ruamel.yaml doesn't support yaml.dump()

[alexiswl]

cwl-utils requirements uses less than <0.19

However yaml.dump was deprecated in version 0.18 and is not supported.

Steps to reproduce

# Install working

pip install cwl-utils==0.32
pip install ruamel.yaml==0.17.40

## Run GraphSplit
cwl-graph-split --outdir workflow/ pipeline.cwl.json 

## Install failing
pip install ruamel.yaml==0.18.0

## Run Graph Split
cwl-graph-split --outdir workflow/ pipeline.cwl.json 

Gives

Click to expand!

Traceback (most recent call last):
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 180, in rewrite
    return rewrite_schemadef(document)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 227, in rewrite_schemadef
    dump([entry], entry_handle, Dumper=RoundTripDumper)
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/ruamel/yaml/main.py", line 1229, in dump
    error_deprecation('dump', 'dump', arg="typ='unsafe', pure=True")
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/ruamel/yaml/main.py", line 1017, in error_deprecation
    sys.exit(1)
SystemExit: 1

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 182, in rewrite
    imports.update(rewrite(value, doc_id))
                   ^^^^^^^^^^^^^^^^^^^^^^
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 135, in rewrite
    imports.update(rewrite(entry, doc_id))
                   ^^^^^^^^^^^^^^^^^^^^^^
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 139, in rewrite
    with SourceLine(document, key, Exception):
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/schema_salad/sourceline.py", line 249, in __exit__
    raise self.makeError(str(exc_value)) from exc_value
Exception: pipeline.cwl.json:208:11: 1

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/media/UMCCR/Projects/202402/schema-testing/venv/bin/cwl-graph-split", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 65, in main
    sys.exit(run(sys.argv[1:]))
             ^^^^^^^^^^^^^^^^^
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 73, in run
    graph_split(
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 113, in graph_split
    imports = rewrite(entry, entry_id)
              ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/cwl_utils/graph_split.py", line 139, in rewrite
    with SourceLine(document, key, Exception):
  File "/media/UMCCR/Projects/202402/schema-testing/venv/lib/python3.11/site-packages/schema_salad/sourceline.py", line 249, in __exit__
    raise self.makeError(str(exc_value)) from exc_value
Exception: pipeline.cwl.json:208:11: 1

pipeline.zip

[mr-c]

Yep,

cwl-utils/cwl_utils/graph_split.py

Line 227 in e3f0704

dump([entry], entry_handle, Dumper=RoundTripDumper)

should be changed to use the yaml_dump function or similar