networkx has no attribute 'utils'

[gwbischof]

handler_registry:
NPY_SEQ: ophyd.sim.NumpySeqHandler

---

AttributeError Traceback (most recent call last)

in ----> 1 a[1] ~/conda_envs/garrett/lib/python3.7/site-packages/intake/catalog/entry.py in __getitem__(self, item) 145 else: 146 item = item[0] --> 147 return self._get_default_source()[item] 148 149 def __repr__(self): ~/conda_envs/garrett/lib/python3.7/site-packages/intake/catalog/entry.py in _get_default_source(self) 112 def _get_default_source(self): 113 """Instantiate DataSource with default agruments""" --> 114 return self() 115 116 @property ~/conda_envs/garrett/lib/python3.7/site-packages/intake/catalog/entry.py in __call__(self, persist, **kwargs) 98 raise ValueError('Persist value (%s) not understood' % persist) 99 persist = persist or self._pmode --> 100 s = self.get(**kwargs) 101 if s.has_been_persisted and persist is not 'never': 102 s2 = s.get_persisted() ~/conda_envs/garrett/lib/python3.7/site-packages/intake/catalog/local.py in get(self, **user_parameters) 272 """Instantiate the DataSource for the given parameters""" 273 plugin, open_args = self._create_open_args(user_parameters) --> 274 data_source = plugin(**open_args) 275 data_source.catalog_object = self._catalog 276 data_source.name = self.name ~/dama/intake-bluesky/intake_bluesky/mongo_normalized.py in __init__(self, metadatastore_db, asset_registry_db, handler_registry, query, **kwargs) 61 self._query = query or {} 62 if handler_registry is None: ---> 63 handler_registry = {} 64 parsed_handler_registry = parse_handler_registry(handler_registry) 65 self.filler = event_model.Filler(parsed_handler_registry) ~/dama/intake-bluesky/intake_bluesky/core.py in parse_handler_registry(handler_registry) 680 if isinstance(handler_str, str): 681 module_name, _, class_name = handler_str.rpartition('.') --> 682 class_ = getattr(importlib.import_module(module_name), class_name) 683 else: 684 class_ = handler_str ~/conda_envs/garrett/lib/python3.7/importlib/__init__.py in import_module(name, package) 125 break 126 level += 1 --> 127 return _bootstrap._gcd_import(name[level:], package, level) 128 129 ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _gcd_import(name, package, level) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _find_and_load(name, import_) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _find_and_load_unlocked(name, import_) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _call_with_frames_removed(f, *args, **kwds) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _gcd_import(name, package, level) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _find_and_load(name, import_) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _find_and_load_unlocked(name, import_) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _load_unlocked(spec) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap_external.py in exec_module(self, module) ~/conda_envs/garrett/lib/python3.7/importlib/_bootstrap.py in _call_with_frames_removed(f, *args, **kwds) ~/conda_envs/garrett/lib/python3.7/site-packages/ophyd/__init__.py in 87 ALL_COMPONENTS, kind_context) 88 from .status import StatusBase ---> 89 from .mca import EpicsMCA, EpicsDXP 90 from .quadem import QuadEM, NSLS_EM, TetrAMM, APS_EM 91 ~/conda_envs/garrett/lib/python3.7/site-packages/ophyd/mca.py in 8 from .device import (Device, Component as C, DynamicDeviceComponent as DDC, 9 Staged, BlueskyInterface, ALL_COMPONENTS, Kind) ---> 10 from .areadetector import EpicsSignalWithRBV as SignalWithRBV 11 12 ~/conda_envs/garrett/lib/python3.7/site-packages/ophyd/areadetector/__init__.py in 6 logger.addHandler(logging.NullHandler()) 7 ----> 8 from .base import * 9 from .cam import * 10 from .detectors import * ~/conda_envs/garrett/lib/python3.7/site-packages/ophyd/areadetector/base.py in 4 import sys 5 from collections import OrderedDict ----> 6 import networkx as nx 7 8 from ..signal import EpicsSignal ~/conda_envs/garrett/lib/python3.7/site-packages/networkx/__init__.py in 112 from networkx.relabel import * 113 --> 114 import networkx.generators 115 from networkx.generators import * 116 ~/conda_envs/garrett/lib/python3.7/site-packages/networkx/generators/__init__.py in 12 from networkx.generators.expanders import * 13 from networkx.generators.geometric import * ---> 14 from networkx.generators.intersection import * 15 from networkx.generators.joint_degree_seq import * 16 from networkx.generators.lattice import * ~/conda_envs/garrett/lib/python3.7/site-packages/networkx/generators/intersection.py in 11 import random 12 import networkx as nx ---> 13 from networkx.algorithms import bipartite 14 from networkx.utils import py_random_state 15 ~/conda_envs/garrett/lib/python3.7/site-packages/networkx/algorithms/__init__.py in 71 import networkx.algorithms.tournament 72 import networkx.algorithms.traversal ---> 73 import networkx.algorithms.tree 74 75 # Make certain functions from some of the previous subpackages available ~/conda_envs/garrett/lib/python3.7/site-packages/networkx/algorithms/tree/__init__.py in ----> 1 from .branchings import * 2 from .coding import * 3 from .mst import * 4 from .recognition import * 5 from .operations import * ~/conda_envs/garrett/lib/python3.7/site-packages/networkx/algorithms/tree/branchings.py in 39 from networkx.utils import py_random_state 40 ---> 41 from .recognition import * 42 43 __all__ = [ ~/conda_envs/garrett/lib/python3.7/site-packages/networkx/algorithms/tree/recognition.py in 86 87 ---> 88 @nx.utils.not_implemented_for('undirected') 89 def is_arborescence(G): 90 """ AttributeError: module 'networkx' has no attribute 'utils'

[gwbischof]

my conda env:

packages in environment at /home/gbischof/conda_envs/bb:

#

Name Version Build Channel

anaconda-client 1.7.2 py37_0 http://alexandria/conda/defaults appdirs 1.4.3 asciitree 0.3.3 asn1crypto 0.24.0 py37_0 http://alexandria/conda/defaults backcall 0.1.0 bluesky 1.5.2 bluesky-browser 0.post100+ge6b8ab7 ca-certificates 2018.03.07 0 http://alexandria/conda/defaults certifi 2018.10.15 py37_0 http://alexandria/conda/defaults cffi 1.11.5 py37he75722e_1 http://alexandria/conda/defaults cftime 1.0.3.4 chardet 3.0.4 py37_1 http://alexandria/conda/defaults cloudpickle 0.8.1 clyent 1.2.2 py37_1 http://alexandria/conda/defaults cryptography 2.4.1 py37h1ba5d50_0 http://alexandria/conda/defaults cycler 0.10.0 dask 1.2.1 decorator 4.3.0 py37_0 http://alexandria/conda/defaults event-model 1.9.0a3 fasteners 0.14.1 historydict 1.2.3 holoviews 1.12.2 idna 2.7 py37_0 http://alexandria/conda/defaults intake 0.4.4 intake-bluesky 0.1.0a5.post1+g2bf76e8 intake-xarray 0.3.0 ipython 7.5.0 ipython_genutils 0.2.0 py37_0 http://alexandria/conda/defaults jedi 0.13.3 Jinja2 2.10.1 jsonschema 2.6.0 py37_0 http://alexandria/conda/defaults jupyter_core 4.4.0 py37_0 http://alexandria/conda/defaults kiwisolver 1.1.0 libedit 3.1.20170329 h6b74fdf_2 http://alexandria/conda/defaults libffi 3.2.1 hd88cf55_4 http://alexandria/conda/defaults libgcc-ng 8.2.0 hdf63c60_1 http://alexandria/conda/defaults libstdcxx-ng 8.2.0 hdf63c60_1 http://alexandria/conda/defaults locket 0.2.0 MarkupSafe 1.1.1 matplotlib 3.0.3 mongoquery 1.3.5 monotonic 1.5 msgpack 0.6.1 msgpack-numpy 0.4.4.2 msgpack-python 0.5.6 nbformat 4.4.0 py37_0 http://alexandria/conda/defaults ncurses 6.1 he6710b0_1 http://alexandria/conda/defaults netCDF4 1.5.1 networkx 2.3 numcodecs 0.6.3 numpy 1.16.3 openssl 1.1.1 h7b6447c_0 http://alexandria/conda/defaults ophyd 1.3.2 pandas 0.24.2 param 1.9.0 parso 0.4.0 partd 0.3.10 pexpect 4.7.0 pickleshare 0.7.5 pip 18.1 py37_0 http://alexandria/conda/defaults prompt-toolkit 2.0.9 ptyprocess 0.6.0 pycparser 2.19 py37_0 http://alexandria/conda/defaults pyepics 3.3.3 Pygments 2.3.1 pymongo 3.8.0 pyopenssl 18.0.0 py37_0 http://alexandria/conda/defaults pyparsing 2.4.0 PyQt5 5.12.1 PyQt5_sip 4.19.15 pysocks 1.6.8 py37_0 http://alexandria/conda/defaults python 3.7.1 h0371630_3 http://alexandria/conda/defaults python-dateutil 2.7.5 py37_0 http://alexandria/conda/defaults python-snappy 0.5.4 pytz 2018.7 py37_0 http://alexandria/conda/defaults pyviz-comms 0.7.2 pyyaml 3.13 py37h14c3975_0 http://alexandria/conda/defaults pyzmq 16.0.4 QtPy 1.7.0 readline 7.0 h7b6447c_5 http://alexandria/conda/defaults requests 2.20.1 py37_0 http://alexandria/conda/defaults setuptools 40.6.2 py37_0 http://alexandria/conda/defaults six 1.11.0 py37_1 http://alexandria/conda/defaults sqlite 3.25.3 h7b6447c_0 http://alexandria/conda/defaults suitcase-jsonl 0.1.1 suitcase-utils 0.1.3 super-state-machine 2.0.2 tk 8.6.8 hbc83047_0 http://alexandria/conda/defaults toolz 0.9.0 tornado 4.5.3 tqdm 4.31.1 traitlets 4.3.2 py37_0 http://alexandria/conda/defaults urllib3 1.23 py37_0 http://alexandria/conda/defaults wcwidth 0.1.7 wheel 0.32.3 py37_0 http://alexandria/conda/defaults xarray 0.12.1 xz 5.2.4 h14c3975_4 http://alexandria/conda/defaults yaml 0.1.7 had09818_2 http://alexandria/conda/defaults zarr 2.3.1 zlib 1.2.11 h7b6447c_3 http://alexandria/conda/defaults

[klauer]

The only line in ophyd is import networkx as nx - what happens when you do that in your environment?

[gwbischof]

same error, I have networkx 2.3 installed

[gwbischof]

hmm same error with 2.2

[klauer]

OK, in that case it's not really an ophyd issue, but we should still see how to resolve it...

Brief search shows potentially related issues: https://stackoverflow.com/questions/49755099/attributeerror-module-networkx-has-no-attribute-utils https://stackoverflow.com/questions/42084985/attributeerror-module-networkx-has-no-attribute-graph

[gwbischof]

I switched back and forth a between 2.2 and 2.3, now it is working with both 2.2 and 2.3. I also reset the kernels when switching versions. I tested with ipython and jupyter notebook. Everything is good now. Maybe the issue was like they stated in your first stackoverflow link: https://stackoverflow.com/a/49811382/6513183

[klauer]

👍 Great! Glad to hear it was resolved, @gwbischof.

[gwbischof]

Thanks for the help