Specify pytest tmpdir in all SLURM tests

[nicolocin]

Currently many pydra tests that doesn't specify cache dirs fail on Openmind. The github actions SLURM CI runs in a docker container which assumes everything runs on one node, which is not the case with distributed SLURM clusters. Adding tmpdir to tests helps with debugging

[nicolocin]

@dorota @satra - I'm not sure whether this is a bug or not. This is from running pytest -vvs --basetemp=/scratch/Thu/nlo/tmpdir2 pydra/engine/tests/test_shelltask.py after I added tmpdir to the tests and updating results_function in this commit ec3e92b1e

==================================================================================== FAILURES ====================================================================================
_____________________________________________________________ test_shell_cmd_inputspec_9[slurm-result_no_submitter] ______________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputspec_9_slu0'), plugin = 'slurm'
results_function = <function result_no_submitter at 0x2b2148cb3320>

    @pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
    def test_shell_cmd_inputspec_9(tmpdir, plugin, results_function):
        """
            providing output name using input_spec (output_file_template in metadata),
            the template has a suffix, the extension of the file will be moved to the end
        """
        cmd = "cp"
        file = tmpdir.mkdir("data_inp").join("file.txt")
        file.write("content")

        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "file_orig",
                    attr.ib(
                        type=File,
                        metadata={"position": 2, "help_string": "new file", "argstr": ""},
                    ),
                ),
                (
                    "file_copy",
                    attr.ib(
                        type=str,
                        metadata={
                            "output_file_template": "{file_orig}_copy",
                            "help_string": "output file",
                            "argstr": "",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        shelly = ShellCommandTask(
            name="shelly", executable=cmd, input_spec=my_input_spec, file_orig=file
        )

        res = results_function(shelly, plugin, tmpdir)
        assert res.output.stdout == ""
        assert res.output.file_copy.exists()
>       assert res.output.file_copy.name == "file_copy.txt"
E       AssertionError: assert 'file.txt' == 'file_copy.txt'
E         - file_copy.txt
E         ?     -----
E         + file.txt

pydra/engine/tests/test_shelltask.py:1177: AssertionError
_______________________________________________________________ test_shell_cmd_inputspec_9[slurm-result_submitter] _______________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputspec_9_slu1'), plugin = 'slurm'
results_function = <function result_submitter at 0x2b2148cb3290>

    @pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
    def test_shell_cmd_inputspec_9(tmpdir, plugin, results_function):
        """
            providing output name using input_spec (output_file_template in metadata),
            the template has a suffix, the extension of the file will be moved to the end
        """
        cmd = "cp"
        file = tmpdir.mkdir("data_inp").join("file.txt")
        file.write("content")

        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "file_orig",
                    attr.ib(
                        type=File,
                        metadata={"position": 2, "help_string": "new file", "argstr": ""},
                    ),
                ),
                (
                    "file_copy",
                    attr.ib(
                        type=str,
                        metadata={
                            "output_file_template": "{file_orig}_copy",
                            "help_string": "output file",
                            "argstr": "",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        shelly = ShellCommandTask(
            name="shelly", executable=cmd, input_spec=my_input_spec, file_orig=file
        )

        res = results_function(shelly, plugin, tmpdir)
        assert res.output.stdout == ""
        assert res.output.file_copy.exists()
>       assert res.output.file_copy.name == "file_copy.txt"
E       AssertionError: assert 'file.txt' == 'file_copy.txt'
E         - file_copy.txt
E         ?     -----
E         + file.txt

pydra/engine/tests/test_shelltask.py:1177: AssertionError
_____________________________________________________________ test_shell_cmd_inputspec_9a[slurm-result_no_submitter] _____________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputspec_9a_sl0'), plugin = 'slurm'
results_function = <function result_no_submitter at 0x2b2148cb3320>

    @pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
    def test_shell_cmd_inputspec_9a(tmpdir, plugin, results_function):
        """
            providing output name using input_spec (output_file_template in metadata)
            and the keep_extension is set to False, so the extension is removed completely.
        """
        cmd = "cp"
        file = tmpdir.join("file.txt")
        file.write("content")

        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "file_orig",
                    attr.ib(
                        type=File,
                        metadata={"position": 2, "help_string": "new file", "argstr": ""},
                    ),
                ),
                (
                    "file_copy",
                    attr.ib(
                        type=str,
                        metadata={
                            "output_file_template": "{file_orig}_copy",
                            "keep_extension": False,
                            "help_string": "output file",
                            "argstr": "",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        shelly = ShellCommandTask(
            name="shelly", executable=cmd, input_spec=my_input_spec, file_orig=file
        )

        res = results_function(shelly, plugin, tmpdir)
        assert res.output.stdout == ""
        assert res.output.file_copy.exists()
>       assert res.output.file_copy.name == "file_copy"
E       AssertionError: assert 'vast-storage_copy' == 'file_copy'
E         - file_copy
E         + vast-storage_copy

pydra/engine/tests/test_shelltask.py:1225: AssertionError
______________________________________________________________ test_shell_cmd_inputspec_9a[slurm-result_submitter] _______________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputspec_9a_sl1'), plugin = 'slurm'
results_function = <function result_submitter at 0x2b2148cb3290>

    @pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
    def test_shell_cmd_inputspec_9a(tmpdir, plugin, results_function):
        """
            providing output name using input_spec (output_file_template in metadata)
            and the keep_extension is set to False, so the extension is removed completely.
        """
        cmd = "cp"
        file = tmpdir.join("file.txt")
        file.write("content")

        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "file_orig",
                    attr.ib(
                        type=File,
                        metadata={"position": 2, "help_string": "new file", "argstr": ""},
                    ),
                ),
                (
                    "file_copy",
                    attr.ib(
                        type=str,
                        metadata={
                            "output_file_template": "{file_orig}_copy",
                            "keep_extension": False,
                            "help_string": "output file",
                            "argstr": "",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        shelly = ShellCommandTask(
            name="shelly", executable=cmd, input_spec=my_input_spec, file_orig=file
        )

        res = results_function(shelly, plugin, tmpdir)
        assert res.output.stdout == ""
        assert res.output.file_copy.exists()
>       assert res.output.file_copy.name == "file_copy"
E       AssertionError: assert 'vast-storage_copy' == 'file_copy'
E         - file_copy
E         + vast-storage_copy

pydra/engine/tests/test_shelltask.py:1225: AssertionError
_____________________________________________________________ test_shell_cmd_inputspec_9b[slurm-result_no_submitter] _____________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputspec_9b_sl0'), plugin = 'slurm'
results_function = <function result_no_submitter at 0x2b2148cb3320>

    @pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
    def test_shell_cmd_inputspec_9b(tmpdir, plugin, results_function):
        """
            providing output name using input_spec (output_file_template in metadata)
            and the keep_extension is set to False, so the extension is removed completely,
            no suffix in the template.
        """
        cmd = "cp"
        file = tmpdir.join("file.txt")
        file.write("content")

        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "file_orig",
                    attr.ib(
                        type=File,
                        metadata={"position": 2, "help_string": "new file", "argstr": ""},
                    ),
                ),
                (
                    "file_copy",
                    attr.ib(
                        type=str,
                        metadata={
                            "output_file_template": "{file_orig}",
                            "keep_extension": False,
                            "help_string": "output file",
                            "argstr": "",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        shelly = ShellCommandTask(
            name="shelly", executable=cmd, input_spec=my_input_spec, file_orig=file
        )

        res = results_function(shelly, plugin, tmpdir)
        assert res.output.stdout == ""
        assert res.output.file_copy.exists()
>       assert res.output.file_copy.name == "file"
E       AssertionError: assert 'vast-storage' == 'file'
E         - file
E         + vast-storage

pydra/engine/tests/test_shelltask.py:1272: AssertionError
______________________________________________________________ test_shell_cmd_inputspec_9b[slurm-result_submitter] _______________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputspec_9b_sl1'), plugin = 'slurm'
results_function = <function result_submitter at 0x2b2148cb3290>

    @pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
    def test_shell_cmd_inputspec_9b(tmpdir, plugin, results_function):
        """
            providing output name using input_spec (output_file_template in metadata)
            and the keep_extension is set to False, so the extension is removed completely,
            no suffix in the template.
        """
        cmd = "cp"
        file = tmpdir.join("file.txt")
        file.write("content")

        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "file_orig",
                    attr.ib(
                        type=File,
                        metadata={"position": 2, "help_string": "new file", "argstr": ""},
                    ),
                ),
                (
                    "file_copy",
                    attr.ib(
                        type=str,
                        metadata={
                            "output_file_template": "{file_orig}",
                            "keep_extension": False,
                            "help_string": "output file",
                            "argstr": "",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        shelly = ShellCommandTask(
            name="shelly", executable=cmd, input_spec=my_input_spec, file_orig=file
        )

        res = results_function(shelly, plugin, tmpdir)
        assert res.output.stdout == ""
        assert res.output.file_copy.exists()
>       assert res.output.file_copy.name == "file"
E       AssertionError: assert 'vast-storage' == 'file'
E         - file
E         + vast-storage

pydra/engine/tests/test_shelltask.py:1272: AssertionError
============================================================================ short test summary info =============================================================================
FAILED pydra/engine/tests/test_shelltask.py::test_shell_cmd_inputspec_9[slurm-result_no_submitter] - AssertionError: assert 'file.txt' == 'file_copy.txt'
FAILED pydra/engine/tests/test_shelltask.py::test_shell_cmd_inputspec_9[slurm-result_submitter] - AssertionError: assert 'file.txt' == 'file_copy.txt'
FAILED pydra/engine/tests/test_shelltask.py::test_shell_cmd_inputspec_9a[slurm-result_no_submitter] - AssertionError: assert 'vast-storage_copy' == 'file_copy'
FAILED pydra/engine/tests/test_shelltask.py::test_shell_cmd_inputspec_9a[slurm-result_submitter] - AssertionError: assert 'vast-storage_copy' == 'file_copy'
FAILED pydra/engine/tests/test_shelltask.py::test_shell_cmd_inputspec_9b[slurm-result_no_submitter] - AssertionError: assert 'vast-storage' == 'file'
FAILED pydra/engine/tests/test_shelltask.py::test_shell_cmd_inputspec_9b[slurm-result_submitter] - AssertionError: assert 'vast-storage' == 'file'
======================================================== 6 failed, 109 passed, 1 skipped, 2 xfailed in 224.84s (0:03:44) =========================================================

[djarecka]

yes, something is definitely wrong

[nicolocin]

@djarecka - I see, should I create a separate issue for this? Seems like the same issue with these tests

FAILED pydra/engine/tests/test_shelltask_inputspec.py::test_shell_cmd_inputs_template_7 - AssertionError: assert ('executable '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo...
FAILED pydra/engine/tests/test_shelltask_inputspec.py::test_shell_cmd_inputs_template_7a - AssertionError: assert ('executable '\n '/net/vast-storage.ib.cluster/scratch/Thu/nl...
FAILED pydra/engine/tests/test_shelltask_inputspec.py::test_shell_cmd_inputs_template_7b - AssertionError: assert ('executable '\n '/net/vast-storage.ib.cluster/scratch/Thu/nl...
FAILED pydra/engine/tests/test_shelltask_inputspec.py::test_shell_cmd_inputs_template_8 - AssertionError: assert ('executable '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo...
FAILED pydra/engine/tests/test_shelltask_inputspec.py::test_shell_cmd_inputs_di - AssertionError: assert ('DenoiseImage -i '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo/tm..

Sample error code:

_______________________________________________________________________ test_shell_cmd_inputs_template_7b ________________________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template2')

    def test_shell_cmd_inputs_template_7b(tmpdir):
        """ additional inputs uses output_file_template with a suffix (no extension)
        keep extension is False (so the extension is removed when creating the output)
        """
        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "inpA",
                    attr.ib(
                        type=File,
                        metadata={
                            "position": 1,
                            "help_string": "inpA",
                            "argstr": "",
                            "mandatory": True,
                        },
                    ),
                ),
                (
                    "outA",
                    attr.ib(
                        type=str,
                        metadata={
                            "position": 2,
                            "help_string": "outA",
                            "argstr": "",
                            "keep_extension": False,
                            "output_file_template": "{inpA}_out",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        inpA_file = tmpdir.join("a_file.txt")
        inpA_file.write("content")
        shelly = ShellCommandTask(
            executable="executable", input_spec=my_input_spec, inpA=inpA_file
        )

        # outA should be formatted in a way that that .txt goes to the end
>       assert (
            shelly.cmdline
            == f"executable {tmpdir.join('a_file.txt')} {str(shelly.output_dir / 'a_file_out')}"
        )
E       AssertionError: assert ('executable '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template2/a_file.txt '\n '/tmp/tmp0b_yq0ba/ShellCommandTask_667f839bced051cf9f8f00a8f4dfc7ec7e46e838d2778d9c6f47f47db3ef0860/vast-storage_out') == ('executable '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template2/a_file.txt '\n '/tmp/tmp0b_yq0ba/ShellCommandTask_667f839bced051cf9f8f00a8f4dfc7ec7e46e838d2778d9c6f47f47db3ef0860/a_file_out')
E         - executable /net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template2/a_file.txt /tmp/tmp0b_yq0ba/ShellCommandTask_667f839bced051cf9f8f00a8f4dfc7ec7e46e838d2778d9c6f47f47db3ef0860/a_file_out
E         ?                                                                                                                                                                                                               ^^^^^^^^^^
E         + executable /net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template2/a_file.txt /tmp/tmp0b_yq0ba/ShellCommandTask_667f839bced051cf9f8f00a8f4dfc7ec7e46e838d2778d9c6f47f47db3ef0860/vast-storage_out
E         ?                                                                                                                                                                                                               ^^^^^^^^^^^^^^^^

pydra/engine/tests/test_shelltask_inputspec.py:1178: AssertionError
________________________________________________________________________ test_shell_cmd_inputs_template_8 ________________________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template3')

    def test_shell_cmd_inputs_template_8(tmpdir):
        """additional inputs uses output_file_template with a suffix and an extension"""
        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "inpA",
                    attr.ib(
                        type=File,
                        metadata={
                            "position": 1,
                            "help_string": "inpA",
                            "argstr": "",
                            "mandatory": True,
                        },
                    ),
                ),
                (
                    "outA",
                    attr.ib(
                        type=str,
                        metadata={
                            "position": 2,
                            "help_string": "outA",
                            "argstr": "",
                            "output_file_template": "{inpA}_out.txt",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        inpA_file = tmpdir.join("a_file.t")
        inpA_file.write("content")
        shelly = ShellCommandTask(
            executable="executable", input_spec=my_input_spec, inpA=inpA_file
        )

        # outA should be formatted in a way that inpA extension is removed and the template extension is used
>       assert (
            shelly.cmdline
            == f"executable {tmpdir.join('a_file.t')} {str(shelly.output_dir / 'a_file_out.txt')}"
        )
E       AssertionError: assert ('executable '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template3/a_file.t '\n '/tmp/tmp92b2a_ex/ShellCommandTask_667f839bced051cf9f8f00a8f4dfc7ec7e46e838d2778d9c6f47f47db3ef0860/vast-storage_out.txt') == ('executable '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template3/a_file.t '\n '/tmp/tmp92b2a_ex/ShellCommandTask_667f839bced051cf9f8f00a8f4dfc7ec7e46e838d2778d9c6f47f47db3ef0860/a_file_out.txt')
E         - executable /net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template3/a_file.t /tmp/tmp92b2a_ex/ShellCommandTask_667f839bced051cf9f8f00a8f4dfc7ec7e46e838d2778d9c6f47f47db3ef0860/a_file_out.txt
E         ?                                                                                                                                                                                                             ^^^^^
E         + executable /net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_template3/a_file.t /tmp/tmp92b2a_ex/ShellCommandTask_667f839bced051cf9f8f00a8f4dfc7ec7e46e838d2778d9c6f47f47db3ef0860/vast-storage_out.txt
E         ?                                                                                                                                                                                                             ^^^^^^^^^^^

pydra/engine/tests/test_shelltask_inputspec.py:1224: AssertionError
____________________________________________________________________________ test_shell_cmd_inputs_di ____________________________________________________________________________

tmpdir = local('/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_di0'), use_validator = None

    def test_shell_cmd_inputs_di(tmpdir, use_validator):
        """ example from #279 """
        my_input_spec = SpecInfo(
            name="Input",
            fields=[
                (
                    "image_dimensionality",
                    attr.ib(
                        type=int,
                        metadata={
                            "help_string": """
                        2/3/4
                        This option forces the image to be treated as a specified-dimensional image.
                        If not specified, the program tries to infer the dimensionality from
                        the input image.
                        """,
                            "allowed_values": [2, 3, 4],
                            "argstr": "-d",
                        },
                    ),
                ),
                (
                    "inputImageFilename",
                    attr.ib(
                        type=File,
                        metadata={
                            "help_string": "A scalar image is expected as input for noise correction.",
                            "argstr": "-i",
                            "mandatory": True,
                        },
                    ),
                ),
                (
                    "noise_model",
                    attr.ib(
                        type=str,
                        metadata={
                            "help_string": """
                        Rician/(Gaussian)
                        Employ a Rician or Gaussian noise model.
                        """,
                            "allowed_values": ["Rician", "Gaussian"],
                            "argstr": "-n",
                        },
                    ),
                ),
                (
                    "maskImageFilename",
                    attr.ib(
                        type=str,
                        metadata={
                            "help_string": "If a mask image is specified, denoising is only performed in the mask region.",
                            "argstr": "-x",
                        },
                    ),
                ),
                (
                    "shrink_factor",
                    attr.ib(
                        type=int,
                        default=1,
                        metadata={
                            "help_string": """
                        (1)/2/3/...
                        Running noise correction on large images can be time consuming.
                        To lessen computation time, the input image can be resampled.
                        The shrink factor, specified as a single integer, describes this
                        resampling. Shrink factor = 1 is the default.
                        """,
                            "argstr": "-s",
                        },
                    ),
                ),
                (
                    "patch_radius",
                    attr.ib(
                        type=int,
                        default=1,
                        metadata={
                            "help_string": "Patch radius. Default = 1x1x1",
                            "argstr": "-p",
                        },
                    ),
                ),
                (
                    "search_radius",
                    attr.ib(
                        type=int,
                        default=2,
                        metadata={
                            "help_string": "Search radius. Default = 2x2x2.",
                            "argstr": "-r",
                        },
                    ),
                ),
                (
                    "correctedImage",
                    attr.ib(
                        type=str,
                        metadata={
                            "help_string": """
                        The output consists of the noise corrected version of the input image.
                        Optionally, one can also output the estimated noise image.
                        """,
                            "output_file_template": "{inputImageFilename}_out",
                        },
                    ),
                ),
                (
                    "noiseImage",
                    attr.ib(
                        type=ty.Union[str, bool],
                        default=False,
                        metadata={
                            "help_string": """
                        The output consists of the noise corrected version of the input image.
                        Optionally, one can also output the estimated noise image.
                        """,
                            "output_file_template": "{inputImageFilename}_noise",
                        },
                    ),
                ),
                (
                    "output",
                    attr.ib(
                        type=str,
                        metadata={
                            "help_string": "Combined output",
                            "argstr": "-o [{correctedImage}, {noiseImage}]",
                            "position": -1,
                            "readonly": True,
                        },
                    ),
                ),
                (
                    "version",
                    attr.ib(
                        type=bool,
                        default=False,
                        metadata={
                            "help_string": "Get Version Information.",
                            "argstr": "--version",
                        },
                    ),
                ),
                (
                    "verbose",
                    attr.ib(
                        type=int,
                        default=0,
                        metadata={"help_string": "(0)/1. Verbose output. ", "argstr": "-v"},
                    ),
                ),
                (
                    "help_short",
                    attr.ib(
                        type=bool,
                        default=False,
                        metadata={
                            "help_string": "Print the help menu (short version)",
                            "argstr": "-h",
                        },
                    ),
                ),
                (
                    "help",
                    attr.ib(
                        type=int,
                        metadata={
                            "help_string": "Print the help menu.",
                            "argstr": "--help",
                        },
                    ),
                ),
            ],
            bases=(ShellSpec,),
        )

        my_input_file = tmpdir.join("a_file.ext")
        my_input_file.write("content")

        # no input provided
        shelly = ShellCommandTask(executable="DenoiseImage", input_spec=my_input_spec)
        with pytest.raises(Exception) as e:
            shelly.cmdline
        assert "mandatory" in str(e.value)

        # input file name, noiseImage is not set, so using default value False
        shelly = ShellCommandTask(
            executable="DenoiseImage",
            inputImageFilename=my_input_file,
            input_spec=my_input_spec,
        )
>       assert (
            shelly.cmdline
            == f"DenoiseImage -i {tmpdir.join('a_file.ext')} -s 1 -p 1 -r 2 -o [{str(shelly.output_dir / 'a_file_out.ext')}]"
        )
E       AssertionError: assert ('DenoiseImage -i '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_di0/a_file.ext '\n '-s 1 -p 1 -r 2 -o '\n '[/tmp/tmp94sb2fnv/ShellCommandTask_73e97c2e37db10b0beab1524ba6041f9729fab3f4fa509464aede51b4105fd84/a_file.ext]') == ('DenoiseImage -i '\n '/net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_di0/a_file.ext '\n '-s 1 -p 1 -r 2 -o '\n '[/tmp/tmp94sb2fnv/ShellCommandTask_73e97c2e37db10b0beab1524ba6041f9729fab3f4fa509464aede51b4105fd84/a_file_out.ext]')
E         - DenoiseImage -i /net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_di0/a_file.ext -s 1 -p 1 -r 2 -o [/tmp/tmp94sb2fnv/ShellCommandTask_73e97c2e37db10b0beab1524ba6041f9729fab3f4fa509464aede51b4105fd84/a_file_out.ext]
E         ?                                                                                                                                                                                                                                       ----
E         + DenoiseImage -i /net/vast-storage.ib.cluster/scratch/Thu/nlo/tmpdir2/test_shell_cmd_inputs_di0/a_file.ext -s 1 -p 1 -r 2 -o [/tmp/tmp94sb2fnv/ShellCommandTask_73e97c2e37db10b0beab1524ba6041f9729fab3f4fa509464aede51b4105fd84/a_file.ext]

pydra/engine/tests/test_shelltask_inputspec.py:1424: AssertionError

[djarecka]

I'm not completely sure if all the test have the same issue. Could you debug it a bit? I'd start from testing the cmdline first