run the CWL v1.2.1 conformance tests

[mr-c]

Uh-oh, there are 378 CWL v1.2 conformance tests, but only 338 are being run (40 are missing!).

[codecov]

Codecov Report

Attention: 8 lines in your changes are missing coverage. Please review.

Comparison is base (0250406) 83.93% compared to head (480e578) 83.81%.

Files	Patch %	Lines
cwltool/singularity.py	38.46%	6 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1942      +/-   ##
==========================================
- Coverage   83.93%   83.81%   -0.12%     
==========================================
  Files          46       46              
  Lines        8190     8198       +8     
  Branches     2175     2177       +2     
==========================================
- Hits         6874     6871       -3     
- Misses        844      853       +9     
- Partials      472      474       +2     

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[mr-c]

2 CWL v1.2 tests failed!

https://github.com/common-workflow-language/cwltool/actions/runs/6864420332/job/18666138132?pr=1942#step:7:375

One should pass with --relax-path-checks; the other I'm not so sure about..

[mr-c]

Yep, --fast-parser is failing the record_with_default test.

@tetron, can you fix this?
cwltool --fast-parser --fast-parser https://github.com/common-workflow-language/cwl-v1.2/raw/1.2.1_proposed/tests/paramref_arguments_roundtrip.cwl fails, drop the --fast-parser and it passes. (Same if it is a local copy of the conformance tests)

INFO /home/michael/cwltool/env3.12/bin/cwltool 3.1.20231114134825.dev5+g9a49a7c4
DEBUG Parsed job order from command line: {
    "__id": "https://github.com/common-workflow-language/cwl-v1.2/raw/1.2.1_proposed/tests/paramref_arguments_roundtrip.cwl",
    "a_record": {
        "fifth": 4200000000000000000000000000000000000000000,
        "first": "y",
        "fourth": 4242424242,
        "second": 23,
        "sixth": {
            "class": "File",
            "path": "whale.txt"
        },
        "third": 2.3
    }
}
DEBUG [job paramref_arguments_roundtrip.cwl] initializing from https://github.com/common-workflow-language/cwl-v1.2/raw/1.2.1_proposed/tests/paramref_arguments_roundtrip.cwl
DEBUG [job paramref_arguments_roundtrip.cwl] {
    "a_record": {
        "fifth": 4200000000000000000000000000000000000000000,
        "first": "y",
        "fourth": 4242424242,
        "second": 23,
        "sixth": {
            "class": "File",
            "location": "whale.txt",
            "basename": "whale.txt",
            "nameroot": "whale",
            "nameext": ".txt"
        },
        "third": 2.3
    }
}
ERROR Input object failed validation:
test:1:1: [Errno 2] No such file or directory: '/home/michael/cwltool_main/whale.txt'
Traceback (most recent call last):
  File "/home/michael/cwltool/cwltool/pathmapper.py", line 169, in visit
    st = os.lstat(deref)
         ^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/michael/cwltool_main/whale.txt'

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

Traceback (most recent call last):
  File "/home/michael/cwltool/cwltool/main.py", line 1301, in main
    (out, status) = real_executor(
                    ^^^^^^^^^^^^^^
  File "/home/michael/cwltool/cwltool/executors.py", line 62, in __call__
    return self.execute(process, job_order_object, runtime_context, logger)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/michael/cwltool/cwltool/executors.py", line 145, in execute
    self.run_jobs(process, job_order_object, logger, runtime_context)
  File "/home/michael/cwltool/cwltool/executors.py", line 220, in run_jobs
    for job in jobiter:
  File "/home/michael/cwltool/cwltool/command_line_tool.py", line 992, in job
    builder.pathmapper = self.make_path_mapper(reffiles, builder.stagedir, runtimeContext, True)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/michael/cwltool/cwltool/command_line_tool.py", line 485, in make_path_mapper
    return PathMapper(reffiles, runtimeContext.basedir, stagedir, separateDirs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/michael/cwltool/cwltool/pathmapper.py", line 95, in __init__
    self.setup(dedup(referenced_files), basedir)
  File "/home/michael/cwltool/cwltool/pathmapper.py", line 198, in setup
    self.visit(
  File "/home/michael/cwltool/cwltool/pathmapper.py", line 158, in visit
    with SourceLine(
  File "/home/michael/cwltool/env3.12/lib/python3.12/site-packages/schema_salad/sourceline.py", line 249, in __exit__
    raise self.makeError(str(exc_value)) from exc_value
schema_salad.exceptions.ValidationException: test:1:1: [Errno 2] No such file or directory: '/home/michael/cwltool_main/whale.txt'