neurodatawithoutborders__pynwb-1669

{
  "status": "ok",
  "stdout": "8:src/pynwb/__init__.py:262:        nwb_version_parts = nwb_version_string.replace(\"-\", \".\").replace(\"_\", \".\").split(\".\")\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": "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": "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",
  "filepath": "src/pynwb/__init__.py",
  "content": "    return BuildManager(type_map)\n\n\n@docval({'name': 'namespace_path', 'type': str, 'doc': 'the path to the YAML with the namespace definition'},\n        returns=\"the namespaces loaded from the given file\", rtype=tuple,\n        is_method=False)\ndef load_namespaces(**kwargs):\n    '''\n    Load namespaces from file\n    '''\n    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": 90,
  "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": "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": "\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)",
  "start_line": 180,
  "end_line": 190,
  "total_lines": 384,
  "is_truncated": false
}

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

{
  "status": "ok",
  "stdout": "13:from hdmf.backends.hdf5 import HDF5IO as _HDF5IO\n194:class NWBHDF5IO(_HDF5IO):\n267:    @docval(*get_docval(_HDF5IO.read),\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "nwb_version: ('2.2.4', (2, 2, 4))\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "Type of nwb_version_string: <class 'str'>\nResult: ('2.2.4', (2, 2, 4))\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "",
  "stderr": "Traceback (most recent call last):\n  File \"<stdin>\", line 9, in <module>\n  File \"<stdin>\", line 3, in get_nwb_version\nTypeError: a bytes-like object is required, not 'str'\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",
  "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": "error",
  "error_type": "CommandError",
  "error_message": "\n==================================== ERRORS ====================================\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=============================== 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/hdf5/test_io.py - RuntimeError: 'core' is not a regis...\n!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!\n1 warning, 1 error in 0.72s\n",
  "details": {
    "stdout": "\n==================================== ERRORS ====================================\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=============================== 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/hdf5/test_io.py - RuntimeError: 'core' is not a regis...\n!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!\n1 warning, 1 error in 0.72s\n",
    "stderr": "",
    "exit_code": 2
  }
}

{
  "status": "ok",
  "stdout": "All tests passed!\n",
  "stderr": "",
  "exit_code": 0,
  "budget_warning": "Only 10 tool call(s) remaining (20/30 used). Finalize your edits and call submit_patch soon."
}

{
  "status": "ok",
  "stdout": "src/pynwb/__init__.py:256:            nwb_version_string = self._file.attrs['nwb_version']\n",
  "stderr": "",
  "exit_code": 0,
  "budget_warning": "Only 9 tool call(s) remaining (21/30 used). Finalize your edits and call submit_patch soon."
}

{
  "status": "ok",
  "stdout": "7:def get_nwb_version(builder: Builder, include_prerelease=False) -> Tuple[int, ...]:\n10:    If the \"nwb_version\" attribute on the root builder equals \"2.5.1\", then (2, 5, 1) is returned.\n11:    If the \"nwb_version\" attribute on the root builder equals \"2.5.1-alpha\" and include_prerelease=False,\n13:    If the \"nwb_version\" attribute on the root builder equals \"2.5.1-alpha\" and include_prerelease=True,\n16:    If the \"nwb_version\" attribute == \"2.0b\" (the only deviation from semantic versioning in the 2.x series), then\n25:    :raises ValueError: if the 'nwb_version' attribute is missing from the root of the NWB file.\n31:    nwb_version = root_builder.attributes.get(\"nwb_version\")\n32:    if nwb_version is None:\n33:        raise ValueError(\"'nwb_version' attribute is missing from the root of the NWB file.\")\n35:    if nwb_version == \"2.0b\":\n40:    nwb_version_match = re.match(r\"(\\d+\\.\\d+\\.\\d+)\", nwb_version)[0]  # trim off any non-numeric symbols at end\n41:    version_list = [int(i) for i in nwb_version_match.split(\".\")]\n43:        prerelease_info = nwb_version[nwb_version.index(\"-\")+1:]\n",
  "stderr": "",
  "exit_code": 0,
  "budget_warning": "Only 8 tool call(s) remaining (22/30 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\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)",
  "start_line": 1,
  "end_line": 45,
  "total_lines": 45,
  "is_truncated": false,
  "budget_warning": "Only 7 tool call(s) remaining (23/30 used). Finalize your edits and call submit_patch soon."
}