Enable parsing struct meta sections

[adamnovak]

Motivation

This should fix #803 and also fix #760, which Toil needs fixed in order to start running tests against the WDL 1.2 spec tests.

Approach

This adds the meta_section productions as allowed peers of struct fields in the grammar for parsing structs, and handles them similarly to how they are handled when they show up in workflow or task blocks when building the object model from the parse tree.

I have some changes to the imports and type specs in here which appeared to be needed to actually import the code on my machine; I'm not sure how the old version actually worked. I don't think I can pull them out of the branch because otherwise the files can't be imported, as far as I can tell.

Checklist

• Add appropriate test(s) to the automatic suite
• Use make pretty to reformat the code with ruff format
• Use make check to statically check the code using ruff check and mypy
• Send PR from a dedicated branch without unrelated edits
• Ensure compatibility with this project's MIT license

[mlin]

See also prior wip #797 but this might well be more complete

[coveralls]

Pull Request Test Coverage Report for Build 18798570385

Details

• 23 of 26 (88.46%) changed or added relevant lines in 2 files are covered.
• 1 unchanged line in 1 file lost coverage.
• Overall coverage decreased (-0.04%) to 95.201%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
WDL/_parser.py	18	19	94.74%
WDL/Tree.py	5	7	71.43%

Files with Coverage Reduction	New Missed Lines	%
WDL/runtime/task.py	1	95.62%

Totals
Change from base Build 18765276648:	-0.04%
Covered Lines:	7479
Relevant Lines:	7856

---

💛 - Coveralls

[mlin]

@adamnovak Can I just ask about the couple of unrelated changes in the type hints and Any-- did you find those necessary to satisfy a certain version of mypy? (the CI here doesn't pin the mypy version, but I can't recall it tripping up in these areas)

[adamnovak]

I was getting type-checking failures without quoting those types, and I think with Any coming from . as well. I thought we just weren't importing the Tree types and also Any just wasn't actually in . somehow, but now I think there must be something wrong with my setup to run the type checking and how it handles imports from ..

[adamnovak]

@mlin I checked again on a fresh install on Python 3.12 and mypy 1.18.2, and it looks like those typing changes aren't actually needed. So I've pulled them out.