Viash 0.6.1

[rcannood]

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 (Container port should be allowed to be of 'number' type #225). Removed the 'Version' helper class.

MINOR CHANGES

• meta["cpus"] is now an integer, meta["memory_*"] are now longs (meta["n_proc"] and meta["memory_*"] are strings #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 (Bugfix/fix exit code #227).

• viash config inject: Fix processing of arguments when argument groups are defined (viash config inject doesn't work when argument groups contain required arguments #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 (VIASH_TEMP must be absolute #242).

• BashScript, CSharpScript, JavaScriptScript, PythonScript, RScript, ScalaScript: Fix quoting issues of certain characters (StringObject escaping bug #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 ";" (Double with multiple: true doesn't seem to work #235).

[codecov]

Codecov Report

Base: 84.68% // Head: 84.72% // Increases project coverage by +0.04% 🎉

Coverage data is based on head (9546f59) compared to base (d7e2107).
Patch coverage: 90.81% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #250      +/-   ##
==========================================
+ Coverage   84.68%   84.72%   +0.04%     
==========================================
  Files          83       84       +1     
  Lines        2840     2907      +67     
  Branches      167      177      +10     
==========================================
+ Hits         2405     2463      +58     
- Misses        435      444       +9     

Impacted Files	Coverage Δ
src/main/scala/io/viash/config/package.scala	100.00% <ø> (ø)
...viash/functionality/arguments/DoubleArgument.scala	0.00% <0.00%> (ø)
...o/viash/functionality/arguments/FileArgument.scala	0.00% <0.00%> (ø)
...iash/functionality/arguments/IntegerArgument.scala	0.00% <0.00%> (ø)
...o/viash/functionality/arguments/LongArgument.scala	0.00% <0.00%> (ø)
...main/scala/io/viash/platforms/NativePlatform.scala	90.00% <ø> (ø)
src/main/scala/io/viash/platforms/Platform.scala	83.33% <ø> (ø)
...iash/platforms/requirements/RubyRequirements.scala	0.00% <ø> (ø)
...main/scala/io/viash/schemas/CollectedSchemas.scala	0.00% <0.00%> (ø)
src/main/scala/io/viash/helpers/Helper.scala	94.44% <50.00%> (-4.05%)	⬇️
... and 35 more

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