Bug 2273607

python-bluepyopt fails to build with pytest 8.


=================================== FAILURES ===================================
_________________ TestNrnSectionCompLocation.test_instantiate __________________

self = <bluepyopt.tests.test_ephys.test_locations.TestNrnSectionCompLocation object at 0x7f9fed13ee70>

    def test_instantiate(self):
        """ephys.locations.NrnSomaDistanceCompLocation: test instantiate"""
    
        # Create a little test class with a soma and two dendritic sections
        class Cell(object):
    
            """Cell class"""
            pass
        cell = Cell()
>       soma = self.sim.neuron.h.Section()
E       AttributeError: 'TestNrnSectionCompLocation' object has no attribute 'sim'

bluepyopt/tests/test_ephys/test_locations.py:68: AttributeError
_________________ TestNrnSeclistCompLocation.test_instantiate __________________

self = <bluepyopt.tests.test_ephys.test_locations.TestNrnSeclistCompLocation object at 0x7f9fed13fe00>

    def test_instantiate(self):
        """ephys.locations.NrnSeclistCompLocation: test instantiate"""
    
        # Create a little test class with a soma and two dendritic sections
        class Cell(object):
            """Cell class"""
            pass
    
        cell = Cell()
>       soma = self.sim.neuron.h.Section()
E       AttributeError: 'TestNrnSeclistCompLocation' object has no attribute 'sim'

bluepyopt/tests/test_ephys/test_locations.py:111: AttributeError
__________________ TestNrnSeclistSecLocation.test_instantiate __________________

self = <bluepyopt.tests.test_ephys.test_locations.TestNrnSeclistSecLocation object at 0x7f9fed13ecf0>

    def test_instantiate(self):
        """ephys.locations.NrnSeclistSecLocation: test instantiate"""
    
        # Create a little test class with a soma and two dendritic sections
        class Cell(object):
            """Cell class"""
            pass
    
        cell = Cell()
>       soma = self.sim.neuron.h.Section()
E       AttributeError: 'TestNrnSeclistSecLocation' object has no attribute 'sim'

bluepyopt/tests/test_ephys/test_locations.py:158: AttributeError
_______________ TestNrnSomaDistanceCompLocation.test_instantiate _______________

self = <bluepyopt.tests.test_ephys.test_locations.TestNrnSomaDistanceCompLocation object at 0x7f9fed13ddf0>

    def test_instantiate(self):
        """ephys.locations.NrnSomaDistanceCompLocation: test instantiate"""
    
        # Create a little test class with a soma and two dendritic sections
        class Cell(object):
    
            """Cell class"""
            pass
        cell = Cell()
>       soma = self.sim.neuron.h.Section()
E       AttributeError: 'TestNrnSomaDistanceCompLocation' object has no attribute 'sim'

bluepyopt/tests/test_ephys/test_locations.py:198: AttributeError
_____________ TestNrnSecSomaDistanceCompLocation.test_instantiate ______________

self = <bluepyopt.tests.test_ephys.test_locations.TestNrnSecSomaDistanceCompLocation object at 0x7f9fed13e6c0>

    def test_instantiate(self):
        """ephys.locations.NrnSomaDistanceCompLocation: test instantiate"""
    
        # Create a little test class with a soma and two dendritic sections
        class Cell(object):
    
            """Cell class"""
            pass
        cell = Cell()
>       soma = self.sim.neuron.h.Section(name="soma[0]")
E       AttributeError: 'TestNrnSecSomaDistanceCompLocation' object has no attribute 'sim'

bluepyopt/tests/test_ephys/test_locations.py:248: AttributeError
____________ TestNrnTrunkSomaDistanceCompLocation.test_instantiate _____________

self = <bluepyopt.tests.test_ephys.test_locations.TestNrnTrunkSomaDistanceCompLocation object at 0x7f9fed13f350>

    def test_instantiate(self):
        """ephys.locations.NrnSomaDistanceCompLocation: test instantiate"""
    
        # Create a little test class with a soma and two dendritic sections
        class Cell(object):
    
            """Cell class"""
            pass
        cell = Cell()
>       soma = self.sim.neuron.h.Section(name="soma[0]")
E       AttributeError: 'TestNrnTrunkSomaDistanceCompLocation' object has no attribute 'sim'

bluepyopt/tests/test_ephys/test_locations.py:303: AttributeError
=============================== warnings summary ===============================
bluepyopt/ephys/create_acc.py:341
  /builddir/build/BUILD/BluePyOpt-6679d3cba959787e253d4667d61e81628c557a55/bluepyopt/ephys/create_acc.py:341: SyntaxWarning: invalid escape sequence '\s'
    nmodl_pattern = '^\s*%s\s+((?:\w+\,\s*)*?\w+)\s*?$'  # NOQA

bluepyopt/tests/test_deapext/test_hype.py::test_hypeIndicatorExact
  /builddir/build/BUILD/BluePyOpt-6679d3cba959787e253d4667d61e81628c557a55/bluepyopt/deapext/hype.py:71: RuntimeWarning: divide by zero encountered in divide
    alpha.append(numpy.prod((k - j) / (Ps - j) / i))

bluepyopt/tests/test_deapext/test_hype.py::test_hypeIndicatorSampled
  /builddir/build/BUILD/BluePyOpt-6679d3cba959787e253d4667d61e81628c557a55/bluepyopt/deapext/hype.py:101: RuntimeWarning: divide by zero encountered in divide
    alpha.append(numpy.prod((k - j) / (nrP - j) / i))

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED bluepyopt/tests/test_ephys/test_locations.py::TestNrnSectionCompLocation::test_instantiate
FAILED bluepyopt/tests/test_ephys/test_locations.py::TestNrnSeclistCompLocation::test_instantiate
FAILED bluepyopt/tests/test_ephys/test_locations.py::TestNrnSeclistSecLocation::test_instantiate
FAILED bluepyopt/tests/test_ephys/test_locations.py::TestNrnSomaDistanceCompLocation::test_instantiate
FAILED bluepyopt/tests/test_ephys/test_locations.py::TestNrnSecSomaDistanceCompLocation::test_instantiate
FAILED bluepyopt/tests/test_ephys/test_locations.py::TestNrnTrunkSomaDistanceCompLocation::test_instantiate
=========== 6 failed, 157 passed, 20 deselected, 3 warnings in 6.93s ===========

https://docs.pytest.org/en/stable/changelog.html

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/thrnciar/pytest/fedora-rawhide-x86_64/07247811-python-bluepyopt/

For all our attempts to build python-bluepyopt with pytest 8, see:
https://copr.fedorainfracloud.org/coprs/thrnciar/pytest/package/python-bluepyopt/

Let us know here if you have any questions.

Pytest 8 is planned to be included in Fedora 41. And this bugzilla is a
heads up before we merge new pytest into rawhide. For more info see a Fedora Change
proposal https://fedoraproject.org/wiki/Changes/Pytest_8

We'd appreciate help from the people who know this package best,
but if you don't want to work on this now, let us know so we can try to work around it on our side.