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Fix optimisation and Queue Shuffle#71

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Neclow merged 21 commits intomainfrom
fix_opt
Jun 11, 2025
Merged

Fix optimisation and Queue Shuffle#71
Neclow merged 21 commits intomainfrom
fix_opt

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@Neclow Neclow commented Jun 11, 2025

  • Fix Queue Shuffle to make it work as it did in previous repos (using a queue system for internal nodes + node code to encode leaves
  • Adapt Queue Shuffle tests and test against legacy code
  • Fix GradME class and make optimisation classes more consistent + more documented
  • Add demo for optimisation schemes using phylo2vec objects
  • Bump rust version: 0.4.0 --> 0.4.1
  • Bump python version: 1.3.0 --> 1.3.1

See PRs #67 #68 #69 #70

Neclow and others added 21 commits June 11, 2025 16:49
* fix: fix queue shuffle and adapt tests

* docs(rust): add comments in queue_shuffle

* style: pre-commit fixes

* docs: add more docs

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fix: fix queue shuffle and adapt tests

* docs(rust): add comments in queue_shuffle

* style: pre-commit fixes

* docs: add more docs

* refactor: make base class and hc class more consistent

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
docs: add demo for optimisation (added to docs) + bump python version
@Neclow Neclow merged commit 1d832b9 into main Jun 11, 2025
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