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Viash 0.9.0-RC7

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@Grifs Grifs released this 13 Aug 12:35
· 94 commits to main since this release
0.9.0-RC7
890d832

Viash 0.9.0-RC7 (2024-08-13): General bugfixes and improvements

These are bug fixes and other improvements that solve some edge case issues and improve the overall user experience and usability of Viash.

BREAKING CHANGES

  • NextflowPlatform: Swap the order of execution of runIf and filter when calling .run(). This means that runIf is now executed before filter (PR #660).

NEW FUNCTIONALITY

  • ExecutableRunner: Add a ---docker_image_id flag to view the Docker image ID of a built executable (PR #741).

  • viash ns query: Add a query filter that allows selecting a single component by its path in a namespace environment (PR #744).

  • config schema: Add label & summary fields for Config, PackageConfig, argument groups, and all argument types (PR #743).

  • NextflowPlatform: Added runIf functionality to runEach (PR #660).

MINOR CHANGES

  • ExecutableRunner: Add parameter docker_automount_prefix to allow for a custom prefix for automounted folders (PR #739).

  • ExecutableRunner: Make Docker runtime arguments configurable via the ---docker_run_args argument (PR #740).

  • export json_schema: Add arguments field to the Config schema (PR #755). Only for the non-strict version, the strict version of the viash config has these values merged into argument_groups.

BUG FIXES

  • platforms: Re-introduce the --platform and --apply_platform arguments to improve backwards compatibility (PR #725).
    When the argument is used, a deprecation warning message is printed on stderr.
    Cannot be used together with --engine or --runner and/or --apply_engine or --apply_runner.

  • nextflow_runner: Fix refactoring error in the findStates() helper function (PR #733).

  • viash ns exec: Fix "relative fields" outputting absolute paths (PR# 737). Additionally, improve path resolution when using the --src argument.

  • viash ns: Fix viash tripping over its toes when it encounters multiple failed configs (PR #761). A dummy config was used as a placeholder, but it always used the name failed, so duplicate config names were generated, which we check for nowadays.

  • bashwrapper: Fix an issue where running viash test which builds the test docker container would ignore test failures but subsequential runs would work correctly (PR #754).

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