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        \"\"\"",
  "start_line": 240,
  "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 4, 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 4, 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",
  "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": "        returns=\"TypeMap loaded for the given extension or NWB core namespace\", rtype=tuple,\n        is_method=False)\ndef get_type_map(**kwargs):\n    '''\n    Get the TypeMap for the given extensions. If no extensions are provided,\n    return the TypeMap for the core namespace\n    '''\n    extensions = getargs('extensions', kwargs)\n    type_map = None\n    if extensions is None:\n        type_map = deepcopy(__TYPE_MAP)\n    else:\n        if isinstance(extensions, TypeMap):\n            type_map = extensions\n        else:\n            type_map = deepcopy(__TYPE_MAP)\n        if isinstance(extensions, list):\n            for ext in extensions:\n                if isinstance(ext, str):\n                    type_map.load_namespaces(ext)\n                elif isinstance(ext, TypeMap):\n                    type_map.merge(ext)\n                else:\n                    raise ValueError('extensions must be a list of paths to namespace specs or a TypeMaps')\n        elif isinstance(extensions, str):\n            type_map.load_namespaces(extensions)\n        elif isinstance(extensions, TypeMap):\n            type_map.merge(extensions)\n    return type_map\n\n\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": 50,
  "end_line": 100,
  "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 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
  }
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "ls: cannot access 'src/pynwb/nwb-schema﴾': No such file or directory\n",
  "details": {
    "stdout": "",
    "stderr": "ls: cannot access 'src/pynwb/nwb-schema﴾': No such file or directory\n",
    "exit_code": 2
  }
}

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

{
  "status": "ok",
  "stdout": ".\n..\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "String version: ('2.2.4', (2, 2, 4))\nBytes version failed: a bytes-like object is required, not 'str'\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",
  "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": "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 3, 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 3, 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": "Traceback (most recent call last):\n  File \"<stdin>\", line 39, in <module>\n  File \"/usr/local/lib/python3.10/site-packages/h5py/_hl/files.py\", line 566, in __init__\n    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)\n  File \"/usr/local/lib/python3.10/site-packages/h5py/_hl/files.py\", line 253, in make_fid\n    fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)\n  File \"h5py/_objects.pyx\", line 54, in h5py._objects.with_phil.wrapper\n  File \"h5py/_objects.pyx\", line 55, in h5py._objects.with_phil.wrapper\n  File \"h5py/h5f.pyx\", line 104, in h5py.h5f.open\nOSError: Unable to synchronously open file (file is already open for read-only)\n",
  "details": {
    "stdout": "Version string: 2.5.1\nVersion tuple: (2, 5, 1)\n",
    "stderr": "Traceback (most recent call last):\n  File \"<stdin>\", line 39, in <module>\n  File \"/usr/local/lib/python3.10/site-packages/h5py/_hl/files.py\", line 566, in __init__\n    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)\n  File \"/usr/local/lib/python3.10/site-packages/h5py/_hl/files.py\", line 253, in make_fid\n    fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)\n  File \"h5py/_objects.pyx\", line 54, in h5py._objects.with_phil.wrapper\n  File \"h5py/_objects.pyx\", line 55, in h5py._objects.with_phil.wrapper\n  File \"h5py/h5f.pyx\", line 104, in h5py.h5f.open\nOSError: Unable to synchronously open file (file is already open for read-only)\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "stdout": "Bytes test - Version string: 2.5.1\nBytes test - Version tuple: (2, 5, 1)\nString test - Version string: 2.5.1\nString test - Version tuple: (2, 5, 1)\n",
  "stderr": "",
  "exit_code": 0
}