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",
  "stdout": "nwb_version_string type: <class 'bytes'>\nCaught expected exception: TypeError: 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": "Comparing b'2.2.4' == '2.0b': False\nCaught exception: TypeError: cannot use a string pattern on a bytes-like object\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "src/pynwb/__init__.py",
  "content": "'''This package will contain functions, classes, and objects\nfor reading and writing data in NWB format\n'''\nimport os.path\nfrom pathlib import Path\nfrom copy import deepcopy\nfrom warnings import warn\nimport h5py\n\nfrom hdmf.spec import NamespaceCatalog\nfrom hdmf.utils import docval, getargs, popargs, get_docval\nfrom hdmf.backends.io import HDMFIO\nfrom hdmf.backends.hdf5 import HDF5IO as _HDF5IO\nfrom hdmf.build import BuildManager, TypeMap\nimport hdmf.common\n\nCORE_NAMESPACE = 'core'\n__core_ns_file_name = 'nwb.namespace.yaml'\n\nfrom .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace  # noqa E402\nfrom .validate import validate  # noqa: F401, E402\n\n\ndef __get_resources():\n    from pkg_resources import resource_filename\n    ret = dict()\n    ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name)\n    return ret\n\n\ndef _get_resources():\n    # LEGACY: Needed to support legacy implementation.\n    return __get_resources()\n\n\n# a global namespace catalog\nglobal __NS_CATALOG\nglobal __TYPE_MAP\n\n__NS_CATALOG = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)\n\nhdmf_typemap = hdmf.common.get_type_map()\n__TYPE_MAP = TypeMap(__NS_CATALOG)\n__TYPE_MAP.merge(hdmf_typemap, ns_catalog=True)\n\n\n@docval({'name': 'extensions', 'type': (str, TypeMap, list),\n         'doc': 'a path to a namespace, a TypeMap, or a list consisting of paths to namespaces and TypeMaps',\n         'default': None},\n        returns=\"TypeMap loaded for the given extension or NWB core namespace\", rtype=tuple,\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": 1,
  "end_line": 100,
  "total_lines": 384,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "src/pynwb/__init__.py:194:class NWBHDF5IO(_HDF5IO):\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": "",
  "details": {
    "stdout": "",
    "stderr": "",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "stdout": "src/pynwb/legacy/map.py:8:        return val.decode('UTF-8')\nsrc/pynwb/_version.py:107:    stdout = process.communicate()[0].strip().decode()\n",
  "stderr": "",
  "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@@ -254,6 +254,8 @@\n         # Get the version string for the NWB file\n         try:\n             nwb_version_string = self._file.attrs['nwb_version']\n+            if isinstance(nwb_version_string, bytes):\n+                nwb_version_string = nwb_version_string.decode('utf-8')\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",
  "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 +31,8 @@\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+    if isinstance(nwb_version, bytes):\n+        nwb_version = nwb_version.decode('utf-8')\n     # handle special non-semver case\n     if nwb_version == \"2.0b\":\n         if not include_prerelease:\n",
  "is_truncated": false
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "/pynwb/src/pynwb/__init__.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n  from pkg_resources import resource_filename\nTraceback (most recent call last):\n  File \"<stdin>\", line 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 \"<stdin>\", 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": "ok",
  "stdout": "src/pynwb/nwb-schema:\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "All get_nwb_version tests passed!\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "All nwb_version_prop tests passed!\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:257:            if isinstance(nwb_version_string, bytes):\nsrc/pynwb/__init__.py:258:                nwb_version_string = nwb_version_string.decode('utf-8')\nsrc/pynwb/__init__.py:264:        nwb_version_parts = nwb_version_string.replace(\"-\", \".\").replace(\"_\", \".\").split(\".\")\nsrc/pynwb/__init__.py:265:        nwb_version = tuple([int(i) if i.isnumeric() else i\nsrc/pynwb/__init__.py:266:                             for i in nwb_version_parts])\nsrc/pynwb/__init__.py:267:        return nwb_version_string, nwb_version\nsrc/pynwb/__init__.py:282:            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:34:    if isinstance(nwb_version, bytes):\nsrc/pynwb/io/utils.py:35:        nwb_version = nwb_version.decode('utf-8')\nsrc/pynwb/io/utils.py:37:    if nwb_version == \"2.0b\":\nsrc/pynwb/io/utils.py:42:    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:43:    version_list = [int(i) for i in nwb_version_match.split(\".\")]\nsrc/pynwb/io/utils.py:45:        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",
  "stdout": " M src/pynwb/__init__.py\n M src/pynwb/io/utils.py\ndiff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py\nindex a5d3bdf..40a0066 100644\n--- a/src/pynwb/__init__.py\n+++ b/src/pynwb/__init__.py\n@@ -254,6 +254,8 @@ class NWBHDF5IO(_HDF5IO):\n         # Get the version string for the NWB file\n         try:\n             nwb_version_string = self._file.attrs['nwb_version']\n+            if isinstance(nwb_version_string, bytes):\n+                nwb_version_string = nwb_version_string.decode('utf-8')\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:\ndiff --git a/src/pynwb/io/utils.py b/src/pynwb/io/utils.py\nindex 23b41b6..b70b1bd 100644\n--- a/src/pynwb/io/utils.py\n+++ b/src/pynwb/io/utils.py\n@@ -31,6 +31,8 @@ def get_nwb_version(builder: Builder, include_prerelease=False) -> Tuple[int, ..\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+    if isinstance(nwb_version, bytes):\n+        nwb_version = nwb_version.decode('utf-8')\n     # handle special non-semver case\n     if nwb_version == \"2.0b\":\n         if not include_prerelease:\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "patch_size": 1270,
  "files_changed": 2
}