rly
commented
4 years ago @lbazan I noticed you might be running Python 3.9 beta. Do you know if this error occurs on your system with Python 3.8?
Closed lbazan closed 3 years ago
rly
commented
4 years ago @lbazan I noticed you might be running Python 3.9 beta. Do you know if this error occurs on your system with Python 3.8?
rly
commented
3 years ago Closing this issue because we cannot reproduce it. Please feel free to reopen it if it occurs again or you have more details about the error.
bendichter
commented
3 years ago @lbazan Thanks for testing on python 3.9! Last we checked there were a few core libraries we rely on that have not yet migrated. We've started automated tests for 3.9 and will include it as a supported python version as soon as all of our dependencies support it.
[0;0;31mERROR in test test_copy_h5py_dataset_h5dataio_input (test_io_hdf5_h5tools.H5IOTest): Traceback (most recent call last): File "/builddir/build/BUILD/hdmf-2.0.1/tests/unit/test_io_hdf5_h5tools.py", line 697, in test_copy_h5py_dataset_h5dataio_input self.assertTrue(isinstance(self.f.get('test_copy', getlink=True), HardLink)) AssertionError: False is not true [0;0;31mERROR in test test_link_h5py_dataset_h5dataio_input (test_io_hdf5_h5tools.H5IOTest): Traceback (most recent call last): File "/builddir/build/BUILD/hdmf-2.0.1/tests/unit/test_io_hdf5_h5tools.py", line 688, in test_link_h5py_dataset_h5dataio_input self.assertTrue(isinstance(self.f.get('test_softlink', getlink=True), SoftLink)) AssertionError: False is not true [0;0;31mERROR in test test_link_h5py_dataset_input (test_io_hdf5_h5tools.H5IOTest): Traceback (most recent call last): File "/builddir/build/BUILD/hdmf-2.0.1/tests/unit/test_io_hdf5_h5tools.py", line 671, in test_link_h5py_dataset_input self.assertTrue(isinstance(self.f.get('test_softlink', getlink=True), SoftLink)) AssertionError: False is not true test_io_hdf5_h5tools.HDF5IOInitFileExistsTest +------------------------------+--------+------------+ | Test name | Output | Status | +------------------------------+--------+------------+ | test_init_file_exists_ok | | [0;0;32mpass | | test_init_wminus_file_exists | | [0;0;32mpass | | test_init_x_file_exists | | [0;0;32mpass | +------------------------------+--------+------------+ test_io_hdf5_h5tools.HDF5IOInitNoFileTest +-------------------------+--------+------------+ | Test name | Output | Status | +-------------------------+--------+------------+ | test_init_no_file_ok | | [0;0;32mpass | | test_init_no_file_r | | [0;0;32mpass | | test_init_no_file_rplus | | [0;0;32mpass | +-------------------------+--------+------------+ test_io_hdf5_h5tools.HDF5IOMultiFileTest +------------------------------------+--------+------------+ | Test name | Output | Status | +------------------------------------+--------+------------+ | test_copy_file_with_external_links | | [0;0;32mpass | +------------------------------------+--------+------------+ test_io_hdf5_h5tools.HDF5IOReadBuilderClosed +------------------+--------+------------+ | Test name | Output | Status | +------------------+--------+------------+ | test_read_closed | | [0;0;32mpass | +------------------+--------+------------+ test_io_hdf5_h5tools.HDF5IOReadData +-------------------+--------+------------+ | Test name | Output | Status | +-------------------+--------+------------+ | test_read_file_ok | | [0;0;32mpass | | test_read_file_w | | [0;0;32mpass | +-------------------+--------+------------+ test_io_hdf5_h5tools.HDF5IOReadNoDataTest +-------------------------+--------+------------+ | Test name | Output | Status | +-------------------------+--------+------------+ | test_read_no_data_a | | [0;0;32mpass | | test_read_no_data_r | | [0;0;32mpass | | test_read_no_data_rplus | | [0;0;32mpass | +-------------------------+--------+------------+ test_io_hdf5_h5tools.HDF5IOWriteFileExists +------------------+--------+------------+ | Test name | Output | Status | +------------------+--------+------------+ | test_write_a | | [0;0;32mpass | | test_write_r | | [0;0;32mpass | | test_write_rplus | | [0;0;32mpass | | test_write_w | | [0;0;32mpass | +------------------+--------+------------+ test_io_hdf5_h5tools.HDF5IOWriteNoFile +------------------------------+--------+------------+ | Test name | Output | Status | +------------------------------+--------+------------+ | test_write_no_file_a_ok | | [0;0;32mpass | | test_write_no_file_w_ok | | [0;0;32mpass | | test_write_no_file_wminus_ok | | [0;0;32mpass | | test_write_no_file_x_ok | | [0;0;32mpass | +------------------------------+--------+------------+ test_io_hdf5_h5tools.TestBuildWriteLinkToLink +---------------------------------------------------------+--------+------------+ | Test name | Output | Status | +---------------------------------------------------------+--------+------------+ | test_external_link_to_external_link: | | [0;0;32mpass | | Test writing a file with external links to external | | | | links. | | | | test_external_link_to_soft_link: | | [0;0;32mpass | | Test writing a file with external links to external | | | | links. | | | +---------------------------------------------------------+--------+------------+ test_io_hdf5_h5tools.TestCacheSpec +-----------------+--------+------------+ | Test name | Output | Status | +-----------------+--------+------------+ | test_cache_spec | | [0;0;32mpass | +-----------------+--------+------------+ test_io_hdf5_h5tools.TestCloseLinks +-----------------------------------+--------+------------+ | Test name | Output | Status | +-----------------------------------+--------+------------+ | test_close_file_with_links | | [0;0;32mpass | | test_double_close_file_with_links | | [0;0;32mpass | +-----------------------------------+--------+------------+ test_io_hdf5_h5tools.TestCpdDatasetRefs +----------------+--------+------------+ | Test name | Output | Status | +----------------+--------+------------+ | test_roundtrip | | [0;0;32mpass | +----------------+--------+------------+ test_io_hdf5_h5tools.TestDatasetRefs +----------------+--------+------------+ | Test name | Output | Status | +----------------+--------+------------+ | test_roundtrip | | [0;0;32mpass | +----------------+--------+------------+ test_io_hdf5_h5tools.TestExport +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_append_data: | | [0;0;32mpass | | Test that exporting a written container after adding | | | | groups, links, and references to it works. | | | | test_append_external_link_copy_data: | | [0;0;32mpass | | Test that exporting a written container after adding a | | | | link with link_data=False copies the data. | | | | test_append_external_link_data: | | [0;0;32mpass | | Test that exporting a written container after adding a | | | | link with link_data=True creates external links. | | | | test_attr_reference: | | [0;0;32mpass | | Test that exporting a written file with attribute | | | | references maintains the references. | | | | test_basic: | | [0;0;32mpass | | Test that exporting a written container works. | | | | test_basic_container: | | [0;0;32mpass | | Test that exporting a written container, passing in the | | | | container arg, works. | | | | test_cache_spec: | | [0;0;32mpass | | Test that exporting with cache_spec works. | | | | test_container_part: | | [0;0;32mpass | | Test that exporting a part of a written container raises | | | | an error. | | | | test_container_unknown: | | [0;0;32mpass | | Test that exporting a container that did not come from | | | | the src_io object raises an error. | | | | test_export_cpd_dset_refs: | | [0;0;32mpass | | Test that exporting a written container with a compound | | | | dataset with references works. | | | | test_export_dset_refs: | | [0;0;32mpass | | Test that exporting a written container with a dataset | | | | of references works. | | | | test_export_io: | | [0;0;32mpass | | Test that exporting a written container using | | | | HDF5IO.export_io works. | | | | test_external_link_dataset: | | [0;0;32mpass | | Test that exporting a written file with external linked | | | | datasets maintains the links. | | | | test_external_link_group: | | [0;0;32mpass | | Test that exporting a written file with external linked | | | | groups maintains the links. | | | | test_external_link_link: | | [0;0;32mpass | | Test that exporting a written file with external links | | | | to external links maintains the links. | | | | test_non_HDF5_src_link_data_true: | | [0;0;32mpass | | Test that exporting with a src_io without a manager | | | | raises an error. | | | | test_non_manager_container: | | [0;0;32mpass | | Test that exporting with a src_io without a manager | | | | raises an error. | | | | test_pop_data: | | [0;0;32mpass | | Test that exporting a written container after removing | | | | an element from it works. | | | | test_pop_linked_group: | | [0;0;32mpass | | Test that exporting a written container after removing a | | | | linked element from it works. | | | | test_soft_link_dataset: | | [0;0;32mpass | | Test that exporting a written file with soft linked | | | | datasets keeps links within the file. | | | | test_soft_link_group: | | [0;0;32mpass | | Test that exporting a written file with soft linked | | | | groups keeps links within the file. | | | | test_wrong_mode: | | [0;0;32mpass | | Test that exporting with a src_io without a manager | | | | raises an error. | | | +--------------------------------------------------------------+--------+------------+ test_io_hdf5_h5tools.TestHDF5IO +------------------------+--------+------------+ | Test name | Output | Status | +------------------------+--------+------------+ | test_constructor | | [0;0;32mpass | | test_set_file_mismatch | | [0;0;32mpass | +------------------------+--------+------------+ test_io_hdf5_h5tools.TestLinkData +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_link_data_false: | | [0;0;32mpass | | Test that the argument link_data=False for write_builder | | | | copies the data. | | | | test_link_data_true: | | [0;0;32mpass | | Test that the argument link_data=True for write_builder | | | | creates an external link. | | | +--------------------------------------------------------------+--------+------------+ test_io_hdf5_h5tools.TestLoadNamespaces +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_load_namespaces_file_no_path: | | [0;0;32mpass | | Test that loading namespaces from an h5py.File not | | | | backed by a file on disk is OK and does not close the | | | | file. | | | | test_load_namespaces_file_path_matched: | | [0;0;32mpass | | Test that loading namespaces given an h5py.File and path | | | | is OK and does not close the file. | | | | test_load_namespaces_file_path_mismatched: | | [0;0;32mpass | | Test that loading namespaces given an h5py.File and path | | | | that are mismatched raises an error. | | | | test_load_namespaces_no_path_no_file: | | [0;0;32mpass | | Test that loading namespaces without a path or file | | | | raises an error. | | | | test_load_namespaces_none_version: | | [0;0;32mpass | | Test that reading a file with a cached namespace and | | | | None version works but raises a warning. | | | | test_load_namespaces_path: | | [0;0;32mpass | | Test that loading namespaces given a path is OK and | | | | returns the correct dictionary. | | | | test_load_namespaces_unversioned: | | [0;0;32mpass | | Test that reading a file with a cached, unversioned | | | | version works but raises a warning. | | | +--------------------------------------------------------------+--------+------------+ test_io_hdf5_h5tools.TestMultiWrite +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_double_write_new_manager: | | [0;0;32mpass | | Test writing to a container in write mode twice using a | | | | new manager without changing the container. | | | | test_double_write_same_manager: | | [0;0;32mpass | | Test writing to a container in write mode twice using | | | | the same manager without changing the container. | | | | test_write_add_append_bucket: | | [0;0;32mpass | | Test appending a container to a file. | | | | test_write_add_append_double_write: | | [0;0;32mpass | | Test using the same IO object to append a container to a | | | | file twice. | | | | test_write_add_write: | | [0;0;32mpass | | Test writing a container, adding to the in-memory | | | | container, then overwriting the same file. | | | +--------------------------------------------------------------+--------+------------+ test_io_hdf5_h5tools.TestNoCacheSpec +--------------------+--------+------------+ | Test name | Output | Status | +--------------------+--------+------------+ | test_no_cache_spec | | [0;0;32mpass | +--------------------+--------+------------+ test_io_hdf5_h5tools.TestReadLink +------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +------------------------------------------------------------+--------+------------+ | test_broken_link: | | [0;0;32mpass | | Test that opening a file with a broken link raises a | | | | warning but is still readable. | | | | test_broken_linked_data: | | [0;0;32mpass | | Test that opening a file with a broken link raises a | | | | warning but is still readable. | | | | test_link_to_link: | | [0;0;32mpass | | Test that link to link gets written and read properly | | | | test_set_link_loc: | | [0;0;32mpass | | Test that Builder location is set when it is read as a | | | | link | | | +------------------------------------------------------------+--------+------------+ test_io_hdf5_h5tools.TestRoundTrip +------------------------------+--------+------------+ | Test name | Output | Status | +------------------------------+--------+------------+ | test_roundtrip_basic | | [0;0;32mpass | | test_roundtrip_empty_dataset | | [0;0;32mpass | | test_roundtrip_empty_group | | [0;0;32mpass | +------------------------------+--------+------------+ test_io_hdf5_h5tools.TestWritten +-------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +-------------------------------------------------------------+--------+------------+ | test_set_written_on_write: | | [0;0;32mpass | | Test that write_builder changes the written flag of the | | | | builder and its children from False to True. | | | +-------------------------------------------------------------+--------+------------+ test_query.LinspaceQueryTest +-----------------------------------------------------+--------+------------+ | Test name | Output | Status | +-----------------------------------------------------+--------+------------+ | test_eq_: | | [0;0;32mpass | | Test wrapper equals magic method | | | | testge: | | [0;0;32mpass | | Test wrapper greater than or equal magic method | | | | testgetitem: | | [0;0;32mpass | | Test wrapper getitem using slice | | | | testgetitemquery: | | [0;0;32mpass | | Test wrapper getitem using query | | | | testgt: | | [0;0;32mpass | | Test wrapper greater than magic method | | | | testle: | | [0;0;32mpass | | Test wrapper less than or equal magic method | | | | testlt: | | [0;0;32mpass | | Test wrapper less than magic method | | | | testne: | | [0;0;32mpass | | Test wrapper not equal magic method | | | | test_get_dataset | | [0;0;32mpass | +-----------------------------------------------------+--------+------------+ testquery.SortedQueryTest +-----------------------------------------------------+--------+------------+ | Test name | Output | Status | +-----------------------------------------------------+--------+------------+ | testeq: | | [0;0;32mpass | | Test wrapper equals magic method | | | | testge: | | [0;0;32mpass | | Test wrapper greater than or equal magic method | | | | testgetitem: | | [0;0;32mpass | | Test wrapper getitem using slice | | | | testgetitemquery: | | [0;0;32mpass | | Test wrapper getitem using query | | | | testgt: | | [0;0;32mpass | | Test wrapper greater than magic method | | | | testle: | | [0;0;32mpass | | Test wrapper less than or equal magic method | | | | testlt__: | | [0;0;32mpass | | Test wrapper less than magic method | | | | test_ne: | | [0;0;32mpass | | Test wrapper not equal magic method | | | | test_get_dataset | | [0;0;32mpass | +-----------------------------------------------------+--------+------------+ utils_test.test_core_DataChunk.DataChunkTests +-------------------------+--------+------------+ | Test name | Output | Status | +-------------------------+--------+------------+ | test_datachunk_astype | | [0;0;32mpass | | test_datachunk_copy | | [0;0;32mpass | | test_datachunk_deepcopy | | [0;0;32mpass | +-------------------------+--------+------------+ utils_test.test_core_DataChunkIterator.DataChunkIteratorTests +-------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +-------------------------------------------------------------+--------+------------+ | test_custom_iter_first_axis | | [0;0;32mpass | | test_custom_iter_last_axis | | [0;0;32mpass | | test_custom_iter_middle_axis | | [0;0;32mpass | | test_custom_iter_mismatched_axis | | [0;0;32mpass | | test_dtype | | [0;0;32mpass | | test_list_none: | | [0;0;32mpass | | Test that DataChunkIterator has no dtype or chunks when | | | | given a list of None. | | | | test_list_none_dtype: | | [0;0;32mpass | | Test that DataChunkIterator has the passed-in dtype and | | | | no chunks when given a list of None. | | | | test_list_numpy_scalar | | [0;0;32mpass | | test_list_scalar | | [0;0;32mpass | | test_maxshape | | [0;0;32mpass | | test_multidimensional_list_first_axis: | | [0;0;32mpass | | Test DataChunkIterator with multidimensional list data, | | | | no buffering, and iterating on the first dimension. | | | | test_multidimensional_list_last_axis: | | [0;0;32mpass | | Test DataChunkIterator with multidimensional list data, | | | | no buffering, and iterating on the last dimension. | | | | test_multidimensional_list_middle_axis: | | [0;0;32mpass | | Test DataChunkIterator with multidimensional list data, | | | | no buffering, and iterating on a middle dimension. | | | | test_none_iter: | | [0;0;32mpass | | Test that DataChunkIterator init sets defaults | | | | correctly and all chunks and recommended shapes are | | | | None. | | | | test_numpy_iter_buffered_first_axis: | | [0;0;32mpass | | Test DataChunkIterator with numpy data, buffering, and | | | | iterating on the first dimension. | | | | test_numpy_iter_buffered_last_axis: | | [0;0;32mpass | | Test DataChunkIterator with numpy data, buffering, and | | | | iterating on the last dimension. | | | | test_numpy_iter_buffered_middle_axis: | | [0;0;32mpass | | Test DataChunkIterator with numpy data, buffering, and | | | | iterating on a middle dimension. | | | | test_numpy_iter_unbuffered_first_axis: | | [0;0;32mpass | | Test DataChunkIterator with numpy data, no buffering, | | | | and iterating on the first dimension. | | | | test_numpy_iter_unbuffered_last_axis: | | [0;0;32mpass | | Test DataChunkIterator with numpy data, no buffering, | | | | and iterating on the last dimension. | | | | test_numpy_iter_unbuffered_middle_axis: | | [0;0;32mpass | | Test DataChunkIterator with numpy data, no buffering, | | | | and iterating on a middle dimension. | | | | test_numpy_iter_unmatched_buffer_size | | [0;0;32mpass | | test_set_maxshape | | [0;0;32mpass | | test_sparse_data_buffer_aligned | | [0;0;32mpass | | test_sparse_data_buffer_notaligned | | [0;0;32mpass | | test_standard_iterator_unbuffered | | [0;0;32mpass | | test_standard_iterator_unmatched_buffersized | | [0;0;32mpass | | test_start_with_none | | [0;0;32mpass | +-------------------------------------------------------------+--------+------------+ utils_test.test_core_DataChunkIterator.DataChunkTests +-----------------------------+--------+------------+ | Test name | Output | Status | +-----------------------------+--------+------------+ | test_astype | | [0;0;32mpass | | test_dtype | | [0;0;32mpass | | test_len_operator_no_data | | [0;0;32mpass | | test_len_operator_with_data | | [0;0;32mpass | +-----------------------------+--------+------------+ utils_test.test_core_DataIO.DataIOTests +-------------------------------------------------+--------+------------+ | Test name | Output | Status | +-------------------------------------------------+--------+------------+ | test_copy | | [0;0;32mpass | | test_dataio_slice_delegation | | [0;0;32mpass | | test_deepcopy | | [0;0;32mpass | | test_set_dataio: | | [0;0;32mpass | | Test that Data.set_dataio works as intended | | | | test_set_dataio_data_already_set: | | [0;0;32mpass | | Test that Data.set_dataio works as intended | | | +-------------------------------------------------+--------+------------+ utils_test.test_core_ShapeValidator.ShapeValidatorResultTests +--------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------+--------+------------+ | test_default_message | | [0;0;32mpass | | test_ensure_use_of_tuples_during_asignment | | [0;0;32mpass | | test_set_error_to_illegal_type | | [0;0;32mpass | +--------------------------------------------+--------+------------+ utils_test.test_core_ShapeValidator.ShapeValidatorTests +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_DataChunkIterator_error_on_undetermined_axis | | [0;0;32mpass | | test_DataChunkIterator_ignore_undetermined_axis | | [0;0;32mpass | | test_DataChunkIterators_match | | [0;0;32mpass | | test_DynamicTableRegion_shape_validation | | [0;0;32mpass | | test_array_all_dimensions_match | | [0;0;32mpass | | test_array_axis_index_out_of_bounds_mutilple_axis | | [0;0;32mpass | | test_array_axis_index_out_of_bounds_single_axis | | [0;0;32mpass | | test_array_dimensions_mismatch | | [0;0;32mpass | | test_array_unequal_number_of_axes_for_comparison | | [0;0;32mpass | | test_array_unequal_number_of_dimensions | | [0;0;32mpass | | test_array_unequal_number_of_dimensions_check_multiple_axesy | | [0;0;32mpass | | test_array_unequal_number_of_dimensions_check_one_axis_only | | [0;0;32mpass | +--------------------------------------------------------------+--------+------------+ utils_test.test_docval.TestDocValidator +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_allow_positional_error | | [0;0;32mpass | | test_allow_positional_warn | | [0;0;32mpass | | test_bad_shape | | [0;0;32mpass | | test_bad_type | | [0;0;32mpass | | test_bool_string_type | | [0;0;32mpass | | test_bool_type | | [0;0;32mpass | | test_catch_dup_names: | | [0;0;32mpass | | Test that docval does not allow duplicate argument names | | | | test_docval_add: | | [0;0;32mpass | | Test that docval works with a single positional | | | | test_docval_add2: | | [0;0;32mpass | | Test that docval works with two positional | | | | test_docval_add2_kw_all_kw_syntax: | | [0;0;32mpass | | Test that docval works with two positional | | | | test_docval_add2_kw_default: | | [0;0;32mpass | | Test that docval works with two positional | | | | test_docval_add2_kw_default_sub: | | [0;0;32mpass | | Test that docval works with a four positional arguments | | | | and | | | | test_docval_add2_kw_default_sub_missing_args: | | [0;0;32mpass | | Test that docval catches missing arguments with a four | | | | positional arguments | | | | test_docval_add2_kw_kw_syntax: | | [0;0;32mpass | | Test that docval works with two positional | | | | test_docval_add2_kw_kwsyntax_sub: | | [0;0;32mpass | | Test that docval works when called with a four | | | | positional | | | | test_docval_add2_kw_kwsyntax_sub_missing_args: | | [0;0;32mpass | | Test that docval catches missing arguments when called | | | | with a four positional | | | | test_docval_add2_kw_kwsyntax_sub_nonetype_arg: | | [0;0;32mpass | | Test that docval catches NoneType when called with a | | | | four positional | | | | test_docval_add2_kw_pos_syntax: | | [0;0;32mpass | | Test that docval works with two positional | | | | test_docval_add2_kw_pos_syntax_missing_args: | | [0;0;32mpass | | Test that docval catches incorrect type with two | | | | positional | | | | test_docval_add2_pos_as_kw: | | [0;0;32mpass | | Test that docval works with two positional | | | | test_docval_add2_w_unicode: | | [0;0;32mpass | | Test that docval works with two positional | | | | test_docval_add_kw: | | [0;0;32mpass | | Test that docval works with a single positional | | | | test_docval_add_missing_args: | | [0;0;32mpass | | Test that docval catches missing argument | | | | test_docval_add_sub: | | [0;0;32mpass | | Test that docval works with a two positional arguments, | | | | test_dup_kw: | | [0;0;32mpass | | Test that docval raises an error if a keyword argument | | | | test_enum_bad_type: | | [0;0;32mpass | | Test that docval with an enum check where the arg type | | | | includes an invalid enum type fails | | | | test_enum_bool_mixed: | | [0;0;32mpass | | Test that the basic usage of an enum check on a tuple of | | | | bool, int, float, and string works | | | | test_enum_float: | | [0;0;32mpass | | Test that the basic usage of an enum check on floats | | | | works | | | | test_enum_forbidden_values: | | [0;0;32mpass | | Test that docval with enum values that include a | | | | forbidden type fails | | | | test_enum_int: | | [0;0;32mpass | | Test that the basic usage of an enum check on ints works | | | | test_enum_none_type: | | [0;0;32mpass | | Test that the basic usage of an enum check on None works | | | | test_enum_single_allowed: | | [0;0;32mpass | | Test that docval with an enum check on a single value | | | | fails | | | | test_enum_str: | | [0;0;32mpass | | Test that the basic usage of an enum check on strings | | | | works | | | | test_enum_str_default: | | [0;0;32mpass | | Test that docval with an enum check on strings and a | | | | default value works | | | | test_enum_str_none_default: | | [0;0;32mpass | | Test that docval with an enum check on strings and a | | | | None default value works | | | | test_enum_uint: | | [0;0;32mpass | | Test that the basic usage of an enum check on uints | | | | works | | | | test_extra_args_dup_kw: | | [0;0;32mpass | | Test that docval raises an error if a keyword argument | | | | test_extra_args_pos_kw: | | [0;0;32mpass | | Test that docval raises an error if too many positional | | | | test_extra_args_pos_kw_ok: | | [0;0;32mpass | | Test that docval does not raise an error if too many | | | | test_extra_args_pos_only: | | [0;0;32mpass | | Test that docval raises an error if too many positional | | | | test_extra_args_pos_only_ok: | | [0;0;32mpass | | Test that docval raises an error if too many positional | | | | test_extra_kwarg: | | [0;0;32mpass | | Test that docval parses arguments when only keyword | | | | test_extra_kwargs_pos_kw: | | [0;0;32mpass | | Test that docval raises an error if extra keyword | | | | test_fmt_docval_args: | | [0;0;32mpass | | Test that fmt_docval_args works | | | | test_fmt_docval_args_allow_extra: | | [0;0;32mpass | | Test that fmt_docval_args works | | | | test_fmt_docval_args_no_docval: | | [0;0;32mpass | | Test that fmt_docval_args raises an error when run on | | | | function without docval | | | | test_get_docval_all: | | [0;0;32mpass | | Test that get_docval returns a tuple of the docval | | | | arguments | | | | test_get_docval_missing_arg: | | [0;0;32mpass | | Test that get_docval throws error if the matching docval | | | | argument is not found | | | | test_get_docval_missing_arg_of_many_ok: | | [0;0;32mpass | | Test that get_docval throws error if the matching docval | | | | arguments is not found | | | | test_get_docval_missing_args: | | [0;0;32mpass | | Test that get_docval throws error if the matching docval | | | | arguments is not found | | | | test_get_docval_none: | | [0;0;32mpass | | Test that get_docval returns an empty tuple if there is | | | | no docval | | | | test_get_docval_none_arg: | | [0;0;32mpass | | Test that get_docval throws error if there is no docval | | | | and an argument name is passed | | | | test_get_docval_one_arg: | | [0;0;32mpass | | Test that get_docval returns the matching docval | | | | argument | | | | test_get_docval_two_args: | | [0;0;32mpass | | Test that get_docval returns the matching docval | | | | arguments in order | | | | test_multi_shape | | [0;0;32mpass | | test_only_kw_arg1_arg2: | | [0;0;32mpass | | Test that docval parses arguments when only keyword | | | | test_only_kw_arg1_arg2_pos: | | [0;0;32mpass | | Test that docval parses arguments when only keyword | | | | test_only_kw_arg1_no_arg2: | | [0;0;32mpass | | Test that docval parses arguments when only keyword | | | | test_only_kw_arg1_pos_no_arg2: | | [0;0;32mpass | | Test that docval parses arguments when only keyword | | | | test_only_kw_arg2_no_arg1: | | [0;0;32mpass | | Test that docval parses arguments when only keyword | | | | test_only_kw_no_args: | | [0;0;32mpass | | Test that docval parses arguments when only keyword | | | | test_uint_string_type: | | [0;0;32mpass | | Test that docval type specification of string 'uint' | | | | matches np.uint of all available precisions. | | | | test_uint_type: | | [0;0;32mpass | | Test that docval type specification of np.uint32 works | | | | as expected. | | | | test_unsupported_docval_term: | | [0;0;32mpass | | Test that docval does not allow setting of arguments | | | +--------------------------------------------------------------+--------+------------+ utils_test.test_docval.TestDocValidatorChain +-------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +-------------------------------------------------------------+--------+------------+ | test_shape_invalid_unpack: | | [0;0;32mpass | | Test that passing an object for an argument with | | | | required shape and object.argument has an invalid shape | | | | test_shape_invalid_unpack_default: | | [0;0;32mpass | | Test that passing an object for an argument with | | | | required shape and a default value and object.argument | | | | has | | | | test_shape_none_unpack: | | [0;0;32mpass | | Test that passing an object for an argument with | | | | required shape and object.argument is None is OK | | | | test_shape_none_unpack_default: | | [0;0;32mpass | | Test that passing an object for an argument with | | | | required shape and a default value and object.argument | | | | is | | | | test_shape_other_unpack: | | [0;0;32mpass | | Test that passing an object for an argument with | | | | required shape and object.argument is an object without | | | | test_shape_other_unpack_default: | | [0;0;32mpass | | Test that passing an object for an argument with | | | | required shape and a default value and object.argument | | | | is | | | | test_shape_valid_unpack: | | [0;0;32mpass | | Test that passing an object for an argument with | | | | required shape tests the shape of object.argument | | | | test_shape_valid_unpack_default: | | [0;0;32mpass | | Test that passing an object for an argument with | | | | required shape and a default value tests the shape of | | | | test_type_arg: | | [0;0;32mpass | | Test that passing an object for an argument that allows | | | | a specific type works | | | | test_type_arg_wrong_type: | | [0;0;32mpass | | Test that passing an object for an argument that does | | | | not match a specific type raises an error | | | +-------------------------------------------------------------+--------+------------+ utils_test.test_docval.TestGetargs +------------------------------+--------+------------+ | Test name | Output | Status | +------------------------------+--------+------------+ | test_arg_not_found_many_args | | [0;0;32mpass | | test_arg_not_found_one_arg | | [0;0;32mpass | | test_last_arg_not_dict | | [0;0;32mpass | | test_many_args_get_all | | [0;0;32mpass | | test_many_args_get_some | | [0;0;32mpass | | test_many_args_reverse | | [0;0;32mpass | | test_many_args_unpack | | [0;0;32mpass | | test_one_arg_first | | [0;0;32mpass | | test_one_arg_second | | [0;0;32mpass | | test_too_few_args | | [0;0;32mpass | +------------------------------+--------+------------+ utils_test.test_docval.TestPopargs +------------------------------+--------+------------+ | Test name | Output | Status | +------------------------------+--------+------------+ | test_arg_not_found_many_args | | [0;0;32mpass | | test_arg_not_found_one_arg | | [0;0;32mpass | | test_last_arg_not_dict | | [0;0;32mpass | | test_many_args_pop_all | | [0;0;32mpass | | test_many_args_pop_some | | [0;0;32mpass | | test_many_args_reverse | | [0;0;32mpass | | test_many_args_unpack | | [0;0;32mpass | | test_one_arg_first | | [0;0;32mpass | | test_one_arg_second | | [0;0;32mpass | | test_too_few_args | | [0;0;32mpass | +------------------------------+--------+------------+ utils_test.test_labelleddict.TestLabelledDict +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_add_basic: | | [0;0;32mpass | | Test add function on object with correct key_attr | | | | test_add_value_missing_key: | | [0;0;32mpass | | Test that add raises an error if the value being set | | | | does not have the attribute key_attr | | | | test_addval_getitem_eqeq: | | [0;0;32mpass | | Test that dict[key_attr == val] returns the single | | | | matching object | | | | test_addval_getitem_eqeq_unknown_key_val: | | [0;0;32mpass | | Test that dict[key_attr == val] where prop3 does not | | | | match any objects in the dict raises an error | | | | test_addval_getitem_eqeq_unknown_val: | | [0;0;32mpass | | Test that dict[key_attr == val] with an unknown val | | | | raises an error even if there are other objects in | | | | test_addval_getitem_other_key: | | [0;0;32mpass | | Test that dict[other_key == val] returns a list of | | | | matching objects | | | | test_addval_getitem_other_key_multi: | | [0;0;32mpass | | Test that dict[other_key == val] returns a list of | | | | matching objects | | | | test_addval_getitem_other_key_none: | | [0;0;32mpass | | Test that dict[other_key == val] raises an error if val | | | | does not equal any of the other_key attribute values | | | | test_constructor: | | [0;0;32mpass | | Test that constructor sets arguments properly | | | | test_constructor_default: | | [0;0;32mpass | | Test that constructor sets default key attribute | | | | test_getitem_eqeq_no_key_attr: | | [0;0;32mpass | | Test that dict[key_attr == val] raises an error if | | | | key_attr is not given | | | | test_getitem_eqeq_no_key_attr_no_val: | | [0;0;32mpass | | Test that dict[key_attr == val] raises an error if | | | | key_attr is not given and val is not given | | | | test_getitem_eqeq_no_val: | | [0;0;32mpass | | Test that dict[key_attr == val] raises an error if val | | | | is not given | | | | test_getitem_eqeq_other_key_attr: | | [0;0;32mpass | | Test that dict[key_attr == val] raises an error if there | | | | are no matches for other_attr == val | | | | test_getitem_eqeq_unknown_val: | | [0;0;32mpass | | Test that dict[key_attr == val] raises an error if there | | | | are no matches for val | | | | test_getitem_unknown_val: | | [0;0;32mpass | | Test that dict[val] raises an error if there are no | | | | matches for val | | | | test_set_key_attr: | | [0;0;32mpass | | Test that the key attribute cannot be set after | | | | initialization | | | | test_setitem_getitem_basic: | | [0;0;32mpass | | Test that setitem and getitem properly set and get the | | | | object | | | | test_setitem_value_missing_key: | | [0;0;32mpass | | Test that setitem raises an error if the value being set | | | | does not have the attribute key_attr | | | | test_setitem_value_wrong_value: | | [0;0;32mpass | | Test that setitem raises an error if the value being set | | | | has a different value for attribute key_attr | | | +--------------------------------------------------------------+--------+------------+ utils_test.test_utils.TestGetDataShape +-------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +-------------------------------------------------------------+--------+------------+ | test_arbitrary_iterable_with_len: | | [0;0;32mpass | | Test get_data_shape with strict_no_data_load=True on an | | | | arbitrary iterable object with len. | | | | test_dataio: | | [0;0;32mpass | | Test get_data_shape on DataIO of various shapes and | | | | maxshape. | | | | test_dci: | | [0;0;32mpass | | Test get_data_shape on DataChunkIterators of various | | | | shapes and maxshape. | | | | test_h5dataset: | | [0;0;32mpass | | Test get_data_shape on h5py.Datasets of various shapes | | | | and maxshape. | | | | test_list: | | [0;0;32mpass | | Test get_data_shape on lists of various shapes. | | | | test_nparray: | | [0;0;32mpass | | Test get_data_shape on numpy arrays of various shapes. | | | | test_other: | | [0;0;32mpass | | Test get_data_shape on miscellaneous edge cases. | | | | test_set: | | [0;0;32mpass | | Test get_data_shape on sets, which have len but are | | | | not subscriptable. | | | | test_strict_no_data_load: | | [0;0;32mpass | | Test get_data_shape with strict_no_data_load=True on | | | | nested lists/tuples is the same as when it is False. | | | | test_string: | | [0;0;32mpass | | Test get_data_shape on strings and collections of | | | | strings. | | | | test_tuple: | | [0;0;32mpass | | Test get_data_shape on tuples of various shapes. | | | +-------------------------------------------------------------+--------+------------+ validator_tests.test_validate.Test1DArrayValidation +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_empty_list: | | [0;0;32mpass | | Test that validator allows an empty list where an array | | | | is specified. | | | | test_empty_nparray: | | [0;0;32mpass | | Test that validator allows an empty numpy array where an | | | | array is specified. | | | | test_scalar: | | [0;0;32mpass | | Test that validator does not allow a scalar where an | | | | array is specified. | | | +--------------------------------------------------------------+--------+------------+ validator_tests.test_validate.TestBasicSpec +-------------------------------------------+--------+------------+ | Test name | Output | Status | +-------------------------------------------+--------+------------+ | test_invalid_incorrect_type_get_validator | | [0;0;32mpass | | test_invalid_incorrect_type_validate | | [0;0;32mpass | | test_invalid_missing | | [0;0;32mpass | | test_valid | | [0;0;32mpass | +-------------------------------------------+--------+------------+ validator_tests.test_validate.TestDateTimeInSpec +--------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------+--------+------------+ | test_invalid_isodatetime | | [0;0;32mpass | | test_invalid_isodatetime_array | | [0;0;32mpass | | test_valid_isodatetime | | [0;0;32mpass | +--------------------------------+--------+------------+ validator_tests.test_validate.TestDtypeValidation +--------------------------------------------------------------+--------+------------+ | Test name | Output | Status | +--------------------------------------------------------------+--------+------------+ | test_ascii_for_utf8: | | [0;0;32mpass | | Test that validator allows ASCII data where UTF8 is | | | | specified. | | | | test_bool_for_numeric: | | [0;0;32mpass | | Test that validator does not allow bool data where | | | | numeric is specified. | | | | test_int64_for_int8: | | [0;0;32mpass | | Test that validator allows int64 data where int8 is | | | | specified. | | | | test_int64_for_numeric: | | [0;0;32mpass | | Test that validator allows int64 data where numeric is | | | | specified. | | | | test_int8_for_int64: | | [0;0;32mpass | | Test that validator does not allow int8 data where int64 | | | | is specified. | | | | test_utf8_for_ascii: | | [0;0;32mpass | | Test that validator does not allow UTF8 where ASCII is | | | | specified. | | | +--------------------------------------------------------------+--------+------------+ validator_tests.test_validate.TestEmptySpec +-------------------------------+--------+------------+ | Test name | Output | Status | +-------------------------------+--------+------------+ | test_invalid_missing_req_type | | [0;0;32mpass | | test_valid | | [0;0;32mpass | +-------------------------------+--------+------------+ validator_tests.test_validate.TestNestedTypes +----------------------------------+--------+------------+ | Test name | Output | Status | +----------------------------------+--------+------------+ | test_invalid_missing_req_group | | [0;0;32mpass | | test_invalid_wrong_name_req_type | | [0;0;32mpass | | test_valid | | [0;0;32mpass | | test_valid_wo_opt_attr | | [0;0;32mpass | +----------------------------------+--------+------------+
2020-08-09 12:40:23,891 - INFO - Ran 692 tests - FAILED (errors=2,failures=3) RPM build errors:
[0;0;31mERROR in test test_append_1_0_5 (back_compat_tests.test_1_1_0.Test1_1_0): Traceback (most recent call last): File "/builddir/build/BUILD/hdmf-2.0.1/tests/unit/back_compat_tests/test_1_1_0.py", line 40, in test_append_1_0_5 read_foofile = io.read() File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 414, in read return call_docval_func(super().read, kwargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 404, in call_docval_func return func(*fargs, fkwargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 560, in func_call return func(args[0], pargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/io.py", line 32, in read f_builder = self.read_builder() File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 560, in func_call return func(args[0], pargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 431, in read_builder f_builder = self.read_group(self.__file, ROOT_NAME, ignore=ignore) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 574, in read_group builder = read_method(sub_h5obj) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 574, in read_group builder = read_method(sub_h5obj) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 574, in __read_group builder = read_method(sub_h5obj) [Previous line repeated 1 more time] File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 582, in read_group ret = GroupBuilder(name, kwargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 560, in func_call return func(args[0], pargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/build/builders.py", line 158, in init super().init(name, attributes, parent, source) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 560, in func_call return func(args[0], pargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/build/builders.py", line 94, in init self.set_attribute(name, val) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 559, in func_call pargs = _check_args(args, kwargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 552, in _check_args raise ExceptionType(msg) TypeError: GroupBuilder.set_attribute: None is not allowed for 'value' (expected 'any type', not None)
[0;0;31mERROR in test test_read_1_0_5 (back_compat_tests.test_1_1_0.Test1_1_0): Traceback (most recent call last): File "/builddir/build/BUILD/hdmf-2.0.1/tests/unit/back_compat_tests/test_1_1_0.py", line 29, in test_read_1_0_5 read_foofile = io.read() File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 414, in read return call_docval_func(super().read, kwargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 404, in call_docval_func return func(*fargs, fkwargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 560, in func_call return func(args[0], pargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/io.py", line 32, in read f_builder = self.read_builder() File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 560, in func_call return func(args[0], pargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 431, in read_builder f_builder = self.read_group(self.__file, ROOT_NAME, ignore=ignore) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 574, in read_group builder = read_method(sub_h5obj) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 574, in read_group builder = read_method(sub_h5obj) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 574, in __read_group builder = read_method(sub_h5obj) [Previous line repeated 1 more time] File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 582, in read_group ret = GroupBuilder(name, kwargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 560, in func_call return func(args[0], pargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/build/builders.py", line 158, in init super().init(name, attributes, parent, source) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 560, in func_call return func(args[0], pargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/build/builders.py", line 94, in init self.set_attribute(name, val) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 559, in func_call pargs = _check_args(args, kwargs) File "/builddir/build/BUILDROOT/python-hdmf-2.0.1-1.fc33.noarch/usr/lib/python3.9/site-packages/hdmf/utils.py", line 552, in _check_args raise ExceptionType(msg) TypeError: GroupBuilder.set_attribute: None is not allowed for 'value' (expected 'any type', not None)
�[0;0;31mERROR in test test_copy_h5py_dataset_h5dataio_input (test_io_hdf5_h5tools.H5IOTest): Traceback (most recent call last): File "/builddir/build/BUILD/hdmf-2.0.1/tests/unit/test_io_hdf5_h5tools.py", line 697, in test_copy_h5py_dataset_h5dataio_input self.assertTrue(isinstance(self.f.get('test_copy', getlink=True), HardLink)) AssertionError: False is not true
�[0;0;31mERROR in test test_link_h5py_dataset_h5dataio_input (test_io_hdf5_h5tools.H5IOTest): Traceback (most recent call last): File "/builddir/build/BUILD/hdmf-2.0.1/tests/unit/test_io_hdf5_h5tools.py", line 688, in test_link_h5py_dataset_h5dataio_input self.assertTrue(isinstance(self.f.get('test_softlink', getlink=True), SoftLink)) AssertionError: False is not true
�[0;0;31mERROR in test test_link_h5py_dataset_input (test_io_hdf5_h5tools.H5IOTest): Traceback (most recent call last): File "/builddir/build/BUILD/hdmf-2.0.1/tests/unit/test_io_hdf5_h5tools.py", line 671, in test_link_h5py_dataset_input self.assertTrue(isinstance(self.f.get('test_softlink', getlink=True), SoftLink)) AssertionError: False is not true