Merge remote-tracking branch 'origin/main' into codegen

.github/workflows/spellcheck.yml

@@ -13,10 +13,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Codespell with annotations
-        uses: codespell-project/actions-codespell@v2.0
+        uses: codespell-project/actions-codespell@v2.1
         with:
           skip: EDAM.owl,foaf.rdf,underscore.js,CODE_OF_CONDUCT.md
-      - uses: rojopolis/spellcheck-github-actions@0.36.0
+      - uses: rojopolis/spellcheck-github-actions@0.41.0
         name: Spellcheck
         # https://github.com/marketplace/actions/github-spellcheck-action
         # To run locally, `pip install pyspelling`, followed by

CommandLineTool.yml

@@ -56,8 +56,7 @@ $graph:
       * CWL has been assigned an official IANA Media Type of [`application/cwl`](https://www.iana.org/assignments/media-types/application/cwl)
         for either JSON or YAML format. For JSON formatted CWL documents, [`application/cwl+json`](https://www.iana.org/assignments/media-types/application/cwl+json)
         has also been assigned and can be used. For specifying a YAML formatted
-        CWL document, one can use `application/cwl+yaml` but that is not an official
-        IANA media-type yet; as of 2023-07-23 the `+yaml` suffix has yet to be approved.
+        CWL document, one can use [`application/cwl+yaml`](https://www.iana.org/assignments/media-types/application/cwl+yaml).
         The above has been documented in the [Syntax](#Syntax) section.
       * There is now an unofficial [JSON Schema for CWL documents](https://github.com/common-workflow-language/cwl-v1.2/blob/1.2.1_proposed/json-schema/cwl.yaml),
         donated by Francis Charette-Migneault. This schema captures much, but not

Process.yml

@@ -8,7 +8,7 @@ $namespaces:
 
 $graph:
 
-- name: "Common Workflow Language, v1.2"
+- name: "Common Workflow Language, v1.2.1"
   type: documentation
   doc: {$include: concepts.md}
 

Workflow.yml

@@ -11,7 +11,7 @@ $graph:
   type: documentation
   doc:
     - |
-      # Common Workflow Language (CWL) Workflow Description, v1.2
+      # Common Workflow Language (CWL) Workflow Description, v1.2.1
 
       This version:
         * https://w3id.org/cwl/v1.2/
@@ -55,8 +55,7 @@ $graph:
       * CWL has been assigned an official IANA Media Type of [`application/cwl`](https://www.iana.org/assignments/media-types/application/cwl)
         for either JSON or YAML format. For JSON formatted CWL documents, [`application/cwl+json`](https://www.iana.org/assignments/media-types/application/cwl+json)
         has also been assigned and can be used. For specifying a YAML formatted
-        CWL document, one can use `application/cwl+yaml` but that is not an official
-        IANA media-type yet; as of 2023-07-23 the `+yaml` suffix has yet to be approved.
+        CWL document, one can use [`application/cwl+yaml`](https://www.iana.org/assignments/media-types/application/cwl+yaml).
         The above has been documented in the [Syntax](#Syntax) section.
       * There is now an unofficial [JSON Schema for CWL documents](https://github.com/common-workflow-language/cwl-v1.2/blob/1.2.1_proposed/json-schema/cwl.yaml),
         donated by Francis Charette-Migneault. This schema captures much, but not

concepts.md

@@ -104,8 +104,7 @@ The official IANA media-type for CWL documents is [`application/cwl`](https://ww
 for either JSON or YAML format. For JSON formatted CWL documents,
 [`application/cwl+json`](https://www.iana.org/assignments/media-types/application/cwl+json)
 can be used. For specifying a YAML formatted CWL document, one can use
-`application/cwl+yaml` but that is not an official IANA media-type yet; as of
-2023-07-23 the `+yaml` suffix has yet to be approved.
+[`application/cwl+yaml`](https://www.iana.org/assignments/media-types/application/cwl+yaml).
 
 CWL documents commonly reference other CWL documents.  Each document
 must declare the `cwlVersion` of that document.  Implementations must

cwl-runner.cwl

@@ -29,6 +29,7 @@ inputs:
 
  processfile:
    type: File?
+   format: [iana:application/cwl, iana:application/cwl+json, iana:application/cwl+yaml]
    doc: |
     The CommandLineTool, ExpressionTool, or Workflow description to run.
     Optional if the jobfile has a `cwl:tool` field to indicate which process

index.md

@@ -1,7 +1,7 @@
-# Common Workflow Language Standards, v1.2
+# Common Workflow Language Standards, v1.2.1
 
 The [User Guide](http://www.commonwl.org/user_guide/) provides a gentle
-introduction to writing CWL command line tools and workflows. Currently the CWL User Guide targets CWL v1.0 only.
+introduction to writing CWL command line tools and workflows.
 
 The CWL [Command Line Tool Description Standard](CommandLineTool.html)
 specifies the document schema and execution semantics for wrapping and

run_test.sh

@@ -51,6 +51,7 @@ SELF=""
 BADGE=""
 TIMEOUT=""
 TAGS=""
+REPORT_URI="https://github.com/common-workflow-language/cwl-$CWL_VER/tree/main/"
 
 while [ -n "$1" ]
 do
@@ -95,7 +96,7 @@ do
             SELF=1
             ;;
         --badgedir=*)
-            BADGE=$arg
+            BADGE="$arg --baseuri=$REPORT_URI"
             ;;
         --timeout=*)
             TIMEOUT=$arg