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))",
  "start_line": 240,
  "end_line": 285,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "src/pynwb/io/utils.py",
  "content": "    :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)",
  "start_line": 25,
  "end_line": 45,
  "total_lines": 45,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "src/pynwb/io/utils.py:7:def get_nwb_version(builder: Builder, include_prerelease=False) -> Tuple[int, ...]:\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/io/file.py",
  "content": "        else:\n            datestr = dob_builder.data\n            date = dateutil_parse(datestr)\n            return date\n\n    @ObjectMapper.constructor_arg(\"age__reference\")\n    def age_reference_none(self, builder, manager):\n        age_builder = builder.get(\"age\")\n        age_reference = None\n        if age_builder is not None:\n            age_reference = age_builder[\"attributes\"].get(\"reference\")\n        if age_reference is None:\n            if get_nwb_version(builder) < (2, 6, 0):\n                return \"unspecified\"  # this is handled specially in Subject.__init__\n            else:\n                return \"birth\"\n        return age_reference",
  "start_line": 220,
  "end_line": 236,
  "total_lines": 236,
  "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": "/workspace/src/pynwb/nwb-schema:\n",
  "stderr": "",
  "exit_code": 0
}

{
  "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 \"<string>\", line 1, 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 \"<string>\", line 1, 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": "error",
  "error_type": "CommandError",
  "error_message": "\n==================================== ERRORS ====================================\n_________ ERROR collecting tests/back_compat/test_import_structure.py __________\ntests/back_compat/test_import_structure.py:3: in <module>\n    import pynwb\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_______________ ERROR collecting tests/back_compat/test_read.py ________________\ntests/back_compat/test_read.py:5: in <module>\n    from pynwb import NWBHDF5IO, validate, TimeSeries\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_____________ ERROR collecting tests/integration/hdf5/test_base.py _____________\ntests/integration/hdf5/test_base.py:5: in <module>\n    from pynwb import TimeSeries, NWBFile, NWBHDF5IO\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____________ ERROR collecting tests/integration/hdf5/test_device.py ____________\ntests/integration/hdf5/test_device.py:1: in <module>\n    from pynwb.device import Device\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___________ ERROR collecting tests/integration/hdf5/test_ecephys.py ____________\ntests/integration/hdf5/test_ecephys.py:3: in <module>\n    from pynwb.ecephys import ElectrodeGroup, ElectricalSeries, FilteredEphys, LFP, Clustering, ClusterWaveforms,\\\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___________ ERROR collecting tests/integration/hdf5/test_icephys.py ____________\ntests/integration/hdf5/test_icephys.py:3: in <module>\n    from pynwb import NWBFile\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____________ ERROR collecting tests/integration/hdf5/test_image.py _____________\ntests/integration/hdf5/test_image.py:3: in <module>\n    from pynwb.device import Device\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______________ ERROR collecting tests/integration/hdf5/test_io.py ______________\ntests/integration/hdf5/test_io.py:7: in <module>\n    from pynwb import NWBFile, TimeSeries, get_manager, NWBHDF5IO, validate\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_____________ ERROR collecting tests/integration/hdf5/test_misc.py _____________\ntests/integration/hdf5/test_misc.py:4: in <module>\n    from pynwb import TimeSeries\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",
  "details": {
    "stdout": "\n==================================== ERRORS ====================================\n_________ ERROR collecting tests/back_compat/test_import_structure.py __________\ntests/back_compat/test_import_structure.py:3: in <module>\n    import pynwb\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_______________ ERROR collecting tests/back_compat/test_read.py ________________\ntests/back_compat/test_read.py:5: in <module>\n    from pynwb import NWBHDF5IO, validate, TimeSeries\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_____________ ERROR collecting tests/integration/hdf5/test_base.py _____________\ntests/integration/hdf5/test_base.py:5: in <module>\n    from pynwb import TimeSeries, NWBFile, NWBHDF5IO\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____________ ERROR collecting tests/integration/hdf5/test_device.py ____________\ntests/integration/hdf5/test_device.py:1: in <module>\n    from pynwb.device import Device\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___________ ERROR collecting tests/integration/hdf5/test_ecephys.py ____________\ntests/integration/hdf5/test_ecephys.py:3: in <module>\n    from pynwb.ecephys import ElectrodeGroup, ElectricalSeries, FilteredEphys, LFP, Clustering, ClusterWaveforms,\\\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___________ ERROR collecting tests/integration/hdf5/test_icephys.py ____________\ntests/integration/hdf5/test_icephys.py:3: in <module>\n    from pynwb import NWBFile\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____________ ERROR collecting tests/integration/hdf5/test_image.py _____________\ntests/integration/hdf5/test_image.py:3: in <module>\n    from pynwb.device import Device\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______________ ERROR collecting tests/integration/hdf5/test_io.py ______________\ntests/integration/hdf5/test_io.py:7: in <module>\n    from pynwb import NWBFile, TimeSeries, get_manager, NWBHDF5IO, validate\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_____________ ERROR collecting tests/integration/hdf5/test_misc.py _____________\ntests/integration/hdf5/test_misc.py:4: in <module>\n    from pynwb import TimeSeries\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",
    "stderr": "",
    "exit_code": 2
  }
}

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

{
  "status": "ok",
  "stdout": "Success with <class 'str'>: ['2', '2', '4']\nFailed with <class 'bytes'>: a bytes-like object is required, not 'str'\n",
  "stderr": "",
  "exit_code": 0
}

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

{
  "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": 45,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "content": "                  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",
  "start_line": 250,
  "end_line": 265,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "occurrences": 1,
  "strategy": "unescaped",
  "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",
  "content": "    :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",
  "start_line": 20,
  "end_line": 30,
  "total_lines": 45,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "src/pynwb/io/utils.py",
  "content": "    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)",
  "start_line": 30,
  "end_line": 45,
  "total_lines": 45,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "src/pynwb/io/utils.py",
  "occurrences": 1,
  "strategy": "unescaped",
  "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": "",
  "details": {
    "stdout": "",
    "stderr": "",
    "exit_code": 1
  }
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "",
  "details": {
    "stdout": "",
    "stderr": "",
    "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/icephys.py",
  "content": "            TimeSeries.__init__,\n            'resolution',\n            'conversion',\n            'timestamps',\n            'starting_time',\n            'rate',\n            'comments',\n            'description',\n            'control',\n            'control_description',\n            'offset',\n        ),\n        {\n            'name': 'sweep_number', 'type': (int, 'uint32', 'uint64'),\n            'doc': 'Sweep number, allows for grouping different PatchClampSeries '\n                   'together via the sweep_table',\n            'default': None,\n        }\n    )\n    def __init__(self, **kwargs):\n        name, data, unit, stimulus_description = popargs('name', 'data', 'unit', 'stimulus_description', kwargs)\n        electrode, gain, sweep_number = popargs('electrode', 'gain', 'sweep_number', kwargs)\n        super().__init__(name, data, unit, **kwargs)\n        self.electrode = electrode\n        self.gain = gain\n        self.stimulus_description = stimulus_description\n\n        if sweep_number is not None:\n            if not (sweep_number >= 0):\n                raise ValueError(\"sweep_number must be a non-negative integer\")\n",
  "start_line": 120,
  "end_line": 150,
  "total_lines": 916,
  "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": "",
  "details": {
    "stdout": "",
    "stderr": "",
    "exit_code": 1
  },
  "budget_warning": "Only 8 tool call(s) remaining (22/30 used). Finalize your edits and call submit_patch soon."
}

{
  "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:        if isinstance(nwb_version_string, bytes):\nsrc/pynwb/__init__.py:263:            nwb_version_string = nwb_version_string.decode('utf-8')\nsrc/pynwb/__init__.py:266:        nwb_version_parts = nwb_version_string.replace(\"-\", \".\").replace(\"_\", \".\").split(\".\")\nsrc/pynwb/__init__.py:267:        nwb_version = tuple([int(i) if i.isnumeric() else i\nsrc/pynwb/__init__.py:268:                             for i in nwb_version_parts])\nsrc/pynwb/__init__.py:269:        return nwb_version_string, nwb_version\nsrc/pynwb/__init__.py:284:            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 isinstance(nwb_version, bytes):\nsrc/pynwb/io/utils.py:36:        nwb_version = nwb_version.decode('utf-8')\nsrc/pynwb/io/utils.py:39:    if nwb_version == \"2.0b\":\nsrc/pynwb/io/utils.py:44:    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:45:    version_list = [int(i) for i in nwb_version_match.split(\".\")]\nsrc/pynwb/io/utils.py:47:        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,
  "budget_warning": "Only 7 tool call(s) remaining (23/30 used). Finalize your edits and call submit_patch soon."
}