openfold3/core/config/msa_pipeline_configs.py:0: error: "DatasetChainData" has no attribute "chains"  [attr-defined]
openfold3/core/data/framework/data_module.py:0: error: "dict[Any, Any]" has no attribute "config"  [attr-defined]
openfold3/core/data/framework/data_module.py:0: error: "dict[Any, Any]" has no attribute "dataset_class"  [attr-defined]
openfold3/core/data/framework/data_module.py:0: error: "dict[Any, Any]" has no attribute "mode"  [attr-defined]
openfold3/core/data/framework/data_module.py:0: error: "dict[Any, Any]" has no attribute "weight"  [attr-defined]
openfold3/core/data/framework/data_module.py:0: error: "list[Tensor]" has no attribute "squeeze"  [attr-defined]
openfold3/core/data/framework/data_module.py:0: error: Argument "compute_settings" to "augment_main_msa_with_query_sequence" has incompatible type "MsaComputationSettings | None"; expected "MsaComputationSettings"  [arg-type]
openfold3/core/data/framework/data_module.py:0: error: Argument "compute_settings" to "preprocess_colabfold_msas" has incompatible type "MsaComputationSettings | None"; expected "MsaComputationSettings"  [arg-type]
openfold3/core/data/framework/data_module.py:0: error: Argument 1 to "parse_data_config" of "DataModule" has incompatible type "list[BaseModel]"; expected "list[dict[Any, Any]]"  [arg-type]
openfold3/core/data/framework/data_module.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[Tensor]")  [assignment]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "crop"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "crop"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "crop"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "None" of "dict[str, Any] | None" has no attribute "template_preprocessor_settings"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "crop"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "crop"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "crop"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "query_set"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Item "dict[str, Any]" of "dict[str, Any] | None" has no attribute "template_preprocessor_settings"  [union-attr]
openfold3/core/data/framework/data_module.py:0: error: Need type annotation for "generators" (hint: "generators: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/framework/data_module.py:0: error: Need type annotation for "next_dataset_indices" (hint: "next_dataset_indices: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/framework/data_module.py:0: error: No overload variant of "__setitem__" of "list" matches argument types "str", "list[Tensor]"  [call-overload]
openfold3/core/data/framework/data_module.py:0: error: No overload variant of "__setitem__" of "list" matches argument types "str", "list[Tensor]"  [call-overload]
openfold3/core/data/framework/data_module.py:0: error: Unsupported operand types for + ("int" and "None")  [operator]
openfold3/core/data/framework/data_module.py:0: note: Possible overload variants:
openfold3/core/data/framework/data_module.py:0: note: Possible overload variants:
openfold3/core/data/framework/data_module.py:0: note: def __setitem__(self, SupportsIndex, dict[str, Tensor], /) -> None
openfold3/core/data/framework/data_module.py:0: note: def __setitem__(self, SupportsIndex, dict[str, Tensor], /) -> None
openfold3/core/data/framework/data_module.py:0: note: def __setitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], Iterable[dict[str, Tensor]], /) -> None
openfold3/core/data/framework/data_module.py:0: note: def __setitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], Iterable[dict[str, Tensor]], /) -> None
openfold3/core/data/framework/single_datasets/abstract_single.py:0: error: "type[SingleDataset]" has no attribute "_registered"  [attr-defined]
openfold3/core/data/framework/single_datasets/abstract_single.py:0: error: Incompatible types in assignment (expression has type "int", variable has type "None")  [assignment]
openfold3/core/data/framework/single_datasets/abstract_single.py:0: error: Need type annotation for "DATASET_REGISTRY" (hint: "DATASET_REGISTRY: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "None" has no attribute "reference_molecule_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "None" has no attribute "structure_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "None" has no attribute "structure_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "None" has no attribute "structure_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "None" has no attribute "structure_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "None" has no attribute "structure_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: Incompatible return value type (got "dict[str, Any]", expected "tuple[dict[Any, Any], AtomArray[Any] | Tensor]")  [return-value]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: Incompatible types in assignment (expression has type "PreprocessingDataCache | DatasetCache", variable has type "None")  [assignment]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: Incompatible types in assignment (expression has type "dict[Never, Never]", variable has type "None")  [assignment]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: Invalid type comment or annotation  [valid-type]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: Need type annotation for "assembly_data" (hint: "assembly_data: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: Need type annotation for "sample_data"  [var-annotated]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: callable? not callable  [misc]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: callable? not callable  [misc]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: callable? not callable  [misc]
openfold3/core/data/framework/single_datasets/base_of3.py:0: error: callable? not callable  [misc]
openfold3/core/data/framework/single_datasets/base_of3.py:0: note: did you mean to use ',' instead of ':' ?
openfold3/core/data/framework/single_datasets/inference.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/framework/single_datasets/inference.py:0: error: Argument 1 to "update" of "MutableMapping" has incompatible type "dict[str, Tensor]"; expected "SupportsKeysAndGetItem[str, AtomArray[Any]]"  [arg-type]
openfold3/core/data/framework/single_datasets/inference.py:0: error: Incompatible types in assignment (expression has type "BiotiteCCDWrapper", variable has type "CIFFile")  [assignment]
openfold3/core/data/framework/single_datasets/inference.py:0: error: Invalid type comment or annotation  [valid-type]
openfold3/core/data/framework/single_datasets/inference.py:0: note: did you mean to use ',' instead of ':' ?
openfold3/core/data/framework/single_datasets/monomer.py:0: error: "None" has no attribute "iloc"  [attr-defined]
openfold3/core/data/framework/single_datasets/monomer.py:0: error: "None" has no attribute "release_connections"  [attr-defined]
openfold3/core/data/framework/single_datasets/monomer.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/framework/single_datasets/monomer.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "None")  [assignment]
openfold3/core/data/framework/single_datasets/monomer.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "None")  [assignment]
openfold3/core/data/framework/single_datasets/monomer.py:0: error: Invalid type comment or annotation  [valid-type]
openfold3/core/data/framework/single_datasets/monomer.py:0: note: did you mean to use ',' instead of ':' ?
openfold3/core/data/framework/single_datasets/pdb.py:0: error: "None" has no attribute "iloc"  [attr-defined]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: "None" has no attribute "release_connections"  [attr-defined]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: "None" has no attribute "structure_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: "None" has no attribute "structure_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: "dict[Any, Any]" has no attribute "disable_non_protein_diffusion_weights"  [attr-defined]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: "dict[Any, Any]" has no attribute "sample_weights"  [attr-defined]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: Argument 1 to "append" of "list" has incompatible type "DatapointType"; expected "str"  [arg-type]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: Incompatible types in assignment (expression has type "list[MoleculeType]", variable has type "str | tuple[str, str]")  [assignment]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: Invalid type comment or annotation  [valid-type]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: No overload variant of "get" of "dict" matches argument types "MoleculeType", "int"  [call-overload]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: No overload variant of "get" of "dict" matches argument types "MoleculeType", "int"  [call-overload]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: No overload variant of "get" of "dict" matches argument types "MoleculeType", "int"  [call-overload]
openfold3/core/data/framework/single_datasets/pdb.py:0: error: No overload variant of "get" of "dict" matches argument types "MoleculeType", "int"  [call-overload]
openfold3/core/data/framework/single_datasets/pdb.py:0: note: Possible overload variants:
openfold3/core/data/framework/single_datasets/pdb.py:0: note: Possible overload variants:
openfold3/core/data/framework/single_datasets/pdb.py:0: note: Possible overload variants:
openfold3/core/data/framework/single_datasets/pdb.py:0: note: Possible overload variants:
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def [_T] get(self, str, _T, /) -> int | _T
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def [_T] get(self, str, _T, /) -> int | _T
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def [_T] get(self, str, _T, /) -> int | _T
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def [_T] get(self, str, _T, /) -> int | _T
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def get(self, str, None = ..., /) -> int | None
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def get(self, str, None = ..., /) -> int | None
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def get(self, str, None = ..., /) -> int | None
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def get(self, str, None = ..., /) -> int | None
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def get(self, str, int, /) -> int
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def get(self, str, int, /) -> int
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def get(self, str, int, /) -> int
openfold3/core/data/framework/single_datasets/pdb.py:0: note: def get(self, str, int, /) -> int
openfold3/core/data/framework/single_datasets/pdb.py:0: note: did you mean to use ',' instead of ':' ?
openfold3/core/data/framework/single_datasets/validation.py:0: error: "None" has no attribute "iloc"  [attr-defined]
openfold3/core/data/framework/single_datasets/validation.py:0: error: "None" has no attribute "release_connections"  [attr-defined]
openfold3/core/data/framework/single_datasets/validation.py:0: error: "None" has no attribute "structure_data"  [attr-defined]
openfold3/core/data/framework/single_datasets/validation.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/framework/single_datasets/validation.py:0: error: Argument 2 to "make_chain_pair_mask_padded" has incompatible type "list[tuple[int, ...]]"; expected "list[tuple[int, int]]"  [arg-type]
openfold3/core/data/framework/single_datasets/validation.py:0: error: Invalid type comment or annotation  [valid-type]
openfold3/core/data/framework/single_datasets/validation.py:0: note: did you mean to use ',' instead of ':' ?
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: "SingleDataset" has no attribute "get_worker_path"  [attr-defined]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: "SingleDataset" has no attribute "name"  [attr-defined]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: "SingleDataset" has no attribute "name"  [attr-defined]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: "SingleDataset" has no attribute "name"  [attr-defined]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: "SingleDataset" has no attribute "name"  [attr-defined]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: Argument 1 to "len" has incompatible type "SingleDataset"; expected "Sized"  [arg-type]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: Argument 1 to "len" has incompatible type "SingleDataset"; expected "Sized"  [arg-type]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: Argument 1 to "len" has incompatible type "SingleDataset"; expected "Sized"  [arg-type]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: Argument 1 to "manual_seed" of "Generator" has incompatible type "int | float"; expected "int"  [arg-type]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: Incompatible default for parameter "epoch_len" (default has type "None", parameter has type "int")  [assignment]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: Value of type "None" is not indexable  [index]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: error: Value of type "None" is not indexable  [index]
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/data/framework/stochastic_sampler_dataset.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/data/io/dataset_cache.py:0: error: Item "DatasetCache" of "PreprocessingDataCache | DatasetCache" has no attribute "_type"  [union-attr]
openfold3/core/data/io/dataset_cache.py:0: error: Item "None" of "bytes | None" has no attribute "decode"  [union-attr]
openfold3/core/data/io/dataset_cache.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "_type"  [union-attr]
openfold3/core/data/io/s3.py:0: error: Argument 1 to "start_s3_client" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/io/s3.py:0: error: Incompatible default for parameter "check_filename_exists" (default has type "None", parameter has type "str")  [assignment]
openfold3/core/data/io/s3.py:0: error: Incompatible return value type (got "IO[Any]", expected "StringIO | BytesIO")  [return-value]
openfold3/core/data/io/s3.py:0: error: Incompatible return value type (got "list[Path]", expected "list[str]")  [return-value]
openfold3/core/data/io/s3.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/data/io/s3.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_mol_type"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_mol_type"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_mol_type"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_rep_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_rep_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_rep_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_rep_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_rep_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_rep_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "chain_id_to_rep_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_chain_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_chain_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_chain_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_chain_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_chain_id"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_main_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_mol_type"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_mol_type"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_mol_type"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_mol_type"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_mol_type"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_paired_msa"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_paired_msa"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_paired_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_paired_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_paired_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_paired_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_paired_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_paired_msa_paths"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_query_seq"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_query_seq"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_query_seq"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_query_seq"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "MsaSampleParserMapper" has no attribute "rep_id_to_query_seq"  [attr-defined]
openfold3/core/data/io/sequence/msa.py:0: error: "create_maps" of "MsaSampleParser" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/core/data/io/sequence/msa.py:0: error: "parse_msas" of "MsaSampleParser" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/core/data/io/sequence/msa.py:0: error: Argument "deletion_matrix" to "from_parsed" of "MsaArray" has incompatible type "list[list[int]]"; expected "ndarray[tuple[Any, ...], dtype[Any]]"  [arg-type]
openfold3/core/data/io/sequence/msa.py:0: error: Argument "deletion_matrix" to "from_parsed" of "MsaArray" has incompatible type "list[list[int]]"; expected "ndarray[tuple[Any, ...], dtype[Any]]"  [arg-type]
openfold3/core/data/io/sequence/msa.py:0: error: Argument 1 to "create_msa_array_collection" of "MsaSampleParser" has incompatible type "None"; expected "MsaSampleParserMapper"  [arg-type]
openfold3/core/data/io/sequence/msa.py:0: error: Function "numpy._core.multiarray.array" is not valid as a type  [valid-type]
openfold3/core/data/io/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "Callable[[list[Path]], dict[str, MsaArray]]", variable has type "partial[dict[str, MsaArray]]")  [assignment]
openfold3/core/data/io/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "Callable[[list[Path]], dict[str, MsaArray]]", variable has type "partial[dict[str, MsaArray]]")  [assignment]
openfold3/core/data/io/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[list[int]]")  [assignment]
openfold3/core/data/io/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[list[int]]")  [assignment]
openfold3/core/data/io/sequence/msa.py:0: error: Signature of "create_maps" incompatible with supertype "MsaSampleParser"  [override]
openfold3/core/data/io/sequence/msa.py:0: error: Signature of "create_maps" incompatible with supertype "MsaSampleParser"  [override]
openfold3/core/data/io/sequence/msa.py:0: error: Signature of "parse_msas" incompatible with supertype "MsaSampleParser"  [override]
openfold3/core/data/io/sequence/msa.py:0: error: Signature of "parse_msas" incompatible with supertype "MsaSampleParser"  [override]
openfold3/core/data/io/sequence/msa.py:0: error: Unexpected keyword argument "input" for "create_maps" of "MsaSampleParser"  [call-arg]
openfold3/core/data/io/sequence/msa.py:0: error: Unexpected keyword argument "maps" for "parse_msas" of "MsaSampleParser"  [call-arg]
openfold3/core/data/io/sequence/msa.py:0: error: Unsupported operand types for / ("None" and "Path")  [operator]
openfold3/core/data/io/sequence/msa.py:0: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
openfold3/core/data/io/sequence/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/io/sequence/msa.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/io/sequence/msa.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/data/io/sequence/msa.py:0: note: Subclass:
openfold3/core/data/io/sequence/msa.py:0: note: Subclass:
openfold3/core/data/io/sequence/msa.py:0: note: Subclass:
openfold3/core/data/io/sequence/msa.py:0: note: Subclass:
openfold3/core/data/io/sequence/msa.py:0: note: Superclass:
openfold3/core/data/io/sequence/msa.py:0: note: Superclass:
openfold3/core/data/io/sequence/msa.py:0: note: Superclass:
openfold3/core/data/io/sequence/msa.py:0: note: Superclass:
openfold3/core/data/io/sequence/msa.py:0: note: def create_maps(self) -> None
openfold3/core/data/io/sequence/msa.py:0: note: def create_maps(self) -> None
openfold3/core/data/io/sequence/msa.py:0: note: def create_maps(self, input: MsaSampleProcessorInputInference) -> MsaSampleParserMapper
openfold3/core/data/io/sequence/msa.py:0: note: def create_maps(self, input: MsaSampleProcessorInputTrain) -> MsaSampleParserMapper
openfold3/core/data/io/sequence/msa.py:0: note: def parse_msas(self) -> None
openfold3/core/data/io/sequence/msa.py:0: note: def parse_msas(self) -> None
openfold3/core/data/io/sequence/msa.py:0: note: def parse_msas(self, maps: MsaSampleParserMapper) -> MsaSampleParserMapper
openfold3/core/data/io/sequence/msa.py:0: note: def parse_msas(self, maps: MsaSampleParserMapper) -> MsaSampleParserMapper
openfold3/core/data/io/sequence/template.py:0: error: Argument "query_aln_str" to "_process_alignment_hits" of "TemplateParser" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/io/sequence/template.py:0: error: Argument "template_alignments" to "_process_alignment_hits" of "TemplateParser" has incompatible type "Sequence[str]"; expected "list[str]"  [arg-type]
openfold3/core/data/io/sequence/template.py:0: error: Argument "template_alignments" to "_process_alignment_hits" of "TemplateParser" has incompatible type "list[str | None]"; expected "list[str]"  [arg-type]
openfold3/core/data/io/sequence/template.py:0: error: Cannot instantiate abstract class "TemplateParser" with abstract attribute "__call__"  [abstract]
openfold3/core/data/io/sequence/template.py:0: error: Incompatible types in assignment (expression has type "Literal[0] | bool | None", variable has type "bool")  [assignment]
openfold3/core/data/io/sequence/template.py:0: error: Incompatible types in assignment (expression has type "int", base class "tuple" defined the type as "Callable[[Any, SupportsIndex, SupportsIndex], int]")  [assignment]
openfold3/core/data/io/sequence/template.py:0: error: Incompatible types in assignment (expression has type "int", base class "tuple" defined the type as "Callable[[Any, SupportsIndex, SupportsIndex], int]")  [assignment]
openfold3/core/data/io/sequence/template.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "tuple[Any, ...]")  [assignment]
openfold3/core/data/io/sequence/template.py:0: error: Item "None" of "str | None" has no attribute "replace"  [union-attr]
openfold3/core/data/io/sequence/template.py:0: error: Item "None" of "str | None" has no attribute "split"  [union-attr]
openfold3/core/data/io/sequence/template.py:0: error: Need type annotation for "aln_row_map" (hint: "aln_row_map: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/io/sequence/template.py:0: error: Need type annotation for "sequences" (hint: "sequences: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/io/sequence/template.py:0: error: Signature of "__call__" incompatible with supertype "TemplateParser"  [override]
openfold3/core/data/io/sequence/template.py:0: error: Signature of "__call__" incompatible with supertype "TemplateParser"  [override]
openfold3/core/data/io/sequence/template.py:0: error: Signature of "__call__" incompatible with supertype "TemplateParser"  [override]
openfold3/core/data/io/sequence/template.py:0: error: Signature of "__call__" incompatible with supertype "TemplateParser"  [override]
openfold3/core/data/io/sequence/template.py:0: error: Value of type "ndarray[tuple[Any, ...], dtype[Any]] | None" is not indexable  [index]
openfold3/core/data/io/sequence/template.py:0: error: Value of type "ndarray[tuple[Any, ...], dtype[Any]] | None" is not indexable  [index]
openfold3/core/data/io/sequence/template.py:0: note: Subclass:
openfold3/core/data/io/sequence/template.py:0: note: Subclass:
openfold3/core/data/io/sequence/template.py:0: note: Subclass:
openfold3/core/data/io/sequence/template.py:0: note: Subclass:
openfold3/core/data/io/sequence/template.py:0: note: Superclass:
openfold3/core/data/io/sequence/template.py:0: note: Superclass:
openfold3/core/data/io/sequence/template.py:0: note: Superclass:
openfold3/core/data/io/sequence/template.py:0: note: Superclass:
openfold3/core/data/io/sequence/template.py:0: note: def __call__(self, alignment_source: Any, query_seq_str: str) -> dict[int, TemplateData]
openfold3/core/data/io/sequence/template.py:0: note: def __call__(self, alignment_source: str | Any, query_seq_str: str, query_entry_id: str | None = ..., query_chain_id: str | None = ...) -> dict[int, TemplateData]
openfold3/core/data/io/sequence/template.py:0: note: def __call__(self, alignment_source: str | Any, query_seq_str: str, query_entry_id: str | None = ..., query_chain_id: str | None = ...) -> dict[int, TemplateData]
openfold3/core/data/io/sequence/template.py:0: note: def __call__(self, alignment_source: str | Any, query_seq_str: str, query_entry_id: str | None = ..., query_chain_id: str | None = ...) -> dict[int, TemplateData]
openfold3/core/data/io/sequence/template.py:0: note: def __call__(self, alignment_source: str | Any, query_seq_str: str, query_entry_id: str | None = ..., query_chain_id: str | None = ...) -> dict[int, TemplateData]
openfold3/core/data/io/sequence/template.py:0: note: def __call__(self, alignment_source: str, query_seq_str: str) -> dict[int, TemplateData]
openfold3/core/data/io/sequence/template.py:0: note: def __call__(self, alignment_source: str, query_seq_str: str, realign: bool = ...) -> dict[int, TemplateData]
openfold3/core/data/io/sequence/template.py:0: note: def __call__(self, cif_file_path: Path, query_seq_str: str, chain_id_seq_map: dict[str, str], entry_id: str | None = ..., specified_chain_id: str | None = ...) -> dict[int, TemplateData]
openfold3/core/data/io/structure/atom_array.py:0: error: Argument 2 to "savez" has incompatible type "**dict[str, ndarray[tuple[Any, int], dtype[floating[Any]]]]"; expected "bool"  [arg-type]
openfold3/core/data/io/structure/atom_array.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, ndarray[tuple[Any, int], dtype[floating[Any]]]]"; expected "bool"  [arg-type]
openfold3/core/data/io/structure/atom_array.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, int], dtype[unsignedinteger[_32Bit]]]", target has type "ndarray[tuple[Any, int], dtype[floating[Any]]]")  [assignment]
openfold3/core/data/io/structure/atom_array.py:0: error: Need type annotation for "atom_array"  [var-annotated]
openfold3/core/data/io/structure/cif.py:0: error: Argument 1 to "open_local_or_s3" has incompatible type "Path | str"; expected "Path"  [arg-type]
openfold3/core/data/io/structure/cif.py:0: error: Argument 1 to "read" of "CIFFile" has incompatible type "StringIO | BytesIO"; expected "PathLike[str] | str | IO[str]"  [arg-type]
openfold3/core/data/io/structure/cif.py:0: error: Incompatible default for parameter "data_block" (default has type "None", parameter has type "str")  [assignment]
openfold3/core/data/io/structure/cif.py:0: error: Incompatible types in assignment (expression has type "BinaryCIFFile", variable has type "CIFFile")  [assignment]
openfold3/core/data/io/structure/cif.py:0: error: Incompatible types in assignment (expression has type "type[BinaryCIFFile]", variable has type "type[CIFFile]")  [assignment]
openfold3/core/data/io/structure/cif.py:0: error: No overload variant of "get_assembly" matches argument types "dict[str, object]", "str"  [call-overload]
openfold3/core/data/io/structure/cif.py:0: error: No overload variant of "get_assembly" matches argument types "dict[str, object]", "str"  [call-overload]
openfold3/core/data/io/structure/cif.py:0: error: No overload variant of "get_structure" matches argument type "dict[str, object]"  [call-overload]
openfold3/core/data/io/structure/cif.py:0: error: No overload variant of "get_structure" matches argument type "dict[str, object]"  [call-overload]
openfold3/core/data/io/structure/cif.py:0: error: No overload variant of "get_structure" matches argument type "dict[str, object]"  [call-overload]
openfold3/core/data/io/structure/cif.py:0: error: callable? not callable  [misc]
openfold3/core/data/io/structure/cif.py:0: error: callable? not callable  [misc]
openfold3/core/data/io/structure/cif.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/data/io/structure/cif.py:0: note: Possible overload variants:
openfold3/core/data/io/structure/cif.py:0: note: Possible overload variants:
openfold3/core/data/io/structure/cif.py:0: note: Possible overload variants:
openfold3/core/data/io/structure/cif.py:0: note: Possible overload variants:
openfold3/core/data/io/structure/cif.py:0: note: Possible overload variants:
openfold3/core/data/io/structure/cif.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/data/io/structure/cif.py:0: note: def get_assembly(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, assembly_id: str | None = ..., *, model: int, data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArray[Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_assembly(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, assembly_id: str | None = ..., *, model: int, data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArray[Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_assembly(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, assembly_id: str | None = ..., model: None = ..., data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArrayStack[Any, Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_assembly(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, assembly_id: str | None = ..., model: None = ..., data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArrayStack[Any, Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_structure(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, model: None = ..., data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArrayStack[Any, Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_structure(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, model: None = ..., data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArrayStack[Any, Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_structure(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, model: None = ..., data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArrayStack[Any, Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_structure(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, model: int, data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArray[Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_structure(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, model: int, data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArray[Any]
openfold3/core/data/io/structure/cif.py:0: note: def get_structure(pdbx_file: CIFFile | CIFBlock | BinaryCIFFile | BinaryCIFBlock, model: int, data_block: str | None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., use_author_fields: bool = ..., include_bonds: bool = ...) -> AtomArray[Any]
openfold3/core/data/io/structure/mol.py:0: error: Missing return statement  [return]
openfold3/core/data/io/structure/pdb.py:0: error: Argument 1 to "open_local_or_s3" has incompatible type "Path | str"; expected "Path"  [arg-type]
openfold3/core/data/io/structure/pdb.py:0: error: Argument 1 to "read" of "PDBFile" has incompatible type "StringIO | BytesIO"; expected "str | PathLike[str] | IO[str]"  [arg-type]
openfold3/core/data/io/structure/pdb.py:0: error: No overload variant of "get_structure" matches argument type "dict[str, object]"  [call-overload]
openfold3/core/data/io/structure/pdb.py:0: error: No overload variant of "get_structure" of "PDBFile" matches argument type "dict[str, object]"  [call-overload]
openfold3/core/data/io/structure/pdb.py:0: note: Possible overload variants:
openfold3/core/data/io/structure/pdb.py:0: note: Possible overload variants:
openfold3/core/data/io/structure/pdb.py:0: note: def get_structure(pdb_file: PDBFile, model: None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] = ..., include_bonds: bool = ...) -> AtomArrayStack[Any, Any]
openfold3/core/data/io/structure/pdb.py:0: note: def get_structure(pdb_file: PDBFile, model: int, altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] = ..., include_bonds: bool = ...) -> AtomArray[Any]
openfold3/core/data/io/structure/pdb.py:0: note: def get_structure(self, model: None = ..., altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., include_bonds: bool = ...) -> AtomArrayStack[Any, Any]
openfold3/core/data/io/structure/pdb.py:0: note: def get_structure(self, model: int, altloc: Literal['first', 'occupancy', 'all'] = ..., extra_fields: Iterable[str] | None = ..., include_bonds: bool = ...) -> AtomArray[Any]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Argument 1 to "append" of "list" has incompatible type "list[tuple[Any, Any, Any]]"; expected "Tensor"  [arg-type]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Argument 1 to "centre_random_augmentation" has incompatible type "list[tuple[Any, Any, Any]]"; expected "Tensor"  [arg-type]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Argument 1 to "concat" has incompatible type "list[list[int]]"; expected "tuple[Tensor, ...] | list[Tensor]"  [arg-type]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Argument 1 to "isnan" has incompatible type "tuple[Any, Any, Any]"; expected "Tensor"  [arg-type]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Argument 2 to "centre_random_augmentation" has incompatible type "list[int]"; expected "Tensor"  [arg-type]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible return value type (got "dict[str, object]", expected "dict[str, Tensor | dict[str, Tensor]]")  [return-value]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[Any]")  [assignment]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[Tensor]")  [assignment]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[int]")  [assignment]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[int]")  [assignment]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[int]")  [assignment]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[list[int]]")  [assignment]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[list[int]]")  [assignment]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[tuple[Any, Any, Any]]")  [assignment]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: No overload variant of "__setitem__" of "list" matches argument types "bool", "float"  [call-overload]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: No overload variant of "any" matches argument type "list[int]"  [call-overload]
openfold3/core/data/pipelines/featurization/conformer.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/featurization/conformer.py:0: note: Possible overload variants:
openfold3/core/data/pipelines/featurization/conformer.py:0: note: Possible overload variants:
openfold3/core/data/pipelines/featurization/conformer.py:0: note: def __setitem__(self, SupportsIndex, tuple[Any, Any, Any], /) -> None
openfold3/core/data/pipelines/featurization/conformer.py:0: note: def __setitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], Iterable[tuple[Any, Any, Any]], /) -> None
openfold3/core/data/pipelines/featurization/conformer.py:0: note: def any(input: Tensor, *, out: Tensor | None = ...) -> Tensor
openfold3/core/data/pipelines/featurization/conformer.py:0: note: def any(input: Tensor, dim: Size | list[int] | tuple[int, ...] | None = ..., keepdim: bool = ..., *, out: Tensor | None = ...) -> Tensor
openfold3/core/data/pipelines/featurization/conformer.py:0: note: def any(input: Tensor, dim: int, keepdim: bool = ..., *, out: Tensor | None = ...) -> Tensor
openfold3/core/data/pipelines/featurization/conformer.py:0: note: def any(input: Tensor, dim: str | EllipsisType | None, keepdim: bool = ..., *, out: Tensor | None = ...) -> Tensor
openfold3/core/data/pipelines/featurization/msa.py:0: error: Argument 1 to "create_features" of "MsaFeaturizerOF3" has incompatible type "dict[str, Tensor]"; expected "MsaFeaturePrecursorOF3"  [arg-type]
openfold3/core/data/pipelines/featurization/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/featurization/pocket_constraints.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "is_atomized"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_component_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_token_index"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/pipelines/featurization/structure.py:0: error: Incompatible return value type (got "dict[str, Tensor]", expected "dict[str, Tensor | dict[str, Tensor]]")  [return-value]
openfold3/core/data/pipelines/featurization/structure.py:0: error: Incompatible types in assignment (expression has type "dict[str, Tensor]", target has type "Tensor")  [assignment]
openfold3/core/data/pipelines/featurization/structure.py:0: error: No overload variant of "ones" matches argument types "Tensor", "dtype"  [call-overload]
openfold3/core/data/pipelines/featurization/structure.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/featurization/structure.py:0: note: "dict" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
openfold3/core/data/pipelines/featurization/structure.py:0: note: Consider using "Mapping" instead, which is covariant in the value type
openfold3/core/data/pipelines/featurization/structure.py:0: note: Perhaps you need a type annotation for "features_target"? Suggestion: "dict[str, Tensor | dict[str, Tensor]]"
openfold3/core/data/pipelines/featurization/structure.py:0: note: Possible overload variants:
openfold3/core/data/pipelines/featurization/structure.py:0: note: def ones(*size: int | SymInt, out: Tensor | None = ..., dtype: dtype | None = ..., layout: layout | None = ..., device: str | device | int | None = ..., pin_memory: bool | None = ..., requires_grad: bool | None = ...) -> Tensor
openfold3/core/data/pipelines/featurization/structure.py:0: note: def ones(*size: int, names: Sequence[str | EllipsisType | None] | None, dtype: dtype | None = ..., layout: layout | None = ..., device: str | device | int | None = ..., pin_memory: bool | None = ..., requires_grad: bool | None = ...) -> Tensor
openfold3/core/data/pipelines/featurization/structure.py:0: note: def ones(size: Sequence[int | SymInt], *, out: Tensor | None = ..., dtype: dtype | None = ..., layout: layout | None = ..., device: str | device | int | None = ..., pin_memory: bool | None = ..., requires_grad: bool | None = ...) -> Tensor
openfold3/core/data/pipelines/featurization/structure.py:0: note: def ones(size: Size | list[int] | tuple[int, ...], *, names: Sequence[str | EllipsisType | None] | None, dtype: dtype | None = ..., layout: layout | None = ..., device: str | device | int | None = ..., pin_memory: bool | None = ..., requires_grad: bool | None = ...) -> Tensor
openfold3/core/data/pipelines/featurization/template.py:0: error: Argument 2 to "create_template_distogram" has incompatible type "Tensor"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/featurization/template.py:0: error: Argument 2 to "create_template_restype" has incompatible type "Tensor"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/featurization/template.py:0: error: Argument 2 to "create_template_unit_vector" has incompatible type "Tensor"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/featurization/template.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/RNA_monomer.py:0: error: Argument "check_filename_exists" to "list_bucket_entries" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/RNA_monomer.py:0: error: Argument "profile" to "list_bucket_entries" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/RNA_monomer.py:0: error: List comprehension has incompatible type List[Path]; expected List[str]  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: "ClusteredDatasetChainData" has no attribute "metric_eligible"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: "ClusteredDatasetInterfaceData" has no attribute "metric_eligible"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Argument "train_dataset_cache" to "assign_homology_labels" has incompatible type "PreprocessingDataCache | DatasetCache"; expected "ClusteredDatasetCache"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Argument 1 to "add_cluster_data" has incompatible type "ValidationDatasetCache"; expected "ClusteredDatasetCache"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Argument 1 to "assign_ligand_model_fits" has incompatible type "dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData]"; expected "ValidationDatasetCache"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Argument 1 to "extend" of "list" has incompatible type "list[ChainDataPoint] | list[InterfaceDataPoint]"; expected "Iterable[ChainDataPoint]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Argument 1 to "extend" of "list" has incompatible type "list[ChainDataPoint] | list[InterfaceDataPoint]"; expected "Iterable[InterfaceDataPoint]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Argument 1 to "get_validation_summary_stats" has incompatible type "dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData]"; expected "dict[str, ValidationDatasetStructureData]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Argument 1 to "select_one_per_cluster" has incompatible type "list[ChainDataPoint]"; expected "list[ChainDataPoint | InterfaceDataPoint]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Argument 1 to "select_one_per_cluster" has incompatible type "list[InterfaceDataPoint]"; expected "list[ChainDataPoint | InterfaceDataPoint]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Enum index should be a string (actual index type "MoleculeType | Any")  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Incompatible types in assignment (expression has type "list[tuple[str, str]]", variable has type "list[ChainDataPoint] | list[InterfaceDataPoint]")  [assignment]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Incompatible types in assignment (expression has type "list[tuple[str, str]]", variable has type "list[ChainDataPoint] | list[InterfaceDataPoint]")  [assignment]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Invalid index type "str" for "dict[MoleculeType, list[ChainDataPoint]]"; expected type "MoleculeType"  [index]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Item "ClusteredDatasetStructureData" of "ClusteredDatasetStructureData | Any" has no attribute "token_count"  [union-attr]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Item "ClusteredDatasetStructureData" of "ClusteredDatasetStructureData | Any" has no attribute "token_count"  [union-attr]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: error: Item "None" of "dict[str, PreprocessingChainData] | None" has no attribute "values"  [union-attr]
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: note: "list" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: note: "list" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: note: Consider using "Sequence" instead, which is covariant
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py:0: note: Consider using "Sequence" instead, which is covariant
openfold3/core/data/pipelines/preprocessing/caches/pdb_weighted.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_weighted.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_weighted.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_weighted.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_weighted.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/pdb_weighted.py:0: error: "None" not callable  [misc]
openfold3/core/data/pipelines/preprocessing/caches/protein_monomer.py:0: error: Argument "check_filename_exists" to "list_bucket_entries" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/protein_monomer.py:0: error: Argument "profile" to "list_bucket_entries" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/caches/protein_monomer.py:0: error: List comprehension has incompatible type List[Path]; expected List[str]  [misc]
openfold3/core/data/pipelines/preprocessing/caches/protein_monomer.py:0: error: Missing positional argument "index" in call to "ProteinMonomerChainData"  [call-arg]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument "best_model_filename" to "DisorderedPreprocessingStructureData" has incompatible type "None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument "chain_map" to "DisorderedPreprocessingStructureData" has incompatible type "None"; expected "dict[str, str]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument "distance_clash_map" to "DisorderedPreprocessingStructureData" has incompatible type "None"; expected "dict[float, bool]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument "distance_clash_map" to "DisorderedPreprocessingStructureData" has incompatible type "None"; expected "dict[float, bool]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument "experimental_method" to "DisorderedPreprocessingStructureData" has incompatible type "None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument "gdt" to "DisorderedPreprocessingStructureData" has incompatible type "None"; expected "float"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument "token_count" to "DisorderedPreprocessingStructureData" has incompatible type "None"; expected "int"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument "transform_array" to "DisorderedPreprocessingStructureData" has incompatible type "None"; expected "list[list[float]]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument 1 to "imap_unordered" of "Pool" has incompatible type "_AF3PreprocessingDisorderedWrapper"; expected "Callable[[tuple[str, DisorderedPreprocessingStructureData]], tuple[str, dict[str, str] | None, dict[float, bool] | None]]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument 1 to "imap_unordered" of "Pool" has incompatible type "_DisorderedMetadataCacheBuilder"; expected "Callable[[tuple[str, PreprocessingStructureData]], DisorderedPreprocessingStructureData]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Argument 2 to "write_multichain_fasta" has incompatible type "dict[int, str]"; expected "dict[str, str]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Cannot infer value of type parameter "KT" of <dict>  [misc]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Incompatible return value type (got "tuple[str, DisorderedPreprocessingStructureData]", expected "DisorderedPreprocessingStructureData")  [return-value]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Incompatible return value type (got "tuple[str, DisorderedPreprocessingStructureData]", expected "DisorderedPreprocessingStructureData")  [return-value]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Incompatible types in assignment (expression has type "dict[Never, Never]", target has type "str")  [assignment]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Incompatible types in assignment (expression has type "float | None", target has type "str")  [assignment]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", target has type "str")  [assignment]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Item "None" of "set[Any] | SharedSet | None" has no attribute "update"  [union-attr]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Key expression in dictionary comprehension has incompatible type "str"; expected type "int"  [misc]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Key expression in dictionary comprehension has incompatible type "str"; expected type "int"  [misc]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Need type annotation for "empty_conformer_dict" (hint: "empty_conformer_dict: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Need type annotation for "output_dict"  [var-annotated]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Need type annotation for "processed_mol_ids"  [var-annotated]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Unsupported operand types for // ("None" and "int")  [operator]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Unsupported target for indexed assignment ("str")  [index]
openfold3/core/data/pipelines/preprocessing/structure.py:0: error: Value of type "Path" is not indexable  [index]
openfold3/core/data/pipelines/preprocessing/structure.py:0: note: "_AF3PreprocessingDisorderedWrapper.__call__" has type "_Wrapped[[Arg(str, 'pdb_id'), Arg(DisorderedPreprocessingStructureData, 'structure_data_entry'), Arg(Path, 'gt_structures_directory'), Arg(Path, 'pred_structures_directory'), Arg(str, 'gt_file_format'), Arg(str, 'pred_file_format'), Arg(Path, 'output_directory'), Arg(CIFFile, 'ccd'), Arg(float, 'pocket_distance_threshold'), Arg(list[float], 'clash_distance_thresholds'), Arg(dict[str, Any], 'transfer_annot_dict'), Arg(list[str], 'delete_annot_list')], tuple[dict[str, str], dict[float, bool]], [Arg(_AF3PreprocessingDisorderedWrapper, 'self'), Arg(tuple[str, DisorderedPreprocessingStructureData], 'input_data')], tuple[str, dict[str, str] | None, dict[float, bool] | None]]"
openfold3/core/data/pipelines/preprocessing/structure.py:0: note: "_DisorderedMetadataCacheBuilder.__call__" has type "_Wrapped[[Arg(str, 'pdb_id'), Arg(PreprocessingStructureData, 'structure_data_entry'), Arg(Path, 'ost_aln_output_directory')], DisorderedPreprocessingStructureData, [Arg(_DisorderedMetadataCacheBuilder, 'self'), Arg(tuple[str, PreprocessingStructureData], 'input_data')], DisorderedPreprocessingStructureData]"
openfold3/core/data/pipelines/preprocessing/structure.py:0: note: Left operand is of type "int | None"
openfold3/core/data/pipelines/preprocessing/structure.py:0: note: Try assigning the literal to a variable annotated as dict[<key>, <val>]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "TemplatePreprocessorInputTrain" has no attribute "aln_path"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: "TemplatePreprocessorInputTrain" has no attribute "query_seq_str"  [attr-defined]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "idx_map" to "TemplateCacheEntry" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "max_release_date" to "check_release_date_max" has incompatible type "datetime | str | None"; expected "datetime"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "max_sequences" to "A3mParser" has incompatible type "None"; expected "int"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "max_sequences" to "CifDirectParser" has incompatible type "None"; expected "int"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "min_release_date_diff" to "check_release_date_diff" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "query_seq_str" to "TemplatePreprocessorInputInference" has incompatible type "Any | str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "query_seq_str" to "TemplatePreprocessorInputInference" has incompatible type "Any | str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "seq_from_aln" to "remap_template_chain_id" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument "seq_from_aln" to "remap_template_chain_id" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "create_residue_idx_map" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]] | Any"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "enumerate" has incompatible type "list[Path] | None"; expected "Iterable[Path]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "imap_unordered" of "Pool" has incompatible type "_OF3TemplateCacheConstructor"; expected "Callable[[_TemplateQueryEntry], None]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "imap_unordered" of "Pool" has incompatible type "_OF3TemplateCacheFilter"; expected "Callable[[_TemplateQueryEntry], TemplateHitCollection]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "imap_unordered" of "Pool" has incompatible type "_OF3TemplatePreCacheConstructor"; expected "Callable[[str | Any], None]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "imap_unordered" of "Pool" has incompatible type "_OF3TemplateStructurePreprocessor"; expected "Callable[[str], None]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "len" has incompatible type "list[Path] | None"; expected "Sized"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "len" has incompatible type "list[Path] | None"; expected "Sized"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "load" has incompatible type "Path | None"; expected "str | bytes | PathLike[str] | PathLike[bytes] | _SupportsReadSeek[bytes]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "parse_hmmsearch_sto" has incompatible type "str | bytes"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "parse_representatives" has incompatible type "PreprocessingDataCache | DatasetCache"; expected "DatasetCache"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "parse_representatives" has incompatible type "PreprocessingDataCache | DatasetCache"; expected "DatasetCache"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "savez_compressed" has incompatible type "Path | None"; expected "str | PathLike[str] | SupportsWrite[bytes]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "set" of "ContextVar" has incompatible type "Logger"; expected "None"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "set" of "ContextVar" has incompatible type "Logger"; expected "None"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "set" of "ContextVar" has incompatible type "Logger"; expected "None"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "set" of "ContextVar" has incompatible type "Logger"; expected "None"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "set" of "ContextVar" has incompatible type "str"; expected "None"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 1 to "setdefault" of "MutableMapping" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "create_residue_idx_map" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]] | Any"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "preprocess_template_structure_for_template" has incompatible type "Path | None"; expected "Path"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, Collection[str]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, Collection[str]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, Collection[str]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, Collection[str]]"; expected "bool"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, Collection[str]]"; expected "bool"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, Collection[str]]"; expected "bool"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[Any, Any]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[Any, Any]]"; expected "bool"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[str, Any]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[str, Any]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[str, Any]]"; expected "bool"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[str, Any]]"; expected "bool"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 3 to "create_residue_idx_map" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 4 to "create_residue_idx_map" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 4 to "preprocess_template_structure_for_template" has incompatible type "list[MoleculeType]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 4 to "preprocess_template_structure_for_template" has incompatible type "list[MoleculeType]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Argument 5 to "_OF3TemplateStructurePreprocessor" has incompatible type "str"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Assignment to variable "_" outside except: block  [misc]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Assignment to variable "_" outside except: block  [misc]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Incompatible return value type (got "dict[tuple[Any, ...], list[Never]]", expected "TemplateHitCollection")  [return-value]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Incompatible return value type (got "dict[tuple[Any, ...], list[Never]]", expected "TemplateHitCollection")  [return-value]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Incompatible types in assignment (expression has type "BiotiteCCDWrapper", variable has type "CIFFile")  [assignment]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Incompatible types in assignment (expression has type "BiotiteCCDWrapper", variable has type "CIFFile")  [assignment]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Incompatible types in assignment (expression has type "DictProxy[Any, Any]", variable has type "dict[Any, Any]")  [assignment]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Incompatible types in assignment (expression has type "DictProxy[Any, Any]", variable has type "dict[Any, Any]")  [assignment]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "str")  [assignment]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "DatasetCache" of "DatasetCache | InferenceQuerySet" has no attribute "queries"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "DatasetCache" of "DatasetCache | InferenceQuerySet" has no attribute "queries"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "DatasetCache" of "DatasetCache | InferenceQuerySet" has no attribute "queries"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "DatasetCache" of "DatasetCache | InferenceQuerySet" has no attribute "queries"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "None" of "Path | None" has no attribute "glob"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "None" of "Path | None" has no attribute "glob"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "None" of "ndarray[tuple[Any, ...], dtype[Any]] | None" has no attribute "astype"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "None" of "ndarray[tuple[Any, ...], dtype[Any]] | None" has no attribute "astype"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "PreprocessingChainData" of "PreprocessingChainData | Any" has no attribute "template_ids"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "PreprocessingChainData" of "PreprocessingChainData | Any" has no attribute "template_ids"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "TemplatePreprocessorInputTrain" of "TemplatePreprocessorInputTrain | TemplatePreprocessorInputInference" has no attribute "aln_path"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "TemplatePreprocessorInputTrain" of "TemplatePreprocessorInputTrain | TemplatePreprocessorInputInference" has no attribute "aln_path"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "TemplatePreprocessorInputTrain" of "TemplatePreprocessorInputTrain | TemplatePreprocessorInputInference" has no attribute "cache_key"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "TemplatePreprocessorInputTrain" of "TemplatePreprocessorInputTrain | TemplatePreprocessorInputInference" has no attribute "query_seq_str"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "TemplatePreprocessorInputTrain" of "TemplatePreprocessorInputTrain | TemplatePreprocessorInputInference" has no attribute "query_seq_str"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "list[_DatedQueryEntry]" of "_DatedQueryEntry | list[_DatedQueryEntry]" has no attribute "query_pdb_chain_id"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "list[_DatedQueryEntry]" of "_DatedQueryEntry | list[_DatedQueryEntry]" has no attribute "query_pdb_chain_id"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "list[_DatedQueryEntry]" of "_DatedQueryEntry | list[_DatedQueryEntry]" has no attribute "query_pdb_chain_id"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "list[_DatedQueryEntry]" of "_DatedQueryEntry | list[_DatedQueryEntry]" has no attribute "query_release_date"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "str" of "str | _DatedQueryEntry" has no attribute "query_pdb_chain_id"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Item "str" of "str | _DatedQueryEntry" has no attribute "query_pdb_chain_id"  [union-attr]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Key expression in dictionary comprehension has incompatible type "tuple[str, ...]"; expected type "tuple[str, str]"  [misc]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Key expression in dictionary comprehension has incompatible type "tuple[str, ...]"; expected type "tuple[str, str]"  [misc]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Missing positional argument "input" in call to "__call__" of "_Wrapped"  [call-arg]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Missing positional argument "input" in call to "__call__" of "_Wrapped"  [call-arg]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Missing positional argument "template_pdb_id" in call to "__call__" of "_Wrapped"  [call-arg]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Missing positional argument "template_pdb_id" in call to "__call__" of "_Wrapped"  [call-arg]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Need type annotation for "inputs" (hint: "inputs: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Need type annotation for "parts" (hint: "parts: list[<type>] = ...")  [var-annotated]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Need type annotation for "processed_cache_keys" (hint: "processed_cache_keys: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Need type annotation for "template_ids_by_cache_key" (hint: "template_ids_by_cache_key: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: No overload variant of "fetch" matches argument types "str", "str", "Path | None"  [call-overload]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported left operand type for / ("None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported left operand type for / ("None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported left operand type for / ("None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported left operand type for / ("None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported left operand type for / ("None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported left operand type for / ("None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported left operand type for / ("None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported left operand type for / ("None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported operand types for + ("object" and "int")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported operand types for + ("object" and "int")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported operand types for + ("object" and "int")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported operand types for + ("str" and "int")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported operand types for + ("str" and "int")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported operand types for + ("str" and "int")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported operand types for > ("float" and "None")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Unsupported operand types for in ("str | None" and "str")  [operator]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Value of type "dict[str, PreprocessingChainData] | None" is not indexable  [index]
openfold3/core/data/pipelines/preprocessing/template.py:0: error: Value of type "dict[str, PreprocessingChainData] | None" is not indexable  [index]
openfold3/core/data/pipelines/preprocessing/template.py:0: note: "_OF3TemplateCacheConstructor.__call__" has type "_Wrapped[[Arg(str, 'query_pdb_chain_id'), Arg(str, 'rep_pdb_chain_id'), Arg(Path, 'template_alignment_file'), Arg(Path, 'template_structures_directory'), Arg(Path, 'template_cache_directory'), Arg(Path, 'template_precache_directory'), Arg(Path, 'query_structures_directory'), Arg(int, 'max_templates_construct'), Arg(str, 'query_structures_filename'), Arg(str, 'query_file_format'), Arg(dict[Any, Any] | None, 's3_client_config'), DefaultArg(Any, 'log_dir')], None, [Arg(_OF3TemplateCacheConstructor, 'self'), Arg(_TemplateQueryEntry, 'input')], None]"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: "_OF3TemplateCacheFilter.__call__" has type "_Wrapped[[Arg(_TemplateQueryEntry, 'input_data'), Arg(Path, 'template_cache_dir'), Arg(int, 'max_templates'), Arg(bool, 'is_core_train'), Arg(datetime | str | None, 'max_release_date'), Arg(int | None, 'min_release_date_diff'), Arg(Path, 'log_dir')], TemplateHitCollection, [Arg(_OF3TemplateCacheFilter, 'self'), Arg(_TemplateQueryEntry, 'input')], TemplateHitCollection]"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: "_OF3TemplatePreCacheConstructor.__call__" has type "_Wrapped[[Arg(str, 'template_pdb_id'), Arg(Path, 'template_structures_directory'), Arg(str, 'template_structures_filename'), Arg(Path, 'template_precache_dir'), Arg(str, 'template_file_format')], None, [Arg(_OF3TemplatePreCacheConstructor, 'self'), Arg(str, 'template_pdb_id')], None]"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: "_OF3TemplateStructurePreprocessor.__call__" has type "_Wrapped[[Arg(str, 'template_pdb_id'), Arg(Path, 'template_structures_directory'), Arg(str, 'template_file_format'), Arg(Path, 'template_structure_array_directory'), Arg(CIFFile, 'ccd'), Arg(ndarray[int, dtype[Any]], 'moltypes_included'), Arg(Path, 'log_dir')], Any, [Arg(_OF3TemplateStructurePreprocessor, 'self'), Arg(str, 'template_pdb_id')], None]"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "Path | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "float | None"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "int | bool | str | Any"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "int | bool | str | Any"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Left operand is of type "int | bool | str | Any"
openfold3/core/data/pipelines/preprocessing/template.py:0: note: Possible overload variants:
openfold3/core/data/pipelines/preprocessing/template.py:0: note: def fetch(pdb_ids: Iterable[str], format: Literal['pdb', 'pdbx', 'cif', 'mmcif', 'bcif', 'fasta'], target_path: None = ..., overwrite: bool = ..., verbose: bool = ..., gzip: bool = ...) -> list[StringIO | BytesIO]
openfold3/core/data/pipelines/preprocessing/template.py:0: note: def fetch(pdb_ids: Iterable[str], format: Literal['pdb', 'pdbx', 'cif', 'mmcif', 'bcif', 'fasta'], target_path: str, overwrite: bool = ..., verbose: bool = ..., gzip: bool = ...) -> list[str]
openfold3/core/data/pipelines/preprocessing/template.py:0: note: def fetch(pdb_ids: str, format: Literal['pdb', 'pdbx', 'cif', 'mmcif', 'bcif', 'fasta'], target_path: None = ..., overwrite: bool = ..., verbose: bool = ..., gzip: bool = ...) -> StringIO | BytesIO
openfold3/core/data/pipelines/preprocessing/template.py:0: note: def fetch(pdb_ids: str, format: Literal['pdb', 'pdbx', 'cif', 'mmcif', 'bcif', 'fasta'], target_path: str, overwrite: bool = ..., verbose: bool = ..., gzip: bool = ...) -> str
openfold3/core/data/pipelines/preprocessing/utils.py:0: error: Incompatible default for parameter "iterable" (default has type "None", parameter has type "Iterable[Any]")  [assignment]
openfold3/core/data/pipelines/preprocessing/utils.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/data/pipelines/preprocessing/utils.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Argument "in_crop_mask" to "ProcessedReferenceMolecule" has incompatible type "ndarray[tuple[Any, ...], dtype[numpy.bool[builtins.bool]]]"; expected "ndarray[builtins.bool, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Argument "permutations" to "ProcessedReferenceMolecule" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "list[ndarray[int, dtype[Any]]] | None"  [arg-type]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Argument 1 to "get_name_match_argsort" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Item "AtomArray[Any]" of "AtomArrayView | AtomArray[Any]" has no attribute "atom_name_unique"  [union-attr]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Item "AtomArray[Any]" of "AtomArrayView | AtomArray[Any]" has no attribute "component_id"  [union-attr]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Item "AtomArray[Any]" of "AtomArrayView | AtomArray[Any]" has no attribute "crop_mask"  [union-attr]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Type argument "bool" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Value of type "DatasetChainData" is not indexable  [index]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Value of type "DatasetReferenceMoleculeData" is not indexable  [index]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: Value of type "DatasetReferenceMoleculeData" is not indexable  [index]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/conformer.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: "None" object is not iterable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: "create_main_msa" of "MsaSampleProcessor" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: "create_paired_msa" of "MsaSampleProcessor" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: "create_query_seq" of "MsaSampleProcessor" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[int, int], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[int, int], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument 1 to "__call__" of "_ConstructorEmpty" has incompatible type "str"; expected "SupportsIndex | Sequence[SupportsIndex]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument 1 to "len" has incompatible type "dict[str, MsaArray] | None"; expected "Sized"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument 1 to "process_msa_pairing_metadata" has incompatible type "Any | list[Any] | ndarray[tuple[Any, ...], dtype[Any]]"; expected "list[str]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument 2 to "expand_paired_row_ids" has incompatible type "dict[str, MsaArray]"; expected "dict[str, ndarray[int, dtype[Any]]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Argument 3 to "map_to_paired_msa_row_id_per_rep" has incompatible type "list[str]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Cannot determine type of "chain_id_to_deletion_mean"  [has-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Cannot determine type of "chain_id_to_main_msa"  [has-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Cannot determine type of "chain_id_to_profile"  [has-type]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Incompatible return value type (got "tuple[Any, Any, Any]", expected "dict[str, MsaArray]")  [return-value]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Incompatible return value type (got "tuple[Any, Any, Any]", expected "dict[str, MsaArray]")  [return-value]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Incompatible return value type (got "tuple[dict[str, MsaArray], dict[str, Any], dict[str, Any]]", expected "dict[str, MsaArray]")  [return-value]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "int")  [assignment]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Item "None" of "dict[str, MsaArray] | None" has no attribute "items"  [union-attr]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Key expression in dictionary comprehension has incompatible type "str"; expected type "int"  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Signature of "create_main_msa" incompatible with supertype "MsaSampleProcessor"  [override]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Signature of "create_paired_msa" incompatible with supertype "MsaSampleProcessor"  [override]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Signature of "create_query_seq" incompatible with supertype "MsaSampleProcessor"  [override]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Too many arguments for "view" of "ndarray"  [call-arg]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Unsupported operand types for + ("str" and "int")  [operator]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Unsupported operand types for > ("str" and "int")  [operator]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Unsupported right operand type for in ("MsaArray | Any")  [operator]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: Value of type "MsaArray | Any" is not indexable  [index]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: Subclass:
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: Subclass:
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: Subclass:
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: Superclass:
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: Superclass:
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: Superclass:
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: def create_main_msa(self, input: MsaSampleProcessorInputInference, msa_array_collection: MsaArrayCollection, chain_id_to_paired_msa: dict[str, MsaArray]) -> dict[str, MsaArray]
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: def create_main_msa(self, input: MsaSampleProcessorInputTrain | MsaSampleProcessorInputInference | None = ..., msa_array_collection: MsaArrayCollection | None = ..., chain_id_to_paired_msa: dict[str, MsaArray] | None = ...) -> None
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: def create_paired_msa(self, input: MsaSampleProcessorInputInference, msa_array_collection: MsaArrayCollection) -> dict[str, MsaArray]
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: def create_paired_msa(self, input: MsaSampleProcessorInputTrain | MsaSampleProcessorInputInference | None = ..., msa_array_collection: MsaArrayCollection | None = ...) -> None
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: def create_query_seq(self, input: MsaSampleProcessorInputInference, msa_array_collection: MsaArrayCollection) -> dict[str, MsaArray]
openfold3/core/data/pipelines/sample_processing/msa.py:0: note: def create_query_seq(self, input: MsaSampleProcessorInputTrain | MsaSampleProcessorInputInference | None = ..., msa_array_collection: MsaArrayCollection | None = ...) -> None
openfold3/core/data/pipelines/sample_processing/structure.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/pipelines/sample_processing/structure.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/pipelines/sample_processing/structure.py:0: error: callable? not callable  [misc]
openfold3/core/data/pipelines/sample_processing/template.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/pipelines/sample_processing/template.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/caches/clustering.py:0: error: Incompatible types in assignment (expression has type "Path", variable has type "str")  [assignment]
openfold3/core/data/primitives/caches/clustering.py:0: error: Need type annotation for "cluster_id_to_size"  [var-annotated]
openfold3/core/data/primitives/caches/clustering.py:0: error: Need type annotation for "non_protein_ident_to_cluster_id"  [var-annotated]
openfold3/core/data/primitives/caches/clustering.py:0: error: Unsupported left operand type for / ("str")  [operator]
openfold3/core/data/primitives/caches/clustering.py:0: error: Unsupported left operand type for / ("str")  [operator]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ClusteredDatasetChainData" has no attribute "metric_eligible"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ClusteredDatasetChainData" has no attribute "source_subset"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ClusteredDatasetChainData" has no attribute "source_subset"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ClusteredDatasetChainData" has no attribute "use_metrics"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ClusteredDatasetChainData" has no attribute "use_metrics"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ClusteredDatasetInterfaceData" has no attribute "low_homology"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ClusteredDatasetInterfaceData" has no attribute "metric_eligible"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ClusteredDatasetInterfaceData" has no attribute "use_metrics"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ValidationDatasetCache" has no attribute "chains"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ValidationDatasetCache" has no attribute "interfaces"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ValidationDatasetCache" has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ValidationDatasetCache" has no attribute "keys"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ValidationDatasetCache" has no attribute "values"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ValidationDatasetStructureData" has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ValidationDatasetStructureData" has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "ValidationDatasetStructureData" has no attribute "values"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "object" has no attribute "cluster_id"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "object" has no attribute "metric_eligible"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "str" has no attribute "name"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "tuple[str, str]" has no attribute "interface_id"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: "tuple[str, str]" has no attribute "pdb_id"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "chain_data" to "check_chain_metric_eligibility" has incompatible type "ClusteredDatasetChainData"; expected "ValidationDatasetChainData"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "chain_dict" to "check_interface_metric_eligibility" has incompatible type "dict[str, ClusteredDatasetChainData]"; expected "dict[str, ValidationDatasetChainData]"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "cluster_id" to "ClusteredDatasetChainData" has incompatible type "None"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "cluster_id" to "ClusteredDatasetInterfaceData" has incompatible type "None"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "cluster_id" to "ValidationDatasetChainData" has incompatible type "None"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "cluster_id" to "ValidationDatasetInterfaceData" has incompatible type "None"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "cluster_size" to "ClusteredDatasetChainData" has incompatible type "None"; expected "int"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "cluster_size" to "ClusteredDatasetInterfaceData" has incompatible type "None"; expected "int"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "cluster_size" to "ValidationDatasetChainData" has incompatible type "None"; expected "int"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "cluster_size" to "ValidationDatasetInterfaceData" has incompatible type "None"; expected "int"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "interface_data" to "check_interface_metric_eligibility" has incompatible type "ClusteredDatasetInterfaceData"; expected "ValidationDatasetInterfaceData"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "low_homology" to "ValidationDatasetChainData" has incompatible type "None"; expected "bool"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "low_homology" to "ValidationDatasetInterfaceData" has incompatible type "None"; expected "bool"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "metric_eligible" to "ValidationDatasetChainData" has incompatible type "None"; expected "bool"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "metric_eligible" to "ValidationDatasetInterfaceData" has incompatible type "None"; expected "bool"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "molecule_type" to "ClusteredDatasetChainData" has incompatible type "MoleculeType | Any"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "molecule_type" to "ValidationDatasetChainData" has incompatible type "MoleculeType | Any"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "reference_mol_dict" to "check_interface_metric_eligibility" has incompatible type "dict[str, DatasetReferenceMoleculeData] | LMDBDict[str, DatasetReferenceMoleculeData]"; expected "ValidationDatasetReferenceMoleculeData"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "reference_molecule_data" to "ValidationDatasetCache" has incompatible type "dict[str, ValidationDatasetReferenceMoleculeData]"; expected "dict[str, DatasetReferenceMoleculeData] | LMDBDict[str, DatasetReferenceMoleculeData]"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument "structure_data" to "ValidationDatasetCache" has incompatible type "dict[str, ValidationDatasetStructureData]"; expected "dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData]"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Argument 1 to "len" has incompatible type "ValidationDatasetCache"; expected "Sized"  [arg-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Function "builtins.callable" is not valid as a type  [valid-type]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible return value type (got "dict[Any, Any]", expected "ValidationDatasetStructureData")  [return-value]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible return value type (got "dict[str, PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData]", expected "dict[str, PreprocessingStructureData] | dict[str, DisorderedPreprocessingStructureData] | dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData] | dict[str, ValidationDatasetStructureData] | LMDBDict[str, ValidationDatasetStructureData] | dict[str, ProteinMonomerStructureData] | LMDBDict[str, ProteinMonomerStructureData] | dict[str, RNAMonomerStructureData] | LMDBDict[str, RNAMonomerStructureData]")  [return-value]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible return value type (got "list[ChainDataPoint | InterfaceDataPoint]", expected "list[ChainDataPoint] | list[InterfaceDataPoint]")  [return-value]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible return value type (got "tuple[PreprocessingDataCache | DatasetCache, dict[str, str]]", expected "tuple[ClusteredDatasetCache, dict[str, str]]")  [return-value]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible return value type (got "tuple[dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData], str | dict[str, ClusteredDatasetChainData], dict[str, dict[str, str]]]", expected "tuple[dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData], dict[str, dict[str, str]]] | tuple[dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData], dict[str, dict[str, ClusteredDatasetChainData]], dict[str, dict[str, str]]]")  [return-value]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible return value type (got "tuple[dict[str, ClusteredDatasetStructureData], defaultdict[Any, dict[Any, Any]]]", expected "dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData] | tuple[dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData], dict[str, ClusteredDatasetChainData]]")  [return-value]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "ClusteredDatasetInterfaceData", variable has type "ClusteredDatasetChainData")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "ClusteredDatasetInterfaceData", variable has type "ClusteredDatasetChainData")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "MoleculeType", variable has type "str")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData] | tuple[dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData], dict[str, ClusteredDatasetChainData]]", variable has type "dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData]")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "dict[str, PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData]", variable has type "dict[str, PreprocessingStructureData] | dict[str, DisorderedPreprocessingStructureData] | dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData] | dict[str, ValidationDatasetStructureData] | LMDBDict[str, ValidationDatasetStructureData] | dict[str, ProteinMonomerStructureData] | LMDBDict[str, ProteinMonomerStructureData] | dict[str, RNAMonomerStructureData] | LMDBDict[str, RNAMonomerStructureData]")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "dict[str, PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData]", variable has type "dict[str, PreprocessingStructureData] | dict[str, DisorderedPreprocessingStructureData] | dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData] | dict[str, ValidationDatasetStructureData] | LMDBDict[str, ValidationDatasetStructureData] | dict[str, ProteinMonomerStructureData] | LMDBDict[str, ProteinMonomerStructureData] | dict[str, RNAMonomerStructureData] | LMDBDict[str, RNAMonomerStructureData]")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "dict[str, PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData]", variable has type "dict[str, PreprocessingStructureData] | dict[str, DisorderedPreprocessingStructureData] | dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData] | dict[str, ValidationDatasetStructureData] | LMDBDict[str, ValidationDatasetStructureData] | dict[str, ProteinMonomerStructureData] | LMDBDict[str, ProteinMonomerStructureData] | dict[str, RNAMonomerStructureData] | LMDBDict[str, RNAMonomerStructureData]")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "dict[str, PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData]", variable has type "dict[str, PreprocessingStructureData] | dict[str, DisorderedPreprocessingStructureData] | dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData] | dict[str, ValidationDatasetStructureData] | LMDBDict[str, ValidationDatasetStructureData] | dict[str, ProteinMonomerStructureData] | LMDBDict[str, ProteinMonomerStructureData] | dict[str, RNAMonomerStructureData] | LMDBDict[str, RNAMonomerStructureData]")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData]")  [assignment]
openfold3/core/data/primitives/caches/filtering.py:0: error: Invalid index type "str" for "dict[MoleculeType, int | None]"; expected type "MoleculeType"  [index]
openfold3/core/data/primitives/caches/filtering.py:0: error: Invalid index type "str" for "dict[MoleculeType, list[Any]]"; expected type "MoleculeType"  [index]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ClusteredDatasetStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "experimental_method"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ClusteredDatasetStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "token_count"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "None" of "dict[str, PreprocessingChainData] | None" has no attribute "items"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "None" of "dict[str, PreprocessingChainData] | None" has no attribute "items"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "None" of "dict[str, PreprocessingChainData] | dict[str, ClusteredDatasetChainData] | dict[str, ValidationDatasetChainData] | dict[str, ProteinMonomerChainData] | dict[str, RNAMonomerChainData] | None" has no attribute "__iter__" (not iterable)  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "None" of "dict[str, PreprocessingChainData] | dict[str, ClusteredDatasetChainData] | dict[str, ValidationDatasetChainData] | dict[str, ProteinMonomerChainData] | dict[str, RNAMonomerChainData] | None" has no attribute "values"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "None" of "list[tuple[str, str]] | None" has no attribute "__iter__" (not iterable)  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "None" of "list[tuple[str, str]] | None" has no attribute "__iter__" (not iterable)  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerChainData" of "PreprocessingChainData | Any | ClusteredDatasetChainData | ProteinMonomerChainData | RNAMonomerChainData" has no attribute "molecule_type"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerChainData" of "PreprocessingChainData | PDBChainData | ProteinMonomerChainData | RNAMonomerChainData" has no attribute "molecule_type"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "experimental_method"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "release_date"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "release_date"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "resolution"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "resolution"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "resolution"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ProteinMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "token_count"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerChainData" of "PreprocessingChainData | Any | ClusteredDatasetChainData | ProteinMonomerChainData | RNAMonomerChainData" has no attribute "molecule_type"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerChainData" of "PreprocessingChainData | PDBChainData | ProteinMonomerChainData | RNAMonomerChainData" has no attribute "molecule_type"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "experimental_method"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "release_date"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "release_date"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "resolution"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "resolution"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "resolution"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "RNAMonomerStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "token_count"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Item "ValidationDatasetStructureData" of "PreprocessingStructureData | ClusteredDatasetStructureData | ValidationDatasetStructureData | ProteinMonomerStructureData | RNAMonomerStructureData" has no attribute "experimental_method"  [union-attr]
openfold3/core/data/primitives/caches/filtering.py:0: error: Need type annotation for "chain_type_to_datapoints"  [var-annotated]
openfold3/core/data/primitives/caches/filtering.py:0: error: Need type annotation for "interface_datapoints_by_type"  [var-annotated]
openfold3/core/data/primitives/caches/filtering.py:0: error: Need type annotation for "unmatched_entries"  [var-annotated]
openfold3/core/data/primitives/caches/filtering.py:0: error: No return value expected  [return-value]
openfold3/core/data/primitives/caches/filtering.py:0: error: Unsupported operand types for < ("date" and "None")  [operator]
openfold3/core/data/primitives/caches/filtering.py:0: error: Unsupported operand types for in ("MoleculeType | Any | str" and "list[MoleculeType]")  [operator]
openfold3/core/data/primitives/caches/filtering.py:0: error: Unsupported operand types for in ("MoleculeType | str | Any" and "tuple[MoleculeType, MoleculeType, MoleculeType]")  [operator]
openfold3/core/data/primitives/caches/filtering.py:0: error: Value of type "ValidationDatasetCache" is not indexable  [index]
openfold3/core/data/primitives/caches/filtering.py:0: error: Value of type "ValidationDatasetCache" is not indexable  [index]
openfold3/core/data/primitives/caches/filtering.py:0: error: Value of type "dict[str, PreprocessingChainData] | dict[str, ClusteredDatasetChainData] | dict[str, ValidationDatasetChainData] | dict[str, ProteinMonomerChainData] | dict[str, RNAMonomerChainData] | None" is not indexable  [index]
openfold3/core/data/primitives/caches/filtering.py:0: error: Value of type dataclass? is not indexable  [index]
openfold3/core/data/primitives/caches/filtering.py:0: error: callable? has no attribute "__name__"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "__delitem__"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "__delitem__"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "keys"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "keys"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "values"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: error: dataclass? has no attribute "values"  [attr-defined]
openfold3/core/data/primitives/caches/filtering.py:0: note: "dict" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
openfold3/core/data/primitives/caches/filtering.py:0: note: Consider using "Mapping" instead, which is covariant in the value type
openfold3/core/data/primitives/caches/filtering.py:0: note: Left operand is of type "date | None"
openfold3/core/data/primitives/caches/filtering.py:0: note: Perhaps you meant "typing.Callable" instead of "callable"?
openfold3/core/data/primitives/caches/format.py:0: error: "type[DatasetCache]" has no attribute "_chain_data_format"  [attr-defined]
openfold3/core/data/primitives/caches/format.py:0: error: "type[DatasetCache]" has no attribute "_interface_data_format"  [attr-defined]
openfold3/core/data/primitives/caches/format.py:0: error: "type[DatasetCache]" has no attribute "_ref_mol_data_format"  [attr-defined]
openfold3/core/data/primitives/caches/format.py:0: error: "type[DatasetCache]" has no attribute "_structure_data_format"  [attr-defined]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "best_model_filename" to "DisorderedPreprocessingStructureData" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "chain_map" to "DisorderedPreprocessingStructureData" has incompatible type "Any | None"; expected "dict[str, str]"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "distance_clash_map" to "DisorderedPreprocessingStructureData" has incompatible type "Any | None"; expected "dict[float, bool]"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "experimental_method" to "DisorderedPreprocessingStructureData" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "experimental_method" to "PreprocessingStructureData" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "gdt" to "DisorderedPreprocessingStructureData" has incompatible type "Any | None"; expected "float"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "token_count" to "DisorderedPreprocessingStructureData" has incompatible type "Any | None"; expected "int"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "token_count" to "PreprocessingStructureData" has incompatible type "Any | None"; expected "int"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument "transform_array" to "DisorderedPreprocessingStructureData" has incompatible type "Any | None"; expected "list[list[float]]"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument 1 to "register_datacache" has incompatible type "type[ClusteredDatasetCache]"; expected "PreprocessingDataCache | DatasetCache"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument 1 to "register_datacache" has incompatible type "type[DisorderedPreprocessingDataCache]"; expected "PreprocessingDataCache | DatasetCache"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument 1 to "register_datacache" has incompatible type "type[PreprocessingDataCache]"; expected "PreprocessingDataCache | DatasetCache"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument 1 to "register_datacache" has incompatible type "type[ProteinMonomerDatasetCache]"; expected "PreprocessingDataCache | DatasetCache"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument 1 to "register_datacache" has incompatible type "type[RNAMonomerDatasetCache]"; expected "PreprocessingDataCache | DatasetCache"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Argument 1 to "register_datacache" has incompatible type "type[ValidationDatasetCache]"; expected "PreprocessingDataCache | DatasetCache"  [arg-type]
openfold3/core/data/primitives/caches/format.py:0: error: Function "dataclasses.dataclass" is not valid as a type  [valid-type]
openfold3/core/data/primitives/caches/format.py:0: error: Function "dataclasses.dataclass" is not valid as a type  [valid-type]
openfold3/core/data/primitives/caches/format.py:0: error: Function "datetime.datetime.date" is not valid as a type  [valid-type]
openfold3/core/data/primitives/caches/format.py:0: error: Function "datetime.datetime.date" is not valid as a type  [valid-type]
openfold3/core/data/primitives/caches/format.py:0: error: Function "datetime.datetime.date" is not valid as a type  [valid-type]
openfold3/core/data/primitives/caches/format.py:0: error: Incompatible types in assignment (expression has type "dict[str, DisorderedPreprocessingStructureData]", base class "PreprocessingDataCache" defined the type as "dict[str, PreprocessingStructureData]")  [assignment]
openfold3/core/data/primitives/caches/format.py:0: error: Item "DatasetCache" of "PreprocessingDataCache | DatasetCache" has no attribute "__name__"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "DatasetCache" of "PreprocessingDataCache | DatasetCache" has no attribute "__name__"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "DatasetCache" of "PreprocessingDataCache | DatasetCache" has no attribute "__name__"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "DatasetCache" of "PreprocessingDataCache | DatasetCache" has no attribute "_type"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "__name__"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "__name__"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "__name__"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "_format_validated"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "_registered"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "_type"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "memoryview[int]" of "bytes | memoryview[int]" has no attribute "decode"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Item "memoryview[int]" of "bytes | memoryview[int]" has no attribute "decode"  [union-attr]
openfold3/core/data/primitives/caches/format.py:0: error: Need type annotation for "DATASET_CACHE_CLASS_REGISTRY" (hint: "DATASET_CACHE_CLASS_REGISTRY: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/primitives/caches/format.py:0: error: dataclass? has no attribute "close"  [attr-defined]
openfold3/core/data/primitives/caches/format.py:0: note: "dict" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
openfold3/core/data/primitives/caches/format.py:0: note: Consider using "Mapping" instead, which is covariant in the value type
openfold3/core/data/primitives/caches/format.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/data/primitives/caches/format.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/data/primitives/caches/format.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/data/primitives/caches/format.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/data/primitives/caches/format.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/data/primitives/caches/homology.py:0: error: Argument "restrict_to_molecule_types" to "get_all_cache_chains" has incompatible type "tuple[MoleculeType] | tuple[MoleculeType, MoleculeType]"; expected "list[MoleculeType] | None"  [arg-type]
openfold3/core/data/primitives/caches/homology.py:0: error: Argument "restrict_to_molecule_types" to "get_all_cache_chains" has incompatible type "tuple[MoleculeType] | tuple[MoleculeType, MoleculeType]"; expected "list[MoleculeType] | None"  [arg-type]
openfold3/core/data/primitives/caches/homology.py:0: error: Argument "val_dataset_cache" to "get_polymer_chain_to_homolog_chains" has incompatible type "ValidationDatasetCache"; expected "ClusteredDatasetCache"  [arg-type]
openfold3/core/data/primitives/caches/homology.py:0: error: Argument 1 to "get_mol_id_to_tanimoto_ligands" has incompatible type "ValidationDatasetCache"; expected "ClusteredDatasetCache"  [arg-type]
openfold3/core/data/primitives/caches/homology.py:0: error: Incompatible types in assignment (expression has type "Path", variable has type "str")  [assignment]
openfold3/core/data/primitives/caches/homology.py:0: error: Need type annotation for "fingerprints" (hint: "fingerprints: list[<type>] = ...")  [var-annotated]
openfold3/core/data/primitives/caches/homology.py:0: error: Need type annotation for "train_mol_id_to_pdb_ids"  [var-annotated]
openfold3/core/data/primitives/caches/homology.py:0: error: Unsupported left operand type for / ("str")  [operator]
openfold3/core/data/primitives/caches/homology.py:0: error: Unsupported left operand type for / ("str")  [operator]
openfold3/core/data/primitives/caches/homology.py:0: error: Unsupported left operand type for / ("str")  [operator]
openfold3/core/data/primitives/caches/homology.py:0: error: Unsupported left operand type for / ("str")  [operator]
openfold3/core/data/primitives/caches/homology.py:0: error: Unsupported left operand type for / ("str")  [operator]
openfold3/core/data/primitives/caches/homology.py:0: error: Unsupported left operand type for / ("str")  [operator]
openfold3/core/data/primitives/caches/lmdb.py:0: error: Item "DatasetCache" of "PreprocessingDataCache | DatasetCache" has no attribute "_type"  [union-attr]
openfold3/core/data/primitives/caches/lmdb.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "_type"  [union-attr]
openfold3/core/data/primitives/caches/lmdb.py:0: error: Item "PreprocessingDataCache" of "PreprocessingDataCache | DatasetCache" has no attribute "name"  [union-attr]
openfold3/core/data/primitives/featurization/msa.py:0: error: "MsaArray" object is not iterable  [misc]
openfold3/core/data/primitives/featurization/msa.py:0: error: "None" object is not iterable  [misc]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "deletion_matrix" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[float64]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "deletion_matrix" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[float64]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "deletion_mean" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[int], dtype[float64]]"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "deletion_mean" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[int], dtype[float64]]"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa_array" to "map_str_array_to_idx_array" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa_index" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[float64]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa_index" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[float64]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa_mask" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[float64]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa_mask" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[float64]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa_profile" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[float64]]"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Argument "msa_profile" to "MsaFeaturePrecursorOF3" has incompatible type "ndarray[tuple[Any, ...], dtype[float64]]"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/msa.py:0: error: Incompatible types in assignment (expression has type "MsaArray | None", variable has type "MsaArray")  [assignment]
openfold3/core/data/primitives/featurization/msa.py:0: error: Incompatible types in assignment (expression has type "MsaArray | None", variable has type "MsaArray")  [assignment]
openfold3/core/data/primitives/featurization/msa.py:0: error: Incompatible types in assignment (expression has type "MsaArray | None", variable has type "MsaArray")  [assignment]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/msa.py:0: error: Unsupported operand types for - ("ndarray[int, dtype[Any]]" and "int")  [operator]
openfold3/core/data/primitives/featurization/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/featurization/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/featurization/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/featurization/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/featurization/padding.py:0: error: Argument 2 to "full" has incompatible type "int | float | None"; expected "int | float | bool | complex"  [arg-type]
openfold3/core/data/primitives/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "is_cyclic"  [attr-defined]
openfold3/core/data/primitives/featurization/structure.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/primitives/featurization/structure.py:0: error: "int" has no attribute "__iter__"; maybe "__int__"? (not iterable)  [attr-defined]
openfold3/core/data/primitives/featurization/structure.py:0: error: Argument 1 to "len" has incompatible type "int"; expected "Sized"  [arg-type]
openfold3/core/data/primitives/featurization/structure.py:0: error: Argument 1 to "zeros" has incompatible type "tuple[Tensor, Tensor]"; expected "Sequence[int | SymInt]"  [arg-type]
openfold3/core/data/primitives/featurization/structure.py:0: error: Argument 1 to "zeros" has incompatible type "tuple[Tensor, Tensor]"; expected "Sequence[int | SymInt]"  [arg-type]
openfold3/core/data/primitives/featurization/structure.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/featurization/structure.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/primitives/featurization/template.py:0: error: Argument "frame_atom_coords" to "OF3TemplateFeaturePrecursor" has incompatible type "ndarray[tuple[int, int, int, int], dtype[Any]]"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/template.py:0: error: Argument "pseudo_beta_atom_coords" to "OF3TemplateFeaturePrecursor" has incompatible type "ndarray[tuple[int, int, int], dtype[Any]]"; expected "ndarray[float, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/featurization/template.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "ndarray[float, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/featurization/template.py:0: error: Need type annotation for "residue_starts"  [var-annotated]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "float" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/featurization/template.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "Atom" has no attribute "component_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "Atom" has no attribute "mol_sym_component_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "Atom" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx_g"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx_g"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "crop_mask"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "crop_mask"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_entity_id"; maybe "entity_id"?  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_component_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_component_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_id"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_token_index"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: "AtomArray[Any]" has no attribute "mol_sym_token_index"  [attr-defined]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Argument 1 to "mol_entity_iter" has incompatible type "Atom"; expected "AtomArray[Any]"  [arg-type]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Argument 1 to "remove_atom_indices" has incompatible type "Atom"; expected "AtomArray[Any]"  [arg-type]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Argument 1 to "renumber_permutations" has incompatible type "list[ndarray[int, dtype[Any]]] | None"; expected "ndarray[tuple[Any, ...], dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Argument 1 to "unique" has incompatible type "list[ndarray[int, dtype[Any]]] | None"; expected "_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]]"  [arg-type]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Incompatible return value type (got "tuple[Atom, AtomArray[Any]]", expected "tuple[AtomArray[Any], AtomArray[Any]]")  [return-value]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Incompatible types in "yield" (actual type "Atom", expected type "AtomArray[Any]")  [misc]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Incompatible types in "yield" (actual type "Atom", expected type "AtomArray[Any]")  [misc]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[ndarray[int, dtype[Any]]] | None")  [assignment]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Need type annotation for "gt_mol_keep_atom_mask" (hint: "gt_mol_keep_atom_mask: list[<type>] = ...")  [var-annotated]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: No overload variant of "__getitem__" of "AtomArray" matches argument type "list[Any]"  [call-overload]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: Value of type "Atom" is not indexable  [index]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/permutation/mol_labels.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/permutation/mol_labels.py:0: note: Possible overload variants:
openfold3/core/data/primitives/permutation/mol_labels.py:0: note: def __getitem__(self, int, /) -> Atom
openfold3/core/data/primitives/permutation/mol_labels.py:0: note: def __getitem__(self, slice[Any, Any, Any] | ndarray[tuple[Any], dtype[integer[Any]]] | ndarray[tuple[Any], dtype[numpy.bool[builtins.bool]]], /) -> AtomArray[int]
openfold3/core/data/primitives/permutation/mol_labels.py:0: note: def __getitem__(self, tuple[EllipsisType, slice[Any, Any, Any] | ndarray[tuple[Any], dtype[integer[Any]]] | ndarray[tuple[Any], dtype[numpy.bool[builtins.bool]]]], /) -> AtomArray[int]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "Dataset[_T_co]" has no attribute "get_worker_path"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "create_all_features"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "create_all_features"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "datapoint_index"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "dataset_cache"; maybe "datapoint_cache"?  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "dataset_cache"; maybe "datapoint_cache"?  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "dataset_cache"; maybe "datapoint_cache"?  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "dataset_cache"; maybe "datapoint_cache"?  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "n_tokens"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "name"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "template"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "LoggingMixin" has no attribute "wrapped_dataset_class"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Cannot determine type of "datapoint_cache"  [has-type]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Cannot determine type of "datapoint_cache"  [has-type]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Cannot determine type of "datapoint_cache"  [has-type]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Incompatible return value type (got "ndarray[tuple[Any, ...], dtype[Any]]", expected "ndarray[str, dtype[Any]]")  [return-value]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "str")  [assignment]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "str")  [assignment]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[str, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Invalid type comment or annotation  [valid-type]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: List item 0 has incompatible type "Any | None"; expected "int"  [list-item]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: List item 0 has incompatible type "Any | None"; expected "int"  [list-item]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: List item 0 has incompatible type "str"; expected "int"  [list-item]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: List item 0 has incompatible type "str"; expected "int"  [list-item]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: List item 0 has incompatible type "str"; expected "int"  [list-item]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: List item 0 has incompatible type "str"; expected "int"  [list-item]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: List item 1 has incompatible type "str"; expected "int"  [list-item]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: List item 1 has incompatible type "str"; expected "int"  [list-item]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Need type annotation for "residue_starts"  [var-annotated]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Need type annotation for "residue_starts_cropped"  [var-annotated]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/quality_control/logging_datasets.py:0: note: did you mean to use ',' instead of ':' ?
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: "list[str]" has no attribute "ravel"  [attr-defined]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Function "builtins.callable" is not valid as a type  [valid-type]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Incompatible default for parameter "mem_enabled" (default has type "ContextVar[bool]", parameter has type "bool")  [assignment]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Incompatible default for parameter "mem_stream" (default has type "ContextVar[None]", parameter has type "Path")  [assignment]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Incompatible default for parameter "runtime_enabled" (default has type "ContextVar[bool]", parameter has type "bool")  [assignment]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Incompatible return value type (got "tuple[None, None]", expected "tuple[ndarray[tuple[Any, ...], dtype[Any]], ndarray[tuple[Any, ...], dtype[Any]]]")  [return-value]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[str]")  [assignment]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[object_]]", variable has type "list[str]")  [assignment]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Need type annotation for "MEM_PROFILED_FUNC_KEYS"  [var-annotated]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: error: Need type annotation for "RUNTIME_DICT"  [var-annotated]
openfold3/core/data/primitives/quality_control/logging_utils.py:0: note: Perhaps you meant "typing.Callable" instead of "callable"?
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "compliance_log"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "compliance_log"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "datasets"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "get_worker_path"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "logger"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "mem_func_token"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "mem_log_token"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "mem_token"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "processed_datapoint_log"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "processed_datapoint_log"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "processed_datapoint_log"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: "Dataset[Any]" has no attribute "runtime_token"  [attr-defined]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: Argument 1 to "len" has incompatible type "str | None"; expected "Sized"  [arg-type]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: Argument 1 to "set" of "ContextVar" has incompatible type "list[str] | str | None"; expected "list[Any]"  [arg-type]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: Incompatible types in assignment (expression has type "LoggerAdapter[Logger]", variable has type "Logger")  [assignment]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: Incompatible types in assignment (expression has type "list[Never]", variable has type "str | None")  [assignment]
openfold3/core/data/primitives/quality_control/worker_config.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "str | None")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/primitives/sequence/msa.py:0: error: "int" object is not iterable  [misc]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[Any, str], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, str], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 1 to "__call__" of "_ConstructorEmpty" has incompatible type "str"; expected "SupportsIndex | Sequence[SupportsIndex]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 1 to "__call__" of "_ConstructorEmpty" has incompatible type "str"; expected "SupportsIndex | Sequence[SupportsIndex]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 1 to "__call__" of "_ConstructorEmpty" has incompatible type "str"; expected "SupportsIndex | Sequence[SupportsIndex]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 1 to "_make_padding_mask" of "MsaArray" has incompatible type "ndarray[str, dtype[Any]]"; expected "ndarray[tuple[Any, ...], dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 1 to "full" has incompatible type "str"; expected "SupportsIndex | Sequence[SupportsIndex]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 1 to "map_str_array_to_idx_array" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 1 to "subset" of "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[bool]]"; expected "ndarray[bool, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 2 to "_num_encode_species" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 3 to "_make_padding_mask" of "MsaArray" has incompatible type "str"; expected "int"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Argument 3 to "_make_padding_mask" of "MsaArray" has incompatible type "str"; expected "int"  [arg-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Cannot determine type of "n_cols"  [has-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Cannot determine type of "n_cols"  [has-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Cannot determine type of "n_cols"  [has-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Cannot determine type of "n_rows"  [has-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Cannot determine type of "n_rows"  [has-type]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible return value type (got "dict[str, ndarray[tuple[int], dtype[Any]]]", expected "dict[str, MsaArray]")  [return-value]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible return value type (got "ndarray[tuple[Any, ...], dtype[int]]", expected "ndarray[int, dtype[Any]]")  [return-value]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible return value type (got "ndarray[tuple[int, int], dtype[Any]]", expected "ndarray[int, dtype[Any]]")  [return-value]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible return value type (got "ndarray[tuple[int], dtype[bool]]", expected "ndarray[bool, dtype[Any]]")  [return-value]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible return value type (got "tuple[dict[str, ndarray[int, dtype[Any]]], ndarray[int, dtype[Any]]]", expected "dict[str, ndarray[int, dtype[Any]]]")  [return-value]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", target has type "ndarray[int, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[Any]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[int, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[int, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[int, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[int, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[str, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[str, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[str, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[int], dtype[int]]", variable has type "ndarray[int, dtype[Any]] | None")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "dict[str, ndarray[int, dtype[Any]]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "ndarray[int, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/sequence/msa.py:0: error: Invalid self argument "ndarray[tuple[Any, ...], dtype[int]]" to attribute function "__iadd__" with type "Callable[[ndarray[tuple[Any, ...], dtype[numpy.bool[builtins.bool]]], _SupportsArray[dtype[numpy.bool[builtins.bool]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool]]]] | builtins.bool | _NestedSequence[builtins.bool]], ndarray[_ShapeT_co, _DTypeT_co]]"  [misc]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "None" of "ndarray[int, dtype[Any]] | None" has no attribute "copy"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "list[Any]" of "Any | list[Any] | ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "columns"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "list[Any]" of "Any | list[Any] | ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "groupby"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "list[Any]" of "Any | list[Any] | ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "iloc"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "ndarray[tuple[Any, ...], dtype[Any]]" of "Any | list[Any] | ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "columns"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "ndarray[tuple[Any, ...], dtype[Any]]" of "Any | list[Any] | ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "groupby"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "ndarray[tuple[Any, ...], dtype[Any]]" of "Any | list[Any] | ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "iloc"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "ndarray[tuple[Any, ...], dtype[Any]]" of "Any | ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "apply"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Item "ndarray[tuple[Any, ...], dtype[Any]]" of "Any | ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "to_numpy"  [union-attr]
openfold3/core/data/primitives/sequence/msa.py:0: error: Name "np.int" is not defined  [name-defined]
openfold3/core/data/primitives/sequence/msa.py:0: error: Need type annotation for "msa_arrays_to_pair" (hint: "msa_arrays_to_pair: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/primitives/sequence/msa.py:0: error: Need type annotation for "msa_arrays_to_pair_i" (hint: "msa_arrays_to_pair_i: list[<type>] = ...")  [var-annotated]
openfold3/core/data/primitives/sequence/msa.py:0: error: Need type annotation for "species" (hint: "species: list[<type>] = ...")  [var-annotated]
openfold3/core/data/primitives/sequence/msa.py:0: error: Need type annotation for "species_to_msa_rows"  [var-annotated]
openfold3/core/data/primitives/sequence/msa.py:0: error: Need type annotation for "used_rows" (hint: "used_rows: set[<type>] = ...")  [var-annotated]
openfold3/core/data/primitives/sequence/msa.py:0: error: No overload variant of "__getitem__" of "list" matches argument type "str"  [call-overload]
openfold3/core/data/primitives/sequence/msa.py:0: error: No overload variant of "__getitem__" of "list" matches argument type "str"  [call-overload]
openfold3/core/data/primitives/sequence/msa.py:0: error: No overload variant of "__getitem__" of "list" matches argument type "str"  [call-overload]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "bool" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "bool" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "bool" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Unsupported operand types for - ("int" and "str")  [operator]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type "int" is not indexable  [index]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type variable "_AnyShapeT" of "__call__" of "_ConstructorEmpty" cannot be "tuple[Any, str]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type variable "_AnyShapeT" of "full" cannot be "tuple[Any, str]"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type variable "_ScalarT" of "__call__" of "_ConstructorEmpty" cannot be "bool"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type variable "_ScalarT" of "__call__" of "_ConstructorEmpty" cannot be "bool"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type variable "_ScalarT" of "__call__" of "_ConstructorEmpty" cannot be "int"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type variable "_ScalarT" of "__call__" of "_ConstructorEmpty" cannot be "int"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type variable "_ScalarT" of "full" cannot be "int"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: Value of type variable "_ScalarT" of "full" cannot be "int"  [type-var]
openfold3/core/data/primitives/sequence/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/sequence/msa.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/sequence/msa.py:0: note: Possible overload variants:
openfold3/core/data/primitives/sequence/msa.py:0: note: Possible overload variants:
openfold3/core/data/primitives/sequence/msa.py:0: note: Possible overload variants:
openfold3/core/data/primitives/sequence/msa.py:0: note: def __getitem__(self, SupportsIndex, /) -> Any
openfold3/core/data/primitives/sequence/msa.py:0: note: def __getitem__(self, SupportsIndex, /) -> Any
openfold3/core/data/primitives/sequence/msa.py:0: note: def __getitem__(self, SupportsIndex, /) -> Any
openfold3/core/data/primitives/sequence/msa.py:0: note: def __getitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], /) -> list[Any]
openfold3/core/data/primitives/sequence/msa.py:0: note: def __getitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], /) -> list[Any]
openfold3/core/data/primitives/sequence/msa.py:0: note: def __getitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], /) -> list[Any]
openfold3/core/data/primitives/sequence/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/primitives/sequence/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/primitives/sequence/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/primitives/sequence/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/primitives/sequence/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/primitives/sequence/template.py:0: error: "None" has no attribute "info"  [attr-defined]
openfold3/core/data/primitives/sequence/template.py:0: error: Argument 1 to "get" of "dict" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/primitives/sequence/template.py:0: error: Argument 2 to "_DatedQueryEntry" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/core/data/primitives/sequence/template.py:0: error: Argument 2 to "_DatedQueryEntry" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/core/data/primitives/sequence/template.py:0: error: Argument 2 to "_DatedQueryEntry" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/core/data/primitives/sequence/template.py:0: error: Argument 2 to "remap_chain_id" has incompatible type "None"; expected "str"  [arg-type]
openfold3/core/data/primitives/sequence/template.py:0: error: Incompatible return value type (got "None", expected "ndarray[int, dtype[Any]]")  [return-value]
openfold3/core/data/primitives/sequence/template.py:0: error: Incompatible return value type (got "None", expected "ndarray[int, dtype[Any]]")  [return-value]
openfold3/core/data/primitives/sequence/template.py:0: error: Need type annotation for "entries" (hint: "entries: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/primitives/sequence/template.py:0: error: Need type annotation for "residue_starts"  [var-annotated]
openfold3/core/data/primitives/sequence/template.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/template.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/template.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/sequence/template.py:0: error: dataclass? has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/sequence/template.py:0: error: dataclass? has no attribute "items"  [attr-defined]
openfold3/core/data/primitives/structure/alignment.py:0: error: Argument "key" to "min" has incompatible type overloaded function; expected "Callable[[Any], SupportsDunderLT[Any] | SupportsDunderGT[Any]]"  [arg-type]
openfold3/core/data/primitives/structure/alignment.py:0: error: Item "tuple[ndarray[tuple[Any, ...], dtype[Any]], ...]" of "ndarray[tuple[Any, ...], dtype[Any]] | tuple[ndarray[tuple[Any, ...], dtype[Any]], ndarray[tuple[Any, ...], dtype[Any]]]" has no attribute "shape"  [union-attr]
openfold3/core/data/primitives/structure/alignment.py:0: error: Need type annotation for "affine_transformation"  [var-annotated]
openfold3/core/data/primitives/structure/alignment.py:0: error: No overload variant of "__getitem__" of "tuple" matches argument type "tuple[slice[None, None, None], int]"  [call-overload]
openfold3/core/data/primitives/structure/alignment.py:0: note: Possible overload variants:
openfold3/core/data/primitives/structure/alignment.py:0: note: def __getitem__(self, SupportsIndex, /) -> ndarray[tuple[Any, ...], dtype[Any]]
openfold3/core/data/primitives/structure/alignment.py:0: note: def __getitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], /) -> tuple[ndarray[tuple[Any, ...], dtype[Any]], ...]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx_arginine_fix"  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx_can_order"  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[Any]" has no attribute "is_atomized"  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[int]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: "AtomArray[int]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Argument 1 to "check_res_id_continuity" has incompatible type "Atom"; expected "AtomArray[Never] | AtomArrayStack[Never, Never]"  [arg-type]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Argument 1 to "get_chain_starts" has incompatible type "Atom"; expected "AtomArray[Never] | AtomArrayStack[Never, Never]"  [arg-type]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Argument 1 to "len" has incompatible type "Atom"; expected "Sized"  [arg-type]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "bondlist"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "bondlist"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "bondlist_arr"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "ca_dists"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "discontinuities"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "distances"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "new_bondlist"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "new_bondlist"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "new_bondlist"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "new_chains"  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Need type annotation for "res_name_to_ref_atoms" (hint: "res_name_to_ref_atoms: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/primitives/structure/cleanup.py:0: error: No overload variant of "roll" matches argument types "Atom", "int", "int"  [call-overload]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Unsupported target for indexed assignment ("ndarray[tuple[Any], dtype[floating[Any]]] | ndarray[tuple[Any, Any], dtype[floating[Any]]] | floating[Any]")  [index]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Value of type "Atom" is not indexable  [index]
openfold3/core/data/primitives/structure/cleanup.py:0: error: Value of type "Atom" is not indexable  [index]
openfold3/core/data/primitives/structure/cleanup.py:0: note: Possible overload variants:
openfold3/core/data/primitives/structure/cleanup.py:0: note: def [_ScalarT: generic[Any]] roll(a: _SupportsArray[dtype[_ScalarT]] | _NestedSequence[_SupportsArray[dtype[_ScalarT]]], shift: SupportsIndex | Sequence[SupportsIndex], axis: SupportsIndex | Sequence[SupportsIndex] | None = ...) -> ndarray[tuple[Any, ...], dtype[_ScalarT]]
openfold3/core/data/primitives/structure/cleanup.py:0: note: def roll(a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], shift: SupportsIndex | Sequence[SupportsIndex], axis: SupportsIndex | Sequence[SupportsIndex] | None = ...) -> ndarray[tuple[Any, ...], dtype[Any]]
openfold3/core/data/primitives/structure/component.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx_coval_comp"  [attr-defined]
openfold3/core/data/primitives/structure/component.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx_coval_comp"  [attr-defined]
openfold3/core/data/primitives/structure/component.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/component.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/component.py:0: error: "int" has no attribute "item"  [attr-defined]
openfold3/core/data/primitives/structure/component.py:0: error: Argument 2 to "component_view_iter_from_metadata" has incompatible type "dict[str, dict[Any, Any]]"; expected "DatasetChainData"  [arg-type]
openfold3/core/data/primitives/structure/component.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/component.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/component.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/component.py:0: error: Need type annotation for "all_bonds"  [var-annotated]
openfold3/core/data/primitives/structure/component.py:0: error: Need type annotation for "bond_list"  [var-annotated]
openfold3/core/data/primitives/structure/component.py:0: error: Need type annotation for "ligand_chain_ids"  [var-annotated]
openfold3/core/data/primitives/structure/component.py:0: error: Value of type "DatasetChainData" is not indexable  [index]
openfold3/core/data/primitives/structure/component.py:0: error: Value of type "_ImplementsGet" is not indexable  [index]
openfold3/core/data/primitives/structure/component.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/conformer.py:0: error: Incompatible return value type (got "ndarray[tuple[Any, ...], dtype[signedinteger[_32Bit | _64Bit]]]", expected "ndarray[int, dtype[Any]]")  [return-value]
openfold3/core/data/primitives/structure/conformer.py:0: error: Incompatible return value type (got "tuple[Any, str, str]", expected "tuple[Any, Literal['default', 'random_init', 'use_fallback'], Literal['rdkit', 'ccd-ideal', 'ccd-model', 'all-nan']]")  [return-value]
openfold3/core/data/primitives/structure/conformer.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/structure/conformer.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/structure/cropping.py:0: error: "AtomArray[Any]" has no attribute "crop_mask"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "AtomArray[Any]" has no attribute "token_center_atom"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "AtomArray[int]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "dict[str, float]" has no attribute "sum"  [attr-defined]
openfold3/core/data/primitives/structure/cropping.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/primitives/structure/cropping.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/primitives/structure/cropping.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/primitives/structure/cropping.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/primitives/structure/cropping.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/primitives/structure/cropping.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/primitives/structure/cropping.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/primitives/structure/cropping.py:0: error: "list" expects 1 type argument, but 2 given  [type-arg]
openfold3/core/data/primitives/structure/cropping.py:0: error: Argument "query_atom_array" to "get_query_interface_atom_pair_idxs" has incompatible type "Atom"; expected "AtomArray[Any]"  [arg-type]
openfold3/core/data/primitives/structure/cropping.py:0: error: Argument 1 to "len" has incompatible type "Atom"; expected "Sized"  [arg-type]
openfold3/core/data/primitives/structure/cropping.py:0: error: Incompatible types in assignment (expression has type "Atom", variable has type "AtomArray[Any]")  [assignment]
openfold3/core/data/primitives/structure/cropping.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "dict[str, float]")  [assignment]
openfold3/core/data/primitives/structure/cropping.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[str]")  [assignment]
openfold3/core/data/primitives/structure/cropping.py:0: error: No overload variant matches argument type "AtomArray[Any]"  [call-overload]
openfold3/core/data/primitives/structure/cropping.py:0: error: No overload variant matches argument type "AtomArray[Any]"  [call-overload]
openfold3/core/data/primitives/structure/cropping.py:0: error: No overload variant matches argument type "AtomArray[Any]"  [call-overload]
openfold3/core/data/primitives/structure/cropping.py:0: error: No overload variant matches argument type "AtomArray[Any]"  [call-overload]
openfold3/core/data/primitives/structure/cropping.py:0: error: No overload variant matches argument types "ndarray[tuple[Any, ...], dtype[Any]]", "dict[str, float]"  [call-overload]
openfold3/core/data/primitives/structure/cropping.py:0: error: Value of type "Atom" is not indexable  [index]
openfold3/core/data/primitives/structure/cropping.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/cropping.py:0: note: Possible overload variants:
openfold3/core/data/primitives/structure/cropping.py:0: note: Possible overload variants:
openfold3/core/data/primitives/structure/cropping.py:0: note: Possible overload variants:
openfold3/core/data/primitives/structure/cropping.py:0: note: Possible overload variants:
openfold3/core/data/primitives/structure/cropping.py:0: note: Possible overload variants:
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> Any
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> Any
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> Any
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> Any
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> Any
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[Any]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[Any]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[Any]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[Any]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[Any]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> int
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> int
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> int
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> int
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: None = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> int
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[signedinteger[_32Bit | _64Bit]]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[signedinteger[_32Bit | _64Bit]]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[signedinteger[_32Bit | _64Bit]]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[signedinteger[_32Bit | _64Bit]]]
openfold3/core/data/primitives/structure/cropping.py:0: note: def choice(self, a: int, size: SupportsIndex | Sequence[SupportsIndex] = ..., replace: bool = ..., p: _SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[numpy.bool[builtins.bool] | integer[Any] | floating[Any]]]] | float | _NestedSequence[float] | None = ...) -> ndarray[tuple[Any, ...], dtype[signedinteger[_32Bit | _64Bit]]]
openfold3/core/data/primitives/structure/interface.py:0: error: "AtomArray[Any]" has no attribute "token_center_atom"  [attr-defined]
openfold3/core/data/primitives/structure/interface.py:0: error: "AtomArray[Any]" has no attribute "token_center_atom"  [attr-defined]
openfold3/core/data/primitives/structure/interface.py:0: error: "AtomArray[Any]" has no attribute "token_center_atom"  [attr-defined]
openfold3/core/data/primitives/structure/interface.py:0: error: Argument 1 to "get_interface_atoms" has incompatible type "Atom"; expected "AtomArray[Any]"  [arg-type]
openfold3/core/data/primitives/structure/interface.py:0: error: Argument 1 to "get_query_interface_atoms" has incompatible type "Atom"; expected "AtomArray[Any]"  [arg-type]
openfold3/core/data/primitives/structure/interface.py:0: error: Argument 2 to "get_query_interface_atoms" has incompatible type "Atom"; expected "AtomArray[Any]"  [arg-type]
openfold3/core/data/primitives/structure/interface.py:0: error: Incompatible return value type (got "None", expected "ndarray[tuple[Any, ...], dtype[Any]] | tuple[ndarray[tuple[Any, ...], dtype[Any]], ndarray[tuple[Any, ...], dtype[Any]]]")  [return-value]
openfold3/core/data/primitives/structure/interface.py:0: error: Incompatible return value type (got "tuple[None, None]", expected "ndarray[tuple[Any, ...], dtype[Any]] | tuple[ndarray[tuple[Any, ...], dtype[Any]], ndarray[tuple[Any, ...], dtype[Any]]]")  [return-value]
openfold3/core/data/primitives/structure/interface.py:0: error: Incompatible types in "yield" (actual type "tuple[tuple[Any, ...], Any | ndarray[tuple[Any, ...], dtype[Any]]]", expected type "tuple[tuple[int, int], ndarray[integer[Any], integer[Any]]]")  [misc]
openfold3/core/data/primitives/structure/interface.py:0: error: Item "None" of "BondList[int] | None" has no attribute "adjacency_matrix"  [union-attr]
openfold3/core/data/primitives/structure/interface.py:0: error: Item "tuple[ndarray[tuple[Any, ...], dtype[Any]], ...]" of "ndarray[tuple[Any, ...], dtype[Any]] | tuple[ndarray[tuple[Any, ...], dtype[Any]], ndarray[tuple[Any, ...], dtype[Any]]]" has no attribute "flatten"  [union-attr]
openfold3/core/data/primitives/structure/interface.py:0: error: Need type annotation for "orig_data_results"  [var-annotated]
openfold3/core/data/primitives/structure/interface.py:0: error: No overload variant of "__getitem__" of "tuple" matches argument type "tuple[slice[None, None, None], int]"  [call-overload]
openfold3/core/data/primitives/structure/interface.py:0: error: Type argument "integer[Any]" of "ndarray" must be a subtype of "dtype[Any]"  [type-var]
openfold3/core/data/primitives/structure/interface.py:0: error: Type argument "integer[Any]" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/structure/interface.py:0: note: Possible overload variants:
openfold3/core/data/primitives/structure/interface.py:0: note: def __getitem__(self, SupportsIndex, /) -> ndarray[tuple[Any, ...], dtype[Any]]
openfold3/core/data/primitives/structure/interface.py:0: note: def __getitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], /) -> tuple[ndarray[tuple[Any, ...], dtype[Any]], ...]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "atom_name_unique"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "atom_name_unique"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "label_asym_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "label_asym_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "label_atom_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "label_comp_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "label_entity_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "label_seq_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[int]" has no attribute "auth_asym_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[int]" has no attribute "label_asym_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: "AtomArray[int]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/labels.py:0: error: Argument 1 to "zip" has incompatible type "list[str]"; expected "Iterable[int]"  [arg-type]
openfold3/core/data/primitives/structure/labels.py:0: error: Argument 1 to "zip" has incompatible type "list[str]"; expected "Iterable[int]"  [arg-type]
openfold3/core/data/primitives/structure/labels.py:0: error: Argument 1 to "zip" has incompatible type "list[str]"; expected "Iterable[int]"  [arg-type]
openfold3/core/data/primitives/structure/labels.py:0: error: Argument 1 to "zip" has incompatible type "list[str]"; expected "Iterable[int]"  [arg-type]
openfold3/core/data/primitives/structure/labels.py:0: error: Argument 2 to "set_annotation" of "_AtomArrayBase" has incompatible type "range"; expected "ndarray[tuple[Any, ...], dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/structure/labels.py:0: error: Argument 2 to "zip" has incompatible type "list[str]"; expected "Iterable[int]"  [arg-type]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "chain_start_idxs"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "chain_start_idxs"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "id_counter"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "residue_starts"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "residue_starts"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: Need type annotation for "source_chain_res_starts"  [var-annotated]
openfold3/core/data/primitives/structure/labels.py:0: error: No return value expected  [return-value]
openfold3/core/data/primitives/structure/labels.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/metadata.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/metadata.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/metadata.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/metadata.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/metadata.py:0: error: Argument 1 to "get_cif_block" has incompatible type "CIFFile | BinaryCIFFile"; expected "CIFFile"  [arg-type]
openfold3/core/data/primitives/structure/metadata.py:0: error: Incompatible return value type (got "dict[Any, int]", expected "dict[str, float]")  [return-value]
openfold3/core/data/primitives/structure/metadata.py:0: error: Incompatible types in assignment (expression has type "list[datetime]", variable has type "ndarray[tuple[Any], dtype[Any]]")  [assignment]
openfold3/core/data/primitives/structure/metadata.py:0: error: Need type annotation for "res_id_to_monomers"  [var-annotated]
openfold3/core/data/primitives/structure/metadata.py:0: error: Value of type "CIFFile | None" is not indexable  [index]
openfold3/core/data/primitives/structure/metadata.py:0: error: Value of type "CIFFile | None" is not indexable  [index]
openfold3/core/data/primitives/structure/metadata.py:0: error: Value of type "CIFFile | None" is not indexable  [index]
openfold3/core/data/primitives/structure/metadata.py:0: note: Perhaps you need a type annotation for "atom_id_to_charge"? Suggestion: "dict[str, float]"
openfold3/core/data/primitives/structure/query.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/query.py:0: error: Argument "atom_array" to "StructureWithReferenceMolecules" has incompatible type "AtomArray[Any] | None"; expected "AtomArray[Any]"  [arg-type]
openfold3/core/data/primitives/structure/query.py:0: error: Argument "atom_array" to "StructureWithReferenceMolecules" has incompatible type "AtomArray[int] | None"; expected "AtomArray[Any]"  [arg-type]
openfold3/core/data/primitives/structure/query.py:0: error: Argument "in_crop_mask" to "ProcessedReferenceMolecule" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[bool, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/structure/query.py:0: error: Argument "sequence" to "structure_with_ref_mols_from_sequence" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/primitives/structure/query.py:0: error: Argument 1 to "connect_via_residue_names" has incompatible type "AtomArray[int] | None"; expected "AtomArray[int | Any] | AtomArrayStack[Any, int | Any]"  [arg-type]
openfold3/core/data/primitives/structure/query.py:0: error: Argument 2 to "isin" has incompatible type "Iterable[str]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
openfold3/core/data/primitives/structure/query.py:0: error: Argument 2 to "set_annotation" of "_AtomArrayBase" has incompatible type "Iterable[str]"; expected "ndarray[tuple[Any, ...], dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/structure/query.py:0: error: Incompatible default for parameter "atoms_to_mask" (default has type "None", parameter has type "Iterable[str]")  [assignment]
openfold3/core/data/primitives/structure/query.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "ndarray[tuple[Any, ...], dtype[Any]]")  [assignment]
openfold3/core/data/primitives/structure/query.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "ndarray[tuple[Any, ...], dtype[Any]]")  [assignment]
openfold3/core/data/primitives/structure/query.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "set[str]")  [assignment]
openfold3/core/data/primitives/structure/query.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "set[str]")  [assignment]
openfold3/core/data/primitives/structure/query.py:0: error: Invalid index type "str | None" for "dict[str, int]"; expected type "str"  [index]
openfold3/core/data/primitives/structure/query.py:0: error: Item "None" of "AtomArray[Any] | None" has no attribute "coord"  [union-attr]
openfold3/core/data/primitives/structure/query.py:0: error: Item "None" of "AtomArray[int] | None" has no attribute "bonds"  [union-attr]
openfold3/core/data/primitives/structure/query.py:0: error: Item "None" of "AtomArray[int] | None" has no attribute "coord"  [union-attr]
openfold3/core/data/primitives/structure/query.py:0: error: Item "None" of "BinaryCIFColumn | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/query.py:0: error: Item "None" of "BinaryCIFColumn | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/query.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/data/primitives/structure/query.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/data/primitives/structure/template.py:0: error: "AtomArray[Any]" has no attribute "label_asym_id"  [attr-defined]
openfold3/core/data/primitives/structure/template.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/template.py:0: error: "AtomArray[int]" has no attribute "token_position"  [attr-defined]
openfold3/core/data/primitives/structure/template.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/primitives/structure/template.py:0: error: "dict" expects 2 type arguments, but 1 given  [type-arg]
openfold3/core/data/primitives/structure/template.py:0: error: Argument "idx_map" to "replace" of "TemplateCacheEntry" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/core/data/primitives/structure/template.py:0: error: Argument 1 to "MoleculeType" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "int"  [arg-type]
openfold3/core/data/primitives/structure/template.py:0: error: Incompatible return value type (got "None", expected "AtomArray[Any]")  [return-value]
openfold3/core/data/primitives/structure/template.py:0: error: Incompatible return value type (got "None", expected "AtomArray[Any]")  [return-value]
openfold3/core/data/primitives/structure/template.py:0: error: Incompatible return value type (got "ndarray[tuple[int], dtype[Any]]", expected "ndarray[int, dtype[Any]]")  [return-value]
openfold3/core/data/primitives/structure/template.py:0: error: Incompatible types in assignment (expression has type "AtomArray[Any]", variable has type "Atom")  [assignment]
openfold3/core/data/primitives/structure/template.py:0: error: Incompatible types in assignment (expression has type "AtomArray[Any]", variable has type "Atom")  [assignment]
openfold3/core/data/primitives/structure/template.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[int, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/structure/template.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[int, dtype[Any]]")  [assignment]
openfold3/core/data/primitives/structure/template.py:0: error: Need type annotation for "cropped_query_res_starts"  [var-annotated]
openfold3/core/data/primitives/structure/template.py:0: error: Need type annotation for "residue_starts"  [var-annotated]
openfold3/core/data/primitives/structure/template.py:0: error: Need type annotation for "template_slices" (hint: "template_slices: list[<type>] = ...")  [var-annotated]
openfold3/core/data/primitives/structure/template.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/structure/template.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/structure/template.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/structure/template.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/primitives/structure/template.py:0: error: Value of type "numpy.bool[builtins.bool] | ndarray[tuple[Any, ...], dtype[numpy.bool[builtins.bool]]]" is not indexable  [index]
openfold3/core/data/primitives/structure/template.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/template.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/template.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/template.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/template.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[Any]" has no attribute "_residue_idx"  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[Any]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[int]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[int]" has no attribute "_residue_idx"  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: "AtomArray[int]" has no attribute "token_id"  [attr-defined]
openfold3/core/data/primitives/structure/tokenization.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/data/primitives/structure/tokenization.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/tokenization.py:0: error: callable? not callable  [misc]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "Atom" has no attribute "_annot"  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "Atom" has no attribute "_annot"  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "Atom" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "Atom" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "Atom" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "Atom" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "AtomArray[Any]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "AtomArray[int]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: "AtomArray[int]" has no attribute "_atom_idx"; maybe "atom_id"?  [attr-defined]
openfold3/core/data/primitives/structure/unresolved.py:0: error: Argument "polymer_type" to "append_unresolved_segment" has incompatible type "str"; expected "Literal['protein', 'nucleic_acid']"  [arg-type]
openfold3/core/data/primitives/structure/unresolved.py:0: error: Argument "polymer_type" to "append_unresolved_segment" has incompatible type "str"; expected "Literal['protein', 'nucleic_acid']"  [arg-type]
openfold3/core/data/primitives/structure/unresolved.py:0: error: Argument "polymer_type" to "append_unresolved_segment" has incompatible type "str"; expected "Literal['protein', 'nucleic_acid']"  [arg-type]
openfold3/core/data/primitives/structure/unresolved.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "merge"  [union-attr]
openfold3/core/data/primitives/structure/unresolved.py:0: error: Need type annotation for "chain_starts"  [var-annotated]
openfold3/core/data/resources/patches.py:0: error: "Atom" has no attribute "_annot"  [attr-defined]
openfold3/core/data/resources/patches.py:0: error: "Atom" has no attribute "_annot"  [attr-defined]
openfold3/core/data/resources/patches.py:0: error: "Atom" has no attribute "_annot"  [attr-defined]
openfold3/core/data/resources/patches.py:0: error: "AtomArray[Any]" has no attribute "_coord"; maybe "coord"?  [attr-defined]
openfold3/core/data/resources/patches.py:0: error: Need type annotation for "array"  [var-annotated]
openfold3/core/data/resources/residues.py:0: error: Argument 1 to "reshape" of "ndarray" has incompatible type "str"; expected "None"  [arg-type]
openfold3/core/data/resources/residues.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "ndarray[str, dtype[Any]]")  [assignment]
openfold3/core/data/resources/residues.py:0: error: Too many arguments for "view" of "ndarray"  [call-arg]
openfold3/core/data/resources/residues.py:0: error: Type argument "int" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/resources/residues.py:0: error: Type argument "str" of "ndarray" must be a subtype of "tuple[int, ...]"  [type-var]
openfold3/core/data/resources/residues.py:0: error: Unsupported operand types for + ("str" and "tuple[int]")  [operator]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: "append" of "list" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: "str" not callable  [operator]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Argument 1 to "append" of "list" has incompatible type "None"; expected "str"  [arg-type]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Argument 1 to "append" of "list" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Argument 1 to "append" of "list" has incompatible type "str"; expected "ChainInput"  [arg-type]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Argument 1 to "get_sequence_hash" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[Any, Any]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[Any, Any]]"; expected "bool"  [arg-type]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Argument 3 to "ChainInput" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible default for parameter "host_url" (default has type "str", parameter has type "Url")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible return value type (got "tuple[dict[Any, Any], dict[Any, str]] | dict[Any, Any]", expected "list[str] | tuple[list[str], list[str]]")  [return-value]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "MsaServerPairingStrategy", variable has type "str")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "None", variable has type "str")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "int", target has type "ChainInput")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "int", variable has type "str")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "int", variable has type "str")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "dict[Any, Any]")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "dict[Any, str]")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "str | None", target has type "str")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "str", target has type "ChainInput")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Incompatible types in assignment (expression has type "str", target has type "ChainInput")  [assignment]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Invalid index type "str | None" for "dict[str, ChainInput]"; expected type "str"  [index]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Invalid index type "str | None" for "dict[str, ChainInput]"; expected type "str"  [index]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Invalid index type "str" for "dict[ChainInput, ChainInput]"; expected type "ChainInput"  [index]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Invalid index type "str" for "dict[ChainInput, ChainInput]"; expected type "ChainInput"  [index]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Invalid index type "str" for "dict[ChainInput, ChainInput]"; expected type "ChainInput"  [index]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Invalid index type "str" for "dict[ChainInput, str]"; expected type "ChainInput"  [index]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Invalid index type "str" for "dict[int, ChainInput]"; expected type "int"  [index]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Need type annotation for "a3m_lines" (hint: "a3m_lines: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Need type annotation for "chain_inputs_seen" (hint: "chain_inputs_seen: set[<type>] = ...")  [var-annotated]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Need type annotation for "template_paths_" (hint: "template_paths_: list[<type>] = ...")  [var-annotated]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Need type annotation for "templates" (hint: "templates: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/data/tools/colabfold_msa_server.py:0: error: Unsupported operand types for + ("str" and "None")  [operator]
openfold3/core/data/tools/colabfold_msa_server.py:0: note: Right operand is of type "str | None"
openfold3/core/data/tools/jackhmmer.py:0: error: Incompatible return value type (got "list[Mapping[str, Any]]", expected "Sequence[Sequence[Mapping[str, Any]]]")  [return-value]
openfold3/core/data/tools/jackhmmer.py:0: error: Need type annotation for "chunked_outputs"  [var-annotated]
openfold3/core/data/tools/kalign.py:0: error: Incompatible return value type (got "list[str] | Any", expected "str")  [return-value]
openfold3/core/data/tools/kalign.py:0: error: Incompatible return value type (got "str", expected "list[str]")  [return-value]
openfold3/core/loss/confidence.py:0: error: Bracketed expression "[...]" is not valid as a type  [valid-type]
openfold3/core/loss/confidence.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[Tensor]")  [assignment]
openfold3/core/loss/diffusion.py:0: error: "float" has no attribute "detach"  [attr-defined]
openfold3/core/loss/diffusion.py:0: error: "float" has no attribute "detach"  [attr-defined]
openfold3/core/loss/diffusion.py:0: error: "float" has no attribute "detach"  [attr-defined]
openfold3/core/loss/diffusion.py:0: error: "float" has no attribute "detach"  [attr-defined]
openfold3/core/loss/diffusion.py:0: error: Bracketed expression "[...]" is not valid as a type  [valid-type]
openfold3/core/loss/diffusion.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/loss/diffusion.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "float")  [assignment]
openfold3/core/loss/diffusion.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "float")  [assignment]
openfold3/core/loss/diffusion.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "float")  [assignment]
openfold3/core/loss/diffusion.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "float")  [assignment]
openfold3/core/loss/diffusion.py:0: error: torch.tensor? has no attribute "expand"  [attr-defined]
openfold3/core/loss/diffusion.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/loss/diffusion.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/loss/loss_module.py:0: error: "list[Any]" has no attribute "shape"  [attr-defined]
openfold3/core/loss/loss_module.py:0: error: "list[Any]" has no attribute "sum"  [attr-defined]
openfold3/core/loss/loss_module.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[Any]")  [assignment]
openfold3/core/loss/loss_utils.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/loss/loss_utils.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/loss/loss_utils.py:0: error: No overload variant of "sum" matches argument type "bool"  [call-overload]
openfold3/core/loss/loss_utils.py:0: error: No overload variant of "sum" matches argument type "int"  [call-overload]
openfold3/core/loss/loss_utils.py:0: error: Unsupported left operand type for * (torch.tensor?)  [operator]
openfold3/core/loss/loss_utils.py:0: error: torch.tensor? has no attribute "expand_as"  [attr-defined]
openfold3/core/loss/loss_utils.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/loss/loss_utils.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/loss/loss_utils.py:0: note: Possible overload variants:
openfold3/core/loss/loss_utils.py:0: note: def sum(input: Tensor, *, dtype: dtype | None = ...) -> Tensor
openfold3/core/loss/loss_utils.py:0: note: def sum(input: Tensor, dim: Sequence[str | EllipsisType | None], keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/loss/loss_utils.py:0: note: def sum(input: Tensor, dim: int | Size | list[int] | tuple[int, ...] | None, keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/alignment.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/core/metrics/confidence.py:0: error: Bracketed expression "[...]" is not valid as a type  [valid-type]
openfold3/core/metrics/confidence.py:0: error: Item "None" of "Tensor | None" has no attribute "unsqueeze"  [union-attr]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument "out_shape" to "select_inter_filter_mask" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument 1 has incompatible type "None"; expected "Tensor | int | float | bool | complex"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Argument 1 to "len" has incompatible type "Sequence[Any] | None"; expected "Sized"  [arg-type]
openfold3/core/metrics/quality.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/metrics/quality.py:0: error: Incompatible return value type (got "Tensor | None", expected "Tensor")  [return-value]
openfold3/core/metrics/quality.py:0: error: Incompatible return value type (got "Tensor | None", expected "Tensor")  [return-value]
openfold3/core/metrics/quality.py:0: error: Incompatible return value type (got "tuple[Tensor | None, Tensor | None]", expected "tuple[Tensor, Tensor]")  [return-value]
openfold3/core/metrics/quality.py:0: error: Incompatible return value type (got "tuple[Tensor | None, Tensor | None]", expected "tuple[Tensor, Tensor]")  [return-value]
openfold3/core/metrics/quality.py:0: error: Incompatible return value type (got "tuple[Tensor | None, Tensor | None]", expected "tuple[Tensor, Tensor]")  [return-value]
openfold3/core/metrics/quality.py:0: error: Incompatible types in assignment (expression has type "None", variable has type "Tensor")  [assignment]
openfold3/core/metrics/quality.py:0: error: Incompatible types in assignment (expression has type "Tensor", target has type "None")  [assignment]
openfold3/core/metrics/quality.py:0: error: Incompatible types in assignment (expression has type "Tensor", target has type "None")  [assignment]
openfold3/core/metrics/quality.py:0: error: Incompatible types in assignment (expression has type "tuple[str, str]", variable has type "str")  [assignment]
openfold3/core/metrics/quality.py:0: error: Item "None" of "Sequence[Any] | None" has no attribute "__iter__" (not iterable)  [union-attr]
openfold3/core/metrics/quality.py:0: error: List item 0 has incompatible type "None"; expected "Tensor"  [list-item]
openfold3/core/metrics/quality.py:0: error: Need type annotation for "metrics" (hint: "metrics: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/metrics/quality.py:0: error: No overload variant of "sum" matches argument types "Any", "int"  [call-overload]
openfold3/core/metrics/quality.py:0: error: No overload variant of "sum" matches argument types "Any", "int"  [call-overload]
openfold3/core/metrics/quality.py:0: error: No overload variant of "sum" matches argument types "None", "int", "bool"  [call-overload]
openfold3/core/metrics/quality.py:0: error: No overload variant of "sum" matches argument types "Tensor", "int"  [call-overload]
openfold3/core/metrics/quality.py:0: error: No overload variant of "sum" matches argument types "Tensor", "int"  [call-overload]
openfold3/core/metrics/quality.py:0: error: Unexpected keyword argument "axis" for overloaded function "sum"  [call-overload]
openfold3/core/metrics/quality.py:0: error: Unexpected keyword argument "axis" for overloaded function "sum"  [call-overload]
openfold3/core/metrics/quality.py:0: error: Unexpected keyword argument "axis" for overloaded function "sum"  [call-overload]
openfold3/core/metrics/quality.py:0: error: Unexpected keyword argument "axis" for overloaded function "sum"  [call-overload]
openfold3/core/metrics/quality.py:0: error: Unpacking a string is disallowed  [str-unpack]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Size" and "tuple[Tensor, Tensor]")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Size" and "tuple[Tensor, Tensor]")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Size" and "tuple[Tensor, Tensor]")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for + ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for - ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for - ("None" and "Tensor")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for / ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for / ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for / ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for < ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Unsupported operand types for < ("Tensor" and "None")  [operator]
openfold3/core/metrics/quality.py:0: error: Value of type torch.tensor? is not indexable  [index]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "bool"  [attr-defined]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "bool"  [attr-defined]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "bool"  [attr-defined]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "bool"  [attr-defined]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "bool"  [attr-defined]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "bool"  [attr-defined]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "expand"  [attr-defined]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/metrics/quality.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Left operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/metrics/quality.py:0: note: Possible overload variants:
openfold3/core/metrics/quality.py:0: note: Possible overload variants:
openfold3/core/metrics/quality.py:0: note: Possible overload variants:
openfold3/core/metrics/quality.py:0: note: Possible overload variants:
openfold3/core/metrics/quality.py:0: note: Possible overload variants:
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: Right operand is of type "float | None"
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, *, dtype: dtype | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, *, dtype: dtype | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, *, dtype: dtype | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, *, dtype: dtype | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, *, dtype: dtype | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: Sequence[str | EllipsisType | None], keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: Sequence[str | EllipsisType | None], keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: Sequence[str | EllipsisType | None], keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: Sequence[str | EllipsisType | None], keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: Sequence[str | EllipsisType | None], keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: int | Size | list[int] | tuple[int, ...] | None, keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: int | Size | list[int] | tuple[int, ...] | None, keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: int | Size | list[int] | tuple[int, ...] | None, keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: int | Size | list[int] | tuple[int, ...] | None, keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/quality.py:0: note: def sum(input: Tensor, dim: int | Size | list[int] | tuple[int, ...] | None, keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/metrics/rasa.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/metrics/rasa.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
openfold3/core/metrics/rasa.py:0: error: "ndarray[tuple[Any, ...], dtype[Any]]" has no attribute "atom_resolved_mask"  [attr-defined]
openfold3/core/metrics/rasa.py:0: error: Argument "vdw_radii" to "sasa" has incompatible type "str"; expected "Literal['ProtOr', 'Single'] | ndarray[tuple[Never], dtype[floating[Any]]]"  [arg-type]
openfold3/core/metrics/rasa.py:0: error: Argument 1 to "apply_residue_wise" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "AtomArray[Never] | AtomArrayStack[Never, Never]"  [arg-type]
openfold3/core/metrics/rasa.py:0: error: Argument 1 to "apply_residue_wise" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "AtomArray[Never] | AtomArrayStack[Never, Never]"  [arg-type]
openfold3/core/metrics/rasa.py:0: error: Argument 1 to "get_residues" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "AtomArray[Any] | AtomArrayStack[Any, Any]"  [arg-type]
openfold3/core/metrics/rasa.py:0: error: Argument 1 to "len" has incompatible type "Atom"; expected "Sized"  [arg-type]
openfold3/core/metrics/rasa.py:0: error: Argument 1 to "len" has incompatible type "Atom"; expected "Sized"  [arg-type]
openfold3/core/metrics/rasa.py:0: error: Argument 1 to "sasa" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "AtomArray[Never]"  [arg-type]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "max_acc_dict" (default has type "None", parameter has type "dict[Any, Any]")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "max_acc_dict" (default has type "None", parameter has type "dict[Any, Any]")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "max_acc_dict" (default has type "None", parameter has type "dict[Any, Any]")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "max_acc_dict" (default has type "None", parameter has type "dict[Any, Any]")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "max_acc_dict" (default has type "None", parameter has type "dict[Any, Any]")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "pdb_id" (default has type "None", parameter has type "str")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "residue_sasa_scale" (default has type "None", parameter has type "str")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "residue_sasa_scale" (default has type "None", parameter has type "str")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "residue_sasa_scale" (default has type "None", parameter has type "str")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible default for parameter "residue_sasa_scale" (default has type "None", parameter has type "str")  [assignment]
openfold3/core/metrics/rasa.py:0: error: Incompatible return value type (got "floating[Any]", expected "float")  [return-value]
openfold3/core/metrics/rasa.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[Any]")  [assignment]
openfold3/core/metrics/rasa.py:0: error: No overload variant of "chain_iter" matches argument type "Atom"  [call-overload]
openfold3/core/metrics/rasa.py:0: error: No overload variant of "chain_iter" matches argument type "Atom"  [call-overload]
openfold3/core/metrics/rasa.py:0: error: Unsupported operand types for > ("list[Any]" and "float")  [operator]
openfold3/core/metrics/rasa.py:0: error: Value of type "Any | None" is not indexable  [index]
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/core/metrics/rasa.py:0: note: Possible overload variants:
openfold3/core/metrics/rasa.py:0: note: Possible overload variants:
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/core/metrics/rasa.py:0: note: def [M: int, N: int] chain_iter(array: AtomArrayStack[M, N]) -> Iterator[AtomArrayStack[M, Any]]
openfold3/core/metrics/rasa.py:0: note: def [M: int, N: int] chain_iter(array: AtomArrayStack[M, N]) -> Iterator[AtomArrayStack[M, Any]]
openfold3/core/metrics/rasa.py:0: note: def [N: int] chain_iter(array: AtomArray[N]) -> Iterator[AtomArray[Any]]
openfold3/core/metrics/rasa.py:0: note: def [N: int] chain_iter(array: AtomArray[N]) -> Iterator[AtomArray[Any]]
openfold3/core/metrics/sample_ranking.py:0: error: Argument "has_frame" to "compute_ptm" has incompatible type "Tensor | None"; expected "Tensor"  [arg-type]
openfold3/core/metrics/sample_ranking.py:0: error: Argument "has_frame" to "compute_ptm" has incompatible type "Tensor | None"; expected "Tensor"  [arg-type]
openfold3/core/metrics/sample_ranking.py:0: error: Dict entry 0 has incompatible type "str": "dict[str, Tensor]"; expected "str": "Tensor"  [dict-item]
openfold3/core/metrics/sample_ranking.py:0: error: Dict entry 1 has incompatible type "str": "dict[str, Tensor]"; expected "str": "Tensor"  [dict-item]
openfold3/core/metrics/sample_ranking.py:0: error: Incompatible return value type (got "dict[str, Tensor]", expected "Tensor")  [return-value]
openfold3/core/metrics/sample_ranking.py:0: error: Incompatible return value type (got "dict[str, dict[Any, Tensor]]", expected "Tensor")  [return-value]
openfold3/core/model/feature_embedders/input_embedders.py:0: error: Argument "no_subsampled_all_msa" to "_subsample_all_msa" of "MSAModuleEmbedder" has incompatible type "int | float"; expected "int"  [arg-type]
openfold3/core/model/feature_embedders/input_embedders.py:0: error: Argument 2 to "split" has incompatible type "list[Tensor]"; expected "int | list[int]"  [arg-type]
openfold3/core/model/feature_embedders/input_embedders.py:0: error: Argument 2 to "split" has incompatible type "list[Tensor]"; expected "int | list[int]"  [arg-type]
openfold3/core/model/feature_embedders/input_embedders.py:0: error: Function "builtins.callable" is not valid as a type  [valid-type]
openfold3/core/model/feature_embedders/input_embedders.py:0: error: Incompatible types in assignment (expression has type "int", variable has type "Tensor")  [assignment]
openfold3/core/model/feature_embedders/input_embedders.py:0: error: Unsupported operand types for * ("Tensor" and Module)  [operator]
openfold3/core/model/feature_embedders/input_embedders.py:0: error: Unsupported operand types for + ("Tensor" and Module)  [operator]
openfold3/core/model/feature_embedders/input_embedders.py:0: error: callable? not callable  [misc]
openfold3/core/model/feature_embedders/input_embedders.py:0: note: Perhaps you meant "typing.Callable" instead of "callable"?
openfold3/core/model/feature_embedders/input_embedders.py:0: note: Right operand is of type "Tensor | Module"
openfold3/core/model/heads/prediction_heads.py:0: error: Argument "feat_dims" to "reshape_inputs" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/model/heads/prediction_heads.py:0: error: Argument "feat_dims" to "reshape_inputs" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/model/heads/prediction_heads.py:0: error: Argument "feat_dims" to "reshape_inputs" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/model/heads/prediction_heads.py:0: error: Argument "feat_dims" to "reshape_inputs" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/model/heads/prediction_heads.py:0: error: Argument "feat_dims" to "reshape_outputs" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/model/heads/prediction_heads.py:0: error: Argument "feat_dims" to "reshape_outputs" has incompatible type "Size"; expected "list[Any]"  [arg-type]
openfold3/core/model/heads/prediction_heads.py:0: error: No overload variant of "sum" matches argument types "Tensor", "int", "bool"  [call-overload]
openfold3/core/model/heads/prediction_heads.py:0: error: Unexpected keyword argument "keepdims" for overloaded function "sum"; did you mean "keepdim"?  [call-overload]
openfold3/core/model/heads/prediction_heads.py:0: error: Unsupported operand types for + ("Size" and "list[Any]")  [operator]
openfold3/core/model/heads/prediction_heads.py:0: note: Possible overload variants:
openfold3/core/model/heads/prediction_heads.py:0: note: def sum(input: Tensor, *, dtype: dtype | None = ...) -> Tensor
openfold3/core/model/heads/prediction_heads.py:0: note: def sum(input: Tensor, dim: Sequence[str | EllipsisType | None], keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/model/heads/prediction_heads.py:0: note: def sum(input: Tensor, dim: int | Size | list[int] | tuple[int, ...] | None, keepdim: bool = ..., *, dtype: dtype | None = ..., out: Tensor | None = ...) -> Tensor
openfold3/core/model/latent/base_blocks.py:0: error: Incompatible types in assignment (expression has type "SwiGLUTransition", variable has type "ReLUTransition")  [assignment]
openfold3/core/model/latent/base_blocks.py:0: error: Incompatible types in assignment (expression has type "SwiGLUTransition", variable has type "ReLUTransition")  [assignment]
openfold3/core/model/latent/base_blocks.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor]")  [index]
openfold3/core/model/latent/base_blocks.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor]")  [index]
openfold3/core/model/latent/base_stacks.py:0: error: Argument "args" to "tune_chunk_size" of "ChunkSizeTuner" has incompatible type "tuple[Tensor, Tensor]"; expected "tuple[Any]"  [arg-type]
openfold3/core/model/latent/base_stacks.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor]")  [index]
openfold3/core/model/latent/base_stacks.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor]")  [index]
openfold3/core/model/latent/evoformer.py:0: error: "None" object is not iterable  [misc]
openfold3/core/model/latent/evoformer.py:0: error: "None" object is not iterable  [misc]
openfold3/core/model/latent/evoformer.py:0: error: "None" object is not iterable  [misc]
openfold3/core/model/latent/evoformer.py:0: error: "None" object is not iterable  [misc]
openfold3/core/model/latent/evoformer.py:0: error: Argument "input_tensors" to "_compute_opm" of "MSABlock" has incompatible type "Sequence[Tensor] | None"; expected "Sequence[Tensor]"  [arg-type]
openfold3/core/model/latent/evoformer.py:0: error: Argument "input_tensors" to "_compute_opm" of "MSABlock" has incompatible type "Sequence[Tensor] | None"; expected "Sequence[Tensor]"  [arg-type]
openfold3/core/model/latent/evoformer.py:0: error: List item 0 has incompatible type "Tensor | None"; expected "Tensor"  [list-item]
openfold3/core/model/latent/evoformer.py:0: error: List item 1 has incompatible type "Tensor | None"; expected "Tensor"  [list-item]
openfold3/core/model/latent/evoformer.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor] | None")  [index]
openfold3/core/model/latent/evoformer.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor] | None")  [index]
openfold3/core/model/latent/evoformer.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor] | None")  [index]
openfold3/core/model/latent/evoformer.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor] | None")  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/evoformer.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: "None" object is not iterable  [misc]
openfold3/core/model/latent/msa_module.py:0: error: "None" object is not iterable  [misc]
openfold3/core/model/latent/msa_module.py:0: error: "None" object is not iterable  [misc]
openfold3/core/model/latent/msa_module.py:0: error: "None" object is not iterable  [misc]
openfold3/core/model/latent/msa_module.py:0: error: Argument "input_tensors" to "_compute_opm" of "MSABlock" has incompatible type "Sequence[Tensor] | None"; expected "Sequence[Tensor]"  [arg-type]
openfold3/core/model/latent/msa_module.py:0: error: Argument "input_tensors" to "_compute_opm" of "MSABlock" has incompatible type "Sequence[Tensor] | None"; expected "Sequence[Tensor]"  [arg-type]
openfold3/core/model/latent/msa_module.py:0: error: Incompatible types in assignment (expression has type "MSAPairWeightedAveraging", variable has type "MSARowAttentionWithPairBias")  [assignment]
openfold3/core/model/latent/msa_module.py:0: error: Incompatible types in assignment (expression has type "None", variable has type "MSARowAttentionWithPairBias")  [assignment]
openfold3/core/model/latent/msa_module.py:0: error: Incompatible types in assignment (expression has type "None", variable has type "ReLUTransition")  [assignment]
openfold3/core/model/latent/msa_module.py:0: error: List item 0 has incompatible type "Tensor | None"; expected "Tensor"  [list-item]
openfold3/core/model/latent/msa_module.py:0: error: List item 1 has incompatible type "Tensor | None"; expected "Tensor"  [list-item]
openfold3/core/model/latent/msa_module.py:0: error: Return type "Tensor" of "_wrap_up" incompatible with return type "Sequence[Tensor]" in supertype "openfold3.core.model.latent.base_stacks.MSAStack"  [override]
openfold3/core/model/latent/msa_module.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor] | None")  [index]
openfold3/core/model/latent/msa_module.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor] | None")  [index]
openfold3/core/model/latent/msa_module.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor] | None")  [index]
openfold3/core/model/latent/msa_module.py:0: error: Unsupported target for indexed assignment ("Sequence[Tensor] | None")  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/msa_module.py:0: error: Value of type "Sequence[Tensor] | None" is not indexable  [index]
openfold3/core/model/latent/pairformer.py:0: error: Argument "args" to "tune_chunk_size" of "ChunkSizeTuner" has incompatible type "tuple[Tensor, Tensor]"; expected "tuple[Any]"  [arg-type]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Argument "n_key" to "convert_single_rep_to_blocks" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Argument "n_key" to "convert_single_rep_to_blocks" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Argument "n_query" to "convert_single_rep_to_blocks" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Argument "n_query" to "convert_single_rep_to_blocks" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Incompatible types in assignment (expression has type "Tensor | None", variable has type "Tensor")  [assignment]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "ada_ln"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "ada_ln"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "ada_ln"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "layer_norm_z"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "linear_ada_out"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "linear_ada_out"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "linear_z"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "linear_z"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "linear_z"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "mha"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "mha"  [union-attr]
openfold3/core/model/layers/attention_pair_bias.py:0: error: Item "None" of "Any | None" has no attribute "mha"  [union-attr]
openfold3/core/model/layers/diffusion_conditioning.py:0: error: Argument "args" to "tune_chunk_size" of "ChunkSizeTuner" has incompatible type "tuple[Tensor, Tensor, Tensor]"; expected "tuple[Any]"  [arg-type]
openfold3/core/model/layers/diffusion_transformer.py:0: error: Incompatible types in assignment (expression has type "CrossAttentionPairBias", variable has type "DiffusionAttentionPairBias")  [assignment]
openfold3/core/model/layers/msa.py:0: error: Argument "z" to "_prep_inputs" of "MSAPairWeightedAveraging" has incompatible type "Tensor | None"; expected "Tensor"  [arg-type]
openfold3/core/model/layers/msa.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/msa.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/msa.py:0: error: Incompatible return value type (got "tuple[Tensor, Any, Tensor | None]", expected "tuple[Tensor, Tensor, Tensor]")  [return-value]
openfold3/core/model/layers/msa.py:0: error: Incompatible types in assignment (expression has type "list[Tensor]", target has type "Tensor")  [assignment]
openfold3/core/model/layers/sequence_local_atom_attention.py:0: error: Argument "c_s" to "NoisyPositionEmbedder" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/model/layers/sequence_local_atom_attention.py:0: error: Argument "c_z" to "NoisyPositionEmbedder" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/model/layers/sequence_local_atom_attention.py:0: error: Item "None" of "Tensor | None" has no attribute "unsqueeze"  [union-attr]
openfold3/core/model/layers/sequence_local_atom_attention.py:0: error: Item "None" of "Tensor | None" has no attribute "unsqueeze"  [union-attr]
openfold3/core/model/layers/sequence_local_atom_attention.py:0: error: Item "None" of "Tensor | None" has no attribute "unsqueeze"  [union-attr]
openfold3/core/model/layers/sequence_local_atom_attention.py:0: error: Item "None" of "Tensor | None" has no attribute "unsqueeze"  [union-attr]
openfold3/core/model/layers/triangular_attention.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_attention.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Argument 2 to "permute_final_dims" has incompatible type "tuple[int, int, int]"; expected "list[int]"  [arg-type]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Signature of "forward" incompatible with supertype "BaseTriangleMultiplicativeUpdate"  [override]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: error: Signature of "forward" incompatible with supertype "BaseTriangleMultiplicativeUpdate"  [override]
openfold3/core/model/layers/triangular_multiplicative_update.py:0: note: Subclass:
openfold3/core/model/layers/triangular_multiplicative_update.py:0: note: Subclass:
openfold3/core/model/layers/triangular_multiplicative_update.py:0: note: Superclass:
openfold3/core/model/layers/triangular_multiplicative_update.py:0: note: Superclass:
openfold3/core/model/layers/triangular_multiplicative_update.py:0: note: def forward(self, z: Tensor, mask: Tensor | None = ..., inplace_safe: bool = ..., _add_with_inplace: bool = ...) -> Tensor
openfold3/core/model/layers/triangular_multiplicative_update.py:0: note: def forward(self, z: Tensor, mask: Tensor | None = ..., inplace_safe: bool = ..., _add_with_inplace: bool = ...) -> Tensor
openfold3/core/model/layers/triangular_multiplicative_update.py:0: note: def forward(self, z: Tensor, mask: Tensor | None = ..., inplace_safe: bool = ..., use_cueq_triangle_kernels: bool = ..., use_triton_triangle_kernels: bool = ..., _add_with_inplace: bool = ..., _inplace_chunk_size: int | None = ...) -> Tensor
openfold3/core/model/layers/triangular_multiplicative_update.py:0: note: def forward(self, z: Tensor, mask: Tensor | None = ..., inplace_safe: bool = ..., use_cueq_triangle_kernels: bool = ..., use_triton_triangle_kernels: bool = ..., _add_with_inplace: bool = ..., _inplace_chunk_size: int | None = ...) -> Tensor
openfold3/core/model/primitives/attention.py:0: error: "None" not callable  [misc]
openfold3/core/model/primitives/attention.py:0: error: Incompatible types in assignment (expression has type "None", variable has type "Callable[[Any, Any, Any, Any, Any, Any], Any]")  [assignment]
openfold3/core/runners/writer.py:0: error: Argument 1 to "write_text" of "Path" has incompatible type "list[str]"; expected "str"  [arg-type]
openfold3/core/runners/writer.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "list[str]")  [assignment]
openfold3/core/runners/writer.py:0: error: Need type annotation for "failed_queries" (hint: "failed_queries: list[<type>] = ...")  [var-annotated]
openfold3/core/utils/atomize_utils.py:0: error: Argument "dim" to "scatter_add_" of "TensorBase" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/utils/atomize_utils.py:0: error: Argument "dim" to "stack" has incompatible type "int | None"; expected "int"  [arg-type]
openfold3/core/utils/atomize_utils.py:0: error: Argument 2 to "pad" has incompatible type "tuple[int, int, int, Tensor]"; expected "Sequence[int]"  [arg-type]
openfold3/core/utils/atomize_utils.py:0: error: Argument 2 to <tuple> has incompatible type "Tensor"; expected "int | SymInt"  [arg-type]
openfold3/core/utils/atomize_utils.py:0: error: Incompatible types in assignment (expression has type "None", variable has type "Tensor")  [assignment]
openfold3/core/utils/atomize_utils.py:0: error: List item 0 has incompatible type "None"; expected "int"  [list-item]
openfold3/core/utils/atomize_utils.py:0: error: No overload variant of "__setitem__" of "list" matches argument types "int", "Tensor"  [call-overload]
openfold3/core/utils/atomize_utils.py:0: note: Possible overload variants:
openfold3/core/utils/atomize_utils.py:0: note: def __setitem__(self, SupportsIndex, None, /) -> None
openfold3/core/utils/atomize_utils.py:0: note: def __setitem__(self, slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None], Iterable[None], /) -> None
openfold3/core/utils/chunk_utils.py:0: error: Argument 1 to "len" has incompatible type "int"; expected "Sized"  [arg-type]
openfold3/core/utils/chunk_utils.py:0: error: Incompatible return value type (got "tuple[int, ...]", expected "tuple[int]")  [return-value]
openfold3/core/utils/chunk_utils.py:0: error: Incompatible types in assignment (expression has type "tuple[slice[int, int, Any], ...]", variable has type "list[slice[int, int, Any]]")  [assignment]
openfold3/core/utils/chunk_utils.py:0: error: List item 0 has incompatible type "tuple[Never, ...]"; expected "tuple[int]"  [list-item]
openfold3/core/utils/chunk_utils.py:0: error: List item 0 has incompatible type "tuple[slice[int, int, Any], ...]"; expected "tuple[int]"  [list-item]
openfold3/core/utils/chunk_utils.py:0: error: List item 0 has incompatible type "tuple[slice[int, int, Any]]"; expected "tuple[int]"  [list-item]
openfold3/core/utils/chunk_utils.py:0: error: No overload variant of "__add__" of "list" matches argument type "tuple[slice[int, int, Any]]"  [operator]
openfold3/core/utils/chunk_utils.py:0: error: No overload variant of "__add__" of "list" matches argument type "tuple[slice[int, int, Any]]"  [operator]
openfold3/core/utils/chunk_utils.py:0: error: No overload variant of "__add__" of "list" matches argument type "tuple[slice[int, int, Any]]"  [operator]
openfold3/core/utils/chunk_utils.py:0: error: No overload variant of "__add__" of "list" matches argument type "tuple[slice[int, int, Any]]"  [operator]
openfold3/core/utils/chunk_utils.py:0: error: No overload variant of "zip" matches argument types "Sequence[int]", "int", "bool"  [call-overload]
openfold3/core/utils/chunk_utils.py:0: note: Possible overload variants:
openfold3/core/utils/chunk_utils.py:0: note: Possible overload variants:
openfold3/core/utils/chunk_utils.py:0: note: Possible overload variants:
openfold3/core/utils/chunk_utils.py:0: note: Possible overload variants:
openfold3/core/utils/chunk_utils.py:0: note: Possible overload variants:
openfold3/core/utils/chunk_utils.py:0: note: def [_S] __add__(self, list[_S], /) -> list[_S | slice[int, int, Any]]
openfold3/core/utils/chunk_utils.py:0: note: def [_S] __add__(self, list[_S], /) -> list[_S | slice[int, int, Any]]
openfold3/core/utils/chunk_utils.py:0: note: def [_S] __add__(self, list[_S], /) -> list[_S | slice[int, int, Any]]
openfold3/core/utils/chunk_utils.py:0: note: def [_S] __add__(self, list[_S], /) -> list[_S | slice[int, int, Any]]
openfold3/core/utils/chunk_utils.py:0: note: def [_T_co, _T1, _T2, _T3, _T4, _T5] zip(Iterable[_T1], Iterable[_T2], Iterable[_T3], Iterable[_T4], Iterable[_T5], /, *, strict: bool = ...) -> zip[tuple[_T1, _T2, _T3, _T4, _T5]]
openfold3/core/utils/chunk_utils.py:0: note: def [_T_co, _T1, _T2, _T3, _T4] zip(Iterable[_T1], Iterable[_T2], Iterable[_T3], Iterable[_T4], /, *, strict: bool = ...) -> zip[tuple[_T1, _T2, _T3, _T4]]
openfold3/core/utils/chunk_utils.py:0: note: def [_T_co, _T1, _T2, _T3] zip(Iterable[_T1], Iterable[_T2], Iterable[_T3], /, *, strict: bool = ...) -> zip[tuple[_T1, _T2, _T3]]
openfold3/core/utils/chunk_utils.py:0: note: def [_T_co, _T1, _T2] zip(Iterable[_T1], Iterable[_T2], /, *, strict: bool = ...) -> zip[tuple[_T1, _T2]]
openfold3/core/utils/chunk_utils.py:0: note: def [_T_co, _T1] zip(Iterable[_T1], /, *, strict: bool = ...) -> zip[tuple[_T1]]
openfold3/core/utils/chunk_utils.py:0: note: def [_T_co] zip(*, strict: bool = ...) -> zip[Any]
openfold3/core/utils/chunk_utils.py:0: note: def [_T_co] zip(Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], /, *iterables: Iterable[Any], strict: bool = ...) -> zip[tuple[Any, ...]]
openfold3/core/utils/chunk_utils.py:0: note: def __add__(self, list[slice[int, int, Any]], /) -> list[slice[int, int, Any]]
openfold3/core/utils/chunk_utils.py:0: note: def __add__(self, list[slice[int, int, Any]], /) -> list[slice[int, int, Any]]
openfold3/core/utils/chunk_utils.py:0: note: def __add__(self, list[slice[int, int, Any]], /) -> list[slice[int, int, Any]]
openfold3/core/utils/chunk_utils.py:0: note: def __add__(self, list[slice[int, int, Any]], /) -> list[slice[int, int, Any]]
openfold3/core/utils/grad_manager.py:0: error: "None" has no attribute "global_rank"  [attr-defined]
openfold3/core/utils/grad_manager.py:0: error: "None" has no attribute "global_step"  [attr-defined]
openfold3/core/utils/grad_manager.py:0: error: "None" has no attribute "global_step"  [attr-defined]
openfold3/core/utils/grad_manager.py:0: error: "None" has no attribute "named_parameters"  [attr-defined]
openfold3/core/utils/grad_manager.py:0: error: Argument 1 has incompatible type "None"; expected "Tensor | int | float | bool | complex"  [arg-type]
openfold3/core/utils/grad_manager.py:0: error: Argument 2 to "maximum" has incompatible type "None"; expected "Tensor"  [arg-type]
openfold3/core/utils/grad_manager.py:0: error: Bracketed expression "[...]" is not valid as a type  [valid-type]
openfold3/core/utils/grad_manager.py:0: error: Incompatible types in assignment (expression has type "Logger", variable has type "None")  [assignment]
openfold3/core/utils/grad_manager.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "None")  [assignment]
openfold3/core/utils/grad_manager.py:0: error: Incompatible types in assignment (expression has type "Trainer", variable has type "None")  [assignment]
openfold3/core/utils/grad_manager.py:0: error: Incompatible types in assignment (expression has type Module, variable has type "None")  [assignment]
openfold3/core/utils/grad_manager.py:0: error: Item "None" of "Any | Tensor | None" has no attribute "float"  [union-attr]
openfold3/core/utils/grad_manager.py:0: error: Item "None" of "MaxMetric | None" has no attribute "compute"  [union-attr]
openfold3/core/utils/grad_manager.py:0: error: Item "None" of "MaxMetric | None" has no attribute "to"  [union-attr]
openfold3/core/utils/grad_manager.py:0: error: Item "None" of "MaxMetric | None" has no attribute "update"  [union-attr]
openfold3/core/utils/grad_manager.py:0: error: Item "None" of "MeanMetric | None" has no attribute "compute"  [union-attr]
openfold3/core/utils/grad_manager.py:0: error: Item "None" of "MeanMetric | None" has no attribute "to"  [union-attr]
openfold3/core/utils/grad_manager.py:0: error: Item "None" of "MeanMetric | None" has no attribute "update"  [union-attr]
openfold3/core/utils/grad_manager.py:0: error: Need type annotation for "_params_to_update" (hint: "_params_to_update: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/utils/grad_manager.py:0: error: Need type annotation for "grad_accumulator" (hint: "grad_accumulator: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/utils/grad_manager.py:0: error: Need type annotation for "parameter_participation_counts" (hint: "parameter_participation_counts: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/core/utils/grad_manager.py:0: error: Unsupported operand types for * ("None" and "float")  [operator]
openfold3/core/utils/grad_manager.py:0: note: Left operand is of type "int | float | None"
openfold3/core/utils/logging_utils.py:0: error: Argument 1 to "set" of "ContextVar" has incompatible type "dict[str, Any] | None"; expected "None"  [arg-type]
openfold3/core/utils/logging_utils.py:0: error: Invalid type: try using Literal[True] instead?  [valid-type]
openfold3/core/utils/logging_utils.py:0: error: Module has no attribute "handlers"; maybe "Handler"?  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: "list[Any]" has no attribute "max"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: "list[list[Any]]" has no attribute "dtype"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: "list[list[Any]]" has no attribute "mean"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: "list[tuple[Any, Any]]" has no attribute "numel"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: "list[tuple[Any, Any]]" has no attribute "numel"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: Argument 1 to "get_least_ambiguous_anchor_candidate" has incompatible type "list[tuple[Any, Any]]"; expected "Tensor"  [arg-type]
openfold3/core/utils/permutation_alignment.py:0: error: Argument 1 to "get_least_ambiguous_anchor_candidate" has incompatible type "list[tuple[Any, Any]]"; expected "Tensor"  [arg-type]
openfold3/core/utils/permutation_alignment.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/utils/permutation_alignment.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/utils/permutation_alignment.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/utils/permutation_alignment.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/utils/permutation_alignment.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/utils/permutation_alignment.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/utils/permutation_alignment.py:0: error: Function "torch._C._VariableFunctions.tensor" is not valid as a type  [valid-type]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible return value type (got "AnchorCandidate | None", expected "AnchorCandidate")  [return-value]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible return value type (got "Tensor", expected "tuple[Tensor, Tensor, int]")  [return-value]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible return value type (got "tuple[Tensor, ...]", expected "tuple[Tensor]")  [return-value]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "int")  [assignment]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[list[Any]]")  [assignment]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[tuple[Any, Any]]")  [assignment]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[tuple[Any, Any]]")  [assignment]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible types in assignment (expression has type "Transformation", variable has type "list[Transformation]")  [assignment]
openfold3/core/utils/permutation_alignment.py:0: error: Incompatible types in assignment (expression has type "dict[Any, Any]", target has type "Tensor")  [assignment]
openfold3/core/utils/permutation_alignment.py:0: error: Need more than 1 value to unpack (2 expected)  [misc]
openfold3/core/utils/permutation_alignment.py:0: error: Need type annotation for "used_gt_sym_ids" (hint: "used_gt_sym_ids: list[<type>] = ...")  [var-annotated]
openfold3/core/utils/permutation_alignment.py:0: error: No overload variant of "split_feats_by_id" matches argument types "list[Any]", "Tensor"  [call-overload]
openfold3/core/utils/permutation_alignment.py:0: error: No overload variant of "split_feats_by_id" matches argument types "list[Tensor]", "Any"  [call-overload]
openfold3/core/utils/permutation_alignment.py:0: error: Overloaded function implementation cannot produce return type of signature 1  [misc]
openfold3/core/utils/permutation_alignment.py:0: error: Overloaded function implementation does not accept all possible parameters of signature 1  [misc]
openfold3/core/utils/permutation_alignment.py:0: error: Single overload definition, multiple required  [misc]
openfold3/core/utils/permutation_alignment.py:0: error: Value of type "bool" is not indexable  [index]
openfold3/core/utils/permutation_alignment.py:0: error: Value of type torch.tensor? is not indexable  [index]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "device"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "dtype"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "expand"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "reshape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "reshape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/core/utils/permutation_alignment.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/utils/permutation_alignment.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/utils/permutation_alignment.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/utils/permutation_alignment.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/utils/permutation_alignment.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/utils/permutation_alignment.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/utils/permutation_alignment.py:0: note: Perhaps you need "Callable[...]" or a callback protocol?
openfold3/core/utils/permutation_alignment.py:0: note: Possible overload variant:
openfold3/core/utils/permutation_alignment.py:0: note: Possible overload variant:
openfold3/core/utils/permutation_alignment.py:0: note: def split_feats_by_id(feats: Tensor, id: Tensor) -> tuple[list[Tensor], Tensor]
openfold3/core/utils/permutation_alignment.py:0: note: def split_feats_by_id(feats: Tensor, id: Tensor) -> tuple[list[Tensor], Tensor]
openfold3/core/utils/rigid_utils.py:0: error: Argument "rot_mats" to "Rotation" has incompatible type "list[Tensor]"; expected "Tensor | None"  [arg-type]
openfold3/core/utils/rigid_utils.py:0: error: Argument 1 to "Rigid" has incompatible type "Rigid"; expected "Rotation | None"  [arg-type]
openfold3/core/utils/rigid_utils.py:0: error: Argument 1 to "Rigid" has incompatible type "Rigid"; expected "Rotation | None"  [arg-type]
openfold3/core/utils/rigid_utils.py:0: error: Argument 1 to "stack" has incompatible type "Tensor"; expected "tuple[Tensor, ...] | list[Tensor]"  [arg-type]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible return value type (got "Rotation", expected "Rigid")  [return-value]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible return value type (got "Rotation", expected "Rigid")  [return-value]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible return value type (got "Rotation", expected "Rigid")  [return-value]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[Tensor]")  [assignment]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible types in assignment (expression has type "Tensor", variable has type "list[list[Any]]")  [assignment]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible types in assignment (expression has type "list[list[Tensor]]", variable has type "Tensor")  [assignment]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible types in assignment (expression has type "tuple[Tensor, ...]", variable has type "Tensor")  [assignment]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible types in assignment (expression has type "tuple[Tensor, ...]", variable has type "Tensor")  [assignment]
openfold3/core/utils/rigid_utils.py:0: error: Incompatible types in assignment (expression has type "tuple[Tensor, ...]", variable has type "Tensor")  [assignment]
openfold3/core/utils/rigid_utils.py:0: error: Item "None" of "Tensor | None" has no attribute "device"  [union-attr]
openfold3/core/utils/rigid_utils.py:0: error: Item "None" of "Tensor | None" has no attribute "shape"  [union-attr]
openfold3/core/utils/rigid_utils.py:0: error: Item "None" of "Tensor | None" has no attribute "shape"  [union-attr]
openfold3/core/utils/rigid_utils.py:0: error: Item "None" of "Tensor | None" has no attribute "to"  [union-attr]
openfold3/core/utils/rigid_utils.py:0: error: The first argument to Callable must be a list of types, parameter specification, or "..."  [valid-type]
openfold3/core/utils/rigid_utils.py:0: error: The first argument to Callable must be a list of types, parameter specification, or "..."  [valid-type]
openfold3/core/utils/rigid_utils.py:0: error: The first argument to Callable must be a list of types, parameter specification, or "..."  [valid-type]
openfold3/core/utils/rigid_utils.py:0: error: The first argument to Callable must be a list of types, parameter specification, or "..."  [valid-type]
openfold3/core/utils/rigid_utils.py:0: note: See https://mypy.readthedocs.io/en/stable/kinds_of_types.html#callable-types-and-lambdas
openfold3/core/utils/rigid_utils.py:0: note: See https://mypy.readthedocs.io/en/stable/kinds_of_types.html#callable-types-and-lambdas
openfold3/core/utils/rigid_utils.py:0: note: See https://mypy.readthedocs.io/en/stable/kinds_of_types.html#callable-types-and-lambdas
openfold3/core/utils/rigid_utils.py:0: note: See https://mypy.readthedocs.io/en/stable/kinds_of_types.html#callable-types-and-lambdas
openfold3/entry_points/experiment_runner.py:0: error: "BaseModel" has no attribute "entity"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "BaseModel" has no attribute "experiment_name"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "BaseModel" has no attribute "group"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "BaseModel" has no attribute "id"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "BaseModel" has no attribute "project"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "ExperimentSettings" has no attribute "skip_existing"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "ExperimentSettings" has no attribute "use_msa_server"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "ExperimentSettings" has no attribute "use_msa_server"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "ExperimentSettings" has no attribute "use_templates"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: "ExperimentSettings" has no attribute "use_templates"  [attr-defined]
openfold3/entry_points/experiment_runner.py:0: error: Argument "datasets" to "DataModuleConfig" has incompatible type "list[TrainingDatasetSpec]"; expected "list[BaseModel]"  [arg-type]
openfold3/entry_points/experiment_runner.py:0: error: Argument "precision" to "OF3DeepSpeedPrecision" has incompatible type "int | str"; expected "Literal['32-true', '16-true', 'bf16-true', '16-mixed', 'bf16-mixed']"  [arg-type]
openfold3/entry_points/experiment_runner.py:0: error: Argument 1 to "equal" has incompatible type "Any | None"; expected "Tensor"  [arg-type]
openfold3/entry_points/experiment_runner.py:0: error: Argument 1 to "store_configs" of "WandbHandler" has incompatible type "ExperimentConfig"; expected "TrainingExperimentConfig"  [arg-type]
openfold3/entry_points/experiment_runner.py:0: error: Incompatible types in assignment (expression has type "Callable[[LightningModule | None, Any | LightningDataModule | None, str | Path | None, bool, LightningDataModule | None, bool | None], list[Mapping[str, float]]]", variable has type "Callable[[LightningModule, Any | LightningDataModule | None, Any | None, LightningDataModule | None, str | Path | None, bool | None], None]")  [assignment]
openfold3/entry_points/experiment_runner.py:0: error: Incompatible types in assignment (expression has type "Callable[[LightningModule | None, Any | LightningDataModule | None, str | Path | None, bool, LightningDataModule | None, bool | None], list[Mapping[str, float]]]", variable has type "Callable[[LightningModule, Any | LightningDataModule | None, Any | None, LightningDataModule | None, str | Path | None, bool | None], None]")  [assignment]
openfold3/entry_points/experiment_runner.py:0: error: Incompatible types in assignment (expression has type "WandbLogger", variable has type "None")  [assignment]
openfold3/entry_points/experiment_runner.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "Literal['debug', 'info', 'warning', 'error'] | None")  [assignment]
openfold3/entry_points/experiment_runner.py:0: error: Item "BaseModel" of "BaseModel | None" has no attribute "id"  [union-attr]
openfold3/entry_points/experiment_runner.py:0: error: Item "BaseModel" of "BaseModel | None" has no attribute "project"  [union-attr]
openfold3/entry_points/experiment_runner.py:0: error: Item "None" of "BaseModel | None" has no attribute "id"  [union-attr]
openfold3/entry_points/experiment_runner.py:0: error: Item "None" of "BaseModel | None" has no attribute "project"  [union-attr]
openfold3/entry_points/experiment_runner.py:0: error: Item "None" of "MPIEnvironment | None" has no attribute "global_rank"  [union-attr]
openfold3/entry_points/experiment_runner.py:0: error: Signature of "run" incompatible with supertype "ExperimentRunner"  [override]
openfold3/entry_points/experiment_runner.py:0: error: Unsupported target for indexed assignment ("dict[str, Any] | None")  [index]
openfold3/entry_points/experiment_runner.py:0: note: "list" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
openfold3/entry_points/experiment_runner.py:0: note: Consider using "Sequence" instead, which is covariant
openfold3/entry_points/experiment_runner.py:0: note: Subclass:
openfold3/entry_points/experiment_runner.py:0: note: Superclass:
openfold3/entry_points/experiment_runner.py:0: note: def run(self) -> Any
openfold3/entry_points/experiment_runner.py:0: note: def run(self, inference_query_set: Any) -> None
openfold3/entry_points/parameters.py:0: error: Argument 1 to "Path" has incompatible type "Path | None"; expected "str | PathLike[str]"  [arg-type]
openfold3/entry_points/parameters.py:0: error: Argument 1 to "Path" has incompatible type "Path | None"; expected "str | PathLike[str]"  [arg-type]
openfold3/entry_points/parameters.py:0: error: Incompatible types in assignment (expression has type "str | Path", variable has type "Path | None")  [assignment]
openfold3/entry_points/validate_rocm.py:0: error: Argument 3 to "_check" has incompatible type "str | None"; expected "str"  [arg-type]
openfold3/entry_points/validate_rocm.py:0: error: Incompatible types in assignment (expression has type "str", variable has type "TorchVersion")  [assignment]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "None" not callable  [misc]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "None" not callable  [misc]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "None" not callable  [misc]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "None" not callable  [misc]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "None" not callable  [misc]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "register_dataset_config" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "register_dataset_config" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "register_dataset_config" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "register_dataset_config" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: "register_dataset_config" does not return a value (it only ever returns None)  [func-returns-value]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: Argument "loss_weights" to "LossConfig" has incompatible type "dict[str, float]"; expected "LossWeights"  [arg-type]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: Argument "loss_weights" to "LossConfig" has incompatible type "dict[str, float]"; expected "LossWeights"  [arg-type]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: Argument "loss_weights" to "LossConfig" has incompatible type "dict[str, float]"; expected "LossWeights"  [arg-type]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: Argument 1 to "get" of "DatasetConfigRegistry" has incompatible type "Any | None"; expected "str"  [arg-type]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: Incompatible types in assignment (expression has type "type[DefaultDatasetConfigSection]", variable has type "BaseModel")  [assignment]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: Need type annotation for "_registry" (hint: "_registry: dict[<type>, <type>] = ...")  [var-annotated]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: No return value expected  [return-value]
openfold3/projects/of3_all_atom/config/dataset_configs.py:0: error: Too few arguments  [call-arg]
openfold3/projects/of3_all_atom/project_entry.py:0: error: Argument 1 to "load_yaml" has incompatible type "Traversable"; expected "Path | str"  [arg-type]
openfold3/projects/of3_all_atom/runner.py:0: error: Argument "logger" to "setup" of "PerSampleGradManager" has incompatible type "lightning_fabric.loggers.logger.Logger | None"; expected "pytorch_lightning.loggers.logger.Logger"  [arg-type]
openfold3/projects/of3_all_atom/runner.py:0: error: Argument "model_class" to "__init__" of "ModelRunner" has incompatible type "type[OpenFold3]"; expected Module  [arg-type]
openfold3/projects/of3_all_atom/runner.py:0: error: Bracketed expression "[...]" is not valid as a type  [valid-type]
openfold3/projects/of3_all_atom/runner.py:0: error: Incompatible default for parameter "log_dir" (default has type "None", parameter has type "Path")  [assignment]
openfold3/projects/of3_all_atom/runner.py:0: error: Item "None" of "PerSampleGradManager | None" has no attribute "accumulate_grad_batches"  [union-attr]
openfold3/projects/of3_all_atom/runner.py:0: error: Item "None" of "PerSampleGradManager | None" has no attribute "setup"  [union-attr]
openfold3/projects/of3_all_atom/runner.py:0: error: Return type "dict[Any, Any]" of "configure_optimizers" incompatible with return type "Optimizer | Sequence[Optimizer] | tuple[Sequence[Optimizer], Sequence[LRScheduler | ReduceLROnPlateau | LRSchedulerConfig]] | OptimizerConfig | OptimizerLRSchedulerConfig | Sequence[OptimizerConfig] | Sequence[OptimizerLRSchedulerConfig] | None" in supertype "pytorch_lightning.core.module.LightningModule"  [override]
openfold3/projects/of3_all_atom/runner.py:0: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
openfold3/projects/of3_all_atom/runner.py:0: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
openfold3/tests/__init__.py:0: error: Module has no attribute "util"  [attr-defined]
openfold3/tests/core/data/io/sequence/msa/test_msa_parsers.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "ndarray[tuple[int, int], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/tests/core/data/io/sequence/msa/test_msa_parsers.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/tests/core/data/io/sequence/test_msa_parsing.py:0: error: Argument 2 to "savez" has incompatible type "**dict[str, ndarray[tuple[Any, ...], dtype[Any]]]"; expected "bool"  [arg-type]
openfold3/tests/core/data/io/sequence/test_msa_parsing.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[()], dtype[Any]]", variable has type "list[list[int]] | None")  [assignment]
openfold3/tests/core/data/io/sequence/test_msa_parsing.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[list[int]] | None")  [assignment]
openfold3/tests/core/data/io/sequence/test_msa_parsing.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[str] | None")  [assignment]
openfold3/tests/core/data/io/sequence/test_msa_parsing.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[str] | None")  [assignment]
openfold3/tests/core/data/pipelines/preprocessing/test_template.py:0: error: Argument "molecule_type" to "Chain" has incompatible type "str"; expected "MoleculeType"  [arg-type]
openfold3/tests/core/data/pipelines/preprocessing/test_template.py:0: error: Argument after ** must be a mapping, not "object"  [arg-type]
openfold3/tests/core/data/primitives/caches/test_lmdb.py:0: error: Need type annotation for "_dict"  [var-annotated]
openfold3/tests/core/data/primitives/sequence/test_msa_array.py:0: error: Argument "deletion_matrix" to "MsaArray" has incompatible type "list[list[int]] | None"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/tests/core/data/primitives/sequence/test_msa_array.py:0: error: Argument "msa" to "MsaArray" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[str, dtype[Any]]"  [arg-type]
openfold3/tests/core/data/primitives/sequence/test_msa_array.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[()], dtype[Any]]", variable has type "list[list[int]] | None")  [assignment]
openfold3/tests/core/data/primitives/sequence/test_msa_array.py:0: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "list[list[int]] | None")  [assignment]
openfold3/tests/core/data/primitives/structure/test_cleanup_bonds.py:0: error: Argument 2 to "BondList" has incompatible type "BondList[Any] | ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[tuple[Never, Never], dtype[integer[Any]]] | None"  [arg-type]
openfold3/tests/test_data/tokenization/construct_tokenization_examples.py:0: error: Argument 3 to "add_unresolved_atoms" has incompatible type "BiotiteCCDWrapper"; expected "CIFFile"  [arg-type]
openfold3/tests/test_structure_from_query.py:0: error: Incompatible types in assignment (expression has type "ndarray[bool, dtype[Any]]", target has type "ndarray[tuple[Any, ...], dtype[Any]]")  [assignment]
openfold3/tests/test_structure_from_query.py:0: error: Incompatible types in assignment (expression has type "ndarray[int, dtype[Any]]", target has type "ndarray[tuple[Any, ...], dtype[Any]]")  [assignment]
openfold3/tests/test_training_full.py:0: error: Item "None" of "IO[Any] | None" has no attribute "__iter__" (not iterable)  [union-attr]
openfold3/tests/test_validation_metrics.py:0: error: torch.tensor? has no attribute "expand"  [attr-defined]
openfold3/tests/test_validation_metrics.py:0: error: torch.tensor? has no attribute "shape"  [attr-defined]
openfold3/tests/utils/custom_assert_utils.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/tests/utils/custom_assert_utils.py:0: error: Item "None" of "BondList[Any] | None" has no attribute "as_array"  [union-attr]
openfold3/tests/utils/custom_assert_utils.py:0: error: Need type annotation for "bondlist_1"  [var-annotated]
openfold3/tests/utils/custom_assert_utils.py:0: error: Need type annotation for "bondlist_2"  [var-annotated]
openfold3/tests/utils/template_helpers.py:0: error: Argument "idx_map" to "TemplateCacheEntry" has incompatible type "ndarray[tuple[Any, ...], dtype[Any]]"; expected "ndarray[int, dtype[Any]]"  [arg-type]
openfold3/tests/utils/template_helpers.py:0: error: Argument 2 to "savez" has incompatible type "**dict[str, ndarray[tuple[Any, ...], dtype[Any]]]"; expected "bool"  [arg-type]
scripts/analysis/run_ost.py:0: error: "list" expects 1 type argument, but 3 given  [type-arg]
scripts/analysis/run_ost.py:0: error: Incompatible types in assignment (expression has type "tuple[Path]", variable has type "tuple[()]")  [assignment]
scripts/data_preprocessing/collect_preprocessed_fastas.py:0: error: Value of type "dict[str, PreprocessingChainData] | None" is not indexable  [index]
scripts/data_preprocessing/create_RNA-monomer_training_dataset_cache.py:0: error: Argument 1 to "parse_s3_config" has incompatible type "dict[Any, Any]"; expected "str"  [arg-type]
scripts/data_preprocessing/create_pdb-disordered_training_dataset_cache_with_templates.py:0: error: Argument "reference_molecule_data" to "ClusteredDatasetCache" has incompatible type "dict[str, PreprocessingReferenceMoleculeData]"; expected "dict[str, DatasetReferenceMoleculeData] | LMDBDict[str, DatasetReferenceMoleculeData]"  [arg-type]
scripts/data_preprocessing/create_pdb-disordered_training_dataset_cache_with_templates.py:0: error: Argument "structure_data" to "ClusteredDatasetCache" has incompatible type "dict[str, PreprocessingStructureData]"; expected "dict[str, ClusteredDatasetStructureData] | LMDBDict[str, ClusteredDatasetStructureData]"  [arg-type]
scripts/data_preprocessing/create_pdb-disordered_training_dataset_cache_with_templates.py:0: error: Invalid index type "str" for "dict[float, bool]"; expected type "float"  [index]
scripts/data_preprocessing/create_pdb-disordered_training_dataset_cache_with_templates.py:0: error: Item "None" of "dict[str, PreprocessingChainData] | None" has no attribute "items"  [union-attr]
scripts/data_preprocessing/create_pdb-disordered_training_dataset_cache_with_templates.py:0: error: Item "None" of "dict[str, PreprocessingChainData] | None" has no attribute "items"  [union-attr]
scripts/data_preprocessing/create_pdb_validation_dataset_cache.py:0: error: Argument "random_seed" to "create_pdb_val_dataset_cache_of3" has incompatible type "int | None"; expected "int"  [arg-type]
scripts/data_preprocessing/create_pdb_validation_dataset_cache.py:0: error: Incompatible types in assignment (expression has type "date", variable has type "str")  [assignment]
scripts/data_preprocessing/create_pdb_validation_dataset_cache.py:0: error: Incompatible types in assignment (expression has type "date", variable has type "str")  [assignment]
scripts/data_preprocessing/create_protein-monomer_training_dataset_cache.py:0: error: Argument 1 to "parse_s3_config" has incompatible type "dict[Any, Any]"; expected "str"  [arg-type]
scripts/data_preprocessing/generate_representatives_from_preparsed.py:0: error: Argument "key" to "sorted" has incompatible type "Callable[[NpzResult], str | None]"; expected "Callable[[NpzResult], SupportsDunderLT[Any] | SupportsDunderGT[Any]]"  [arg-type]
scripts/data_preprocessing/generate_representatives_from_preparsed.py:0: error: Incompatible return value type (got "str | None", expected "SupportsDunderLT[Any] | SupportsDunderGT[Any]")  [return-value]
scripts/data_preprocessing/generate_representatives_from_preparsed.py:0: error: Invalid index type "tuple[str | None, str | None]" for "dict[tuple[str, str], NpzResult]"; expected type "tuple[str, str]"  [index]
scripts/data_preprocessing/preparse_alignments_of3.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[Any, Any]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
scripts/data_preprocessing/preparse_alignments_of3.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[Any, Any]]"; expected "bool"  [arg-type]
scripts/data_preprocessing/preparse_monomer_msas_from_s3.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[Any, Any]]"; expected "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str]"  [arg-type]
scripts/data_preprocessing/preparse_monomer_msas_from_s3.py:0: error: Argument 2 to "savez_compressed" has incompatible type "**dict[str, dict[Any, Any]]"; expected "bool"  [arg-type]
scripts/data_preprocessing/preparse_monomer_msas_from_s3.py:0: error: Argument 3 to "_MsaPreparser" has incompatible type "str"; expected "dict[str, str]"  [arg-type]
scripts/data_preprocessing/preparse_monomer_msas_from_s3.py:0: error: Invalid index type "str" for "str"; expected type "SupportsIndex | slice[SupportsIndex | None, SupportsIndex | None, SupportsIndex | None]"  [index]
scripts/data_preprocessing/preparse_monomer_structures_from_s3.py:0: error: Argument "s3_config" to "preprocess_pdb_monomer_distilation" has incompatible type "str"; expected "dict[Any, Any]"  [arg-type]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Argument "clash_distance_thresholds" to "preprocess_pdb_disordered_of3" has incompatible type "str"; expected "list[float]"  [arg-type]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Argument "delete_annot_list" to "preprocess_pdb_disordered_of3" has incompatible type "str"; expected "list[str]"  [arg-type]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Argument "transfer_annot_dict" to "preprocess_pdb_disordered_of3" has incompatible type "str"; expected "dict[str, Any]"  [arg-type]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Incompatible return value type (got "tuple[str, str, str]", expected "tuple[list[float], dict[str, Any], list[str]]")  [return-value]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Incompatible types in assignment (expression has type "dict[str, Any]", variable has type "str")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Incompatible types in assignment (expression has type "list[Never]", variable has type "str")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Incompatible types in assignment (expression has type "list[float]", variable has type "str")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Incompatible types in assignment (expression has type "list[float]", variable has type "str")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "str")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py:0: error: Incompatible types in assignment (expression has type "list[str]", variable has type "str")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_compare_structures.py:0: error: Argument 1 to "imap_unordered" of "Pool" has incompatible type "_OSTCompareStructuresWrapper"; expected "Callable[[str], None]"  [arg-type]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_compare_structures.py:0: error: Incompatible types in assignment (expression has type "list[str | Any]", variable has type "set[str | Any]")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_compare_structures.py:0: note: "_OSTCompareStructuresWrapper.__call__" has type "_Wrapped[[Arg(str, 'pdb_id'), Arg(Path, 'gt_structures_directory'), Arg(Path, 'pred_structures_directory'), Arg(Literal['cif', 'pdb'], 'gt_structure_file_format'), Arg(Path, 'alignment_output_directory'), Arg(str | None, 'gt_biounit_id'), Arg(str | None, 'pred_biounit_id'), Arg(Logger, 'logger')], None, [Arg(_OSTCompareStructuresWrapper, 'self'), Arg(str, 'pdb_id')], None]"
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py:0: error: "AtomArray[Any]" has no attribute "molecule_type_id"  [attr-defined]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py:0: error: Argument "moltypes" to "UnresolvedResidueCounter" has incompatible type "str"; expected "list[MoleculeType]"  [arg-type]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py:0: error: Incompatible types in assignment (expression has type "None", variable has type "list[Path | Any]")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py:0: error: Incompatible types in assignment (expression has type "list[MoleculeType]", variable has type "str")  [assignment]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py:0: error: Item "None" of "Path | None" has no attribute "iterdir"  [union-attr]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py:0: error: Item "None" of "Path | None" has no attribute "iterdir"  [union-attr]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py:0: error: Need type annotation for "entry_ids" (hint: "entry_ids: list[<type>] = ...")  [var-annotated]
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py:0: error: Need type annotation for "n_res_unresolved_counts" (hint: "n_res_unresolved_counts: list[<type>] = ...")  [var-annotated]
scripts/data_preprocessing/preprocess_pdb_of3.py:0: error: Argument "log_level" to "preprocess_cif_dir_of3" has incompatible type "Literal['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']"; expected "int"  [arg-type]
scripts/data_preprocessing/preprocess_rfam.py:0: error: Need type annotation for "counts"  [var-annotated]
scripts/data_preprocessing/preprocess_template_alignments_new_of3.py:0: error: Argument "input_set" to "TemplatePreprocessor" has incompatible type "InferenceQuerySet | None"; expected "DatasetCache | InferenceQuerySet"  [arg-type]
scripts/data_preprocessing/preprocess_template_alignments_new_of3.py:0: error: Argument "mode" to "TemplatePreprocessorSettings" has incompatible type "str"; expected "Literal['train', 'predict']"  [arg-type]
scripts/data_preprocessing/preprocess_template_alignments_new_of3.py:0: error: Item "None" of "InferenceQuerySet | None" has no attribute "model_dump_json"  [union-attr]
scripts/data_preprocessing/preprocess_template_alignments_old_of3.py:0: error: Argument "max_release_date" to "filter_template_cache_of3" has incompatible type "str"; expected "datetime | None"  [arg-type]
scripts/data_preprocessing/preprocess_template_alignments_old_of3.py:0: error: Argument "s3_client_config" to "create_template_cache_of3" has incompatible type "str | None"; expected "dict[Any, Any] | None"  [arg-type]
scripts/data_preprocessing/preprocess_template_alignments_old_of3.py:0: error: Incompatible types in assignment (expression has type "dict[Any, Any]", variable has type "str | None")  [assignment]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: "Logger" has no attribute "extra"  [attr-defined]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: "SamplerDataset" has no attribute "next_dataset_indices"  [attr-defined]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Argument "datasets" to "DataModuleConfig" has incompatible type "list[TrainingDatasetSpec]"; expected "list[BaseModel]"  [arg-type]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Argument "datasets" to "SamplerDataset" has incompatible type "Sequence[Dataset[Any]]"; expected "Sequence[SingleDataset]"  [arg-type]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Argument "seed" to "OF3DistributedSampler" has incompatible type "int | None"; expected "int"  [arg-type]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Argument "subset_to_examples" to "init_datasets_with_logging" has incompatible type "str"; expected "list[str]"  [arg-type]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Argument "type_to_init" to "init_datasets_with_logging" has incompatible type "None"; expected "DatasetMode"  [arg-type]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Argument 1 to "manual_seed" of "Generator" has incompatible type "int | None"; expected "int"  [arg-type]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Argument 1 to "parse_data_config" of "DataModule" has incompatible type "list[BaseModel]"; expected "list[dict[Any, Any]]"  [arg-type]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Incompatible types in assignment (expression has type "ConcatDataset[Never]", variable has type "SamplerDataset")  [assignment]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: error: Item "None" of "WorkerInfo | None" has no attribute "dataset"  [union-attr]
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: note: "list" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
scripts/data_preprocessing/run_data_pipeline_treadmill.py:0: note: Consider using "Sequence" instead, which is covariant
scripts/datasets/pdb_subset_helpers.py:0: error: Need type annotation for "names" (hint: "names: set[<type>] = ...")  [var-annotated]
scripts/datasets/select_smoke_validation_set.py:0: error: Need type annotation for "candidates"  [var-annotated]
scripts/dev/build_release_date_cache.py:0: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
scripts/dev/check_release_dates.py:0: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs  [annotation-unchecked]
scripts/validate_msas.py:0: error: Please use "Callable[[<parameters>], <return type>]" or "Callable"  [misc]
