Viash 0.1.0

Changes to functionality and the native/docker platforms

New Release
Author

Viash Team

Published

May 14, 2020

What’s new?

Changes to functionality.yaml

  • ftype has been renamed to function_type. The value for this field is also being checked.
  • platform has been removed.
  • Instead, the first resource listed is expected to have type: r_script, type: bash_script, type: python_script, or type: executable. The other resources are expected to have type: file by default, and are left untouched by Viash.
  • in the arguments, field flagValue has been removed. Instead, use type: boolean_true and type: boolean_false to achieve the same effect.

Changes to platform_(docker/native).yaml

  • The r: packages: field has been renamed to r: cran:.

Full changelog

MAJOR CHANGES

  • Refactoring of the Functionality class as discussed in VIP1 (#1). This has resulted in a lot of internal changes, but the changes with regard to the yaml definitions are relatively minor. See the section below for more info.

MINOR CHANGES

  • Updated the functionality.yamls under atoms/ and src/test/ to reflect these aforementioned changes.
  • Allow for bioconductor and other repositories in the R environment.
  • Add support for pip versioning syntax.

BUG FIXES

  • Do not quote passthrough flags.
  • Allow for spaces inside of Docker volume paths.

DOCUMENTATION

  • Updated the README.md.
  • Provide some small examples at doc/examples.