Viash 0.5.10.1

BUG FIX

• NextflowPlatform: Fix passthrough of organization field.

Viash 0.5.10

MAJOR CHANGES

• viash_install:

  • Added --log_prefix: This prefix is used to determine the path of the log files for viash_build, viash_test and viash_push.
  • Added --organization: Id of the organisation to be used in the Docker image name, i.e. <registry>/<organization>/<namespace><namespace_sep><name>.
  • Added --target_image_source: Url to the Git repo in which this project resides.
  • Removed --log.

• viash_build:

  • Reduce code duplication by contructing the command with Bash Arrays.
  • Renamed --platforms to --platform.
  • Added --organization: Id of the organisation to be used in the Docker image name, i.e. <registry>/<organization>/<namespace><namespace_sep><name>.
  • Added --target_image_source: Url to the Git repo in which this project resides.
  • Changed default of --log from log.txt to .viash_build_log.txt.
  • Added --verbose: Print out the underlying viash ns build command before running it.

• viash_test:

  • Reduce code duplication by contructing the command with Bash Arrays.
  • Renamed --platforms to --platform.
  • Added --organization: Id of the organisation to be used in the Docker image name, i.e. <registry>/<organization>/<namespace><namespace_sep><name>.
  • Added --target_image_source: Url to the Git repo in which this project resides.
  • Changed default of --log from log.txt to .viash_test_log.txt.
  • Changed default of --tsv from log.tsv to .viash_test_log.tsv.
  • Added --verbose: Print out the underlying viash ns test command before running it.

• viash_push:

  • Reduce code duplication by contructing the command with Bash Arrays.
  • Added --organization: Id of the organisation to be used in the Docker image name, i.e. <registry>/<organization>/<namespace><namespace_sep><name>.
  • Changed default of --log from log.txt to .viash_push_log.txt.
  • Added --verbose: Print out the underlying viash ns build command before running it.

MINOR CHANGES

• NextflowPlatform: Added the organization field to the nextflow platform as well.

Viash 0.5.9

NEW FEATURES

• viash run: A long running Viash component can be interrupted by pressing
  CTRL-C or by sending it an INT or SIGINT signal.

• DockerPlatform: Automatically add a few labels based on metadata to Dockerfile.

• DockerPlatform: Added value target_image_source for setting the source of
  the target image. This is used for defining labels in the dockerfile.
  Example:

  target_image_source: https://github.com/foo/bar

MINOR CHANGES

• viash ns list: Added --format yaml/json argument to be able to return the
  output as a json as well. Useful for when jq is installed but yq is not. Example:

    viash ns list -p docker -f json | jq '.[] | .info.config'
  

• viash config view: Same as above.

DEPRECATION

• CLI: Deprecated -P flag use -p intead.

• DockerPlatform: Deprecated version value.

Viash 0.5.8

NEW FUNCTIONALITY

• DockerPlatform: Allow defining a container's organisation. Example:

    - type: docker
      registry: ghcr.io
      organisation: viash-io
      image: viash
      tag: "1.0"
      target_registry: ghcr.io
      target_organization: viash-io

• DockerRequirement: Add label instructions. Example:
  setup: [ [ type: docker, label: [ "foo BAR" ]]]

• Config: In specific places, allow parsing a value as a list of values. Fixes #97.
  This mostly applies to list values in DockerPlatform, but also to author roles.
  Examples:

  functionality:
    name: foo
    authors:
      - name: Alice
        role: author # can be a string or a list
  platforms:
    - type: docker
      port: "80:80" # can be a string or a list
      setup:
        - type: r
          packages: incgraph # can be a string or a list

BREAKING CHANGES

• viash test: This command doesn't automatically add the resources dir to the path.

BUG FIXES

• Functionality: Fix .functionality.add_resources_to_path not being picked up correctly.

• AptRequirement: Set DEBIAN_FRONTEND=noninteractive by default. This can be turned off by specifying:

    - type: apt
      packages: [ foo, bar ]
      interactive: true

MINOR CHANGES

• Main: Slightly better error messages when parsing of viash yaml file fails.
  Before:

  $ viash test src/test/resources/testbash/config_failed_build.vsh.yaml 
  Exception in thread "main" DecodingFailure(Unexpected field: [package]; valid fields: packages, interactive, type, List(DownField(apt), DownArray, DownField(platforms)))
  

  After:

  $ viash test src/test/resources/testbash/config_failed_build.vsh.yaml 
  Error parsing 'file:///path/to/viash/src/test/resources/testbash/config_failed_build.vsh.yaml'. Details:
  Unexpected field: [package]; valid fields: packages, interactive, type: DownField(apt),DownArray,DownField(platforms)
  

Viash 0.5.7

BREAKING CHANGES

• viash config: An argument's example now needs to be of the same type as the argument itself.
  For example, [ type: integer, name: foo, example: 10 ] is valid, whereas
  [ type: integer, name: foo, example: bar ] is not, as 'bar' cannot be cast to an integer.

NEW FUNCTIONALITY

• viash config inject: A command for inserting a Viash header into your script.

• DockerPlatform: Added a requirement setup for installing through yum. Example:
  setup: [ [ type: yum, packages: [ wget] ] ]

• DockerPlatform: Allow using copy and add instructions. Example:
  setup: [ [ type: docker, add: [ "http://foo.bar ." ]]]

BUG FIXES

• ViashTest: Fix verbosity passthrough.

• --help: Fix repeated usage flag when printing the help.

Viash 0.5.6

BREAKING CHANGES

• BashWrapper: Forbidden flags -v, --verbose, --verbosity have been renamed to ---v, ---verbose, ---verbosity.

MINOR CHANGES

• Set version of helper scripts to the same version as Viash.

• DockerPlatform: Produce helpful warning message when Docker image can't be found remotely (#94).

• DockerPlatform: Produce helpful error message when Docker isn't installed or the daemon is not running (#94 bis).

BUG FIXES

• viash_install:

  • Passing Viash path as a string instead of as a file to ensure the path is not converted to an absolute path
  • Switch from Docker backend to a Native backend, 'unzip' and 'wget' are required.
  • Correctly set the log file for viash_test.

• DockerPlatform: Added sleep workaround to avoid concurrency issue where a file is executed to
  build docker containers but apparently still in the process of being written.

• DockerPlatform: Fix order issue of ---verbose flag in combination with ---setup, allowing to run
  viash run config.vsh.yaml -- ---setup cb ---verbose and actually get output.

Viash 0.5.5

BREAKING CHANGES

• Functionality: The resources dir no longer automatically added to the PATH variable.
  To alter this behaviour, set .functionality.add_resources_to_path to true.

MINOR CHANGES

• Bash Script: only define variables which have values.

• CSharp Test Component: Change Docker image to dataintuitive/dotnet-script to have more control over the lifecycle of
  versioned tags.

• Updated Code of Conduct from v2.0 to v2.1.

BUG FIXES

• Viash namespace: Fix incorrect output path when the parent directory of a Viash component is not equal to the value of
  .functionality.name.

Viash 0.5.4

BREAKING CHANGES

• NextFlowPlatform: The default caching mechanism is now what NextFlow uses as default. In order to replicate earlier caching, cache: deep should be specified in the Viash config file.

NEW FEATURES

• NextFlowPlatform: Added cache directive to specify the typing of caching to be performed.

viash 0.5.3

NEW FEATURES

• Similar to par, each script now also has a meta list. meta contains meta information about the component
  or the execution thereof. It currently has the following fields:

  • meta["resources_dir"]: Path to the directory containing the resources
  • meta["functionality_name"]: Name of the component

• NextFlowPlatform: Export VIASH_TEMP environment variable.

BUG FIXES

• NextFlowPlatform: Fix output formatting when separate_multiple_outputs is false.

viash 0.5.2

This is a small release containing two small features and a bug fix.

MINOR CHANGES

• DockerPlatform: Added run_args field to allow setting docker run arguments.

• NextFlowPlatform: Added argument separate_multiple_outputs to allow not separating the outputs generated by a
  component with multiple outputs as separate events on the channel.

BUG FIX

• IO: Allow overwriting directory resources upon rebuild.