Build branch fix-integration-tests with version dev (2dbe3b72)

Build pipeline: vsh-ci-dev-k8tz4

Source commit: 2dbe3b7231

Source message: Fix pointers to test resources

schemas/author.yaml

@@ -0,0 +1 @@
+$ref: "defs_common.yaml#/definitions/Author"

schemas/defs_common.yaml

@@ -0,0 +1,395 @@
+definitions:
+  Config:
+    description: "A Viash configuration is a YAML file which contains metadata to\
+      \ describe the behaviour and build target(s) of a component.  \nWe commonly\
+      \ name this file `config.vsh.yaml` in our examples, but you can name it however\
+      \ you choose.  \n"
+    type: "object"
+    properties:
+      label:
+        description: "A clean version of the component's name. This is only used for\
+          \ documentation."
+        type: "string"
+      license:
+        description: "The license of the package."
+        type: "string"
+      authors:
+        description: "A list of authors. An author must at least have a name, but\
+          \ can also have a list of roles, an e-mail address, and a map of custom\
+          \ properties.\n\nSuggested values for roles are:\n \n| Role | Abbrev. |\
+          \ Description |\n|------|---------|-------------|\n| maintainer | mnt |\
+          \ for the maintainer of the code. Ideally, exactly one maintainer is specified.\
+          \ |\n| author | aut | for persons who have made substantial contributions\
+          \ to the software. |\n| contributor | ctb| for persons who have made smaller\
+          \ contributions (such as code patches).\n| datacontributor | dtc | for persons\
+          \ or organisations that contributed data sets for the software\n| copyrightholder\
+          \ | cph | for all copyright holders. This is a legal concept so should use\
+          \ the legal name of an institution or corporate body.\n| funder | fnd |\
+          \ for persons or organizations that furnished financial support for the\
+          \ development of the software\n\nThe [full list of roles](https://www.loc.gov/marc/relators/relaterm.html)\
+          \ is extremely comprehensive.\n"
+        type: "array"
+        items:
+          type: object
+          properties:
+            __merge__:
+              type: string
+              pattern: "^/src/authors/.*\\.yaml$"
+            roles:
+              description: |
+                  Role of the author. Possible values:
+
+                  * `"author"`: Authors who have made substantial contributions to the component.
+                  * `"maintainer"`: The maintainer of the component.
+                  * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.).
+              type: array
+              items:
+                enum: [maintainer, author, contributor]
+      status:
+        description: "Allows setting a component to active, deprecated or disabled."
+        $ref: "defs_viash.yaml#/definitions/Status"
+      requirements:
+        description: "Computational requirements related to running the component.\
+          \ \n`cpus` specifies the maximum number of (logical) cpus a component is\
+          \ allowed to use., whereas\n`memory` specifies the maximum amount of memory\
+          \ a component is allowed to allicate. Memory units must be\nin B, KB, MB,\
+          \ GB, TB or PB for SI units (1000-base), or KiB, MiB, GiB, TiB or PiB for\
+          \ binary IEC units (1024-base)."
+        $ref: "defs_viash.yaml#/definitions/ComputationalRequirements"
+      repositories:
+        description: "(Pre-)defines repositories that can be used as repository in\
+          \ dependencies.\nAllows reusing repository definitions in case it is used\
+          \ in multiple dependencies."
+        type: "array"
+        items:
+          $ref: "defs_viash.yaml#/definitions/RepositoryWithName"
+      dependencies:
+        description: "Allows listing Viash components required by this Viash component"
+        type: "array"
+        items:
+          $ref: "defs_viash.yaml#/definitions/Dependency"
+      summary:
+        description: "A one-sentence summary of the component. This is only used for\
+          \ documentation."
+        type: "string"
+      runners:
+        description: "A list of runners to execute target artifacts.\n\n - ExecutableRunner\n\
+          \ - NextflowRunner\n"
+        type: "array"
+        items:
+          $ref: "defs_viash.yaml#/definitions/Runner"
+      name:
+        description: "Name of the component and the filename of the executable when\
+          \ built with `viash build`."
+        type: "string"
+      argument_groups:
+        description: "A grouping of the arguments, used to display the help message.\n\
+          \n - `name: foo`, the name of the argument group. \n - `description: Description\
+          \ of foo`, a description of the argument group. Multiline descriptions are\
+          \ supported.\n - `arguments: [arg1, arg2, ...]`, list of the arguments.\n\
+          \n"
+        type: "array"
+        items:
+          $ref: "defs_viash.yaml#/definitions/ArgumentGroup"
+      description:
+        description: "A description of the component. This is only used for documentation.\
+          \ Multiline descriptions are supported."
+        type: "string"
+      usage:
+        description: "A description on how to use the component. This will be displayed\
+          \ with `--help` under the 'Usage:' section."
+        type: "string"
+      info:
+        description: "Structured information. Can be any shape: a string, vector,\
+          \ map or even nested map."
+        type: "object"
+      version:
+        description: "Version of the component. This field will be used to version\
+          \ the executable and the Docker container."
+        type: "string"
+      links:
+        description: "External links of the component."
+        $ref: "defs_viash.yaml#/definitions/Links"
+      references:
+        description: "References to external resources related to the component."
+        $ref: "defs_viash.yaml#/definitions/References"
+      engines:
+        description: "A list of engine environments to execute target artifacts in.\n\
+          \n - NativeEngine\n - DockerEngine\n"
+        type: "array"
+        items:
+          $ref: "defs_viash.yaml#/definitions/Engine"
+      resources:
+        description: "Resources are files that support the component. The first resource\
+          \ should be a script that will be executed when the component is run. Additional\
+          \ resources will be copied to the same directory.\n\nCommon properties:\n\
+          \n * type: `file` / `r_script` / `python_script` / `bash_script` / `javascript_script`\
+          \ / `scala_script` / `csharp_script`, 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`.\n * dest: filename, the resulting name\
+          \ 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.\n * path: `path/to/file`, the path\
+          \ of the input file. Can be a relative or an absolute path, or a URI. Mutually\
+          \ exclusive with `text`.\n * text: ...multiline text..., the content of\
+          \ the resulting file specified as a string. Mutually exclusive with `path`.\n\
+          \ * is_executable: `true` / `false`, whether the resulting resource file\
+          \ should be made executable.\n"
+        type: "array"
+        items:
+          $ref: "defs_viash.yaml#/definitions/Resource"
+      keywords:
+        description: "The keywords of the components."
+        type: "array"
+        items:
+          type: "string"
+      test_resources:
+        description: "One or more scripts to be used to test the component behaviour\
+          \ when `viash test` is invoked. Additional files of type `file` will be\
+          \ made available only during testing. Each test script should expect no\
+          \ command-line inputs, be platform-independent, and return an exit code\
+          \ >0 when unexpected behaviour occurs during testing. See Unit Testing for\
+          \ more info."
+        type: "array"
+        items:
+          $ref: "defs_viash.yaml#/definitions/Resource"
+      namespace:
+        description: "Namespace this component is a part of. See the Namespaces guide\
+          \ for more information on namespaces."
+        type: "string"
+      arguments:
+        description: "A list of arguments for this component. For each argument, a\
+          \ type and a name must be specified. Depending on the type of argument,\
+          \ different properties can be set. See these reference pages per type for\
+          \ more information:  \n\n - string\n - file\n - integer\n - double\n - boolean\n\
+          \ - boolean_true\n - boolean_false\n"
+        type: "array"
+        items:
+          $ref: "defs_viash.yaml#/definitions/Argument"
+      __merge__:
+        $ref: "#/definitions/Merge"
+    required:
+    - "name"
+    additionalProperties: false
+  Merge:
+    type: string
+    description: Path to a YAML file to inherit values from.
+    oneOf:
+      - type: array
+      - type: string
+  FileFormat:
+    description: 'File format metadata'
+    type: object
+    required: [label, file_format]
+    properties:
+      label:
+        $ref: "defs_common.yaml#/definitions/Label"
+      summary: 
+        $ref: "defs_common.yaml#/definitions/Summary"
+      file_format:
+        oneOf:
+          - type: object
+            required: [type]
+            additionalProperties: false
+            properties:
+              type:
+                const: h5ad
+              X:
+                $ref: "#/definitions/AnnDataSlot"
+              layers:
+                type: array
+                items:
+                  $ref: "#/definitions/AnnDataSlot"
+              var:
+                type: array
+                items:
+                  $ref: "#/definitions/AnnDataSlot"
+              varm:
+                type: array
+                items:
+                  $ref: "#/definitions/AnnDataSlot"
+              varp:
+                type: array
+                items:
+                  $ref: "#/definitions/AnnDataSlot"
+              obs:
+                type: array
+                items:
+                  $ref: "#/definitions/AnnDataSlot"
+              obsm:
+                type: array
+                items:
+                  $ref: "#/definitions/AnnDataSlot"
+              obsp:
+                type: array
+                items:
+                  $ref: "#/definitions/AnnDataSlot"
+              uns:
+                type: array
+                items:
+                  oneOf:
+                    - $ref: "#/definitions/AnnDataSlot"
+                    - $ref: "#/definitions/AnnDataSlotObject"
+          - type: object
+            required: [type, mod]
+            additionalProperties: false
+            properties:
+              type:
+                const: h5mu
+              mod:
+                type: object
+                additionalProperties: false
+                properties:
+                  rna:
+                    "#/definitions/AnnData"
+                  atac:
+                    "#/definitions/AnnData"
+                  prot:
+                    "#/definitions/AnnData"
+                  vdj:
+                    "#/definitions/AnnData"
+                  vdj_t:
+                    "#/definitions/AnnData"
+                  vdj_b:
+                    "#/definitions/AnnData"
+                  gdo:
+                    "#/definitions/AnnData"
+                  hto:
+                    "#/definitions/AnnData"
+  MuData:
+    required: [mod]
+    additionalProperties: false
+    properties:
+      mod:
+        type: object
+        additionalProperties: false
+        properties:
+          rna:
+            "#/definitions/AnnData"
+          atac:
+            "#/definitions/AnnData"
+          prot:
+            "#/definitions/AnnData"
+          vdj:
+            "#/definitions/AnnData"
+          vdj_t:
+            "#/definitions/AnnData"
+          vdj_b:
+            "#/definitions/AnnData"
+          gdo:
+            "#/definitions/AnnData"
+          hto:
+            "#/definitions/AnnData"
+  AnnData:
+    additionalProperties: false
+    properties:
+      X:
+        $ref: "#/definitions/AnnDataSlot"
+      layers:
+        type: array
+        items:
+          $ref: "#/definitions/AnnDataSlot"
+      var:
+        type: array
+        items:
+          $ref: "#/definitions/AnnDataSlot"
+      varm:
+        type: array
+        items:
+          $ref: "#/definitions/AnnDataSlot"
+      varp:
+        type: array
+        items:
+          $ref: "#/definitions/AnnDataSlot"
+      obs:
+        type: array
+        items:
+          $ref: "#/definitions/AnnDataSlot"
+      obsm:
+        type: array
+        items:
+          $ref: "#/definitions/AnnDataSlot"
+      obsp:
+        type: array
+        items:
+          $ref: "#/definitions/AnnDataSlot"
+      uns:
+        type: array
+        items:
+          oneOf:
+            - $ref: "#/definitions/AnnDataSlot"
+            - $ref: "#/definitions/AnnDataSlotObject"
+  AnnDataSlot:
+    properties:
+      type:
+        enum: [integer, double, string, boolean]
+      name:
+        type: string
+        description: A unique identifier.
+        pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$"
+      description:
+        type: string
+      required:
+        type: boolean
+    required: [type, name, description, required]
+  AnnDataSlotObject:
+    properties:
+      type:
+        enum: [object]
+      name:
+        type: string
+        description: A unique identifier.
+        pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$"
+      description:
+        type: string
+      required:
+        type: boolean
+    required: [type, name, description, required]
+
+  # added specific properties to the author info
+  Author:
+    description: Author metadata.
+    type: object
+    additionalProperties: false
+    properties:
+      name:
+        description: Full name of the author, usually in the name of FirstName MiddleName LastName.
+        type: string
+      info:
+        description: Additional information on the author
+        type: object
+        additionalProperties: false
+        required: [role, links, organizations]
+        properties:
+          links:
+            type: object
+            additionalProperties: false
+            required: github
+            properties:
+              github:
+                type: string
+              orcid:
+                type: string
+              email:
+                type: string
+              twitter:
+                type: string
+              linkedin:
+                type: string
+          role:
+            description: Role in the organisation
+            enum: ["Core Team Member", "Contributor"]
+          organizations:
+            type: array
+            minItems: 1
+            items:
+              type: object
+              additionalProperties: false
+              required: [name, href, role]
+              properties:
+                name:
+                  type: string
+                href:
+                  type: string
+                role:
+                  type: string

schemas/file_format.yaml

@@ -0,0 +1,56 @@
+
+title: File API
+description: A file format specification file.
+type: "object"
+properties:
+  info:
+    $ref: "defs_common.yaml#/definitions/FileFormat"
+  create_parent:
+    description: "If the output filename is a path and it does not exist, create\
+      \ it before executing the script (only for `direction: output`)."
+    type: "boolean"
+  default:
+    anyOf:
+    - description: "The default value when no argument value is provided. This\
+        \ will not work if the [`required`](#required) property is enabled."
+      type: "string"
+    - description: "The default value when no argument value is provided. This\
+        \ will not work if the [`required`](#required) property is enabled."
+      type: "array"
+      items:
+        type: "string"
+  example:
+    anyOf:
+    - description: "An example value for this argument. If no [`default`](#default)\
+        \ property was specified, this will be used for that purpose."
+      type: "string"
+    - description: "An example value for this argument. If no [`default`](#default)\
+        \ property was specified, this will be used for that purpose."
+      type: "array"
+      items:
+        type: "string"
+  description:
+    description: "A description of the argument. This will be displayed with `--help`."
+    type: "string"
+  multiple_sep:
+    description: "The delimiter character for providing [`multiple`](#multiple)\
+      \ values. `:` by default."
+    type: "string"
+  multiple:
+    description: "Treat the argument value as an array. Arrays can be passed using\
+      \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\
+      \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\
+      \ property. `false` by default."
+    type: "boolean"
+  type:
+    description: "A `file` type argument has a string value that points to a file\
+      \ or folder path."
+    const: "file"
+  required:
+    description: "Make the value for this argument required. If set to `true`,\
+      \ an error will be produced if no value was provided. `false` by default."
+    type: "boolean"
+  __merge__:
+    $ref: "defs_common.yaml#/definitions/Merge"
+required:  [type, info]
+additionalProperties: false

schemas/package_config.yaml

@@ -0,0 +1 @@
+$ref: "defs_viash.yaml#/definitions/PackageConfig"

schemas/viash_config.yaml

@@ -0,0 +1,2 @@
+oneOf:
+  - $ref: "defs_common.yaml#/definitions/Config"