make FakeRng return correct values and get exactly identical trees.
Fixed the docstring comment for the argmax option in NJTreeBuilder for clarification Co-authored-by: Mattes Mrzik <[email protected]>
…/rust-phylo into feature/stochastic-tree-builder
Fixied comment to clarify how FakeRng::shuffle works
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Currently changes functionality so that you have to instantiate to use with methods. Not a consistent implementation with methods or associated functions yet, going to move to methods most likely. Distance function argument being developed right now.