glotzerlab__signac-185

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "Traceback (most recent call last):\n  File \"<stdin>\", line 15, 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": "Printing job.doc...\n",
    "stderr": "Traceback (most recent call last):\n  File \"<stdin>\", line 15, 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()\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()",
  "start_line": 130,
  "end_line": 180,
  "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))\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",
  "start_line": 1,
  "end_line": 50,
  "total_lines": 281,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "./signac/core/h5store.py:79:    import numpy    # h5py depends on numpy, so this is safe.\n./signac/core/h5store.py:108:        grp[key] = numpy.bytes_(value)\n./signac/core/h5store.py:111:    elif type(value).__module__ == numpy.__name__:\n./signac/core/h5store.py:258:      * numpy arrays\n./signac/core/json.py:11:    import numpy\n./signac/core/json.py:43:            if isinstance(o, numpy.number):\n./signac/core/json.py:45:            elif isinstance(o, numpy.ndarray):\n./signac/common/tqdm/_tqdm_pandas.py:21:    >>> import numpy as np\n./signac/common/tqdm/_tqdm.py:456:        >>> import numpy as np\n./tests/test_numpy_integration.py:7:    import numpy    # noqa\n./tests/test_numpy_integration.py:13:@unittest.skipIf(not NUMPY, 'test requires the numpy package')\n./tests/test_numpy_integration.py:18:            a = numpy.float32(i) if i % 2 else numpy.float64(i)\n./tests/test_numpy_integration.py:19:            b = numpy.float64(i) if i % 2 else numpy.float32(i)\n./tests/test_numpy_integration.py:28:            self.project.open_job(dict(a=numpy.array([i]))).init()\n./tests/test_numpy_integration.py:31:            self.assertEqual(numpy.array([i]), job.sp.a)\n./tests/test_numpy_integration.py:36:            job.doc.array = numpy.ones(3) * i\n./tests/test_numpy_integration.py:39:            self.assertTrue(((numpy.array([i, i, i]) == job.doc.array).all()))\n./tests/test_h5store.py:45:    import numpy    # noqa\n./tests/test_h5store.py:86:                raise unittest.SkipTest(\"This test requires the numpy package.\")\n./tests/test_h5store.py:87:            numpy.testing.assert_array_equal(a, b)\n./tests/test_h5store.py:137:        'numpy_float_array': numpy.array([-1.5, 0, 1.5], dtype=float),\n./tests/test_h5store.py:138:        'numpy_int_array': numpy.array([-1, 0, 1], dtype=int),\n./tests/test_h5store.py:389:                        self.assertTrue(isinstance(v, (array, numpy.ndarray)))\n./tests/test_h5store.py:580:@unittest.skipIf(not NUMPY, 'requires numpy package')\n./tests/test_h5store.py:587:            numpy.random.rand(8, size), index=[string.ascii_letters[i] for i in range(8)])\n./tests/test_h5store.py:610:@unittest.skipIf(not NUMPY, 'requires numpy package')\n./tests/test_h5store.py:617:            numpy.random.rand(8, size), index=[string.ascii_letters[i] for i in range(8)]))\n./tests/test_h5store.py:729:@unittest.skipIf(not NUMPY, 'requires numpy package')\n./tests/test_h5store.py:737:        times = numpy.zeros(200)\n./tests/test_h5store.py:754:        msg += format_row('mean', numpy.mean)\n./tests/test_h5store.py:755:        msg += format_row('median', numpy.median)\n./tests/test_h5store.py:756:        msg += format_row('25 percentile', partial(numpy.percentile, q=25))\n./tests/test_h5store.py:757:        msg += format_row('75 percentile', partial(numpy.percentile, q=75))\n./tests/test_h5store.py:759:            numpy.percentile(times, 25) / numpy.percentile(self.baseline_time, 75),\n./tests/test_h5store.py:763:        times = numpy.zeros(200)\n./tests/test_h5store.py:775:        times = numpy.zeros(200)\n./tests/test_h5store.py:795:        times = numpy.zeros(200)\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "signac/core/json.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.\nfrom __future__ import absolute_import\nimport logging\n\nlogger = logging.getLogger(__name__)\nmsg = \"Using '{}' package for JSON encoding/decoding.\"\n\ntry:\n    import numpy\n    NUMPY = True\nexcept ImportError:\n    NUMPY = False\n\ntry:\n    import rapidjson as json\n    from rapidjson import Encoder\n\n    class JSONEncoder(Encoder):",
  "start_line": 1,
  "end_line": 20,
  "total_lines": 66,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "True\nFalse\nTrue\nFalse\n",
  "stderr": "",
  "exit_code": 0
}

{
  "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 +140,17 @@\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+                    try:\n+                        import numpy as np\n+                        if np.array_equal(old[key], new[key]):\n+                            continue\n+                    except ImportError:\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": "ok",
  "stdout": "Printing job.doc...\n{'my_array': array([0, 1, 2])}\n",
  "stderr": "",
  "exit_code": 0
}

{
  "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-edge'. 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-edge'. Path '/workspace' already contains a conflicting project configuration.\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "stdout": "Case 1 (same array): [0 1 2]\nCase 2 (diff array): [3 4 5]\nCase 3 (numpy to list same): [0, 1, 2]\nCase 4 (numpy to list diff): [0, 1, 3]\nCase 5 (list to numpy same): [0 1 2]\nCase 6 (list to numpy diff): [0 1 3]\nCase 7 (nested numpy): {'a': array([1, 2])}\nCase 8 (nested numpy same): {'a': array([1, 2])}\nCase 9 (nested numpy diff): {'a': array([1, 3])}\nFinal doc: {'my_array': [0, 1, 3], 'my_list': array([0, 1, 3]), 'nested': {'a': array([1, 3])}}\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "...                                                                      [100%]\n3 passed in 0.35s\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "tests/test_synced_attrdict.py:10:from signac.core.synceddict import _SyncedDict\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "........................                                                 [100%]\n24 passed in 0.18s\n",
  "stderr": "",
  "exit_code": 0
}

{
  "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__)",
  "start_line": 1,
  "end_line": 20,
  "total_lines": 289,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "        if type(root) == cls:\n                    if old[key] == new[key]:\n                            assert type(value) == type(self)\n            return self() == other()\n            return self() == other\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "115:        if type(root) == cls:\n144:                    if old[key] == new[key]:\n176:                            assert type(value) == type(self)\n284:            return self() == other()\n286:            return self() == other\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "content": "\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):",
  "start_line": 270,
  "end_line": 288,
  "total_lines": 289,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "signac/core/synceddict.py",
  "content": "            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):",
  "start_line": 230,
  "end_line": 260,
  "total_lines": 289,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "113:    def _convert_to_dict(cls, root):\n119:                    ret[k] = cls._convert_to_dict(root[k])\n123:                root[k] = cls._convert_to_dict(root[k])\n125:            return [cls._convert_to_dict(item) for item in root]\n262:        return self._convert_to_dict(self._data).values()\n266:        return self._convert_to_dict(self._data).items()\n276:            return self._convert_to_dict(self._data.copy())\n",
  "stderr": "",
  "exit_code": 0,
  "budget_warning": "Only 10 tool call(s) remaining (20/30 used). Finalize your edits and call submit_patch soon."
}