Fix bionemo-size-aware-batching, standardize pyproject.toml's & dependencies #284
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malcolmgreaves
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jstjohn,
polinabinder1,
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DejunL,
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malcolmgreaves
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Oct 8, 2024
DejunL
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jstjohn
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Hey @DejunL, PR feedback that is at the level of nits shouldn't be review blocking. Do you have any review-blocking feedback for this PR? Or was the rejection here accidental?
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@malcolmgreaves I just don't like maintaining the import in the API doc. It's not executable code to import anything for |
DejunL
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DejunL
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@malcolmgreaves approved as my comments are not blocking but I'd like to remove those "..." from the README's API doc (see the inline comments above) |
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Ok I can revert those code changes, np. Thank you @DejunL ! |
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…dencies Fix `bionemo-size-aware-batching`'s dependencies: was missing required `bionemo-core` dependency for `torch`! Also includes minor tweaks and touch-ups to its README.md. Fix dependencies of `bionemo-fw` that are already specified by `bionemo-core` (PyTorch Lightning). Standardizes the format & structure of all pyproject.toml files under sub-packages/. Makes sure that every bionemo sub-package depends on bionemo-core (minus bionemo-core itself). Make sure that `bionemo-fw` depends on every other bionemo sub-package (minus intentional exceptions). Eensures that the top level pyproject.toml (`"bionemo-meta"`) correctly lists all bionemo sub-packages in the workspace. Specifically, fixes `tool.uv.sources`, `project.dependencies`, and `tool.pyright`. Finally, fixes a few errors from linting with `ruff` that somehow were not caught during previous PRs.
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Fix
bionemo-size-aware-batching's dependencies: was missing requiredbionemo-coredependency fortorch!Also includes minor tweaks and touch-ups to its README.md.
Fix dependencies of
bionemo-fwthat are already specified bybionemo-core(PyTorch Lightning).Standardizes the format & structure of all pyproject.toml files under sub-packages/.
Makes sure that every bionemo sub-package depends on bionemo-core (minus bionemo-core itself).
Make sure that
bionemo-fwdepends on every other bionemo sub-package (minus intentional exceptions).Additionally, ensures that the top level pyproject.toml (
"bionemo-meta") correctly lists all bionemosub-packages in the workspace. Specifically, fixes
tool.uv.sources,project.dependencies, andtool.pyright.