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Test failed hdmf 1.5.0 #245

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lbazan opened this issue Jan 8, 2020 · 10 comments
Closed

Test failed hdmf 1.5.0 #245

lbazan opened this issue Jan 8, 2020 · 10 comments
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category: bug errors in the code or code behavior

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@lbazan
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lbazan commented Jan 8, 2020 •
edited by rly
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  • /usr/bin/python3 test.py -v
    ======================================================================
    2020-01-08 21:01:18,398 - INFO - running hdmf unit tests
    EEEEEEEEEEEEEEEEEEEEEEEEEEE
    [0;0;36mStatus:
    �[0;0;31mError: 27
    �[0;0;36mDescription:
    �[0;0;36mSummary:
    +------------------------------------------+-------+------+------+-------+
    | Test group/Test case | Count | Pass | Fail | Error |
    +------------------------------------------+-------+------+------+-------+
    unittest.loader._FailedTest 27 0 0 27
    Total 27 0 0 27
    +------------------------------------------+-------+------+------+-------+
    unittest.loader._FailedTest 
      +-----------------------------+--------+-------------+
  |          Test name          | Output |    Status   |
  +-----------------------------+--------+-------------+
  | test_1_1_0                  |        | �[0;0;31merror       |
  | test_io_build_builders      |        | �[0;0;31merror       |
  | test_io_manager             |        | �[0;0;31merror       |
  | test_io_map                 |        | �[0;0;31merror       |
  | test_io_map_data            |        | �[0;0;31merror       |
  | test_common                 |        | �[0;0;31merror       |
  | test_sparse                 |        | �[0;0;31merror       |
  | test_table                  |        | �[0;0;31merror       |
  | test_attribute_spec         |        | �[0;0;31merror       |
  | test_dataset_spec           |        | �[0;0;31merror       |
  | test_dtype_spec             |        | �[0;0;31merror       |
  | test_group_spec             |        | �[0;0;31merror       |
  | test_load_namespace         |        | �[0;0;31merror       |
  | test_ref_spec               |        | �[0;0;31merror       |
  | test_spec_catalog           |        | �[0;0;31merror       |
  | test_spec_write             |        | �[0;0;31merror       |
  | test_container              |        | �[0;0;31merror       |
  | test_io_hdf5                |        | �[0;0;31merror       |
  | test_io_hdf5_h5tools        |        | �[0;0;31merror       |
  | test_query                  |        | �[0;0;31merror       |
  | test_core_DataChunk         |        | �[0;0;31merror       |
  | test_core_DataChunkIterator |        | �[0;0;31merror       |
  | test_core_DataIO            |        | �[0;0;31merror       |
  | test_core_ShapeValidator    |        | �[0;0;31merror       |
  | test_docval                 |        | �[0;0;31merror       |
  | test_labelleddict           |        | �[0;0;31merror       |
  | test_validate               |        | �[0;0;31merror       |
  +-----------------------------+--------+-------------+
    �[0;0;31mERROR in test back_compat_tests.test_1_1_0 (unittest.loader._FailedTest):
    ImportError: Failed to import test module: back_compat_tests.test_1_1_0
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/back_compat_tests/test_1_1_0.py", line 5, in
    from tests.unit.test_io_hdf5_h5tools import _get_manager
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/test_io_hdf5_h5tools.py", line 18, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test build_tests.test_io_build_builders (unittest.loader._FailedTest):
    ImportError: Failed to import test module: build_tests.test_io_build_builders
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/build_tests/test_io_build_builders.py", line 2, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test build_tests.test_io_manager (unittest.loader._FailedTest):
    ImportError: Failed to import test module: build_tests.test_io_manager
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/build_tests/test_io_manager.py", line 5, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test build_tests.test_io_map (unittest.loader._FailedTest):
    ImportError: Failed to import test module: build_tests.test_io_map
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/build_tests/test_io_map.py", line 7, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test build_tests.test_io_map_data (unittest.loader._FailedTest):
    ImportError: Failed to import test module: build_tests.test_io_map_data
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/build_tests/test_io_map_data.py", line 5, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test common.test_common (unittest.loader._FailedTest):
    ImportError: Failed to import test module: common.test_common
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/common/test_common.py", line 2, in
    from hdmf.common import get_type_map
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test common.test_sparse (unittest.loader._FailedTest):
    ImportError: Failed to import test module: common.test_sparse
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/common/test_sparse.py", line 1, in
    from hdmf.common import CSRMatrix
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test common.test_table (unittest.loader._FailedTest):
    ImportError: Failed to import test module: common.test_table
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/common/test_table.py", line 1, in
    from hdmf.common import DynamicTable, VectorData, ElementIdentifiers, DynamicTableRegion
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test spec_tests.test_attribute_spec (unittest.loader._FailedTest):
    ImportError: Failed to import test module: spec_tests.test_attribute_spec
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/spec_tests/test_attribute_spec.py", line 4, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test spec_tests.test_dataset_spec (unittest.loader._FailedTest):
    ImportError: Failed to import test module: spec_tests.test_dataset_spec
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/spec_tests/test_dataset_spec.py", line 4, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test spec_tests.test_dtype_spec (unittest.loader._FailedTest):
    ImportError: Failed to import test module: spec_tests.test_dtype_spec
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/spec_tests/test_dtype_spec.py", line 2, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test spec_tests.test_group_spec (unittest.loader._FailedTest):
    ImportError: Failed to import test module: spec_tests.test_group_spec
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/spec_tests/test_group_spec.py", line 4, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test spec_tests.test_load_namespace (unittest.loader._FailedTest):
    ImportError: Failed to import test module: spec_tests.test_load_namespace
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/spec_tests/test_load_namespace.py", line 6, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test spec_tests.test_ref_spec (unittest.loader._FailedTest):
    ImportError: Failed to import test module: spec_tests.test_ref_spec
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/spec_tests/test_ref_spec.py", line 4, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test spec_tests.test_spec_catalog (unittest.loader._FailedTest):
    ImportError: Failed to import test module: spec_tests.test_spec_catalog
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/spec_tests/test_spec_catalog.py", line 4, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test spec_tests.test_spec_write (unittest.loader._FailedTest):
    ImportError: Failed to import test module: spec_tests.test_spec_write
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/spec_tests/test_spec_write.py", line 7, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test test_container (unittest.loader._FailedTest):
    ImportError: Failed to import test module: test_container
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/test_container.py", line 4, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test test_io_hdf5 (unittest.loader._FailedTest):
    ImportError: Failed to import test module: test_io_hdf5
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/test_io_hdf5.py", line 10, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test test_io_hdf5_h5tools (unittest.loader._FailedTest):
    ImportError: Failed to import test module: test_io_hdf5_h5tools
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/test_io_hdf5_h5tools.py", line 18, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test test_query (unittest.loader._FailedTest):
    ImportError: Failed to import test module: test_query
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/test_query.py", line 8, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test utils_test.test_core_DataChunk (unittest.loader._FailedTest):
    ImportError: Failed to import test module: utils_test.test_core_DataChunk
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/utils_test/test_core_DataChunk.py", line 5, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test utils_test.test_core_DataChunkIterator (unittest.loader._FailedTest):
    ImportError: Failed to import test module: utils_test.test_core_DataChunkIterator
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/utils_test/test_core_DataChunkIterator.py", line 4, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test utils_test.test_core_DataIO (unittest.loader._FailedTest):
    ImportError: Failed to import test module: utils_test.test_core_DataIO
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/utils_test/test_core_DataIO.py", line 6, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test utils_test.test_core_ShapeValidator (unittest.loader._FailedTest):
    ImportError: Failed to import test module: utils_test.test_core_ShapeValidator
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/utils_test/test_core_ShapeValidator.py", line 4, in
    from hdmf.common.table import DynamicTable, DynamicTableRegion, VectorData
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test utils_test.test_docval (unittest.loader._FailedTest):
    ImportError: Failed to import test module: utils_test.test_docval
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/utils_test/test_docval.py", line 4, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test utils_test.test_labelleddict (unittest.loader._FailedTest):
    ImportError: Failed to import test module: utils_test.test_labelleddict
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/utils_test/test_labelleddict.py", line 2, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    �[0;0;31mERROR in test validator_tests.test_validate (unittest.loader._FailedTest):
    ImportError: Failed to import test module: validator_tests.test_validate
    Traceback (most recent call last):
    File "/usr/lib64/python3.8/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
    File "/usr/lib64/python3.8/unittest/loader.py", line 377, in _get_module_from_name
    import(name)
    File "/builddir/build/BUILD/hdmf-1.5.0/tests/unit/validator_tests/test_validate.py", line 9, in
    from hdmf.testing import TestCase
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/init.py", line 1, in
    from .testcase import TestCase, TestH5RoundTripMixin # noqa: F401
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/testing/testcase.py", line 11, in
    from ..common import validate as common_validate, get_manager
    File "/builddir/build/BUILDROOT/python-hdmf-1.5.0-1.fc32.noarch/usr/lib/python3.8/site-packages/hdmf/common/init.py", line 112, in
    raise RuntimeError("Unable to load a TypeMap - no namespace file found")
    RuntimeError: Unable to load a TypeMap - no namespace file found
    ======================================================================
    2020-01-08 21:01:18,770 - INFO - Ran 27 tests - FAILED (errors=27)
@lbazan lbazan added the category: bug errors in the code or code behavior label Jan 8, 2020
@lbazan
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lbazan commented Jan 8, 2020

oh sorry the big letter... my apologize!

@lbazan
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lbazan commented Jan 8, 2020

Using hdmf 1.5.1 the test continue with error.

Cheers,

@rly
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rly commented Jan 8, 2020

Hi @lbazan, did you do a git clone or download the source? If from source, from where did you download it?

@lbazan
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lbazan commented Jan 8, 2020

Hi @lbazan, did you do a git clone or download the source? If from source, from where did you download it?

Download the tar.gz https://github.com/hdmf-dev/hdmf/archive/1.5.1.tar.gz

@rly
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rly commented Jan 8, 2020

HDMF uses git submodules, and unfortunately, when GitHub automatically makes archive files for each release, the archives do not include the submodule contents, which are necessary for using HDMF. See

To get around this, we release our own source tarball with each release. Here is the URL for 1.5.1, which includes the required submodule contents:
https://github.com/hdmf-dev/hdmf/releases/download/1.5.1/hdmf-1.5.1.tar.gz

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rly commented Jan 8, 2020

See #195 for more info.

@lbazan
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lbazan commented Jan 8, 2020

Hi @rly

The test run ok but only 1 issue

2020-01-08 21:46:26,757 - INFO - Ran 464 tests - FAILED (failures=1)
/usr/lib/python3.8/site-packages/pytz/init.py:515: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/share/zoneinfo/zone.tab' mode='r' encoding='UTF-8'>
common_timezones = [l.split()[2]
ResourceWarning: Enable tracemalloc to get the object allocation traceback

https://kojipkgs.fedoraproject.org//work/tasks/7163/40297163/build.log

Cheers,

@rly
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rly commented Jan 9, 2020

Thanks. It looks like HDMF works slightly differently under python 3.8 than 3.7, such that a test breaks. I'll look into it.

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rly commented Jan 9, 2020

Specifically, the numpy implementation of np.array appears to have changed. Previously, calling the np.array function on an object would call the __array__ attribute of the object. In DataIO, we override the __array__ method to handle that case. However, now, for some reason, np.array calls the __array_struct__ attribute of the object.

@rly rly mentioned this issue Jan 9, 2020
Merged
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rly commented Jan 11, 2020

This should now be fixed through #247 and #248.

@rly rly closed this as completed Jan 11, 2020
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