Bump miniwdl from 1.12.0 to 1.12.1 (#5030)

* Bump miniwdl from 1.12.0 to 1.12.1

Bumps [miniwdl](https://github.com/chanzuckerberg/miniwdl) from 1.12.0 to 1.12.1.
- [Release notes](https://github.com/chanzuckerberg/miniwdl/releases)
- [Commits](chanzuckerberg/miniwdl@v1.12.0...v1.12.1)

---
updated-dependencies:
- dependency-name: miniwdl
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Linting.

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: DailyDreaming <[email protected]>

requirements-wdl.txt

@@ -1,3 +1,3 @@
-miniwdl==1.12.0
+miniwdl==1.12.1
 wdlparse==0.1.0
 graphlib-backport==1.0 ; python_version < '3.9'

src/toil/wdl/wdltoil.py

@@ -54,6 +54,7 @@
 import WDL.runtime.config
 from configargparse import ArgParser
 from WDL._util import byte_size_units
+from WDL.Tree import ReadSourceResult
 from WDL.CLI import print_error
 from WDL.runtime.backend.docker_swarm import SwarmContainer
 from WDL.runtime.backend.singularity import SingularityContainer
@@ -396,7 +397,7 @@ def potential_absolute_uris(uri: str, path: List[str], importer: Optional[WDL.Tr
         # If we come back it didn't work
         failures.add(candidate_uri)
 
-async def toil_read_source(uri: str, path: List[str], importer: Optional[WDL.Tree.Document]) -> WDL.ReadSourceResult:
+async def toil_read_source(uri: str, path: List[str], importer: Optional[WDL.Tree.Document]) -> ReadSourceResult:
     """
     Implementation of a MiniWDL read_source function that can use any
     filename or URL supported by Toil.
@@ -430,7 +431,7 @@ async def toil_read_source(uri: str, path: List[str], importer: Optional[WDL.Tre
             continue
 
         # Return our result and its URI. TODO: Should we de-URI files?
-        return WDL.ReadSourceResult(string_data, candidate_uri)
+        return ReadSourceResult(string_data, candidate_uri)
 
     # If we get here we could not find it anywhere. Do exactly what MiniWDL
     # does:
@@ -3451,7 +3452,7 @@ def main() -> None:
                 # have to cast from more specific to less specific ones here.
                 # The miniwld values_from_json function can evaluate
                 # expressions in the inputs or something.
-                WDLTypeDeclBindings = WDL.Env.Bindings[Union[WDL.Tree.Decl, WDL.Type.Base]]
+                WDLTypeDeclBindings = WDL.Env.Bindings[WDL.Tree.Decl] | WDL.Env.Bindings[WDL.Type.Base]
                 input_bindings = WDL.values_from_json(
                     inputs,
                     cast(WDLTypeDeclBindings, target.available_inputs),