Viash 0.6.1

Minor improvements in functionality

New Release
Author

Viash Team

Published

October 3, 2022

What’s new?

This release contains mostly minor improvements of functionality released in Viash 0.6.0. Most notably:

  • Support was added for type: long arguments

  • meta["n_proc"] has been renamed to meta["cpus"]. meta["cpus"] is now an integer, whereas meta["memory_*"] are now longs.

  • viash ns exec is able to recognise {platform} and {namespace} fields.

  • And various bug fixes and improvements to documentation and unit testing.

Full changelog

BREAKING CHANGES

  • Deprecated usage resources_dir variable inside scripts, use meta["resources_dir"] instead (or $meta_resources_dir in Bash, or meta$resources_dir in R).

  • Deprecated meta["n_proc"] in favour for meta["cpus"].

NEW FUNCTIONALITY

  • viash ns exec: Added two more fields:

    • {platform}: the platform name (if applicable)
    • {namespace}: the namespace of the component

  • LongArgument: Added support for 64-bit integers with type: long as opposed to type: integer which are 32-bit integers.

MAJOR CHANGES

  • Allow passing integers/doubles/booleans to string parameters (#225). Removed the ‘Version’ helper class.

MINOR CHANGES

  • meta["cpus"] is now an integer, meta["memory_*"] are now longs (#224).

  • DockerPlatform: Only store author names in the authors metadata.

  • NextflowPlatform: Only store author names in the authors metadata.

  • Argument[_]: Turn multiple_sep from Char into String.

INTERNAL CHANGES

  • All meta[...] variables are now processed similar to Argument[_]s, instead of using custom code to convert object types and detect Docker mounts.

  • Escaper: Make more generic Escaper helper class.

DOCUMENTATION

  • Hardcoded URLs pointing to viash.io in the documentation annotations were replaced with a new keyword system.

  • Replaced references to “DSL” with “Dynamic Config Modding” in the --help output.

  • Added an example for Ruby based Docker setups.

BUG FIXES

  • viash ns: Reverse exit code outputs, was returning 1 when everything was OK and 0 when errors were detected (PR #227).

  • viash config inject: Fix processing of arguments when argument groups are defined (#231).

  • Fixed a few typos in the CLI.

  • Fixed the formatting of ns exec documentation.

  • VDSL3: Fix stub functionality.

  • VDSL3: Fix error during error message.

  • viash test: Fix issue where VIASH_TEMP could not be a relative directory when running viash test (#242).

  • BashScript, CSharpScript, JavaScriptScript, PythonScript, RScript, ScalaScript: Fix quoting issues of certain characters (#113).

DEPRECATION

  • NextflowPlatform: Deprecate --param_list_format parameter.

TESTING

  • BashScript, CSharpScript, JavaScriptScript, PythonScript, RScript, ScalaScript: Implement more rigorous testing of which characters are escaped.

  • BashWrapper: Escape usage of multiple_sep. This fixes various checks and transformations not working when when multiple_sep is set to ";" (#235).