Viash 0.3.1

Add authors field to config, added registry fields to Docker platform config, ...

Full changelog: #

NEW FEATURES #

• Functionality: Added list of authors field. Example:

functionality:
  authors:
    - name: Bob Cando
      roles: [maintainer, author]
      email: bob@cando.com
      props: {github: bobcando, orcid: XXXAAABBB}

• Docker Platform: Allow specifying the registry with target_registry. Example:

- type: docker
  image: bash:4.0
  target_registry: foo.io
  target_image: bar
  target_tag: 0.1

• Docker Platform: version is now a synonym for target_tag. If both version and target_tag are not defined, functionality.version will be used instead.

• Docker Platform: Can change the Docker Setup Strategy by specifying

  • in the yaml: setup_strategy: xxx
  • on command-line: ---docker_setup_strategy xxx or ---dss xxx

  Allowed values for the setup strategy are:

  • alwaysbuild / build: build the image from the dockerfile (DEFAULT)
  • alwayscachedbuild / cachedbuild: build the image from the dockerfile, with caching
  • alwayspull / pull: pull the image from a registry
  • alwayspullelsebuild / pullelsebuild: try to pull the image from a registry, else build it
  • alwayspullelsecachedbuild / pullelsecachedbuild: try to pull the image from a registry, else build it with caching
  • ifneedbebuild: if the image does not exist locally, build the image
  • ifneedbecachedbuild: if the image does not exist locally, build the image with caching
  • ifneedbepull: if the image does not exist locally, pull the image
  • ifneedbepullelsebuild: if the image does not exist locally, pull the image else build it
  • ifneedbepullelsecachedbuild: if the image does not exist locally, pull the image else build it with caching
  • donothing / meh: do not build or pull anything

MAJOR CHANGES #

• License: viash is now licensed under GPL-3.

MINOR CHANGES #

• CLI: Allow parameters before and after specifying a viash config yaml. For example, both following commands now work. Up until now, only the latter would work.

  • viash run config.vsh.yaml -p docker
  • viash run -p docker config.vsh.yaml

• Functionality: Arguments field can now be omitted.

• Scripts: Wrapped scripts now contain a minimal header at the top.

BUG FIXES #

• NXF viash build: Do not assume each config yaml has at least one test.

• Scripts: Fix Docker chown failing when multiple outputs are defined (#21).

• JavaScriptRequirements: Fix type getting set to "python" when unparsing.

• viash run . ---debug: Debug session should now work again

• Native ---setup: Fix missing newlines when running native ---setup commands.

• Main: Fix crashing when no arguments are supplied.

• Namespace: Show error message when the config file can't be parsed.

• Executable resource: Fix Docker automount handling for Executable resources.

TESTING #

• YAML: Test invertibility of parsing/unparsing config objects.