Fix use of extensions in $graph

Fixes #2114

Author: mr-c

MANIFEST.in

@@ -64,6 +64,7 @@ include cwltool/schemas/v1.3.0-dev1/salad/schema_salad/metaschema/*.md
 include cwltool/extensions.yml
 include cwltool/extensions-v1.1.yml
 include cwltool/extensions-v1.2.yml
+include cwltool/extensions-v1.3.yml
 include cwltool/jshint/jshint_wrapper.js
 include cwltool/jshint/jshint.js
 include cwltool/hello.simg

cwltool/main.py

@@ -645,16 +645,19 @@ def setup_schema(
         ext10 = files("cwltool").joinpath("extensions.yml").read_text("utf-8")
         ext11 = files("cwltool").joinpath("extensions-v1.1.yml").read_text("utf-8")
         ext12 = files("cwltool").joinpath("extensions-v1.2.yml").read_text("utf-8")
+        ext13 = files("cwltool").joinpath("extensions-v1.3.yml").read_text("utf-8")
         use_custom_schema("v1.0", "http://commonwl.org/cwltool", ext10)
         use_custom_schema("v1.1", "http://commonwl.org/cwltool", ext11)
         use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext12)
+        use_custom_schema("v1.3.0-dev1", "http://commonwl.org/cwltool", ext13)
         use_custom_schema("v1.2.0-dev1", "http://commonwl.org/cwltool", ext11)
         use_custom_schema("v1.2.0-dev2", "http://commonwl.org/cwltool", ext11)
         use_custom_schema("v1.2.0-dev3", "http://commonwl.org/cwltool", ext11)
     else:
         use_standard_schema("v1.0")
         use_standard_schema("v1.1")
         use_standard_schema("v1.2")
+        use_standard_schema("v1.3.0-dev1")
         use_standard_schema("v1.2.0-dev1")
         use_standard_schema("v1.2.0-dev2")
         use_standard_schema("v1.2.0-dev3")

tests/test_ext.py

@@ -285,3 +285,10 @@ def test_ext_validation_no_namespace_warning() -> None:
         "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you "
         "missing a $namespaces section?"
     ) not in stderr
+
+
+def test_ext_in_dollarsign_graph() -> None:
+    error_code, stdout, stderr = get_main_output(
+        ["--validate", "--enable-ext", get_data("tests/wf/hello_gpu.cwl")]
+    )
+    assert error_code == 0

tests/wf/hello_gpu.cwl

@@ -0,0 +1,52 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+$graph:
+
+- class: Workflow
+  id: main
+  label: Test GPU
+  doc: |
+    Print GPU info.
+  s:keywords: gpu
+  s:softwareVersion: 0.1.0
+
+  inputs: []
+
+  outputs:
+    echo:
+      type: File
+      outputSource: node_hello/echo
+
+  steps:
+    node_hello:
+      in: []
+      run: '#hello-cl'
+      out:
+      - echo
+
+- class: CommandLineTool
+  id: hello-cl
+  s:softwareVersion: 1.0.0
+
+  baseCommand: nvidia-smi
+  arguments: []
+
+  requirements:
+    cwltool:CUDARequirement:
+      cudaVersionMin: "12.0"
+      cudaComputeCapability: "7.5"
+      cudaDeviceCountMin: 1
+      cudaDeviceCountMax: 4
+  inputs: []
+
+  outputs:
+    echo:
+      type: File
+      outputBinding:
+        glob: output.txt
+  stdout: output.txt
+
+$namespaces:
+  cwltool: http://commonwl.org/cwltool#
+  s: https://schema.org/