Merge arguments into argument_groups in preparse step

[Grifs]

Describe your changes

Merge arguments into argument_groups in preparse step

Issue ticket number and link

Closes #573

Checklist before requesting a review

• I have performed a self-review of my code

• Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• Relevant unit tests have been added

[codecov]

Codecov Report

Attention: 3 lines in your changes are missing coverage. Please review.

Files	Coverage Δ
src/main/scala/io/viash/ViashConfig.scala	70.37% <100.00%> (+12.47%)	⬆️
src/main/scala/io/viash/ViashNamespace.scala	85.54% <100.00%> (ø)
src/main/scala/io/viash/ViashTest.scala	96.61% <ø> (ø)
src/main/scala/io/viash/cli/CLIConf.scala	98.79% <100.00%> (ø)
...n/scala/io/viash/functionality/Functionality.scala	93.75% <100.00%> (+6.90%)	⬆️
.../viash/functionality/dependencies/Dependency.scala	81.25% <ø> (ø)
...h/functionality/dependencies/LocalRepository.scala	100.00% <ø> (ø)
src/main/scala/io/viash/helpers/Helper.scala	98.55% <100.00%> (ø)
src/main/scala/io/viash/schemas/JsonSchema.scala	89.14% <100.00%> (+0.17%)	⬆️
...rc/main/scala/io/viash/functionality/package.scala	97.61% <96.96%> (+2.61%)	⬆️
... and 1 more

... and 1 file with indirect coverage changes

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[rcannood]

This is a scary set of changes, but I guess it's okay since all the tests pass!

Optionally we could rename allArguments to simply arguments, since arguments has no other function other than provide documentation. WDYT?

[Grifs]

Optionally we could rename allArguments to simply arguments, since arguments has no other function other than provide documentation. WDYT?

I guess that should be fine. There is a certain risk that it's a bit obfuscated that the arguments from the config isn't the same as the arguments function in functionality though. WDYT?

Edit: I believe tying the documentation of arguments and the function allArguments renamed as arguments won't work out of the box as I believe functions' documentation won't be picked up when the documentation is generated.

[rcannood]

Arguably the same could be said about the argument groups itself :p