Viash 0.6.4 – Viash

What’s new?

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.

Full changelog

BREAKING CHANGES

Config: Viash configs whose filenames start with a . are ignored (PR #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 (PR #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 (PR #295).
Config merging: __inherits__ has been renamed to __merge__.

NEW FUNCTIONALITY

You can switch versions of Viash using the VIASH_VERSION environment variable (PR #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 (PR #291 and PR #293).
FileArgument: Added create_parent option, which will check if the directory of an output file exists and create it if necessary (PR #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 (PR #302).
NextflowPlatform: Add DataflowHelper.nf as a retrievable resource in Viash (PR #301).
NextflowPlatform: During a stubrun, argument requirements are turned off and the publishDir, cpus, memory, and label directives are also removed from the process (PR #301).
NextflowPlatform: Added a filter processing argument to filter the incoming channel after the map, mapData, mapId and mapPassthrough have been applied (PR #296).

NextflowPlatform: Added the Viash config to the Nextflow module for later introspection (PR #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 (PR #295).

EXPERIMENTAL FEATURES

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