Fix mypy error on bool expressions

[davelopez]

This will hopefully get rid of the mypy error in test_galaxy_packages on dev.

+ make mypy
mypy galaxy tests
galaxy/util/bool_expressions.py:139: error: Incompatible types in assignment
(expression has type "ParserElement", variable has type "Forward")  [assignment]
            self.boolExpr: Forward = infixNotation(
                                     ^
Found 1 error in 1 file (checked 80 source files)
make: *** [Makefile:96: mypy] Error 1

I'm a bit confused though with which version of mypy are we using across tests. If I run tox -e mypy I don't catch this error, but a different one shows instead...

(.venv) davelopez@davelopez:~/dev/galaxy$ tox -e mypy
mypy installed: attrs==21.4.0,flake8==4.0.1,flake8-bugbear==21.11.29,flake8-import-order==0.18.1,importlib-metadata==4.2.0,mccabe==0.6.1,mypy==0.910,mypy-extensions==0.4.3,pycodestyle==2.8.0,pyflakes==2.4.0,toml==0.10.2,typed-ast==1.4.3,types-bleach==4.1.4,types-boto==2.49.5,types-contextvars==2.4.1,types-cryptography==3.3.11,types-dataclasses==0.6.3,types-docutils==0.17.3,types-enum34==1.1.2,types-ipaddress==1.0.2,types-Markdown==3.3.11,types-paramiko==2.8.7,types-pkg-resources==0.1.3,types-python-dateutil==2.8.5,types-PyYAML==6.0.2,types-requests==2.27.2,types-six==1.16.8,typing_extensions==4.0.1,zipp==3.7.0
mypy run-test-pre: PYTHONHASHSEED='3439307142'
mypy run-test: commands[0] | mypy test lib
lib/galaxy/workflow/modules.py:1901: error: "Dataset" has no attribute "element_identifier"  [attr-defined]
                                replacement.element_identifier = temp.element_identifier  # type: ignore[union-attr]
                                ^
Found 1 error in 1 file (checked 1429 source files)

How to test the changes?

• This is a refactoring of components with existing test coverage.

License

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• I agree to allow the Galaxy committers to license these and all my past contributions to the core galaxy codebase under the MIT license. If this condition is an issue, uncheck and just let us know why with an e-mail to galaxy-committers@lists.galaxyproject.org.

[davelopez]

@nsoranzo, do you also get the error above in the description when you run tox -e mypy or is there something wrong with my local setup?

[nsoranzo]

Nothing wrong on your setup, it's also breaking package tests: https://app.circleci.com/pipelines/github/galaxyproject/galaxy/22397/workflows/1fde08f2-96f2-4829-97eb-121af7df63dc/jobs/168660