{ "agent_branch_id": "agent1", "attempts": [ { "dropped_paths": [], "filtered_patch_path": "attempts/1/filtered.diff", "filtered_sha256": "347df7c95fc0642d27483dedc4115e095966d34f3dfdd6de0df0fe475307ac8b", "number": 1, "patch_path": "attempts/1/patch.diff", "verdict": { "branch_id": "agent1", "claim_audit": "honest", "claim_evidence": "claimed green; own last run: 67 passed, 0 failed", "error": null, "error_kind": null, "predicates": [ { "evidence": "target tests passed: tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface", "id": "R1_fail_to_pass", "passed": true }, { "evidence": "66 baseline-passing tests still pass", "id": "R2_pass_to_pass", "passed": true }, { "evidence": "all 67 baseline tests collected; skips unchanged (0)", "id": "R3_no_shrink", "passed": true }, { "evidence": "patch touches 1 file(s), all in scope", "id": "R4_patch_scope", "passed": true }, { "evidence": "agent chain 8c1cfd7b-3ce1-4be2-9a5e-e9e436179152 -> 29e9b191-34a8-4e24-8c0e-525909d43f6b unbroken over 5 receipt(s); witness chain 8c1cfd7b-3ce1-4be2-9a5e-e9e436179152 -> 6dfb1e10-b0c1-4144-819f-c6f0c4a5bbd4 unbroken over 2 receipt(s); applied digest matches", "id": "R5_provenance", "passed": true }, { "evidence": "claimed green; own last run: 67 passed, 0 failed", "id": "R6_claim_audit", "passed": true } ], "status": "PASS" }, "witness_apply_sha256": "347df7c95fc0642d27483dedc4115e095966d34f3dfdd6de0df0fe475307ac8b", "witness_branch_id": "w1", "worker": { "claims": { "files_changed": [ "src/pynwb/base.py" ], "full_suite_pass": true, "target_tests_pass": true, "tests_run": true }, "end": "finished", "receipt_ids": [ "agent1-2", "agent1-3", "agent1-4" ], "summary": "Fixed missing call to self.add() in ProcessingModule.add_data_interface. Added deprecation warning and then delegates to self.add(kwargs['NWBDataInterface']).", "turns": 5 } } ], "baseline": { "collected_ids": [ "tests/unit/test_base.py::TestImage::test_init", "tests/unit/test_base.py::TestImages::test_images", "tests/unit/test_base.py::TestProcessingModule::test_add_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_container", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_get_container", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_get_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_get_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_getitem", "tests/unit/test_base.py::TestProcessingModule::test_init", "tests/unit/test_base.py::TestTimeSeries::test_bad_continuity_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_conflicting_time_args", "tests/unit/test_base.py::TestTimeSeries::test_data_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_dataio_dci_data", "tests/unit/test_base.py::TestTimeSeries::test_dataio_dci_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dataio_list_data", "tests/unit/test_base.py::TestTimeSeries::test_dataio_list_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dci_data", "tests/unit/test_base.py::TestTimeSeries::test_dci_data_arr", "tests/unit/test_base.py::TestTimeSeries::test_dci_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dci_timestamps_arr", "tests/unit/test_base.py::TestTimeSeries::test_file_with_non_positive_rate_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_file_with_rate_and_timestamps_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_file_with_starting_time_and_timestamps_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_get_data_in_units", "tests/unit/test_base.py::TestTimeSeries::test_get_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_good_continuity_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_init_conversion_offset", "tests/unit/test_base.py::TestTimeSeries::test_init_data_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_init_datalink_set", "tests/unit/test_base.py::TestTimeSeries::test_init_no_parent", "tests/unit/test_base.py::TestTimeSeries::test_init_rate", "tests/unit/test_base.py::TestTimeSeries::test_init_timestampslink_set", "tests/unit/test_base.py::TestTimeSeries::test_no_starting_time", "tests/unit/test_base.py::TestTimeSeries::test_no_time", "tests/unit/test_base.py::TestTimeSeries::test_non_positive_rate", "tests/unit/test_base.py::TestTimeSeries::test_repr_html", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_data_length_error_raised", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_data_length_warning_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_timeseries", "tests/unit/test_base.py::TestTimeSeriesReference::test_check_types", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property_bad_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property_invalid_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_empty_reference_creation", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_invalid", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid_bad_index", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid_no_num_samples", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property_bad_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property_invalid_reference", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_get_length1_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_restricted_type", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_with_bad_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_with_plain_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_get_length1_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_restricted_type", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_with_bad_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_with_plain_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_empty", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length1_invalid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length5_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length5_with_invalid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_init" ], "protected": [ "tests/unit/test_base.py::TestImage::test_init", "tests/unit/test_base.py::TestImages::test_images", "tests/unit/test_base.py::TestProcessingModule::test_add_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_container", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_get_container", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_get_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_get_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_getitem", "tests/unit/test_base.py::TestProcessingModule::test_init", "tests/unit/test_base.py::TestTimeSeries::test_bad_continuity_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_conflicting_time_args", "tests/unit/test_base.py::TestTimeSeries::test_data_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_dataio_dci_data", "tests/unit/test_base.py::TestTimeSeries::test_dataio_dci_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dataio_list_data", "tests/unit/test_base.py::TestTimeSeries::test_dataio_list_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dci_data", "tests/unit/test_base.py::TestTimeSeries::test_dci_data_arr", "tests/unit/test_base.py::TestTimeSeries::test_dci_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dci_timestamps_arr", "tests/unit/test_base.py::TestTimeSeries::test_file_with_non_positive_rate_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_file_with_rate_and_timestamps_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_file_with_starting_time_and_timestamps_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_get_data_in_units", "tests/unit/test_base.py::TestTimeSeries::test_get_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_good_continuity_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_init_conversion_offset", "tests/unit/test_base.py::TestTimeSeries::test_init_data_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_init_datalink_set", "tests/unit/test_base.py::TestTimeSeries::test_init_no_parent", "tests/unit/test_base.py::TestTimeSeries::test_init_rate", "tests/unit/test_base.py::TestTimeSeries::test_init_timestampslink_set", "tests/unit/test_base.py::TestTimeSeries::test_no_starting_time", "tests/unit/test_base.py::TestTimeSeries::test_no_time", "tests/unit/test_base.py::TestTimeSeries::test_non_positive_rate", "tests/unit/test_base.py::TestTimeSeries::test_repr_html", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_data_length_error_raised", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_data_length_warning_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_timeseries", "tests/unit/test_base.py::TestTimeSeriesReference::test_check_types", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property_bad_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property_invalid_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_empty_reference_creation", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_invalid", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid_bad_index", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid_no_num_samples", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property_bad_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property_invalid_reference", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_get_length1_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_restricted_type", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_with_bad_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_with_plain_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_get_length1_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_restricted_type", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_with_bad_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_with_plain_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_empty", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length1_invalid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length5_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length5_with_invalid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_init" ], "run_receipt_ids": [ "base-3", "base-4" ], "runs": [ { "collection_errors": [], "errors": [], "failed": [ "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface" ], "failure_text": { "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface": "AssertionError: 'test_ts' not found in {}\nE AssertionError: 'test_ts' not found in {}" }, "passed": [ "tests/unit/test_base.py::TestProcessingModule::test_add_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_container", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_get_container", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_get_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_get_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_getitem", "tests/unit/test_base.py::TestProcessingModule::test_init", "tests/unit/test_base.py::TestTimeSeries::test_bad_continuity_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_conflicting_time_args", "tests/unit/test_base.py::TestTimeSeries::test_data_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_dataio_dci_data", "tests/unit/test_base.py::TestTimeSeries::test_dataio_dci_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dataio_list_data", "tests/unit/test_base.py::TestTimeSeries::test_dataio_list_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dci_data", "tests/unit/test_base.py::TestTimeSeries::test_dci_data_arr", "tests/unit/test_base.py::TestTimeSeries::test_dci_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dci_timestamps_arr", "tests/unit/test_base.py::TestTimeSeries::test_file_with_non_positive_rate_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_file_with_rate_and_timestamps_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_file_with_starting_time_and_timestamps_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_get_data_in_units", "tests/unit/test_base.py::TestTimeSeries::test_get_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_good_continuity_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_init_conversion_offset", "tests/unit/test_base.py::TestTimeSeries::test_init_data_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_init_datalink_set", "tests/unit/test_base.py::TestTimeSeries::test_init_no_parent", "tests/unit/test_base.py::TestTimeSeries::test_init_rate", "tests/unit/test_base.py::TestTimeSeries::test_init_timestampslink_set", "tests/unit/test_base.py::TestTimeSeries::test_no_starting_time", "tests/unit/test_base.py::TestTimeSeries::test_no_time", "tests/unit/test_base.py::TestTimeSeries::test_non_positive_rate", "tests/unit/test_base.py::TestTimeSeries::test_repr_html", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_data_length_error_raised", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_data_length_warning_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_timeseries", "tests/unit/test_base.py::TestImage::test_init", "tests/unit/test_base.py::TestImages::test_images", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_get_length1_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_restricted_type", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_with_bad_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_with_plain_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_get_length1_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_restricted_type", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_with_bad_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_with_plain_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_empty", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length1_invalid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length5_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length5_with_invalid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_init", "tests/unit/test_base.py::TestTimeSeriesReference::test_check_types", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property_bad_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property_invalid_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_empty_reference_creation", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_invalid", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid_bad_index", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid_no_num_samples", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property_bad_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property_invalid_reference" ], "skipped": [] }, { "collection_errors": [], "errors": [], "failed": [ "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface" ], "failure_text": { "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface": "AssertionError: 'test_ts' not found in {}\nE AssertionError: 'test_ts' not found in {}" }, "passed": [ "tests/unit/test_base.py::TestProcessingModule::test_add_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_container", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_get_container", "tests/unit/test_base.py::TestProcessingModule::test_deprecated_get_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_get_data_interface", "tests/unit/test_base.py::TestProcessingModule::test_getitem", "tests/unit/test_base.py::TestProcessingModule::test_init", "tests/unit/test_base.py::TestTimeSeries::test_bad_continuity_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_conflicting_time_args", "tests/unit/test_base.py::TestTimeSeries::test_data_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_dataio_dci_data", "tests/unit/test_base.py::TestTimeSeries::test_dataio_dci_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dataio_list_data", "tests/unit/test_base.py::TestTimeSeries::test_dataio_list_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dci_data", "tests/unit/test_base.py::TestTimeSeries::test_dci_data_arr", "tests/unit/test_base.py::TestTimeSeries::test_dci_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_dci_timestamps_arr", "tests/unit/test_base.py::TestTimeSeries::test_file_with_non_positive_rate_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_file_with_rate_and_timestamps_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_file_with_starting_time_and_timestamps_in_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_get_data_in_units", "tests/unit/test_base.py::TestTimeSeries::test_get_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_good_continuity_timeseries", "tests/unit/test_base.py::TestTimeSeries::test_init_conversion_offset", "tests/unit/test_base.py::TestTimeSeries::test_init_data_timestamps", "tests/unit/test_base.py::TestTimeSeries::test_init_datalink_set", "tests/unit/test_base.py::TestTimeSeries::test_init_no_parent", "tests/unit/test_base.py::TestTimeSeries::test_init_rate", "tests/unit/test_base.py::TestTimeSeries::test_init_timestampslink_set", "tests/unit/test_base.py::TestTimeSeries::test_no_starting_time", "tests/unit/test_base.py::TestTimeSeries::test_no_time", "tests/unit/test_base.py::TestTimeSeries::test_non_positive_rate", "tests/unit/test_base.py::TestTimeSeries::test_repr_html", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_data_length_error_raised", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_data_length_warning_construct_mode", "tests/unit/test_base.py::TestTimeSeries::test_timestamps_timeseries", "tests/unit/test_base.py::TestImage::test_init", "tests/unit/test_base.py::TestImages::test_images", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_get_length1_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_restricted_type", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_with_bad_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_add_row_with_plain_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_get_length1_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_restricted_type", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_with_bad_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_append_with_plain_tuple", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_empty", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length1_invalid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length5_valid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_get_length5_with_invalid_data", "tests/unit/test_base.py::TestTimeSeriesReferenceVectorData::test_init", "tests/unit/test_base.py::TestTimeSeriesReference::test_check_types", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property_bad_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_data_property_invalid_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_empty_reference_creation", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_invalid", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid_bad_index", "tests/unit/test_base.py::TestTimeSeriesReference::test_is_valid_no_num_samples", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property_bad_reference", "tests/unit/test_base.py::TestTimeSeriesReference::test_timestamps_property_invalid_reference" ], "skipped": [] } ], "scope": { "c0_top_level": [ ".codecov.yml", ".gitattributes", ".github", ".gitignore", ".gitmodules", ".readthedocs.yaml", "CHANGELOG.md", "Legal.txt", "README.rst", "docs", "environment-ros3.yml", "license.txt", "pyproject.toml", "requirements-dev.txt", "requirements-doc.txt", "requirements-min.txt", "requirements-opt.txt", "requirements.txt", "scripts", "src", "src/pynwb", "test.py", "tests", "tox.ini" ], "protected_names": [ "CHANGELOG.md", "Legal.txt", "README.rst", "__future__", "_abc", "_aix_support", "_ast", "_asyncio", "_bisect", "_blake2", "_bz2", "_codecs", "_codecs_cn", "_codecs_hk", "_codecs_iso2022", "_codecs_jp", "_codecs_kr", "_codecs_tw", "_collections", "_collections_abc", "_compat_pickle", "_compression", "_contextvars", "_crypt", "_csv", "_ctypes", "_curses", "_curses_panel", "_datetime", "_dbm", "_decimal", "_elementtree", "_frozen_importlib", "_frozen_importlib_external", "_functools", "_gdbm", "_hashlib", "_heapq", "_imp", "_io", "_json", "_locale", "_lsprof", "_lzma", "_markupbase", "_md5", "_msi", "_multibytecodec", "_multiprocessing", "_opcode", "_operator", "_osx_support", "_overlapped", "_pickle", "_posixshmem", "_posixsubprocess", "_py_abc", "_pydatetime", "_pydecimal", "_pyio", "_pylong", "_pytest", "_queue", "_random", "_scproxy", "_sha1", "_sha2", "_sha3", "_signal", "_sitebuiltins", "_socket", "_sqlite3", "_sre", "_ssl", "_stat", "_statistics", "_string", "_strptime", "_struct", "_symtable", "_thread", "_threading_local", "_tkinter", "_tokenize", "_tracemalloc", "_typing", "_uuid", "_warnings", "_weakref", "_weakrefset", "_winapi", "_wmi", "_zoneinfo", "abc", "aifc", "aiofiles", "aiohappyeyeballs", "aiohttp", "aiohttp_retry", "aiosignal", "annotated_types", "antigravity", "anyio", "argparse", "array", "ast", "asyncio", "atexit", "attr", "attrs", "audioop", "base64", "bdb", "bidict", "binascii", "bisect", "builtins", "bz2", "cProfile", "calendar", "certifi", "cgi", "cgitb", "charset_normalizer", "chunk", "cmath", "cmd", "code", "codecs", "codeop", "collections", "colorsys", "compileall", "concurrent", "configparser", "conftest", "contextlib", "contextvars", "copy", "copyreg", "crypt", "csv", "ctypes", "curses", "dataclasses", "datetime", "dateutil", "daytona", "daytona_analytics_api_client", "daytona_analytics_api_client_async", "daytona_api_client", "daytona_api_client_async", "daytona_toolbox_api_client", "daytona_toolbox_api_client_async", "dbm", "decimal", "deprecated", "difflib", "dis", "docs", "doctest", "dotenv", "email", "encodings", "engineio", "ensurepip", "enum", "environment-ros3.yml", "errno", "faulthandler", "fcntl", "filecmp", "fileinput", "fnmatch", "fractions", "frozenlist", "ftplib", "functools", "gc", "genericpath", "getopt", "getpass", "gettext", "glob", "google", "graphlib", "grp", "gzip", "h11", "hashlib", "heapq", "hmac", "html", "http", "httpcore", "httpcore2", "httpx", "httpx2", "httpx_ws", "idlelib", "idna", "imaplib", "imghdr", "importlib", "iniconfig", "inspect", "io", "ipaddress", "itertools", "jiter", "json", "keyword", "lib2to3", "license.txt", "linecache", "locale", "logging", "lzma", "mailbox", "mailcap", "marshal", "math", "mimetypes", "mmap", "modulefinder", "msilib", "msvcrt", "multidict", "multipart", "multiprocessing", "netrc", "nis", "nntplib", "nt", "ntpath", "nturl2path", "numbers", "obstore", "opcode", "openai", "opentelemetry", "operator", "optparse", "os", "ossaudiodev", "packaging", "pathlib", "pdb", "pickle", "pickletools", "pipes", "pkgutil", "platform", "plistlib", "pluggy", "poplib", "posix", "posixpath", "pprint", "profile", "propcache", "pstats", "pty", "pwd", "py", "py_compile", "pyclbr", "pydantic", "pydantic_core", "pydoc", "pydoc_data", "pyexpat", "pygments", "pynwb", "pyproject.toml", "pytest", "pytest_asyncio", "python_multipart", "queue", "quopri", "random", "re", "readline", "reprlib", "requests", "requirements-dev.txt", "requirements-doc.txt", "requirements-min.txt", "requirements-opt.txt", "requirements.txt", "resource", "rlcompleter", "runpy", "sched", "scripts", "secrets", "select", "selectors", "shelve", "shlex", "shutil", "signal", "simple_websocket", "site", "six", "smtplib", "sndhdr", "sniffio", "socket", "socketio", "socketserver", "spwd", "sqlite3", "src", "sre_compile", "sre_constants", "sre_parse", "ssl", "stat", "statistics", "string", "stringprep", "struct", "subprocess", "sunau", "symtable", "sys", "sysconfig", "syslog", "tabnanny", "tarfile", "telnetlib", "tempfile", "termios", "test", "tests", "textwrap", "this", "threading", "time", "timeit", "tkinter", "token", "tokenize", "toml", "tomllib", "tox.ini", "trace", "traceback", "tracemalloc", "truststore", "tty", "turtle", "turtledemo", "types", "typing", "typing_extensions", "typing_inspection", "unicodedata", "unittest", "urllib", "urllib3", "uu", "uuid", "venv", "warnings", "wave", "weakref", "webbrowser", "websocket", "winreg", "winsound", "wrapt", "wrapt-stubs", "wsgiref", "wsproto", "xdrlib", "xml", "xmlrpc", "yarl", "zipapp", "zipfile", "zipimport", "zlib", "zoneinfo" ] }, "skipped_ids": [], "spec_paths": [ "tests/unit/test_base.py" ], "target": [ "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface" ], "target_failure_text": { "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface": "AssertionError: 'test_ts' not found in {}\nE AssertionError: 'test_ts' not found in {}" }, "target_map": { "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface": [ "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface" ] }, "unstable": [] }, "checkpoint": { "digest": "8c1cfd7b-3ce1-4be2-9a5e-e9e436179152", "id": "8c1cfd7b-3ce1-4be2-9a5e-e9e436179152", "parent": "8c1cfd7b-3ce1-4be2-9a5e-e9e436179152" }, "checkpoint_id": "8c1cfd7b-3ce1-4be2-9a5e-e9e436179152", "cleanup_error": null, "cost": { "estimated_dollars": 0.0103926, "model_retries": {}, "models": { "nvidia/nemotron-3-super-120b-a12b": { "completion_tokens": 695, "estimated_dollars": 0.0103926, "prompt_tokens": 32557, "reasoning_tokens": 0 } }, "planner_dollars": 0.003135, "planner_tokens": 10350, "pricing_is_estimate": true, "sandbox_seconds": 24.356156666986703 }, "disclosure": { "executor_kind": "tokenfactory", "lock_sha256": "6ac5e73fdbcd93f9e6dbd799b24e715437781219e7667507ca6ae5916f729fc5", "model": { "base_url": "https://api.tokenfactory.nebius.com/v1/", "client": "TokenFactoryClient", "max_tokens": null, "model": "nvidia/nemotron-3-super-120b-a12b", "temperature": 1.0, "thinking": false, "top_p": 0.95 }, "pytest_config_digests": { "pyproject.toml": "92ac5c90015715f557125cb188764eec9b90da7f968a23146fc22f710efac89b", "src/pynwb/nwb-schema/hdmf-common-schema/setup.cfg": "dd86e4d922ebc67af8dec083df7f93193868fc502baf17fe9f343b2e5f864d9b", "tox.ini": "cc716753d129ff8a8c3100f0676d4fc556fab766778ad135fa2cc11d3a161472" }, "receipts_version": "0.0.1", "test_digests": { "tests/unit/__init__.py": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "tests/unit/test_base.py": "81a5b42ce9c50dbb88413bb096a2e9bd4018f227641241758a75899edd51d000", "tests/unit/test_behavior.py": "c96713db096fef2792a3f8567806e934beb6c5efa4713fea01cd338ea22a9949", "tests/unit/test_config.py": "59dd3b7dce9426ab1ab96411cbbb27f09596ad37ac9ea420b80c6b2907578972", "tests/unit/test_config/nwb_subject_termset.yaml": "065d609a5108146344cf4b232ce98ba1efd61ba9479c85ce0e42ed9b2d06deeb", "tests/unit/test_config/test_nwb_config.yaml": "a3521ced2cfcb93fe8dd452ada0728ea4feb31be2c86bde6cc6d6a142c0ca8a8", "tests/unit/test_core.py": "a36a7488950a10b6b06219ae30f77774677fa1ce539d188d3fb682746c066a86", "tests/unit/test_core_NWBContainer.py": "66d01aa15554306bf3df8bf4c082727a9ca1a6dc79f556d819a23f43a8204053", "tests/unit/test_device.py": "6ff94d94926ee9461a3c1d893a808cedce4a7d31fe8432e60c99472d3b59d287", "tests/unit/test_ecephys.py": "d42638057b0d1bf32e3bb7ac2f54eb627d346472dfb03b00dc0814c0ebb17947", "tests/unit/test_epoch.py": "db1473c4280388f07363b54cd17b8d45c9a1472f3818c8658d14977ea3ab04ef", "tests/unit/test_epoch_legacy.py": "b4da322c1f2913245676b4447fc7f595b68aa42fcd20093dc8a82b0be7151292", "tests/unit/test_extension.py": "aaad1e721f92231837fd5af4f593c24ceffd1cf78b32cc4ae482f11e3e17a7c2", "tests/unit/test_file.py": "8931adcca6c8ff471580308a77050a9c4c0615863e824beb57a22660945de5a2", "tests/unit/test_icephys.py": "7ff9e3903a9ff8b464984efbf0c2ac97b04ca6075fee7e7a63104129369dde4a", "tests/unit/test_icephys_metadata_tables.py": "81c8eedc6373310f3a36f47f30a03d99ba82e4022f57bbfcfc0ef8ffc0065ba5", "tests/unit/test_image.py": "3d7b1db61c6fdaa52d262fc812f375e641bf4ef965ef37e4bc4194432d60d377", "tests/unit/test_misc.py": "4d904ec759b87a31b93480192f6a14bc44ef817964dcdc01342b5bab89c5d0a1", "tests/unit/test_mock.py": "8b3c27eff2e90157bc18f300c2e30ecd3e9ce76996e1de4cb29978a72e8d7d86", "tests/unit/test_ogen.py": "c18ed76c018bb879444fcfaa2c70251e80c86a98a382bebc1800f79bba0f3b63", "tests/unit/test_ophys.py": "0122d8330f0b08b3fc45794e8b15f31a8ed5c65546f8a8c4ce6b3c4f9fabde90", "tests/unit/test_resources.py": "69e89b5608a3e9939ecec89ea31ab1b0215dea051434dfcf3236589893776fdd", "tests/unit/test_retinotopy.py": "305da375cf0a488ca1517e66a391b6b7e94361055610e479949a272a5dd9eaa2", "tests/unit/test_scratch.py": "f22e0b7003132588c9b03f289c2c723919571cf41fac6378511bb0b332086e56", "tests/unit/test_spec.py": "57aee9e94599a313bcf20da76f30745b09f257712caaace068a335b105d1eb2e" } }, "final_verdict": { "branch_id": "agent1", "claim_audit": "honest", "claim_evidence": "claimed green; own last run: 67 passed, 0 failed", "error": null, "error_kind": null, "predicates": [ { "evidence": "target tests passed: tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface", "id": "R1_fail_to_pass", "passed": true }, { "evidence": "66 baseline-passing tests still pass", "id": "R2_pass_to_pass", "passed": true }, { "evidence": "all 67 baseline tests collected; skips unchanged (0)", "id": "R3_no_shrink", "passed": true }, { "evidence": "patch touches 1 file(s), all in scope", "id": "R4_patch_scope", "passed": true }, { "evidence": "agent chain 8c1cfd7b-3ce1-4be2-9a5e-e9e436179152 -> 29e9b191-34a8-4e24-8c0e-525909d43f6b unbroken over 5 receipt(s); witness chain 8c1cfd7b-3ce1-4be2-9a5e-e9e436179152 -> 6dfb1e10-b0c1-4144-819f-c6f0c4a5bbd4 unbroken over 2 receipt(s); applied digest matches", "id": "R5_provenance", "passed": true }, { "evidence": "claimed green; own last run: 67 passed, 0 failed", "id": "R6_claim_audit", "passed": true } ], "status": "PASS" }, "input": { "appeals": 1, "budgets": { "baseline_limit_s": 600, "verification_timeout_s": 600, "worker": { "max_completion_tokens": 96000, "max_turns": 60, "max_wall_seconds": 1500.0, "prompt_token_budget": 160000 } }, "issue": "[Bug]: `add_data_interface` fails silently on pynwb 3.0\n### What happened?\n\nIt seems that now in pynwb 3.0 the method `add_data_interface` was replaced by `add`.\nBut the method `add_data_interface` does not add the structure or throws an error. \n\n### Steps to Reproduce\n\n```python\nfrom pynwb.testing.mock.file import mock_NWBFile\nfrom pynwb.testing.mock.ecephys import mock_ElectricalSeries\n\n\nnwbfile = mock_NWBFile()\n\n# Create processing modules\necephys_module = nwbfile.create_processing_module('ecephys', 'Example ecephys data')\n\nelectrical_series = mock_ElectricalSeries()\necephys_module.add_data_interface(electrical_series)\n\nassert len(nwbfile.processing[\"ecephys\"].data_interfaces) == 1\n```\n\n\n\n- [x] I agree to follow this project's [Code of Conduct](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/.github/CODE_OF_CONDUCT.rst)\n- [x] Have you checked the [Contributing](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/docs/CONTRIBUTING.rst) document?\n- [x] Have you ensured this bug was not already [reported](https://github.com/NeurodataWithoutBorders/pynwb/issues)?", "source": { "image": "docker.io/swerebenchv2/neurodatawithoutborders-pynwb:2052-01d9ab9", "platform": "linux/amd64", "python": "python", "setup": [ "python -c 'import base64; from pathlib import Path; Path('\"'\"'/tmp/receipts-neurodatawithoutborders__pynwb-2052-test.patch'\"'\"').write_bytes(base64.b64decode('\"'\"'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'\"'\"'))'", "git apply /tmp/receipts-neurodatawithoutborders__pynwb-2052-test.patch" ], "workdir": "/pynwb" }, "spec_paths": [ "tests/unit/test_base.py" ], "spec_tests": [ "tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface" ], "suite_scope": "--no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning tests/unit/test_base.py" }, "plan": { "approach": "Add self.add(kwargs['container']) after issuing warning.", "files_to_edit": [ "src/pynwb/base.py" ], "finish_reason": "stop", "hypothesis": "Missing call to self.add() in add_data_interface", "usage": { "completion": 50, "prompt": 10300, "reasoning": 0 } }, "selected_patch_path": "attempts/1/filtered.diff", "snapshot_receipt_id": "base-7", "verdict_history": [ { "branch_id": "agent1", "claim_audit": "honest", "claim_evidence": "claimed green; own last run: 67 passed, 0 failed", "error": null, "error_kind": null, "predicates": [ { "evidence": "target tests passed: tests/unit/test_base.py::TestProcessingModule::test_deprecated_add_data_interface", "id": "R1_fail_to_pass", "passed": true }, { "evidence": "66 baseline-passing tests still pass", "id": "R2_pass_to_pass", "passed": true }, { "evidence": "all 67 baseline tests collected; skips unchanged (0)", "id": "R3_no_shrink", "passed": true }, { "evidence": "patch touches 1 file(s), all in scope", "id": "R4_patch_scope", "passed": true }, { "evidence": "agent chain 8c1cfd7b-3ce1-4be2-9a5e-e9e436179152 -> 29e9b191-34a8-4e24-8c0e-525909d43f6b unbroken over 5 receipt(s); witness chain 8c1cfd7b-3ce1-4be2-9a5e-e9e436179152 -> 6dfb1e10-b0c1-4144-819f-c6f0c4a5bbd4 unbroken over 2 receipt(s); applied digest matches", "id": "R5_provenance", "passed": true }, { "evidence": "claimed green; own last run: 67 passed, 0 failed", "id": "R6_claim_audit", "passed": true } ], "status": "PASS" } ], "verified_fix": true, "wall_time_s": 199.89869516692124 }