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Update Mypy to 1.11.2 and fix new signature override errors #18811

Merged
merged 8 commits into from
Sep 14, 2024
Merged

Update Mypy to 1.11.2 and fix new signature override errors #18811

merged 8 commits into from
Sep 14, 2024

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nsoranzo
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Extracted from #18578 , since it's going to be overwritten by the bot tomorrow.

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@nsoranzo
Move standard library import to top
cb0e3ed
@nsoranzo
Remove declarative mapping from imperatively mapped `LibraryDatasetDa…
f6c6a37 
…tasetAssociation` class

See galaxyproject#18773 (review)
@nsoranzo
Fix signature override of GenomeFilterMixin._add_parsers() method
440fbd6 
Fix 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
```
@nsoranzo
Fix signature override of DatasetAssociationSerializer.serialize() …
ed336d8 
…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
```
@nsoranzo
Fix signature override of DatabaseOperationTool.produce_outputs() m…
fd5ca34 
…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
```
@nsoranzo
Fix signature override of WorkflowModule.save_to_step() method
0b4fee5 
Fix 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
```
@nsoranzo
Fix signature override of Tool.exec_after_process() method
7154daf 
Fix 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
@nsoranzo
Update mypy to 1.11.2
1f8260d 
Remove now unneeded `type: ignore` .
@nsoranzo nsoranzo added kind/bug kind/refactoring cleanup or refactoring of existing code, no functional changes labels Sep 13, 2024
@github-actions github-actions bot added this to the 24.2 milestone Sep 13, 2024
@mvdbeek mvdbeek merged commit 948f38b into galaxyproject:dev Sep 14, 2024
55 of 56 checks passed
@nsoranzo nsoranzo deleted the mypy_1.11 branch September 14, 2024 17:53
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@jmchilton jmchilton jmchilton approved these changes

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area/database Galaxy's database or data access layer area/dependencies area/jobs area/tool-framework area/util area/workflows kind/bug kind/refactoring cleanup or refactoring of existing code, no functional changes
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3 participants
@nsoranzo @jmchilton @mvdbeek