Viash

BUG FIX

* `NextflowPlatform`: Fix passthrough of `organization` field.

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.

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:
yaml
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.

NEW FUNCTIONALITY

* `DockerPlatform`: Allow defining a container's organisation. Example:
yaml
- 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:
yaml
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:
yaml
- 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)

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.

* `YumRequirement`: Added a requirement setup for installing through yum. Example:
`setup: [ [ type: yum, packages: [ wget] ] ]`

* `DockerRequirement`: 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.

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.