ESM openfold_utils type hints #20544
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The documentation is not available anymore as the PR was closed or merged. |
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Wow, this is really comprehensive! All of your edits seem good, and thanks for catching those duplicate functions! The code is failing some of our code style checks, but I believe I can fix that for you, hang on! |
Member
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I think the other issues are just old issues with our repo - they'll be fixed if you pull from upstream on your fork's |
use isinstance builtin instead of 'type(x) is y'; add assertions to aid in type inferencing; use bools instead of ints in _get_minimal_slice_set for improved type clarity; refactor to avoid re-assigning to the same variable with a different type
refactor to avoid re-assigning to the same variable with a different type
refactor to avoid re-assigning to the same variable with a different type
refactor to avoid re-assigning to the same variable with a different type; fix Callable, Tuple type hints; match conditional structure to other methods; fix return type on Rotation.cat and Rotation.unsqueeze
overload for tree_map; use insinstance builtin instead of 'type(x) is y'; export dict_multimap, flatten_final_dims, permute_final_dims in openfold_utils
add FIXME for attempted string mutation; add missing None check in get_pdb_headers; fix potentially unbound variable 'chain_tag' in to_pdb; modify get_pdb_headers return type
hints on collection constants; remove magic trailing comma to reduce number of lines; change list -> tuple for rigid_group_atom_positions for improved hinting
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@ringohoffman Looks good to me now! Are you okay with me merging it? |
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I'm good if you are! |
Rocketknight1
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Dec 5, 2022
mpierrau
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Dec 15, 2022
* add type annotations for esm chunk_utils use isinstance builtin instead of 'type(x) is y'; add assertions to aid in type inferencing; use bools instead of ints in _get_minimal_slice_set for improved type clarity; refactor to avoid re-assigning to the same variable with a different type * add type annotations for esm data_transforms refactor to avoid re-assigning to the same variable with a different type * add type annotations for esm feats utils refactor to avoid re-assigning to the same variable with a different type * add type annotations for esm loss utils * add/fix type annotations for esm rigit_utils refactor to avoid re-assigning to the same variable with a different type; fix Callable, Tuple type hints; match conditional structure to other methods; fix return type on Rotation.cat and Rotation.unsqueeze * add type annotations for esm tensor_utils overload for tree_map; use insinstance builtin instead of 'type(x) is y'; export dict_multimap, flatten_final_dims, permute_final_dims in openfold_utils * add type annotations for esm protein utils add FIXME for attempted string mutation; add missing None check in get_pdb_headers; fix potentially unbound variable 'chain_tag' in to_pdb; modify get_pdb_headers return type * add type annotations for esm residue constants hints on collection constants; remove magic trailing comma to reduce number of lines; change list -> tuple for rigid_group_atom_positions for improved hinting * code style fixup Co-authored-by: Matt <[email protected]>
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What does this PR do?
This PR generally adds type hints for the files located at
src/transformers/models/esm/openfold_utils/.dict_multimap,flatten_final_dims,permute_final_dimsin__init__.pysince these functions are currently duplicated in src/transformers/models/esm/modeling_esmfold.py; exporting these fromopenfold_utilsshould allow us to remove these duplicatestype(x) is yto use the builtinisinstance(x, y)assertstatements to to narrow typesFIXMEstatement at an apparent bug inprotein.pyin which string mutation is attemptedRelated: #16059
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Who can review?
@Rocketknight1