Update Mypy to 1.11.2 and fix new signature override errors #18811
Commits on Sep 13, 2024
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Remove declarative mapping from imperatively mapped `LibraryDatasetDa…
…tasetAssociation` class See galaxyproject#18773 (review)
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Fix signature override of
GenomeFilterMixin._add_parsers()methodFix the following mypy 1.11 error: ``` lib/galaxy/managers/history_contents.py:638: error: Signature of "_add_parsers" incompatible with supertype "GenomeFilterMixin" [override] def _add_parsers(self): ^ lib/galaxy/managers/history_contents.py:638: note: Superclass: lib/galaxy/managers/history_contents.py:638: note: def _add_parsers(self, database_connection: str) -> Any lib/galaxy/managers/history_contents.py:638: note: Subclass: lib/galaxy/managers/history_contents.py:638: note: def _add_parsers(self) -> Any ``` -
Fix signature override of
DatasetAssociationSerializer.serialize()……method Fix the following mypy 1.11 errors: ``` lib/galaxy/managers/hdas.py:616: error: Signature of "serialize" incompatible with supertype "DatasetAssociationSerializer" [override] def serialize(self, hda, keys, user=None, **context): ^ lib/galaxy/managers/hdas.py:616: note: Superclass: lib/galaxy/managers/hdas.py:616: note: def serialize(self, item: Any, keys: Any, **context: Any) -> Any lib/galaxy/managers/hdas.py:616: note: Subclass: lib/galaxy/managers/hdas.py:616: note: def serialize(self, hda: Any, keys: Any, user: Any = ..., **context: Any) -> Any lib/galaxy/managers/hdas.py:616: error: Signature of "serialize" incompatible with supertype "ModelSerializer" [override] def serialize(self, hda, keys, user=None, **context): ^ lib/galaxy/managers/hdas.py:616: note: Superclass: lib/galaxy/managers/hdas.py:616: note: def serialize(self, item: Any, keys: Any, **context: Any) -> Any lib/galaxy/managers/hdas.py:616: note: Subclass: lib/galaxy/managers/hdas.py:616: note: def serialize(self, hda: Any, keys: Any, user: Any = ..., **context: Any) -> Any ``` -
Fix signature override of
DatabaseOperationTool.produce_outputs()m……ethod Fix the following mypy 1.11 errors: ``` lib/galaxy/tools/__init__.py:3989: error: Signature of "produce_outputs" incompatible with supertype "DatabaseOperationTool" [override] def produce_outputs(self, trans, out_data, output_collections, inc... ^ lib/galaxy/tools/__init__.py:3989: note: Superclass: lib/galaxy/tools/__init__.py:3989: note: def produce_outputs(self, trans: Any, out_data: Any, output_collections: Any, incoming: Any, history: Any, **kwds: Any) -> Any lib/galaxy/tools/__init__.py:3989: note: Subclass: lib/galaxy/tools/__init__.py:3989: note: def produce_outputs(self, trans: Any, out_data: Any, output_collections: Any, incoming: Any, history: Any, tag_handler: Any, **kwds: Any) -> Any lib/galaxy/tools/__init__.py:4026: error: Signature of "produce_outputs" incompatible with supertype "DatabaseOperationTool" [override] def produce_outputs(self, trans, out_data, output_collections, inc... ^ lib/galaxy/tools/__init__.py:4026: note: Superclass: lib/galaxy/tools/__init__.py:4026: note: def produce_outputs(self, trans: Any, out_data: Any, output_collections: Any, incoming: Any, history: Any, **kwds: Any) -> Any lib/galaxy/tools/__init__.py:4026: note: Subclass: lib/galaxy/tools/__init__.py:4026: note: def produce_outputs(self, trans: Any, out_data: Any, output_collections: Any, incoming: Any, history: Any, tag_handler: Any, **kwds: Any) -> Any ``` -
Fix signature override of
WorkflowModule.save_to_step()methodFix the following mypy 1.11 errors: ``` lib/galaxy/workflow/modules.py:650: error: Signature of "save_to_step" incompatible with supertype "WorkflowModule" [override] def save_to_step(self, step, **kwd): ^ lib/galaxy/workflow/modules.py:650: note: Superclass: lib/galaxy/workflow/modules.py:650: note: def save_to_step(self, step: Any, detached: Any = ...) -> Any lib/galaxy/workflow/modules.py:650: note: Subclass: lib/galaxy/workflow/modules.py:650: note: def save_to_step(self, step: Any, **kwd: Any) -> Any lib/galaxy/workflow/modules.py:1030: error: Signature of "save_to_step" incompatible with supertype "WorkflowModule" [override] def save_to_step(self, step, **kwd): ^ lib/galaxy/workflow/modules.py:1030: note: Superclass: lib/galaxy/workflow/modules.py:1030: note: def save_to_step(self, step: Any, detached: Any = ...) -> Any lib/galaxy/workflow/modules.py:1030: note: Subclass: lib/galaxy/workflow/modules.py:1030: note: def save_to_step(self, step: Any, **kwd: Any) -> Any lib/galaxy/workflow/modules.py:1680: error: Signature of "save_to_step" incompatible with supertype "WorkflowModule" [override] def save_to_step(self, step, **kwd): ^ lib/galaxy/workflow/modules.py:1680: note: Superclass: lib/galaxy/workflow/modules.py:1680: note: def save_to_step(self, step: Any, detached: Any = ...) -> Any lib/galaxy/workflow/modules.py:1680: note: Subclass: lib/galaxy/workflow/modules.py:1680: note: def save_to_step(self, step: Any, **kwd: Any) -> Any ``` -
Fix signature override of
Tool.exec_after_process()methodFix the following mypy 1.11 error: ``` lib/galaxy/tools/__init__.py:3212: error: Signature of "exec_after_process" incompatible with supertype "Tool" [override] def exec_after_process(self, app, inp_data, out_data, param_dict, ... ^ lib/galaxy/tools/__init__.py:3212: note: Superclass: lib/galaxy/tools/__init__.py:3212: note: def exec_after_process(self, app: Any, inp_data: Any, out_data: Any, param_dict: Any, job: Any = ..., **kwds: Any) -> Any lib/galaxy/tools/__init__.py:3212: note: Subclass: lib/galaxy/tools/__init__.py:3212: note: def exec_after_process(self, app: Any, inp_data: Any, out_data: Any, param_dict: Any, job: Any, final_job_state: Any = ..., **kwds: Any) -> Any ``` Also: - Add some type annotions - Small refactorings
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