Error importing Kami.Hierarchy

[hmedina]

I get an error when trying to import Kami Hierarchy. For both Kami and ReGraph, I am on branch master and up to date (as of this posting).

hmedina@Hector-Surface:~$ cd KAMI-python/
hmedina@Hector-Surface:~/KAMI-python$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean
hmedina@Hector-Surface:~/KAMI-python$ cd ../ReGraph/
hmedina@Hector-Surface:~/ReGraph$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean
hmedina@Hector-Surface:~/ReGraph$ python3
Python 3.5.2 (default, Nov 23 2017, 16:37:01)
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from kami.entities import (Gene, Region, Site, Residue, State, RegionActor, SiteActor)
>>> from kami.interactions import (Binding, Modification)
>>> from kami.hierarchy import (KamiHierarchy)
Traceback (most recent call last):
  File "/home/hmedina/ReGraph/regraph/primitives.py", line 75, in add_nodes_from
    node_id, node_attrs = n
ValueError: too many values to unpack (expected 2)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/hmedina/.local/lib/python3.5/site-packages/kami-0.1-py3.5.egg/kami/hierarchy.py", line 13, in <module>
    from kami.resources import default_components
  File "/home/hmedina/.local/lib/python3.5/site-packages/kami-0.1-py3.5.egg/kami/resources/default_components.py", line 2, in <module>
    from kami.resources import (metamodels,
  File "/home/hmedina/.local/lib/python3.5/site-packages/kami-0.1-py3.5.egg/kami/resources/metamodels.py", line 20, in <module>
    "action"
  File "/home/hmedina/ReGraph/regraph/primitives.py", line 78, in add_nodes_from
    add_node(graph, n)
  File "/home/hmedina/ReGraph/regraph/primitives.py", line 50, in add_node
    graph.node[node_id] = new_attrs
TypeError: 'NodeView' object does not support item assignment
>>>

As this is a Kami call, I'm filing it here, even though all the errors arise on ReGraph calls. If this should be posted to the ReGraph issues page, kindly let me know.

[eugeniashurko]

The second exception (TypeError: 'NodeView' object does not support item assignment) is related to the fact that at the moment ReGraph is implemented using NetworkX v1, and I think you have NetworkX v2 installed. In the second version the result of graph.node[node_id] is not a dictionary object (as in v1), but a 'NodeView' object. Please, try to check which version of nx you have installed, try to downgrade it to v1, and tell me if both errors persist.

[hmedina]

I had the latest stable release of NetworkX, version 2.1 After uninstalling v2.1 to force loading of the already installed v1.11, I get no errors.

Side note, is there a way of making ReGraph call the legacy version of NetworkX, if multiple are installed? ReGraph's setup.py file correctly states the dependency as 1.11, so pip handles the installation correctly.