Add manifest.contributors config option

docs/reference/config.md

@@ -614,7 +614,7 @@ The following settings are available:
 : :::{versionadded} 24.04.0
   :::
 : *Used only by the {ref}`slurm-executor`, {ref}`lsf-executor`, {ref}`pbs-executor` and {ref}`pbspro-executor` executors.*
-: Allows specifying the project or organisation account that should be charged for running the pipeline jobs.
+: Allows specifying the project or organization account that should be charged for running the pipeline jobs.
 
 `executor.cpus`
 : The maximum number of CPUs made available by the underlying system. Used only by the `local` executor.
@@ -1144,8 +1144,22 @@ The `manifest` scope allows you to define some meta-data information needed when
 The following settings are available:
 
 `manifest.author`
+: :::{deprecated} 24.09.0-edge
+  Use `manifest.contributors` instead.
+  :::
 : Project author name (use a comma to separate multiple names).
 
+`manifest.contributors`
+: :::{versionadded} 24.09.0-edge
+  :::
+: List of project contributors. Should be a list of maps. The following fields are supported in the contributor map:
+  - `name`: the contributor's name 
+  - `affiliation`: the contributor's affiliated organization
+  - `email`: the contributor's email address
+  - `github`: the contributor's GitHub URL
+  - `contribution`: list of contribution types, each element can be one of `'author'`, `'maintainer'`, or `'contributor'`
+  - `orcid`: the contributor's [ORCID](https://orcid.org/) URL
+
 `manifest.defaultBranch`
 : Git repository default branch (default: `master`).
 
@@ -1170,9 +1184,6 @@ The following settings are available:
 `manifest.mainScript`
 : Project main script (default: `main.nf`).
 
-`manifest.maintainer`
-: Project maintainer name (use a comma to separate multiple names).
-
 `manifest.name`
 : Project short name.
 
@@ -1189,8 +1200,8 @@ The following settings are available:
   manifest.nextflowVersion = '!>=1.2'       // with ! prefix, stop execution if current version does not match required version.
   ```
 
-`manifest.organisation`
-: Project organisation
+`manifest.organization`
+: Project organization
 
 `manifest.recurseSubmodules`
 : Pull submodules recursively from the Git repository.

modules/nextflow/src/main/groovy/nextflow/config/Manifest.groovy

@@ -16,9 +16,13 @@
 
 package nextflow.config
 
+import java.util.stream.Collectors
 
 import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
 import groovy.util.logging.Slf4j
+import nextflow.exception.AbortOperationException
+
 import static nextflow.Const.DEFAULT_BRANCH
 import static nextflow.Const.DEFAULT_MAIN_FILE_NAME
 /**
@@ -63,6 +67,21 @@ class Manifest {
         target.author
     }
 
+    List<Contributor> getContributors() {
+        if( !target.contributors )
+            return Collections.emptyList()
+
+        try {
+            final contributors = target.contributors as List<Map>
+            return contributors.stream()
+                .map(opts -> new Contributor(opts))
+                .collect(Collectors.toList())
+        }
+        catch( ClassCastException | IllegalArgumentException e ){
+            throw new AbortOperationException("Invalid config option `manifest.contributors` -- should be a list of maps")
+        }
+    }
+
     String getMainScript() {
         target.mainScript ?: DEFAULT_MAIN_FILE_NAME
     }
@@ -102,25 +121,24 @@ class Manifest {
         target.docsUrl
     }
 
-    String getIcon(){
+    String getIcon() {
         target.icon
     }
 
-    String getMaintainer(){
-        target.maintainer
-    }
-
-    String getOrganisation(){
-        target.organisation
+    String getOrganization() {
+        target.organization
     }
 
-    String getLicense(){
+    String getLicense() {
         target.license
     }
 
     Map toMap() {
         final result = new HashMap(15)
         result.author = getAuthor()
+        result.contributors = getContributors().stream()
+            .map(c -> c.toMap())
+            .collect(Collectors.toList())
         result.defaultBranch = getDefaultBranch()
         result.description = getDescription()
         result.homePage = homePage
@@ -131,9 +149,49 @@ class Manifest {
         result.doi = getDoi()
         result.docsUrl = getDocsUrl()
         result.icon = getIcon()
-        result.maintainer = getMaintainer()
-        result.organisation = getOrganisation()
+        result.organization = getOrganization()
         result.license = getLicense()
         return result
     }
+
+    @EqualsAndHashCode
+    static class Contributor {
+        String name
+        String affiliation
+        String email
+        String github
+        Set<ContributionType> contribution
+        String orcid
+
+        Contributor(Map opts) {
+            name = opts.name as String
+            affiliation = opts.affiliation as String
+            email = opts.email as String
+            github = opts.github as String
+            contribution = (opts.contribution as List<String>).stream()
+                .map(c -> ContributionType.valueOf(c.toUpperCase()))
+                .collect(Collectors.toSet())
+            orcid = opts.orcid as String
+        }
+
+        Map toMap() {
+            final result = new HashMap(6)
+            result.name = name
+            result.affiliation = affiliation
+            result.email = email
+            result.github = github
+            result.contribution = contribution.stream()
+                .map(c -> c.toString().toLowerCase())
+                .sorted()
+                .collect(Collectors.toList())
+            result.orcid = orcid
+            return result
+        }
+    }
+
+    static enum ContributionType {
+        AUTHOR,
+        MAINTAINER,
+        CONTRIBUTOR
+    }
 }

modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy

@@ -64,7 +64,7 @@ class AssetManager {
 
     /**
      * The pipeline name. It must be in the form {@code username/repo} where 'username'
-     * is a valid user name or organisation account, while 'repo' is the repository name
+     * is a valid user name or organization account, while 'repo' is the repository name
      * containing the pipeline code
      */
     private String project

modules/nextflow/src/test/groovy/nextflow/config/ManifestTest.groovy

@@ -16,7 +16,10 @@
 
 package nextflow.config
 
+import nextflow.exception.AbortOperationException
 import spock.lang.Specification
+
+import static nextflow.config.Manifest.ContributionType
 /**
  *
  * @author Paolo Di Tommaso <[email protected]>
@@ -26,49 +29,126 @@ class ManifestTest extends Specification {
     def 'should check manifest object' () {
 
         given:
-        def MAN = [author: 'pablo', nextflowVersion: '1.2.3', name: 'foo',
-                   maintainer: 'john', organisation: 'My Organisation', icon: 'icon.png',
-                   docsUrl: 'https://docs.io', license: 'Apache v2']
+        def MAP = [
+            author: 'pablo',
+            contributors: [
+                [
+                    name: 'Alice', 
+                    affiliation: 'University', 
+                    email: '[email protected]',
+                    contribution: ['author', 'maintainer'],
+                    orcid: 'https://orcid.org/0000-0000-0000-0000'
+                ],
+                [
+                    name: 'Bob', 
+                    affiliation: 'Company', 
+                    email: '[email protected]',
+                    contribution: ['contributor'],
+                ]
+            ],
+            nextflowVersion: '1.2.3',
+            name: 'foo',
+            organization: 'My Organization',
+            icon: 'icon.png',
+            docsUrl: 'https://docs.io',
+            license: 'Apache v2'
+        ]
         when:
-        def manifest = new Manifest(MAN)
+        def manifest = new Manifest(MAP)
         then:
-        manifest.with {
-            author == 'pablo'
-            nextflowVersion == '1.2.3'
-            name == 'foo'
-            maintainer == 'john'
-            organisation == 'My Organisation'
-            icon == 'icon.png'
-            docsUrl == 'https://docs.io'
-            license == 'Apache v2'
-        }
+        manifest.author == 'pablo'
+        manifest.contributors.size() == 2
+        manifest.contributors[0].name == 'Alice'
+        manifest.contributors[0].affiliation == 'University'
+        manifest.contributors[0].email == '[email protected]'
+        manifest.contributors[0].contribution == [ContributionType.AUTHOR, ContributionType.MAINTAINER] as Set
+        manifest.contributors[0].orcid == 'https://orcid.org/0000-0000-0000-0000'
+        manifest.contributors[1].name == 'Bob'
+        manifest.contributors[1].affiliation == 'Company'
+        manifest.contributors[1].email == '[email protected]'
+        manifest.contributors[1].contribution == [ContributionType.CONTRIBUTOR] as Set
+        manifest.nextflowVersion == '1.2.3'
+        manifest.name == 'foo'
+        manifest.organization == 'My Organization'
+        manifest.icon == 'icon.png'
+        manifest.docsUrl == 'https://docs.io'
+        manifest.license == 'Apache v2'
 
     }
 
     def 'should check empty manifest' () {
 
-        // check empty manifest
         when:
         def manifest = new Manifest(new ConfigObject())
         then:
-        manifest.with {
-            homePage == null
-            defaultBranch == 'master'
-            description == null
-            author == null
-            mainScript == 'main.nf'
-            gitmodules == null
-            nextflowVersion == null
-            version == null
-            name == null
-            maintainer == null
-            docsUrl == null
-            organisation == null
-            icon == null
-            license == null
-        }
+        manifest.homePage == null
+        manifest.defaultBranch == 'master'
+        manifest.description == null
+        manifest.author == null
+        manifest.contributors == []
+        manifest.mainScript == 'main.nf'
+        manifest.gitmodules == null
+        manifest.nextflowVersion == null
+        manifest.version == null
+        manifest.name == null
+        manifest.docsUrl == null
+        manifest.organization == null
+        manifest.icon == null
+        manifest.license == null
+
+    }
+
+    def 'should convert manifest to map' () {
 
+        when:
+        def MAP = [
+            name: 'Alice', 
+            affiliation: 'University', 
+            email: '[email protected]',
+            contribution: ['author', 'maintainer'],
+            orcid: 'https://orcid.org/0000-0000-0000-0000'
+        ]
+        then:
+        new Manifest.Contributor(MAP).toMap() == [
+            name: 'Alice', 
+            affiliation: 'University', 
+            email: '[email protected]',
+            github: null,
+            contribution: ['author', 'maintainer'],
+            orcid: 'https://orcid.org/0000-0000-0000-0000'
+        ]
     }
 
+    def 'should throw error on invalid manifest' () {
+        when:
+        def manifest = new Manifest([
+            contributors: [ 'Alice' ]
+        ])
+        manifest.contributors
+        then:
+        thrown(AbortOperationException)
+
+        when:
+        manifest = new Manifest([
+            contributors: [[
+                name: 'Alice',
+                contribution: 'author'
+            ]]
+        ])
+        manifest.contributors
+        then:
+        thrown(AbortOperationException)
+
+        when:
+        manifest = new Manifest([
+            contributors: [[
+                name: 'Alice',
+                contribution: [ 'owner' ]
+            ]]
+        ])
+        manifest.contributors
+        then:
+        thrown(AbortOperationException)
+    }
 
 }