Viash 0.6.3 – Viash

What’s new?

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

viash ns list now only returns a config just once instead of once per platform.
A functionality’s info field can contain any data structures. An .info field was added to arguments as well.
Bug fixes for using Viash with podman, Nextflow>=22.10 and R<4.0.
Experimental support for inheriting from config partials.

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.
Testbenches: Add exit code to helper method testMainWithStdErr.
Testbenches: Add testbench to verify viash underscore components (viash_build, viash_install, viash_push, viash_skeleton, viash_test).
Testbenches: Update viash underscore component tests to use $meta_executable.
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).
Underscore component tests: Fix tests for viash_skeleton and viash_test components.
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 (PR #271). 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