Upgrade miniwdl to 1.15.0 and refresh WDL unit test skip lists (#5377)

[annagiroti]

miniwdl 1.15.0 adds parsing support for WDL 1.2 hints sections, unblocking several previously-skipped conformance unit tests and letting most nested-input tests run. Removes 30 entries across the WDL 1.1 and 1.2 unsupported-test lists that now pass, and updates the remaining entries' comments to reflect their current (rather than pre-upgrade) failure reasons.

miniwdl 1.15.0 also changed CallCache.put()'s signature, adding two new required keyword arguments, inputs and add_paths. Threads the actual input bindings through to all three call sites (task cache, workflow cache, and the write_* file cache) so cache entries record real inputs; add_paths is passed empty since Toil doesn't track that concept yet.

Addresses #5377

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[adamnovak]

This looks OK, but I think for the return codes ones we might be removing information that's still maybe accurate.

I think the CI failed due to the code not type checking against the new MiniWDL, so you might need to fix that.

[adamnovak]

Has MiniWDL 1.15 learned about return_codes? I think the Got: codes are probably right for these and it's the expected codes that are wrong.

[adamnovak]

This looks OK, but we probably want to redesign our own caching stuff a bit if the MiniWDL caching now needs the inputs and not just the key.

[adamnovak]

If we now need to pass the whole input bindings to the cache, we probably should move responsibility for computing the key inside this function.

[adamnovak]

I looked a little at the failing tests.

I think basic_directory is failing because now the WDL code is seeing absolute paths, and its regex in out wdl-conformance-tests repo doesn't have a .* before the first item:

https://github.com/DataBiosphere/wdl-conformance-tests/blob/d3e05db85696f5c5c5a5f5e1785c64fb2229b097/conformance.yaml#L1233

@annagiroti I invited you to that repo so you should be able to fix it there. You can run that test in that repo with:

 python3 run.py --versions 1.2 --id basic_directory --runner toil-wdl-runner

For the spec tests, the test_map test has started failing with a bunc of complaints about:

	WDL.Error.EvalError: source-relative File/Directory path resolution requires runtime context

I'm not sure why, but you can run it with:

python3 setup_unit_tests.py --version 1.2 --repo https://github.com/adamnovak/wdl.git --branch patch-3 --force-pull
python3 run_unit.py --versions 1.2 --id test_map

(This grabs a patched version of the spec tests that has openwdl/wdl#799 so it actually contains only parse-able JSON. You could also set up the pinned version of the spec tests that Toil is using.)