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Viash 0.6.4
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@rcannood rcannood released this 30 Nov 12:57
0.6.4
718c7a6

This release adds features related to managing Viash projects and
allows for better runtime introspection of Nextflow VDSL3 modules.

The most notable changes are:

  • You can switch versions of Viash using the VIASH_VERSION
    environment variable! Example:

    VIASH_VERSION=0.6.0 viash --version

    More importantly, you can specify the version of Viash you want
    in a project config. See below for more info.

  • Introducing Viash project config files as an experimental feature.
    It allows storing project-related settings in a _viash.yaml
    config file which you should store at the root of your repository.
    Example:

    viash_version: 0.6.4
source: src
target: target
config_mods: |
  .platforms[.type == 'docker'].target_registry := 'ghcr.io'
  .platforms[.type == 'docker'].target_organization := 'viash-io'
  .platforms[.type == 'docker'].namespace_separator := '/'
  .platforms[.type == 'docker'].target_image_source := 'https://github.com/viash-io/viash'

  • It's now possible to specify in which order Viash will merge
    Viash configs. Example:

    functionality:
  name: foo
  arguments:
    - __merge__: obj_input.yaml
      name: "--one"
    - __merge__: [., obj_input.yaml]
      name: "--two"
    - __merge__: [obj_input.yaml, .]
     name: "--three"

Please take note of the following breaking changes:

  • Passing non-existent paths to a Viash component will cause the
    component to generate an error when no file or folder is found.
    Set must_exist to false to revert to the previous behaviour.

  • The arguments --write_meta/-w and --meta/-m no longer exist,
    because every viash build/run/test run will generate a
    .config.vsh.yaml meta file.

BREAKING CHANGES

  • Config: Viash configs whose filenames start with a . are ignored (#291).

  • viash build: --write_meta/-m and --meta/-m arguments have been removed.
    Instead, the .config.vsh.yaml file is always created when building Viash components (#293).

  • FileArgument: Default setting of must_exist was changed from false to true.
    As such, the component will throw an error by default if an input file or output file
    is missing (#295).

  • Config merging: __inherits__ has been renamed to __merge__.

NEW FUNCTIONALITY

  • You can switch versions of Viash using the VIASH_VERSION
    environment variable (#304)! Example:

    VIASH_VERSION=0.6.0 viash --version

  • Traceability: Running viash build and viash test creates a .config.vsh.yaml file
    by default, which contains the processed config of the component. As a side effect,
    this allows for reading in the .config.vsh.yaml from within the component to learn
    more about the component being tested (#291 and #293).

  • FileArgument: Added create_parent option, which will check if the directory of an output
    file exists and create it if necessary (#295).

MINOR CHANGES

  • viash run, viash test: When running or testing a component, Viash will add an extension
    to the temporary file that is created. Before: /tmp/viash-run-wdckjnce,
    now: /tmp/viash-run-wdckjnce.py (#302).

  • NextflowPlatform: Add DataflowHelper.nf as a retrievable resource in Viash (#301).

  • NextflowPlatform: During a stubrun, argument requirements are turned off and
    the publishDir, cpus, memory, and label directives are also removed
    from the process (#301).

  • NextflowPlatform: Added a filter processing argument to filter the incoming channel after
    the map, mapData, mapId and mapPassthrough have been applied (#296).

  • NextflowPlatform: Added the Viash config to the Nextflow module for later introspection (#296).
    For example:

    include { foo } from "$targetDir/path/foo/main.nf"

foo.run(filter: { tup ->
  def preferredNormalization = foo.config.functionality.info.preferred_normalization
  tup.normalization_id == preferredNormalization
})

BUG FIXES

  • BashWrapper: Don't overwrite meta values when trailing arguments are provided (#295).

EXPERIMENTAL FEATURES

  • Viash Project: Viash will automatically search for a _viash.yaml file in the directory of
    a component and its parent directories (#294).

    Contents of _viash.yaml:

    source: src
target: target
config_mods: |
  .platforms[.type == 'docker'].target_registry := 'ghcr.io'
  .platforms[.type == 'docker'].target_organization := 'viash-io'
  .platforms[.type == 'docker'].namespace_separator := '/'
  .platforms[.type == 'docker'].target_image_source := 'https://github.com/viash-io/viash'

  • Config merging: Allow specifying the order in which Viash will merge configs (#289).
    If . is not in the list of inherited objects, it will be added at the end.

    Contents of config.vsh.yaml:

    functionality:
  name: foo
  arguments:
    - __merge__: obj_input.yaml
      name: "--one"
    - __merge__: [., obj_input.yaml]
      name: "--two"
    - __merge__: [obj_input.yaml, .]
      name: "--three"

    Contents of obj_input.yaml:

    type: file
name: --input
description: A h5ad file

    Output of viash config view config.vsh.yaml (stripped irrelevant bits):

    functionality:
  arguments:
  - type: "file"
    name: "--one"
    description: "A h5ad file"
  - type: "file"
    name: "--input"
    description: "A h5ad file"
  - type: "file"
    name: "--three"
    description: "A h5ad file"
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