Unpin & upgrade cwl-utils version

[mr-c]

Fixes #39

[codecov]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (b1c02bb) 97.25% compared to head (e1a51b3) 97.26%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #40   +/-   ##
=======================================
  Coverage   97.25%   97.26%           
=======================================
  Files          11       11           
  Lines        1786     1790    +4     
=======================================
+ Hits         1737     1741    +4     
  Misses         49       49           

Impacted Files	Coverage Δ
src/runcrate/convert.py	97.57% <100.00%> (+<0.01%)	⬆️
tests/test_cwlprov_crate_builder.py	99.87% <100.00%> (+<0.01%)	⬆️

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[simleo]

Thanks for this @mr-c! There's one weird thing that puzzles me: if I set up a local environment like this:

python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install wheel
pip install -e .
pip install pytest
pytest tests/

Then three tests fail:

============================================================================ test session starts ============================================================================
platform linux -- Python 3.8.10, pytest-7.3.1, pluggy-1.0.0
rootdir: /tmp/runcrate
collected 27 items                                                                                                                                                          

tests/test_cli.py .......FFF                                                                                                                                          [ 37%]
tests/test_cwlprov_crate_builder.py ...............                                                                                                                   [ 92%]
tests/test_step_mapping.py ..                                                                                                                                         [100%]

================================================================================= FAILURES ==================================================================================
_______________________________________________________________________________ test_cli_run ________________________________________________________________________________

data_dir = PosixPath('/tmp/runcrate/tests/data'), tmpdir = PosixPath('/tmp/pytest-of-simleo/pytest-14/test_cli_run0')
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7ff314d00d30>

    def test_cli_run(data_dir, tmpdir, monkeypatch):
        crate_dir = data_dir / "type-zoo-run-1-crate"
        runner = CliRunner()
        args = ["run", str(crate_dir)]
        monkeypatch.chdir(str(tmpdir))
        result = runner.invoke(cli, args)
>       assert result.exit_code == 0
E       AssertionError: assert 1 == 0
E        +  where 1 = <Result FileNotFoundError(2, 'No such file or directory')>.exit_code

/tmp/runcrate/tests/test_cli.py:120: AssertionError
__________________________________________________________________________ test_cli_run_dir_array ___________________________________________________________________________

data_dir = PosixPath('/tmp/runcrate/tests/data'), tmpdir = PosixPath('/tmp/pytest-of-simleo/pytest-14/test_cli_run_dir_array0')
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7ff314d00ca0>

    def test_cli_run_dir_array(data_dir, tmpdir, monkeypatch):
        crate_dir = data_dir / "dirarray-run-1-crate"
        runner = CliRunner()
        args = ["run", str(crate_dir)]
        monkeypatch.chdir(str(tmpdir))
        result = runner.invoke(cli, args)
>       assert result.exit_code == 0
E       AssertionError: assert 1 == 0
E        +  where 1 = <Result FileNotFoundError(2, 'No such file or directory')>.exit_code

/tmp/runcrate/tests/test_cli.py:133: AssertionError
__________________________________________________________________________ test_cli_run_file_array __________________________________________________________________________

data_dir = PosixPath('/tmp/runcrate/tests/data'), tmpdir = PosixPath('/tmp/pytest-of-simleo/pytest-14/test_cli_run_file_array0')
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7ff314d0b730>

    def test_cli_run_file_array(data_dir, tmpdir, monkeypatch):
        crate_dir = data_dir / "no-output-run-1-crate"
        runner = CliRunner()
        args = ["run", str(crate_dir)]
        monkeypatch.chdir(str(tmpdir))
        result = runner.invoke(cli, args)
>       assert result.exit_code == 0
E       AssertionError: assert 1 == 0
E        +  where 1 = <Result FileNotFoundError(2, 'No such file or directory')>.exit_code

/tmp/runcrate/tests/test_cli.py:142: AssertionError
========================================================================== short test summary info ==========================================================================
FAILED tests/test_cli.py::test_cli_run - AssertionError: assert 1 == 0
FAILED tests/test_cli.py::test_cli_run_dir_array - AssertionError: assert 1 == 0
FAILED tests/test_cli.py::test_cli_run_file_array - AssertionError: assert 1 == 0
======================================================================= 3 failed, 24 passed in 1.40s ========================================================================

However, if I run tox -e test, all tests pass! Can you reproduce this? Do you have any clue as to why it might be happening?

[simleo]

@mr-c on a different note, please add your copyright statement to the top of convert.py and your info to the authors section of CITATION.cff

[simleo]

However, if I run tox -e test, all tests pass! Can you reproduce this? Do you have any clue as to why it might be happening?

@mr-c Sorry about this, I forgot that cwlref-runner is an additional requirement for the tests.

[mr-c]

Thanks for this @mr-c! There's one weird thing that puzzles me: if I set up a local environment like this:

python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install wheel
pip install -e .
pip install pytest
pytest tests/

Then three tests fail:

You'll need cwlref-runner as well, yeah?

  File "/home/michael/src/runcrate/src/runcrate/run.py", line 212, in run_crate
    subprocess.check_call(args)
  File "/usr/lib/python3.11/subprocess.py", line 408, in check_call
    retcode = call(*popenargs, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/subprocess.py", line 389, in call
    with Popen(*popenargs, **kwargs) as p:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/subprocess.py", line 1024, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.11/subprocess.py", line 1901, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'cwl-runner'

[simleo]

You'll need cwlref-runner as well, yeah?

Yes, thank you

[mr-c]

@mr-c on a different note, please add your copyright statement to the top of convert.py and your info to the authors section of CITATION.cff

Done! Shall I merge?