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CHANGELOG_0.10.md

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Viash 0.x.x (yyyy-MM-dd): TODO Add title

TODO add summary

NEW FEATURES

  • Nextflow runner: specifying a non-existent argument as a hashmap key for fromState and toState now raises an error (PR #793).

  • config run: Add option to run a component using a package bundle downloaded from ViashHub (PR #816). This allows for running a component without having to build it first. Example: viash run vsh://toolbox@v0.1.0/yq -- --input input.yaml --output output.yaml.

  • Parameter passing: Add support for unsetting argument values and computational requirements at runtime (PR #762, fixes #375).

    • Pass the literal UNDEFINED (unquoted) to set a single-value argument to undefined/null: ./my_component --arg UNDEFINED
    • Pass UNDEFINED_ITEM as a value in a multi-value argument to represent a missing item: ./my_component --args "value1;UNDEFINED_ITEM;value3"
    • Unset computational requirements with ---cpus UNDEFINED or ---memory UNDEFINED
    • Quote the values ('"UNDEFINED"' or "'UNDEFINED'") to pass the literal string UNDEFINED instead of null.

BREAKING CHANGES

  • Nextflow runner: remove deprecated map, mapId, mapData, mapPassthrough and renameKeys arguments (PR #792).

  • Nextflow runner: remove helper functions: setWorkflowArguments, getWorkflowArguments, strictMap, passthroughMap, passthroughFlatMap, passthroughFilter, channelFromParams, runComponents (PRs #792, #811).

  • Remove deprecated functionality functionality and platforms (PR #832).

  • Bash scripts: Arguments with multiple: true are now stored as bash arrays instead of semicolon-separated strings (PR #762). Update scripts to use array syntax: for item in "${par_inputs[@]}"; do ... instead of IFS splitting.

BUG FIXES

  • NextflowRunner: Automatically convert integers to doubles when argument type is double (port of PR #824, PR #825).

  • Parameter passing: Fix handling of special characters in argument values (PR #762, fixes #619, #705, #763, #821, #840).

    • Backticks in argument values no longer cause command substitution
    • Backslash-quote sequences (\') no longer break Python syntax
    • Dollar signs, newlines, and other special characters are properly preserved

MINOR FIXES

  • Executable: Add more info to the --help (PR #802).

INTERNAL CHANGES

  • Parameter passing: Switch from code injection to JSON-based parameter passing (PR #762). Instead of injecting argument values directly into script code, values are now stored in a JSON file (params.json) and parsed at runtime using language-specific JSON parsers. This approach is more robust, easier to debug, and handles special characters (backticks, quotes, newlines) correctly.