[Debian-med-packaging] Bug#954496: python-humanfriendly is fixed but there is a remaining (or new) test suite error

[Andreas Tille]

Hi Michael,

I checked the situation in cwltool git and got:


=================================== FAILURES ===================================
_____________________ test_load_graph_fragment_from_packed _____________________
[gw2] linux -- Python 3.7.7 /usr/bin/python3.7

    def test_load_graph_fragment_from_packed():
        """Loading a fragment from packed with update."""
        loadingContext = LoadingContext()
        uri = Path(get_data("tests/wf/packed-with-loadlisting.cwl")).as_uri() + "#main"
        try:
            with open(get_data("cwltool/extensions.yml"), "r") as res:
                use_custom_schema("v1.0", "http://commonwl.org/cwltool", res.read())
    
            # The updater transforms LoadListingRequirement from an
            # extension (in v1.0) to a core feature (in v1.1) but there
            # was a bug when loading a packed workflow and loading a
            # specific fragment it would get the un-updated document.
            # This recreates that case and asserts that we are using the
            # updated document like we should.
    
>           tool = load_tool(uri, loadingContext)

cwltool/tests/test_load_tool.py:105: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
cwltool/load_tool.py:436: in load_tool
    return make_tool(uri, loadingContext)
cwltool/load_tool.py:414: in make_tool
    tool = loadingContext.construct_tool_object(processobj, loadingContext)
cwltool/workflow.py:61: in default_make_tool
    return Workflow(toolpath_object, loadingContext)
cwltool/workflow.py:716: in __init__
    step, index, loadingContext, loadingContext.prov_obj
cwltool/workflow.py:762: in make_workflow_step
    return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <cwltool.workflow.WorkflowStep object at 0x7fa566554590>
toolpath_object = ordereddict([('in', [ordereddict([('source', 'file:///build/cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loa...step.cwl'), ('id', 'file:///build/cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl#main/step1')])
pos = 0
loadingContext = <cwltool.context.LoadingContext object at 0x7fa5665a8e10>
parentworkflowProv = None

    def __init__(
        self,
        toolpath_object,  # type: Dict[str, Any]
        pos,  # type: int
        loadingContext,  # type: LoadingContext
        parentworkflowProv=None,  # type: Optional[ProvenanceProfile]
    ):  # type: (...) -> None
        """Initialize this WorkflowStep."""
        if "id" in toolpath_object:
            self.id = toolpath_object["id"]
        else:
            self.id = "#step" + str(pos)
    
        loadingContext = loadingContext.copy()
    
        loadingContext.requirements = copy.deepcopy(
            getdefault(loadingContext.requirements, [])
        )
        assert loadingContext.requirements is not None  # nosec
        loadingContext.requirements.extend(toolpath_object.get("requirements", []))
        loadingContext.requirements.extend(
            get_overrides(getdefault(loadingContext.overrides_list, []), self.id).get(
                "requirements", []
            )
        )
    
        hints = copy.deepcopy(getdefault(loadingContext.hints, []))
        hints.extend(toolpath_object.get("hints", []))
        loadingContext.hints = hints
    
        try:
            if isinstance(toolpath_object["run"], MutableMapping):
                self.embedded_tool = loadingContext.construct_tool_object(
                    toolpath_object["run"], loadingContext
                )  # type: Process
            else:
                loadingContext.metadata = {}
                self.embedded_tool = load_tool(toolpath_object["run"], loadingContext)
        except validate.ValidationException as vexc:
            if loadingContext.debug:
                _logger.exception("Validation exception")
            raise WorkflowException(
                "Tool definition %s failed validation:\n%s"
                % (toolpath_object["run"], indent(str(vexc)))
>           ) from vexc
E           cwltool.errors.WorkflowException: Tool definition file:///build/cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl#16169-step.cwl failed validation:
E           ../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl:3:9:    checking object
E                                                                                                      `../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl#main`
E           ../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl:5:11:     checking field
E                                                                                                        `requirements`
E           ../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl:6:13:       checking item
E           ../../../../cwltool-3.0.20200324120055%2Bdfsg/tests/wf/packed-with-loadlisting.cwl:8:15:         Field `class`
E                                                                                                            contains undefined
E                                                                                                            reference to
E                                                                                                            `http://commonwl.org/cwltool#LoadListingRequirement`

cwltool/workflow.py:850: WorkflowException
=============================== warnings summary ===============================
/usr/lib/python3/dist-packages/rdflib/plugins/sparql/compat.py:8
/usr/lib/python3/dist-packages/rdflib/plugins/sparql/compat.py:8
  /usr/lib/python3/dist-packages/rdflib/plugins/sparql/compat.py:8: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working
    from collections import Mapping, MutableMapping  # was added in 2.6

-- Docs: https://docs.pytest.org/en/latest/warnings.html
======== 1 failed, 224 passed, 100 skipped, 2 warnings in 90.13 seconds ========
E: pybuild pybuild:352: test: plugin custom failed with: exit code=1: cd /build/cwltool-3.0.20200324120055+dfsg; export PATH=/build/cwltool-3.0.20200324120055+dfsg/debian/python3-cwltool/usr/bin:/usr/sbin:/usr/b


can you have a look?

Kind regards

       Andreas.

----- Forwarded message from Debian testing autoremoval watch <noreply at release.debian.org> -----

Date: Mon, 30 Mar 2020 04:39:17 +0000
From: Debian testing autoremoval watch <noreply at release.debian.org>
To: cwltool at packages.debian.org
Subject: cwltool is marked for autoremoval from testing

cwltool 2.0.20200224214940+dfsg-1 is marked for autoremoval from testing on 2020-05-05

It is affected by these RC bugs:
954496: cwltool: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.7 3.8" returned exit code 13


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