Viash

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`.

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.

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`.

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.

NEW FEATURES

* `CSharpScript`: Added support for C scripts (`type: "csharp_script"`) to viash.

MINOR CHANGES

* `NextFlowPlatform`: Added `directive_cpus`, `directive_max_forks`, `directive_memory` and `directive_time` parameters.

BUG FIXES

* `BashWrapper`: Refactor escaping descriptions, usages, defaults, and examples (34).

* `NextFlowPlatform`: Refactor escaping descriptions, usages, defaults and examples (75).

* `NextFlowPlatform`: Add argument to output path to avoid naming conflicts for components with multiple output files (76).

* `NextFlowPlatform`, `renderCLI()`: Only add flag to rendered command when boolean_true is actually true (78).

* `DockerPlatform`: Only chown when output file exists.

TESTING

* `viash build`: Capture stdout messages when errors are expected, so that they don't clutter the expected output.

* `viash build`: Check `--help` description output on the whole text instead of per letter or word basis.

* `TestingAllComponentsSuite`: Only testing bash natively, because other dependencies might not be available.

BREAKING CHANGES

* `DockerPlatform`: A Docker setup will be performed by default. Default strategy has been changed to `ifneedbepullelsecachedbuild` (57).
`---setup` strategy has been removed and `---docker_setup_strategy` has been renamed to `---setup`.
This change allows running a component for the first time. During first time setup, the Docker container will be pulled or built automatically.

* `NativePlatform`: Deprecated the native setup field.

MAJOR CHANGES

* `NXF`: This version changes the handling logic for arguments. An argument can be either `required` or not and can have a `default: ...` value or not. Checks are implemented to verify that required arguments are effectively provided _during_ pipeline running.

* `NXF`: If one sticks to long-option argments in the viash config, for all arguments that are _required_, the way of specifying the arguments on the CLI is identical for the Docker and NextFlow platforms. Non-required arguments can still be accessed from CLI using `--<component_name>__<argument_name> ...`.

* `NXF`: Running a module as a standalone pipeline has become easier.

* `viash run`: Implement verbosity levels (58). viash executables now have 7 levels of verbosity: emergency, alert, critical, error, warning, notice, info, debug.
The default verbosity level is 'notice'. Passing `-v` or `--verbose` bumps up the verbosity level by one, `-vv` by two. The verbosity level can be set manually by passing `--verbosity x`.

MINOR CHANGES

* `Docker Platform`: Added `privileged` argument, allowing to run docker with the `--privileged` flag.

* `Docker Requirements`: Allow specifying environment variables in the Dockerfile.

* Config modding: Added a `+0=` operator to prepend items to a list.

* `viash run`: Added a `--version` flag to viash executables for viewing the version of the component.

* `Functionality`: Added checks on the functionality and argument names.

* `viash run`: Added examples to functionality and arguments. Reworked `--help` formatting to include more information and be more consistent (56).

BUG FIXES

* `Docker R Requirements`: Install `remotes` when using `{ type: r, packages: [ foo ] }`.

* `config`: Throw error when user made a typo in the viash config (62).

TESTING

* `NXF`: Add an end-to-end test for running a nextflow pipeline using viash components.

* `Docker`: Reorganized viash docker build testbench into a main testbench with smaller auxiliary testbenches to keep them more manageable and clear what happens where.

* `viash ns`: Added a basic testbench for namespace tests.