neurodatawithoutborders__pynwb-1669

{
  "status": "ok",
  "stdout": "src/pynwb/icephys.py:15:def ensure_unit(self, name, current_unit, unit, nwb_version):\nsrc/pynwb/icephys.py:25:            % (current_unit, self.__class__.__name__, name, unit, nwb_version))\nsrc/pynwb/icephys.py:218:    def _ensure_stimulus_description(self, name, current_stim_desc, stim_desc, nwb_version):\nsrc/pynwb/icephys.py:228:                % (current_stim_desc, self.__class__.__name__, name, stim_desc, nwb_version))\nsrc/pynwb/__init__.py:245:    def nwb_version(self):\nsrc/pynwb/__init__.py:251:                  and strings, e.g., (2, 5, 1, beta). (None, None) will be returned if the nwb_version\nsrc/pynwb/__init__.py:256:            nwb_version_string = self._file.attrs['nwb_version']\nsrc/pynwb/__init__.py:262:        nwb_version_parts = nwb_version_string.replace(\"-\", \".\").replace(\"_\", \".\").split(\".\")\nsrc/pynwb/__init__.py:263:        nwb_version = tuple([int(i) if i.isnumeric() else i\nsrc/pynwb/__init__.py:264:                             for i in nwb_version_parts])\nsrc/pynwb/__init__.py:265:        return nwb_version_string, nwb_version\nsrc/pynwb/__init__.py:280:            file_version_str, file_version = self.nwb_version\nsrc/pynwb/io/utils.py:7:def get_nwb_version(builder: Builder, include_prerelease=False) -> Tuple[int, ...]:\nsrc/pynwb/io/utils.py:10:    If the \"nwb_version\" attribute on the root builder equals \"2.5.1\", then (2, 5, 1) is returned.\nsrc/pynwb/io/utils.py:11:    If the \"nwb_version\" attribute on the root builder equals \"2.5.1-alpha\" and include_prerelease=False,\nsrc/pynwb/io/utils.py:13:    If the \"nwb_version\" attribute on the root builder equals \"2.5.1-alpha\" and include_prerelease=True,\nsrc/pynwb/io/utils.py:16:    If the \"nwb_version\" attribute == \"2.0b\" (the only deviation from semantic versioning in the 2.x series), then\nsrc/pynwb/io/utils.py:25:    :raises ValueError: if the 'nwb_version' attribute is missing from the root of the NWB file.\nsrc/pynwb/io/utils.py:31:    nwb_version = root_builder.attributes.get(\"nwb_version\")\nsrc/pynwb/io/utils.py:32:    if nwb_version is None:\nsrc/pynwb/io/utils.py:33:        raise ValueError(\"'nwb_version' attribute is missing from the root of the NWB file.\")\nsrc/pynwb/io/utils.py:35:    if nwb_version == \"2.0b\":\nsrc/pynwb/io/utils.py:40:    nwb_version_match = re.match(r\"(\\d+\\.\\d+\\.\\d+)\", nwb_version)[0]  # trim off any non-numeric symbols at end\nsrc/pynwb/io/utils.py:41:    version_list = [int(i) for i in nwb_version_match.split(\".\")]\nsrc/pynwb/io/utils.py:43:        prerelease_info = nwb_version[nwb_version.index(\"-\")+1:]\nsrc/pynwb/io/file.py:8:from .utils import get_nwb_version\nsrc/pynwb/io/file.py:232:            if get_nwb_version(builder) < (2, 6, 0):\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "content": "                manager = get_manager()\n        # Open the file\n        super().__init__(path, manager=manager, mode=mode, file=file_obj, comm=comm, driver=driver)\n\n    @property\n    def nwb_version(self):\n        \"\"\"\n        Get the version of the NWB file opened via this NWBHDF5IO object.\n\n        :returns: Tuple consisting of: 1) the original version string as stored in the file and\n                  2) a tuple with the parsed components of the version string, consisting of integers\n                  and strings, e.g., (2, 5, 1, beta). (None, None) will be returned if the nwb_version\n                  is missing, e.g., in the case when no data has been written to the file yet.\n        \"\"\"\n        # Get the version string for the NWB file\n        try:\n            nwb_version_string = self._file.attrs['nwb_version']\n        #  KeyError occurs  when the file is empty (e.g., when creating a new file nothing has been written)\n        #  or when the HDF5 file is not a valid NWB file\n        except KeyError:\n            return None, None\n        # Parse the version string\n        nwb_version_parts = nwb_version_string.replace(\"-\", \".\").replace(\"_\", \".\").split(\".\")\n        nwb_version = tuple([int(i) if i.isnumeric() else i\n                             for i in nwb_version_parts])\n        return nwb_version_string, nwb_version\n\n    @docval(*get_docval(_HDF5IO.read),\n            {'name': 'skip_version_check', 'type': bool, 'doc': 'skip checking of NWB version', 'default': False})\n    def read(self, **kwargs):\n        \"\"\"\n        Read the NWB file from the IO source.\n\n        :raises TypeError: If the NWB file version is missing or not supported\n\n        :return: NWBFile container\n        \"\"\"\n        # Check that the NWB file is supported\n        skip_verison_check = popargs('skip_version_check', kwargs)\n        if not skip_verison_check:\n            file_version_str, file_version = self.nwb_version\n            if file_version is None:\n                raise TypeError(\"Missing NWB version in file. The file is not a valid NWB file.\")\n            if file_version[0] < 2:\n                raise TypeError(\"NWB version %s not supported. PyNWB supports NWB files version 2 and above.\" %\n                                str(file_version_str))",
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  "end_line": 285,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "src/pynwb/io/utils.py",
  "content": "import re\nfrom typing import Tuple\n\nfrom hdmf.build import Builder\n\n\ndef get_nwb_version(builder: Builder, include_prerelease=False) -> Tuple[int, ...]:\n    \"\"\"Get the version of the NWB file from the root of the given builder, as a tuple.\n\n    If the \"nwb_version\" attribute on the root builder equals \"2.5.1\", then (2, 5, 1) is returned.\n    If the \"nwb_version\" attribute on the root builder equals \"2.5.1-alpha\" and include_prerelease=False,\n    then (2, 5, 1) is returned.\n    If the \"nwb_version\" attribute on the root builder equals \"2.5.1-alpha\" and include_prerelease=True,\n    then (2, 5, 1, \"alpha\") is returned.\n\n    If the \"nwb_version\" attribute == \"2.0b\" (the only deviation from semantic versioning in the 2.x series), then\n    if include_prerelease=True, (2, 0, 0, \"b\") is returned; else, (2, 0, 0) is returned.\n\n    :param builder: Any builder within an NWB file.\n    :type builder: Builder\n    :param include_prerelease: Whether to include prerelease information in the returned tuple.\n    :type include_prerelease: bool\n    :return: The version of the NWB file, as a tuple.\n    :rtype: tuple\n    :raises ValueError: if the 'nwb_version' attribute is missing from the root of the NWB file.\n    \"\"\"\n    temp_builder = builder\n    while temp_builder.parent is not None:\n        temp_builder = temp_builder.parent\n    root_builder = temp_builder\n    nwb_version = root_builder.attributes.get(\"nwb_version\")\n    if nwb_version is None:\n        raise ValueError(\"'nwb_version' attribute is missing from the root of the NWB file.\")\n    # handle special non-semver case\n    if nwb_version == \"2.0b\":\n        if not include_prerelease:\n            return (2, 0, 0)\n        else:\n            return (2, 0, 0, \"b\")\n    nwb_version_match = re.match(r\"(\\d+\\.\\d+\\.\\d+)\", nwb_version)[0]  # trim off any non-numeric symbols at end\n    version_list = [int(i) for i in nwb_version_match.split(\".\")]\n    if include_prerelease:\n        prerelease_info = nwb_version[nwb_version.index(\"-\")+1:]\n        version_list.append(prerelease_info)\n    return tuple(version_list)",
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  "total_lines": 45,
  "is_truncated": false
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "/pynwb/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 2, in <module>\n  File \"/pynwb/src/pynwb/__init__.py\", line 109, in <module>\n    raise RuntimeError(\nRuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n",
  "details": {
    "stdout": "",
    "stderr": "/pynwb/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 2, in <module>\n  File \"/pynwb/src/pynwb/__init__.py\", line 109, in <module>\n    raise RuntimeError(\nRuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "stdout": "src/pynwb/nwb-schema:\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "content": "    namespace_path = getargs('namespace_path', kwargs)\n    return __TYPE_MAP.load_namespaces(namespace_path)\n\n\n# load the core namespace, i.e. base NWB specification\n__resources = __get_resources()\nif os.path.exists(__resources['namespace_path']):\n    load_namespaces(__resources['namespace_path'])\nelse:\n    raise RuntimeError(\n        \"'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to \"\n        \"use the --recurse_submodules flag when cloning. See developer installation instructions here: \"\n        \"https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\"\n    )\n\n\ndef available_namespaces():\n    \"\"\"Returns all namespaces registered in the namespace catalog\"\"\"\n    return __NS_CATALOG.namespaces\n\n",
  "start_line": 100,
  "end_line": 120,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "24:def __get_resources():\n33:    return __get_resources()\n105:__resources = __get_resources()\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "content": "from .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace  # noqa E402\nfrom .validate import validate  # noqa: F401, E402\n\n\ndef __get_resources():\n    from pkg_resources import resource_filename\n    ret = dict()\n    ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name)\n    return ret\n\n\ndef _get_resources():\n    # LEGACY: Needed to support legacy implementation.\n    return __get_resources()\n\n",
  "start_line": 20,
  "end_line": 35,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "/workspace/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 2, in <module>\n  File \"/workspace/src/pynwb/__init__.py\", line 109, in <module>\n    raise RuntimeError(\nRuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n",
  "details": {
    "stdout": "",
    "stderr": "/workspace/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 2, in <module>\n  File \"/workspace/src/pynwb/__init__.py\", line 109, in <module>\n    raise RuntimeError(\nRuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "stdout": "Caught expected error: a bytes-like object is required, not 'str'\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "content": "            # ns_catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)\n            # super().load_namespaces(ns_catalog, path)\n            # tm = TypeMap(ns_catalog)\n            # tm.copy_mappers(get_type_map())\n        else:\n            if manager is not None and extensions is not None:\n                raise ValueError(\"'manager' and 'extensions' cannot be specified together\")\n            elif extensions is not None:\n                manager = get_manager(extensions=extensions)\n            elif manager is None:\n                manager = get_manager()",
  "start_line": 230,
  "end_line": 240,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "194:class NWBHDF5IO(_HDF5IO):\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "",
  "details": {
    "stdout": "",
    "stderr": "",
    "exit_code": 1
  }
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "",
  "details": {
    "stdout": "",
    "stderr": "",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "content": "    If mapper_cls is not specified, returns a decorator for registering an ObjectMapper class as the mapper for\n    container_cls. If mapper_cls is specified, register the class as the mapper for container_cls\n    \"\"\"\n    container_cls, mapper_cls = getargs('container_cls', 'mapper_cls', kwargs)\n\n    def _dec(cls):\n        __TYPE_MAP.register_map(container_cls, cls)\n        return cls\n    if mapper_cls is None:\n        return _dec\n    else:\n        _dec(mapper_cls)\n\n\n@docval({'name': 'neurodata_type', 'type': str, 'doc': 'the neurodata_type to get the NWBContainer class for'},\n        {'name': 'namespace', 'type': str, 'doc': 'the namespace the neurodata_type is defined in'},\n        is_method=False)\ndef get_class(**kwargs):\n    \"\"\"\n    Parse the YAML file for a given neurodata_type that is a subclass of NWBContainer and automatically generate its\n    python API. This will work for most containers, but is known to not work for descendants of MultiContainerInterface\n    and DynamicTable, so these must be defined manually (for now). `get_class` infers the API mapping directly from the\n    specification. If you want to define a custom mapping, you should not use this function and you should define the\n    class manually.\n\n    Examples:\n\n    Generating and registering an extension is as simple as::\n\n        MyClass = get_class('MyClass', 'ndx-my-extension')\n\n    `get_class` defines only the `__init__` for the class. In cases where you want to provide additional methods for\n    querying, plotting, etc. you can still use `get_class` and attach methods to the class after-the-fact, e.g.::\n\n        def get_sum(self, a, b):\n            return self.feat1 + self.feat2\n\n        MyClass.get_sum = get_sum\n\n    \"\"\"\n    neurodata_type, namespace = getargs('neurodata_type', 'namespace', kwargs)\n    return __TYPE_MAP.get_dt_container_cls(neurodata_type, namespace)\n\n\nclass NWBHDF5IO(_HDF5IO):\n\n    @docval({'name': 'path', 'type': (str, Path), 'doc': 'the path to the HDF5 file', 'default': None},\n            {'name': 'mode', 'type': str,\n             'doc': 'the mode to open the HDF5 file with, one of (\"w\", \"r\", \"r+\", \"a\", \"w-\", \"x\")',\n             'default': 'r'},\n            {'name': 'load_namespaces', 'type': bool,",
  "start_line": 150,
  "end_line": 200,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "content": "'''This package will contain functions, classes, and objects\nfor reading and writing data in NWB format\n'''\nimport os.path\nfrom pathlib import Path\nfrom copy import deepcopy\nfrom warnings import warn\nimport h5py\n\nfrom hdmf.spec import NamespaceCatalog\nfrom hdmf.utils import docval, getargs, popargs, get_docval\nfrom hdmf.backends.io import HDMFIO\nfrom hdmf.backends.hdf5 import HDF5IO as _HDF5IO\nfrom hdmf.build import BuildManager, TypeMap\nimport hdmf.common\n\nCORE_NAMESPACE = 'core'\n__core_ns_file_name = 'nwb.namespace.yaml'\n\nfrom .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace  # noqa E402\nfrom .validate import validate  # noqa: F401, E402\n\n\ndef __get_resources():\n    from pkg_resources import resource_filename\n    ret = dict()\n    ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name)\n    return ret\n\n\ndef _get_resources():\n    # LEGACY: Needed to support legacy implementation.\n    return __get_resources()\n\n\n# a global namespace catalog\nglobal __NS_CATALOG\nglobal __TYPE_MAP\n\n__NS_CATALOG = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)\n\nhdmf_typemap = hdmf.common.get_type_map()\n__TYPE_MAP = TypeMap(__NS_CATALOG)\n__TYPE_MAP.merge(hdmf_typemap, ns_catalog=True)\n\n\n@docval({'name': 'extensions', 'type': (str, TypeMap, list),\n         'doc': 'a path to a namespace, a TypeMap, or a list consisting of paths to namespaces and TypeMaps',\n         'default': None},\n        returns=\"TypeMap loaded for the given extension or NWB core namespace\", rtype=tuple,",
  "start_line": 1,
  "end_line": 50,
  "total_lines": 384,
  "is_truncated": false
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{
  "status": "ok",
  "stdout": "tests/unit/test_epoch_legacy.py:77:                infile.attrs['nwb_version'] = '2.3.0'\ntests/integration/hdf5/test_io.py:59:                      'nwb_version': DatasetBuilder('nwb_version', '1.0.6'),\ntests/integration/hdf5/test_io.py:166:                      'nwb_version': DatasetBuilder('nwb_version', '1.0.6'),\ntests/integration/hdf5/test_io.py:421:    def test_nwb_version_property(self):\ntests/integration/hdf5/test_io.py:422:        \"\"\"Test reading of files with missing nwb_version\"\"\"\ntests/integration/hdf5/test_io.py:425:            self.assertTupleEqual(io.nwb_version, (None, None))\ntests/integration/hdf5/test_io.py:436:                io.attrs['nwb_version'] = ver[0]\ntests/integration/hdf5/test_io.py:437:            # Assert expected result for nwb_version tuple\ntests/integration/hdf5/test_io.py:439:                self.assertEqual(io.nwb_version[0], ver[0])\ntests/integration/hdf5/test_io.py:440:                self.assertTupleEqual(io.nwb_version[1], ver[1])\ntests/integration/hdf5/test_io.py:443:            del io.attrs['nwb_version']\ntests/integration/hdf5/test_io.py:445:            self.assertTupleEqual(io.nwb_version, (None, None))\ntests/integration/hdf5/test_io.py:447:    def test_check_nwb_version_ok(self):\ntests/integration/hdf5/test_io.py:452:            self.assertIsNotNone(io.nwb_version[0])\ntests/integration/hdf5/test_io.py:453:            self.assertIsNotNone(io.nwb_version[1])\ntests/integration/hdf5/test_io.py:454:            self.assertGreater(io.nwb_version[1][0], 1)\ntests/integration/hdf5/test_io.py:458:    def test_check_nwb_version_missing_version(self):\ntests/integration/hdf5/test_io.py:459:        \"\"\"Test reading of files with missing nwb_version\"\"\"\ntests/integration/hdf5/test_io.py:465:            del io.attrs['nwb_version']\ntests/integration/hdf5/test_io.py:477:    def test_check_nwb_version_old_version(self):\ntests/integration/hdf5/test_io.py:484:            io.attrs['nwb_version'] = \"1.0.5\"\ntests/integration/utils/test_io_utils.py:5:from pynwb.io.utils import get_nwb_version\ntests/integration/utils/test_io_utils.py:11:    def test_get_nwb_version(self):\ntests/integration/utils/test_io_utils.py:14:        builder1.set_attribute(name=\"nwb_version\", value=\"2.0.0\")\ntests/integration/utils/test_io_utils.py:17:        assert get_nwb_version(builder1) == (2, 0, 0)\ntests/integration/utils/test_io_utils.py:18:        assert get_nwb_version(builder2) == (2, 0, 0)\ntests/integration/utils/test_io_utils.py:20:    def test_get_nwb_version_missing(self):\ntests/integration/utils/test_io_utils.py:21:        \"\"\"Get the NWB version from a builder where the root builder does not have an nwb_version attribute.\"\"\"\ntests/integration/utils/test_io_utils.py:26:        with pytest.raises(ValueError, match=\"'nwb_version' attribute is missing from the root of the NWB file.\"):\ntests/integration/utils/test_io_utils.py:27:            get_nwb_version(builder1)\ntests/integration/utils/test_io_utils.py:29:        with pytest.raises(ValueError, match=\"'nwb_version' attribute is missing from the root of the NWB file.\"):\ntests/integration/utils/test_io_utils.py:30:            get_nwb_version(builder1)\ntests/integration/utils/test_io_utils.py:32:    def test_get_nwb_version_prerelease_false(self):\ntests/integration/utils/test_io_utils.py:35:        builder1.set_attribute(name=\"nwb_version\", value=\"2.0.0-alpha\")\ntests/integration/utils/test_io_utils.py:36:        assert get_nwb_version(builder1) == (2, 0, 0)\ntests/integration/utils/test_io_utils.py:38:    def test_get_nwb_version_prerelease_true1(self):\ntests/integration/utils/test_io_utils.py:41:        builder1.set_attribute(name=\"nwb_version\", value=\"2.0.0-alpha\")\ntests/integration/utils/test_io_utils.py:42:        assert get_nwb_version(builder1, include_prerelease=True) == (2, 0, 0, \"alpha\")\ntests/integration/utils/test_io_utils.py:44:    def test_get_nwb_version_prerelease_true2(self):\ntests/integration/utils/test_io_utils.py:47:        builder1.set_attribute(name=\"nwb_version\", value=\"2.0.0-alpha.sha-test.5114f85\")\ntests/integration/utils/test_io_utils.py:48:        assert get_nwb_version(builder1, include_prerelease=True) == (2, 0, 0, \"alpha.sha-test.5114f85\")\ntests/integration/utils/test_io_utils.py:50:    def test_get_nwb_version_20b(self):\ntests/integration/utils/test_io_utils.py:53:        builder1.set_attribute(name=\"nwb_version\", value=\"2.0b\")\ntests/integration/utils/test_io_utils.py:54:        assert get_nwb_version(builder1) == (2, 0, 0)\ntests/integration/utils/test_io_utils.py:55:        assert get_nwb_version(builder1, include_prerelease=True) == (2, 0, 0, \"b\")\n",
  "stderr": "grep: tests/back_compat/1.1.2_str_pub.nwb: binary file matches\ngrep: tests/back_compat/1.0.2_str_pub.nwb: binary file matches\ngrep: tests/back_compat/1.5.1_timeseries_no_unit.nwb: binary file matches\ngrep: tests/back_compat/1.1.2_str_experimenter.nwb: binary file matches\ngrep: tests/back_compat/1.1.0_str_experimenter.nwb: binary file matches\ngrep: tests/back_compat/2.1.0_imageseries_non_external_format.nwb: binary file matches\ngrep: tests/back_compat/1.0.3_str_pub.nwb: binary file matches\ngrep: tests/back_compat/1.5.1_timeseries_no_data.nwb: binary file matches\ngrep: tests/back_compat/1.0.2_str_experimenter.nwb: binary file matches\ngrep: tests/back_compat/1.0.3_str_experimenter.nwb: binary file matches\ngrep: tests/back_compat/1.5.1_imageseries_no_data.nwb: binary file matches\ngrep: tests/back_compat/1.1.0_str_pub.nwb: binary file matches\ngrep: tests/back_compat/2.2.0_subject_no_age__reference.nwb: binary file matches\ngrep: tests/back_compat/2.1.0_nwbfile_with_extension.nwb: binary file matches\ngrep: tests/back_compat/1.0.3_nwbfile.nwb: binary file matches\ngrep: tests/back_compat/1.5.1_imageseries_no_unit.nwb: binary file matches\ngrep: tests/back_compat/1.1.2_nwbfile.nwb: binary file matches\ngrep: tests/back_compat/1.0.2_nwbfile.nwb: binary file matches\ngrep: tests/back_compat/2.1.0_imageseries_no_data.nwb: binary file matches\ngrep: tests/back_compat/1.1.0_nwbfile.nwb: binary file matches\ngrep: tests/back_compat/2.1.0_imageseries_nonmatch_starting_frame.nwb: binary file matches\n",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "occurrences": 1,
  "strategy": "exact",
  "diff": "--- a/src/pynwb/__init__.py\n+++ b/src/pynwb/__init__.py\n@@ -258,6 +258,10 @@\n         #  or when the HDF5 file is not a valid NWB file\n         except KeyError:\n             return None, None\n+        \n+        if isinstance(nwb_version_string, bytes):\n+            nwb_version_string = nwb_version_string.decode('utf-8')\n+\n         # Parse the version string\n         nwb_version_parts = nwb_version_string.replace(\"-\", \".\").replace(\"_\", \".\").split(\".\")\n         nwb_version = tuple([int(i) if i.isnumeric() else i\n",
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "src/pynwb/io/utils.py",
  "occurrences": 1,
  "strategy": "exact",
  "diff": "--- a/src/pynwb/io/utils.py\n+++ b/src/pynwb/io/utils.py\n@@ -31,6 +31,10 @@\n     nwb_version = root_builder.attributes.get(\"nwb_version\")\n     if nwb_version is None:\n         raise ValueError(\"'nwb_version' attribute is missing from the root of the NWB file.\")\n+\n+    if isinstance(nwb_version, bytes):\n+        nwb_version = nwb_version.decode('utf-8')\n+\n     # handle special non-semver case\n     if nwb_version == \"2.0b\":\n         if not include_prerelease:\n",
  "is_truncated": false
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "/pynwb/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 2, in <module>\n  File \"/pynwb/src/pynwb/__init__.py\", line 109, in <module>\n    raise RuntimeError(\nRuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n",
  "details": {
    "stdout": "",
    "stderr": "/pynwb/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 2, in <module>\n  File \"/pynwb/src/pynwb/__init__.py\", line 109, in <module>\n    raise RuntimeError(\nRuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n",
    "exit_code": 1
  },
  "budget_warning": "Only 10 tool call(s) remaining (20/30 used). Finalize your edits and call submit_patch soon."
}

{
  "status": "ok",
  "filepath": "src/pynwb/io/utils.py",
  "content": "import re\nfrom typing import Tuple\n\nfrom hdmf.build import Builder\n\n\ndef get_nwb_version(builder: Builder, include_prerelease=False) -> Tuple[int, ...]:\n    \"\"\"Get the version of the NWB file from the root of the given builder, as a tuple.\n\n    If the \"nwb_version\" attribute on the root builder equals \"2.5.1\", then (2, 5, 1) is returned.\n    If the \"nwb_version\" attribute on the root builder equals \"2.5.1-alpha\" and include_prerelease=False,\n    then (2, 5, 1) is returned.\n    If the \"nwb_version\" attribute on the root builder equals \"2.5.1-alpha\" and include_prerelease=True,\n    then (2, 5, 1, \"alpha\") is returned.\n\n    If the \"nwb_version\" attribute == \"2.0b\" (the only deviation from semantic versioning in the 2.x series), then\n    if include_prerelease=True, (2, 0, 0, \"b\") is returned; else, (2, 0, 0) is returned.\n\n    :param builder: Any builder within an NWB file.\n    :type builder: Builder",
  "start_line": 1,
  "end_line": 20,
  "total_lines": 49,
  "is_truncated": false,
  "budget_warning": "Only 9 tool call(s) remaining (21/30 used). Finalize your edits and call submit_patch soon."
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "/workspace/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 1, in <module>\n  File \"/workspace/src/pynwb/__init__.py\", line 109, in <module>\n    raise RuntimeError(\nRuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n",
  "details": {
    "stdout": "",
    "stderr": "/workspace/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 1, in <module>\n  File \"/workspace/src/pynwb/__init__.py\", line 109, in <module>\n    raise RuntimeError(\nRuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n",
    "exit_code": 1
  },
  "budget_warning": "Only 8 tool call(s) remaining (22/30 used). Finalize your edits and call submit_patch soon."
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "\n==================================== ERRORS ====================================\n__________ ERROR collecting tests/integration/utils/test_io_utils.py ___________\ntests/integration/utils/test_io_utils.py:5: in <module>\n    from pynwb.io.utils import get_nwb_version\n/pynwb/src/pynwb/__init__.py:109: in <module>\n    raise RuntimeError(\nE   RuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n=============================== warnings summary ===============================\n../pynwb/src/pynwb/__init__.py:25\n  /pynwb/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n    from pkg_resources import resource_filename\n\n-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html\n=========================== short test summary info ============================\nERROR tests/integration/utils/test_io_utils.py - RuntimeError: 'core' is not ...\n!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!\n1 warning, 1 error in 0.63s\n",
  "details": {
    "stdout": "\n==================================== ERRORS ====================================\n__________ ERROR collecting tests/integration/utils/test_io_utils.py ___________\ntests/integration/utils/test_io_utils.py:5: in <module>\n    from pynwb.io.utils import get_nwb_version\n/pynwb/src/pynwb/__init__.py:109: in <module>\n    raise RuntimeError(\nE   RuntimeError: 'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to use the --recurse_submodules flag when cloning. See developer installation instructions here: https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n=============================== warnings summary ===============================\n../pynwb/src/pynwb/__init__.py:25\n  /pynwb/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n    from pkg_resources import resource_filename\n\n-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html\n=========================== short test summary info ============================\nERROR tests/integration/utils/test_io_utils.py - RuntimeError: 'core' is not ...\n!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!\n1 warning, 1 error in 0.63s\n",
    "stderr": "",
    "exit_code": 2
  },
  "budget_warning": "Only 7 tool call(s) remaining (23/30 used). Finalize your edits and call submit_patch soon."
}

{
  "status": "ok",
  "stdout": "Testing get_nwb_version...\nResult for b'2.0.0': (2, 0, 0)\nResult for b'2.5.1-alpha' (prerelease=True): (2, 5, 1, 'alpha')\nResult for b'2.0b' (prerelease=True): (2, 0, 0, 'b')\nAll tests passed!\n",
  "stderr": "",
  "exit_code": 0,
  "budget_warning": "Only 6 tool call(s) remaining (24/30 used). Finalize your edits and call submit_patch soon."
}