0.9.1 release

.github/workflows/gh-pages.yml

@@ -44,9 +44,9 @@ jobs:
       #   with:
       #     python-version: "3.10"
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
 
-      - uses: viash-io/viash-actions/setup@v5
+      - uses: viash-io/viash-actions/setup@v6
 
       - name: Install dependencies via renv restore
         run: |

_src/automation/config_pages_settings.yaml

@@ -10,6 +10,7 @@ structure:
   'ArgumentGroup': ./argumentGroup
   'Links': ./links
   'References': ./references
+  'Scope': ./scope
 
   'Platform': ./deprecated/platforms/index
   'NativePlatform': ./deprecated/platforms/native/index

_viash.yaml

@@ -1,4 +1,4 @@
-viash_version: 0.9.0
+viash_version: 0.9.1
 
 source: _src
 target: _target

blog/posts/viash-0.9.1/index.qmd

@@ -0,0 +1,44 @@
+---
+title: "Viash 0.9.1"
+subtitle: "Enhanced nextflow support and Scala 3 update"
+date: "2024-12-16"
+categories: [ New Release ]
+author: Viash Team
+---
+
+## What's new?
+
+Workflows can now publish results asynchronously by emitting multiple output channels. These results will then be merged into a published output behind the screens.
+Dependencies will use the new dedicated git url instead of the top level domain name.
+
+## Full changelog
+
+### NEW FEATURES
+
+* `Nextflow` runner: allow emitting multiple output channels (PR #736).
+
+* `Scope`: Add a `scope` field to the config (PR #782). This allows tuning how the components is built for release.
+
+### MINOR CHANGES
+
+* `viash-hub`: Change the url for viash-hub Git access to packages.viash-hub.com (PR #774).
+
+* `RRequirements`: Allow single quotes to be used again in the `.script` field (PR #771).
+
+* `scala`: Update Scala to Scala 3 (PR #759).
+  For most of the code, this was a minor update, so no breaking changes are expected.
+  The biggest change is how the exporting of the schema is done, but this has no impact on the user.
+  However, switching to Scala 3 allows for additional features and improvements in the future.
+
+* `--help`: Component `--help` messages will now display what built in `---` options are available (PR #784).
+
+### BUG FIXES
+
+* `config build`: Fix a bug where a missing main script would cause a stack trace instead of a proper error message (PR #776).
+  The error message showed the path of the missing resource but it was easy to miss given the stack trace, besides it shouldn't have been a stack trace anyway.
+
+* `RRequirements`: Treat warnings as errors when installing R dependencies in Docker engines (PR #771).
+
+* `Nextflow` runner: fix false-positive error when output argument arguments `required: true` 
+  are incorrectly flagged as missing input arguments (PR #778).
+

reference/config/arguments/file.qmd

@@ -206,7 +206,8 @@ my_component --my_files=firstFile.csv,anotherFile.csv,yetAnother.csv
 
 **Default**: `True`
 
-Checks whether the file or folder exists. For input files, this check will happen before the execution of the script, while for output files the check will happen afterwards.
+Checks whether the file or folder exists. For input files, this check will happen
+before the execution of the script, while for output files the check will happen afterwards.
 
 **Example:**
 

reference/config/arguments/index.qmd

@@ -33,3 +33,9 @@ arguments:
     type: string
 
 ```
+
+## type
+
+**Type**: `String`
+
+Specifies the type of the argument.

reference/config/deprecated/platforms/index.qmd

@@ -25,3 +25,9 @@ platforms:
       label: [lowcpu, midmem]
 
 ```
+
+## type
+
+**Type**: `String`
+
+Specifies the type of the platform.

reference/config/engines/docker/setup/index.qmd

@@ -14,3 +14,9 @@ Requirements for installing the following types of packages:
  - [Ruby](/reference/config/engines/docker/setup/rubyRequirements.html)
  - [yum](/reference/config/engines/docker/setup/yumRequirements.html)
 
+
+## type
+
+**Type**: `String`
+
+Specifies the type of the requirement specification.

reference/config/engines/docker/setup/rRequirements.qmd

@@ -178,3 +178,17 @@ Specifies which packages to install using a generic URI.
 ```yaml
 url: [ https://github.com/hadley/stringr/archive/HEAD.zip ]
 ```
+
+## warnings_as_errors
+
+**Type**: `Boolean`
+
+**Default**: `True`
+
+Specifies whether to treat warnings as errors. Default: true.
+
+**Example:**
+
+```yaml
+warnings_as_errors: true
+```

reference/config/engines/index.qmd

@@ -21,3 +21,21 @@ engines:
   - type: native
 
 ```
+
+## id
+
+**Type**: `String`
+
+Id of the engine.
+
+**Example:**
+
+```yaml
+id: foo
+```
+
+## type
+
+**Type**: `String`
+
+Specifies the type of the engine.

reference/config/index.qmd

@@ -478,6 +478,17 @@ A list of runners to execute target artifacts.
  - [NextflowRunner](/reference/config/runners/nextflow/#)
 
 
+## scope
+
+**Type**: `Either ScopeEnum or Scope`
+
+**Default**: `public`
+
+Defines the scope of the component.
+`test`: only available during testing; components aren't published.
+`private`: only meant for internal use within a workflow or other component.
+`public`: core component or workflow meant for general use.
+
 ## status
 
 **Type**: `Status`

reference/config/repositories/index.qmd

@@ -36,3 +36,25 @@ dependencies:
       tag: 0.3.0
 
 ```
+
+## path
+
+**Type**: `String`
+
+**Default**: `Empty`
+
+Defines a subfolder of the repository to use as base to look for the dependency components.
+
+## tag
+
+**Type**: `String`
+
+**Default**: `Empty`
+
+Defines which version of the dependency component to use. Typically this can be a specific tag, branch or commit hash.
+
+## type
+
+**Type**: `String`
+
+Defines the repository type. This determines how the repository will be fetched and handled.

reference/config/resources/index.qmd

@@ -25,3 +25,41 @@ resources:
     path: resource1.txt
 
 ```
+
+## dest
+
+**Type**: `String`
+
+**Default**: `Empty`
+
+Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter.
+
+## is_executable
+
+**Type**: `Boolean`
+
+**Default**: `Empty`
+
+Whether the resulting resource file should be made executable.
+
+## path
+
+**Type**: `String`
+
+**Default**: `Empty`
+
+The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`.
+
+## text
+
+**Type**: `String`
+
+**Default**: `Empty`
+
+The content of the resulting file specified as a string. Mutually exclusive with `path`.
+
+## type
+
+**Type**: `String`
+
+Specifies the type of the resource. The first resource cannot be of type `file`. When the type is not specified, the default type is simply `file`.

reference/config/runners/index.qmd

@@ -20,3 +20,21 @@ runners:
   - type: nextflow
 
 ```
+
+## id
+
+**Type**: `String`
+
+Id of the runner.
+
+**Example:**
+
+```yaml
+id: foo
+```
+
+## type
+
+**Type**: `String`
+
+Specifies the type of the runner.

reference/config/scope.qmd

@@ -0,0 +1,25 @@
+---
+title: "Scope"
+search: true
+---
+
+Defines the scope of the component.
+`test`: only available during testing; components aren't published.
+`private`: only meant for internal use within a workflow or other component.
+`public`: core component or workflow meant for general use.
+
+## image
+
+**Type**: `ScopeEnum`
+
+test: image is only used during testing and is transient
+private: image is published in the registry
+public: image is published in the registry
+
+## target
+
+**Type**: `ScopeEnum`
+
+test: target folder is only used during testing and is transient
+private: target folder can be published in target/private or target/dependencies/private
+public: target is published in target/executable or target/nextflow