viash v0.1.0

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.
• BUG FIX: Do not quote passthrough flags.
• BUG FIX: Allow for spaces inside of Docker volume paths.
• DOCUMENTATION: Updated the README.md.
• DOCUMENTATION: Provide some small examples at doc/examples.
• MINOR CHANGES: Allow for bioconductor and other repositories in the R environment.
• MINOR CHANGES: Add support for pip versioning syntax.

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:.