neurodatawithoutborders__pynwb-1669

{
  "status": "ok",
  "stdout": "245:    def nwb_version(self):\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()\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        \"\"\"",
  "start_line": 230,
  "end_line": 270,
  "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": "    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",
  "filepath": "src/pynwb/__init__.py",
  "content": "\n@docval(*get_docval(get_type_map),\n        returns=\"the namespaces loaded from the given file\", rtype=tuple,\n        is_method=False)\ndef get_manager(**kwargs):\n    '''\n    Get a BuildManager to use for I/O using the given extensions. If no extensions are provided,\n    return a BuildManager that uses the core namespace\n    '''\n    type_map = get_type_map(**kwargs)\n    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)",
  "start_line": 80,
  "end_line": 100,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "24:def __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\n# a global namespace catalog\nglobal __NS_CATALOG\nglobal __TYPE_MAP\n\n__NS_CATALOG = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)",
  "start_line": 20,
  "end_line": 40,
  "total_lines": 384,
  "is_truncated": false
}

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

{
  "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/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
}

{
  "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": "/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": "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 15, in <module>\n  File \"/workspace/src/pynwb/__init__.py\", line 107, in <module>\n    load_namespaces(__resources['namespace_path'])\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/utils.py\", line 672, in func_call\n    return func(**pargs)\n  File \"/workspace/src/pynwb/__init__.py\", line 101, in load_namespaces\n    return __TYPE_MAP.load_namespaces(namespace_path)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/utils.py\", line 668, in func_call\n    return func(args[0], **pargs)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/build/manager.py\", line 482, in load_namespaces\n    deps = self.__ns_catalog.load_namespaces(**kwargs)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/utils.py\", line 668, in func_call\n    return func(args[0], **pargs)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/spec/namespace.py\", line 529, in load_namespaces\n    namespaces = reader.read_namespace(namespace_path)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/spec/namespace.py\", line 202, in read_namespace\n    with open(namespace_path, 'r') as stream:\nFileNotFoundError: [Errno 2] No such file or directory: '/workspace/src/pynwb/nwb-schema/core/nwb.namespace.yaml'\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 15, in <module>\n  File \"/workspace/src/pynwb/__init__.py\", line 107, in <module>\n    load_namespaces(__resources['namespace_path'])\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/utils.py\", line 672, in func_call\n    return func(**pargs)\n  File \"/workspace/src/pynwb/__init__.py\", line 101, in load_namespaces\n    return __TYPE_MAP.load_namespaces(namespace_path)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/utils.py\", line 668, in func_call\n    return func(args[0], **pargs)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/build/manager.py\", line 482, in load_namespaces\n    deps = self.__ns_catalog.load_namespaces(**kwargs)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/utils.py\", line 668, in func_call\n    return func(args[0], **pargs)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/spec/namespace.py\", line 529, in load_namespaces\n    namespaces = reader.read_namespace(namespace_path)\n  File \"/usr/local/lib/python3.10/site-packages/hdmf/spec/namespace.py\", line 202, in read_namespace\n    with open(namespace_path, 'r') as stream:\nFileNotFoundError: [Errno 2] No such file or directory: '/workspace/src/pynwb/nwb-schema/core/nwb.namespace.yaml'\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "filepath": "src/pynwb/io/utils.py",
  "content": "        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": 40,
  "end_line": 49,
  "total_lines": 49,
  "is_truncated": false
}

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

{
  "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
}

{
  "status": "ok",
  "filepath": "src/pynwb/icephys.py",
  "content": "def ensure_unit(self, name, current_unit, unit, nwb_version):\n    \"\"\"A helper to ensure correct unit used.\n\n    Issues a warning with details if `current_unit` is to be ignored, and\n    `unit` to be used instead.\n    \"\"\"\n    if current_unit != unit:\n        warnings.warn(\n            \"Unit '%s' for %s '%s' is ignored and will be set to '%s' \"\n            \"as per NWB %s.\"\n            % (current_unit, self.__class__.__name__, name, unit, nwb_version))\n    return unit\n\n\n@register_class('IntracellularElectrode', CORE_NAMESPACE)\nclass IntracellularElectrode(NWBContainer):\n    \"\"\"Describes an intracellular electrode and associated metadata.\"\"\"\n\n    __nwbfields__ = ('cell_id',\n                     'slice',\n                     'seal',\n                     'description',\n                     'location',\n                     'resistance',\n                     'filtering',\n                     'initial_access_resistance',\n                     'device')\n\n    @docval({'name': 'name', 'type': str, 'doc': 'the name of this electrode'},\n            {'name': 'device', 'type': Device, 'doc': 'the device that was used to record from this electrode'},\n            {'name': 'description', 'type': str,\n             'doc': 'Recording description, description of electrode (e.g.,  whole-cell, sharp, etc).'},\n            {'name': 'slice', 'type': str, 'doc': 'Information about slice used for recording.', 'default': None},\n            {'name': 'seal', 'type': str, 'doc': 'Information about seal used for recording.', 'default': None},\n            {'name': 'location', 'type': str,\n             'doc': 'Area, layer, comments on estimation, stereotaxis coordinates (if in vivo, etc).', 'default': None},\n            {'name': 'resistance', 'type': str, 'doc': 'Electrode resistance, unit: Ohm.', 'default': None},\n            {'name': 'filtering', 'type': str, 'doc': 'Electrode specific filtering.', 'default': None},\n            {'name': 'initial_access_resistance', 'type': str, 'doc': 'Initial access resistance.', 'default': None},\n            {'name': 'cell_id', 'type': str, 'doc': 'Unique ID of cell.', 'default': None}\n            )\n    def __init__(self, **kwargs):\n        keys_to_set = (\n            'slice',\n            'seal',\n            'description',\n            'location',\n            'resistance',\n            'filtering',\n            'initial_access_resistance',\n            'device',\n            'cell_id'\n        )\n        args_to_set = popargs_to_dict(keys_to_set, kwargs)\n        super().__init__(**kwargs)\n\n        for key, val in args_to_set.items():\n            setattr(self, key, val)\n\n\n@register_class('PatchClampSeries', CORE_NAMESPACE)\nclass PatchClampSeries(TimeSeries):\n    '''\n    Stores stimulus or response current or voltage. Superclass definition for patch-clamp data\n    (this class should not be instantiated directly).\n    '''\n\n    __nwbfields__ = (\n        'electrode',\n        'gain',\n        'stimulus_description',\n        'sweep_number',\n    )\n\n    @docval(\n        *get_docval(TimeSeries.__init__, 'name'),  # required\n        {\n            \"name\": \"data\",\n            \"type\": (\"array_data\", \"data\", TimeSeries),\n            \"doc\": \"The data values. The first dimension must be time.\",\n            \"shape\": (None,),\n        },   # required\n        {\n            'name': 'unit',\n            'type': str,\n            'doc': 'The base unit of measurement (should be SI unit)',\n        },  # required\n        {\n            'name': 'electrode',\n            'type': IntracellularElectrode,\n            'doc': 'IntracellularElectrode group that describes the electrode that was '\n                   'used to apply or record this data.',\n        },    # required\n        {\n            'name': 'gain',\n            'type': float,\n            'doc': 'Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)',\n        },  # required\n        {\n            'name': 'stimulus_description',\n            'type': str,\n            'doc': 'the stimulus name/protocol',\n            'default': \"N/A\",\n        },\n        *get_docval(\n            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\n            self.sweep_number = sweep_number\n\n\n@register_class('CurrentClampSeries', CORE_NAMESPACE)\nclass CurrentClampSeries(PatchClampSeries):\n    '''\n    Stores voltage data recorded from intracellular current-clamp recordings. A corresponding\n    CurrentClampStimulusSeries (stored separately as a stimulus) is used to store the current\n    injected.\n    '''\n\n    __nwbfields__ = ('bias_current',\n                     'bridge_balance',\n                     'capacitance_compensation')",
  "start_line": 15,
  "end_line": 164,
  "total_lines": 916,
  "is_truncated": true
}