Skip to content

Viash 0.6.1
Compare
Choose a tag to compare
@rcannood rcannood released this 03 Oct 13:38
· 1206 commits to main since this release
0.6.1
4e18fe9
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

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.

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 (#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).

Assets 8
Loading