glotzerlab__signac-185

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "Traceback (most recent call last):\n  File \"<stdin>\", line 14, in <module>\n  File \"/workspace/signac/core/synceddict.py\", line 264, in __str__\n    return str(self())\n  File \"/workspace/signac/core/synceddict.py\", line 271, in __call__\n    self._synced_load()\n  File \"/workspace/signac/core/synceddict.py\", line 157, in _synced_load\n    self.load()\n  File \"/workspace/signac/core/synceddict.py\", line 165, in load\n    self._dfs_update(self._data, data)\n  File \"/workspace/signac/core/synceddict.py\", line 143, in _dfs_update\n    if old[key] == new[key]:\nValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()\n",
  "details": {
    "stdout": "",
    "stderr": "Traceback (most recent call last):\n  File \"<stdin>\", line 14, in <module>\n  File \"/workspace/signac/core/synceddict.py\", line 264, in __str__\n    return str(self())\n  File \"/workspace/signac/core/synceddict.py\", line 271, in __call__\n    self._synced_load()\n  File \"/workspace/signac/core/synceddict.py\", line 157, in _synced_load\n    self.load()\n  File \"/workspace/signac/core/synceddict.py\", line 165, in load\n    self._dfs_update(self._data, data)\n  File \"/workspace/signac/core/synceddict.py\", line 143, in _dfs_update\n    if old[key] == new[key]:\nValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "content": "        self._suspend_sync_ += 1\n        yield\n        self._suspend_sync_ -= 1\n\n    def _load(self):\n        return None\n\n    def _save(self):\n        pass\n\n    def _dfs_update(self, old, new):\n        for key in new:\n            if key in old:\n                if old[key] == new[key]:\n                    continue\n                elif isinstance(new[key], Mapping) and isinstance(old[key], Mapping):\n                    self._dfs_update(old[key], new[key])\n                    continue\n            old[key] = self._dfs_convert(new[key])\n        remove = set()\n        for key in old:\n            if key not in new:\n                remove.add(key)\n        for key in remove:\n            del old[key]\n\n    def _synced_load(self):\n        self.load()\n\n    def load(self):\n        if self._suspend_sync_ <= 0:\n            if self._parent is None:\n                data = self._load()\n                if data is not None:\n                    with self._suspend_sync():\n                        self._dfs_update(self._data, data)\n                    for value in self._data:\n                        if isinstance(value, Mapping):\n                            assert type(value) == type(self)\n            else:\n                self._parent.load()",
  "start_line": 130,
  "end_line": 170,
  "total_lines": 281,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "content": "# Copyright (c) 2018 The Regents of the University of Michigan\n# All rights reserved.\n# This software is licensed under the BSD 3-Clause License.\n\"Synchronized dictionary.\"\nimport logging\nfrom contextlib import contextmanager\nfrom functools import wraps\nfrom copy import deepcopy\n\nfrom ..common import six\n\nif six.PY2:\n    from collections import Mapping\n    from collections import MutableMapping\nelse:\n    from collections.abc import Mapping\n    from collections.abc import MutableMapping\n\n\nlogger = logging.getLogger(__name__)\n\n\nclass _SyncedList(list):\n\n    def __init__(self, iterable, parent):\n        self._parent = parent\n        super(_SyncedList, self).__init__(iterable)\n\n    def __deepcopy__(self, memo):\n        ret = type(self)([], deepcopy(self._parent, memo))",
  "start_line": 1,
  "end_line": 30,
  "total_lines": 281,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "signac/core/utility.py",
  "content": "# Copyright (c) 2017 The Regents of the University of Michigan\n# All rights reserved.\n# This software is licensed under the BSD 3-Clause License.\nimport re\nimport subprocess\n\n\ndef get_subject_from_certificate(fn_certificate):\n    try:\n        cert_txt = subprocess.check_output(\n            ['openssl', 'x509', '-in', fn_certificate,\n             '-inform', 'PEM', '-subject', '-nameopt', 'RFC2253']).decode()\n    except subprocess.CalledProcessError:\n        msg = \"Unable to retrieve subject from certificate '{}'.\"\n        raise RuntimeError(msg.format(fn_certificate))\n    else:\n        lines = cert_txt.split('\\n')\n        assert lines[0].startswith('subject=')\n        return lines[0][len('subject='):].strip()\n\n\nclass Version(dict):\n    \"\"\"Utility class to manage revision control numbers.\"\"\"\n\n    def __init__(self, major=0, minor=0, change=0,\n                 postrelease='', prerelease='final'):\n        if prerelease > 'final':\n            raise ValueError('illegal pre-release tag', prerelease)\n        super(Version, self).__init__(major=major, minor=minor,\n                                      change=change, postrelease=postrelease,\n                                      prerelease=prerelease)\n\n    def to_tuple(self):\n        return self['major'], self['minor'], self['change'],\\\n            self['prerelease'], self['postrelease']\n\n    def __lt__(self, other):\n        return self.to_tuple() < other.to_tuple()\n\n    def __eq__(self, other):\n        return self.to_tuple() == other.to_tuple()\n\n    def __str__(self):\n        return '{major}.{minor}{postrelease}.{change}{prerelease}'.format(\n            **self)\n\n    def __repr__(self):\n        return \"Version({})\".format(','.join(\n            ('{}={}'.format(k, v) for k, v in self.items())))\n\n\ndef parse_version(version_str):\n    \"\"\"Parse a version number into a version object.\"\"\"\n    p = re.compile(\n        r\"(?P<major>[0-9]*)\\.(?P<minor>[0-9]*)((?P<postrelease>-?\\w*)\"\n        r\"\\.(?P<change>[0-9])(?P<prerelease>\\w*))?\")\n    r = p.match(version_str)\n    v = r.groupdict()\n    version = Version(**{\n        'major': int(v.get('major') or 0),\n        'minor': int(v.get('minor') or 0),\n        'change': int(v.get('change') or 0),\n        'postrelease': str(v.get('postrelease') or ''),\n        'prerelease': str(v.get('prerelease') or 'final'),\n    })\n    return version",
  "start_line": 1,
  "end_line": 66,
  "total_lines": 66,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "occurrences": 1,
  "strategy": "exact",
  "diff": "--- a/signac/core/synceddict.py\n+++ b/signac/core/synceddict.py\n@@ -140,9 +140,12 @@\n     def _dfs_update(self, old, new):\n         for key in new:\n             if key in old:\n-                if old[key] == new[key]:\n-                    continue\n-                elif isinstance(new[key], Mapping) and isinstance(old[key], Mapping):\n+                try:\n+                    if old[key] == new[key]:\n+                        continue\n+                except ValueError:\n+                    pass\n+                if isinstance(new[key], Mapping) and isinstance(old[key], Mapping):\n                     self._dfs_update(old[key], new[key])\n                     continue\n             old[key] = self._dfs_convert(new[key])\n",
  "is_truncated": false
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "Traceback (most recent call last):\n  File \"/workspace/signac/contrib/project.py\", line 1468, in init_project\n    assert project.get_id() == str(name)\nAssertionError\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"<stdin>\", line 10, in <module>\n  File \"/workspace/signac/contrib/project.py\", line 1857, in init_project\n    return Project.init_project(name=name, root=root, workspace=workspace, make_dir=make_dir)\n  File \"/workspace/signac/contrib/project.py\", line 1477, in init_project\n    name, os.path.abspath(root)))\nRuntimeError: Failed to initialize project 'dfs-update-bug-fix'. Path '/workspace' already contains a conflicting project configuration.\n",
  "details": {
    "stdout": "",
    "stderr": "Traceback (most recent call last):\n  File \"/workspace/signac/contrib/project.py\", line 1468, in init_project\n    assert project.get_id() == str(name)\nAssertionError\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"<stdin>\", line 10, in <module>\n  File \"/workspace/signac/contrib/project.py\", line 1857, in init_project\n    return Project.init_project(name=name, root=root, workspace=workspace, make_dir=make_dir)\n  File \"/workspace/signac/contrib/project.py\", line 1477, in init_project\n    name, os.path.abspath(root)))\nRuntimeError: Failed to initialize project 'dfs-update-bug-fix'. Path '/workspace' already contains a conflicting project configuration.\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "stdout": "{'my_array': [0, 1, 2]}\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "Traceback (most recent call last):\n  File \"<stdin>\", line 15, in <module>\nAttributeError: 'Job' object has no attribute 'save'\n",
  "details": {
    "stdout": "",
    "stderr": "Traceback (most recent call last):\n  File \"<stdin>\", line 15, in <module>\nAttributeError: 'Job' object has no attribute 'save'\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "content": "            for k in root:\n                root[k] = self._dfs_convert(root[k])\n        elif isinstance(root, Mapping):\n            ret = type(self)(parent=self)\n            with ret._suspend_sync():\n                for k in root:\n                    ret[k] = root[k]\n            return ret\n        elif type(root) is list:\n            return _SyncedList(root, self)\n        return root\n\n    @classmethod\n    def _convert_to_dict(cls, root):\n        \"Convert (nested) values to dict.\"\n        if type(root) == cls:\n            ret = dict()\n            with root._suspend_sync():\n                for k in root:\n                    ret[k] = cls._convert_to_dict(root[k])\n            return ret\n        elif type(root) is dict:\n            for k in root:\n                root[k] = cls._convert_to_dict(root[k])\n        elif type(root) is _SyncedList:\n            return [cls._convert_to_dict(item) for item in root]\n        return root\n\n    @contextmanager\n    def _suspend_sync(self):\n        self._suspend_sync_ += 1",
  "start_line": 100,
  "end_line": 130,
  "total_lines": 284,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "content": "\n    def __getattribute__(self, name):\n        outer = super(_SyncedList, self).__getattribute__(name)\n\n        if name in ('append', 'clear', 'extend', 'insert', 'pop',\n                    'remove', 'reverse', 'sort'):\n\n            @wraps(outer)\n            def outer_wrapped_in_load_and_save(*args, **kwargs):\n                if hasattr(self, '_parent'):\n                    self._parent.load()\n                    ret = outer(*args, **kwargs)\n                    self._parent.save()\n                    return ret\n                else:\n                    return outer(*args, **kwargs)\n\n            return outer_wrapped_in_load_and_save\n        else:\n            return outer\n\n\nclass _SyncedDict(MutableMapping):\n\n    def __init__(self, initialdata=None, parent=None):\n        self._suspend_sync_ = 1\n        self._parent = parent\n        super(_SyncedDict, self).__init__()\n        if initialdata is None:\n            self._data = dict()\n        else:\n            self._data = {\n                self._validate_key(k): self._dfs_convert(v)\n                for k, v in initialdata.items()\n            }\n        self._suspend_sync_ = 0\n\n    @staticmethod\n    def _validate_key(key):\n        \"Emit a warning or raise an exception if key is invalid. Returns key.\"\n        if '.' in key:\n            from ..errors import InvalidKeyError\n            raise InvalidKeyError(\n                \"\\nThe use of '.' (dots) in keys is invalid.\\n\\n\"\n                \"See https://signac.io/document-wide-migration/ \"\n                \"for a recipe on how to replace dots in existing keys.\")\n        return key\n\n    def _dfs_convert(self, root):\n        if type(root) is type(self):\n            for k in root:",
  "start_line": 50,
  "end_line": 100,
  "total_lines": 284,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "content": "# Copyright (c) 2018 The Regents of the University of Michigan\n# All rights reserved.\n# This software is licensed under the BSD 3-Clause License.\n\"Synchronized dictionary.\"\nimport logging\nfrom contextlib import contextmanager\nfrom functools import wraps\nfrom copy import deepcopy\n\nfrom ..common import six\n\nif six.PY2:\n    from collections import Mapping\n    from collections import MutableMapping\nelse:\n    from collections.abc import Mapping\n    from collections.abc import MutableMapping\n\n\nlogger = logging.getLogger(__name__)\n\n\nclass _SyncedList(list):\n\n    def __init__(self, iterable, parent):\n        self._parent = parent\n        super(_SyncedList, self).__init__(iterable)\n\n    def __deepcopy__(self, memo):\n        ret = type(self)([], deepcopy(self._parent, memo))\n        for item in self:\n            super(_SyncedList, ret).append(deepcopy(item, memo))\n        return ret\n\n    def __getitem__(self, key):\n        self._parent.load()\n        ret = super(_SyncedList, self).__getitem__(key)\n        return ret\n\n    def __setitem__(self, key, value):\n        self._parent.load()\n        ret = super(_SyncedList, self).__setitem__(key, value)\n        self._parent.save()\n        return ret\n\n    def __delitem__(self, key):\n        self._parent.load()\n        super(_SyncedList, self).__delitem__(key)\n        self._parent.save()\n\n    def __getattribute__(self, name):\n        outer = super(_SyncedList, self).__getattribute__(name)\n\n        if name in ('append', 'clear', 'extend', 'insert', 'pop',\n                    'remove', 'reverse', 'sort'):\n\n            @wraps(outer)\n            def outer_wrapped_in_load_and_save(*args, **kwargs):\n                if hasattr(self, '_parent'):\n                    self._parent.load()\n                    ret = outer(*args, **kwargs)\n                    self._parent.save()\n                    return ret\n                else:\n                    return outer(*args, **kwargs)\n\n            return outer_wrapped_in_load_and_save\n        else:\n            return outer\n\n\nclass _SyncedDict(MutableMapping):\n\n    def __init__(self, initialdata=None, parent=None):\n        self._suspend_sync_ = 1\n        self._parent = parent\n        super(_SyncedDict, self).__init__()\n        if initialdata is None:\n            self._data = dict()\n        else:\n            self._data = {\n                self._validate_key(k): self._dfs_convert(v)\n                for k, v in initialdata.items()\n            }\n        self._suspend_sync_ = 0\n\n    @staticmethod\n    def _validate_key(key):\n        \"Emit a warning or raise an exception if key is invalid. Returns key.\"\n        if '.' in key:\n            from ..errors import InvalidKeyError\n            raise InvalidKeyError(\n                \"\\nThe use of '.' (dots) in keys is invalid.\\n\\n\"\n                \"See https://signac.io/document-wide-migration/ \"\n                \"for a recipe on how to replace dots in existing keys.\")\n        return key\n\n    def _dfs_convert(self, root):\n        if type(root) is type(self):\n            for k in root:\n                root[k] = self._dfs_convert(root[k])\n        elif isinstance(root, Mapping):\n            ret = type(self)(parent=self)\n            with ret._suspend_sync():\n                for k in root:\n                    ret[k] = root[k]\n            return ret\n        elif type(root) is list:\n            return _SyncedList(root, self)\n        return root\n\n    @classmethod\n    def _convert_to_dict(cls, root):\n        \"Convert (nested) values to dict.\"\n        if type(root) == cls:\n            ret = dict()\n            with root._suspend_sync():\n                for k in root:\n                    ret[k] = cls._convert_to_dict(root[k])\n            return ret\n        elif type(root) is dict:\n            for k in root:\n                root[k] = cls._convert_to_dict(root[k])\n        elif type(root) is _SyncedList:\n            return [cls._convert_to_dict(item) for item in root]\n        return root\n\n    @contextmanager\n    def _suspend_sync(self):\n        self._suspend_sync_ += 1\n        yield\n        self._suspend_sync_ -= 1\n\n    def _load(self):\n        return None\n\n    def _save(self):\n        pass\n\n    def _dfs_update(self, old, new):\n        for key in new:\n            if key in old:\n                try:\n                    if old[key] == new[key]:\n                        continue\n                except ValueError:\n                    pass\n                if isinstance(new[key], Mapping) and isinstance(old[key], Mapping):\n                    self._dfs_update(old[key], new[key])\n                    continue",
  "start_line": 1,
  "end_line": 150,
  "total_lines": 284,
  "is_truncated": true
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "content": "            old[key] = self._dfs_convert(new[key])\n        remove = set()\n        for key in old:\n            if key not in new:\n                remove.add(key)\n        for key in remove:\n            del old[key]\n\n    def _synced_load(self):\n        self.load()\n\n    def load(self):\n        if self._suspend_sync_ <= 0:\n            if self._parent is None:\n                data = self._load()\n                if data is not None:\n                    with self._suspend_sync():\n                        self._dfs_update(self._data, data)\n                    for value in self._data:\n                        if isinstance(value, Mapping):\n                            assert type(value) == type(self)\n            else:\n                self._parent.load()\n\n    def _synced_save(self):\n        self.save()\n\n    def save(self):\n        if self._suspend_sync_ <= 0:\n            if self._parent is None:\n                self._save()\n            else:\n                self._parent.save()\n\n    def __setitem__(self, key, value):\n        self._synced_load()\n        with self._suspend_sync():\n            self._data[self._validate_key(key)] = self._dfs_convert(value)\n        self._synced_save()\n        return value\n\n    def __getitem__(self, key):\n        self._synced_load()\n        return self._data[key]\n\n    def get(self, key, default=None):\n        self._synced_load()\n        return self._data.get(key, default)\n\n    def pop(self, key, default=None):\n        self._synced_load()\n        ret = self._data.pop(key, default)\n        self._synced_save()\n        return ret\n\n    def popitem(self):\n        self._synced_load()\n        key, value = self._data.popitem()\n        self._synced_save()\n        return key, value._as_dict()\n\n    def setdefault(self, key, default=None):\n        self._synced_load()\n        ret = self._data.setdefault(key, self._dfs_convert(default))\n        self._synced_save()\n        return ret\n\n    def __delitem__(self, key):\n        self._synced_load()\n        del self._data[key]\n        self._synced_save()\n\n    def clear(self):\n        with self._suspend_sync():\n            self._data.clear()\n        self._synced_save()\n\n    def _update(self, mapping):\n        with self._suspend_sync():\n            for key in mapping.keys():\n                self[key] = mapping[key]\n\n    def update(self, mapping):\n        self._synced_load()\n        self._update(mapping)\n        self._synced_save()\n\n    def __len__(self):\n        self._synced_load()\n        return len(self._data)\n\n    def __contains__(self, key):\n        self._synced_load()\n        return key in self._data\n\n    def __iter__(self):\n        self._synced_load()\n        with self._suspend_sync():\n            return iter(self._data)\n\n    def keys(self):\n        self._synced_load()\n        return self._data.keys()\n\n    def values(self):\n        self._synced_load()\n        return self._convert_to_dict(self._data).values()\n\n    def items(self):\n        self._synced_load()\n        return self._convert_to_dict(self._data).items()\n\n    def __repr__(self):\n        return repr(self())\n\n    def __str__(self):\n        return str(self())\n\n    def _as_dict(self):\n        with self._suspend_sync():\n            return self._convert_to_dict(self._data.copy())\n\n    def __call__(self):\n        self._synced_load()\n        return self._as_dict()\n\n    def __eq__(self, other):\n        if isinstance(other, type(self)):\n            return self() == other()\n        else:\n            return self() == other\n\n    def __ne__(self, other):\n        return not self.__eq__(other)",
  "start_line": 151,
  "end_line": 284,
  "total_lines": 284,
  "is_truncated": false
}