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phylo2vec.opt imported GradME eagerly, so any import from it needed jax, optax, tqdm and rpy2. GradME is now imported in a try block: without these, the rest of phylo2vec.opt imports, and asking for GradME raises an ImportError that says what to install. Since only GradME needs them, the [opt] extras are renamed [gradme]. joblib is dropped from them, as it is already a core dependency. The test task now runs the docstring examples of the phylo2vec.opt modules that need no extras, instead of skipping the whole package. BREAKING CHANGE: the [opt] extras are now [gradme]. `pip install phylo2vec[opt]` only warns that the extra does not exist and installs phylo2vec without the GradME dependencies. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Code Review Summary
| Analyzer | Status | Updated (UTC) | Details |
|---|---|---|---|
| Rust |  |
Nov 6, 2026 2:14p.m. | Review ↗ |
| Python | |
Nov 6, 2026 2:14p.m. | Review ↗ |
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Moved to sbhattlab#228 |
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Summary
phylo2vec.optimportedGradMEeagerly, so importing anything from it required jax, optax, tqdm and rpy2. This preparesphylo2vec.optfor the upcoming BME functions, which need none of them.opt/__init__.pyimportsGradMEandgradme_lossin atryblock. Without the extras, the rest ofphylo2vec.optimports normally, andfrom phylo2vec.opt import GradMEraises anImportErrorthat names the extras to install (chained to the original error).__all__andlist_methods()only include GradME when it can be imported.[opt]extras are renamed[gradme], since only GradME needs them.joblibis dropped from them, as it is already a core dependency.pixi run testnow runs the docstring examples inphylo2vec.opt, except in the modules that need the extras or numba (_gradme.py,_gradme_losses.py,utils.py,_beagle_losses.py).[gradme].tests/test_opt.pychecks the import behaviour with jax hidden, in a separate interpreter.Locally, the new tests and the package doctests pass; the doctest run now includes the
list_methodsexample.Breaking change
pip install phylo2vec[opt]no longer installs the GradME dependencies: pip warns that the extra does not exist and installs phylo2vec alone. Usepip install phylo2vec[gradme]instead.Not in this PR
numba, imported by
opt/_beagle_losses.py, is not declared in any dependency list.