Viash 0.6.3

Quality-of-life improvements in Viash.

New Release
Author

Viash Team

Published

November 9, 2022

This release features contains mostly quality of life improvements and some experimental functionality. Most notably:

Full changelog

MAJOR CHANGES

  • Config: Made major internal changes w.r.t. how config files are read and at which point a platform (native, docker, nextflow) is applied to the functionality script. The only visible side effect is that viash ns list will output each config only once instead of multiple times.

  • Functionality: Structured annotation can be added to a functionality and its arguments using the info field. Example:

    functionality:
      name: foo
      info:
        site: https://abc.xyz
        tags: [ one, two, three ]
      arguments:
        - name: --foo
          type: string
          info:
            foo: bar
            a:
              b:
                c

MINOR CHANGES

  • BashWrapper: Allow printing the executor command by adding ---verbose ---verbose to a viash run or an executable.

  • Testbenches: Rework MainBuildAuxiliaryNativeParameterCheck to create stimulus files and loop over the file from bash instead of looping natively. This prevents creating thousands of new processes which would only test a single parameter. Note this still calls the main script for each stimulus separately, but that was the case anyway, only much much worse.

  • Testbenches: Split some grouped test benches into slightly smaller test benches that group tested functionality better.

  • Annotations: Complete the config schema annotations. Make sure all arguments are documented. Added an annotation internalFunctionality and undocumented for arguments that should not be documented. Added a testbench that verifies that all arguments are in fact annotated, skipping those that are not in the class constructor. Adds a hierarchy field in the __this__ member to list the relation of the own and parent classes.

  • viash ns exec: Allow choosing whether the {platform} field should be filled in, based on the --apply_platform parameter.

BUG FIXES

  • DockerPlatform: Remove duplicate auto-mounts (#257).

  • NextflowVDSL3Platform: Fix ‘Module scriptPath has not been defined yet’ error when Nextflow>=22.10 (#269).

  • config inject: Doesn’t work when must_exist == true (#273).

  • RScript: Fix compatibility issue where the new character escaping in r_script required R>=4.0 (#275). Escaping is now handled without using the new r'(foo)' notation.

DEPRECATION

  • DockerRequirements: The resources: setting has been deprecated and will be removed in Viash 0.7.0. Please use copy: instead.

  • DockerRequirements: The privileged: setting has been deprecated and will be removed in Viash 0.7.0. Please use run_args: "--privileged" instead.

EXPERIMENTAL FUNCTIONALITY

  • Config: Any part of a Viash config can use inheritance to fill data (#259). For example: Contents of src/test/config.vsh.yaml:

    __inherits__: ../api/base.yaml
    functionality:
      name: test
      resources:
        - type: bash_script
          path: script.sh
          text: |
            echo Copying $par_input to $par_output
            cp $par_input $par_output

    Contents of src/api/base.yaml:

    functionality:
      arguments:
        - name: "--input"
          type: file
        - name: "--output"
          type: file
          direction: output

    The resulting yaml will be:

    functionality:
      name: test
      arguments:
        - name: "--input"
          type: file
        - name: "--output"
          type: file
          direction: output
      resources:
        - type: bash_script
          path: script.sh
          text: |
            echo Copying $par_input to $par_output
            cp $par_input $par_output