when a py2cytoscape version, compatible with Python 3.7.1, will be available?

[empet]

Recently I installed py2cytoscape and worked with it under an environment with python 3.6.4. Meanwhile I updated the networkx library, via conda, and without notice it installed Python 3.7.1 along with other dependencies. The Python 3.7 was a major release and a lot of python packages that worked with 3.6.4 display errors under python 3.7.1. So I updated numpy, scipy, pandas, etc.

Unfortunately py2cytoscape hasn't yet a version compatible with 3.7.1, and I cannot use it anymore. Could we hope that in the near future such a version will be available?

[jorgeboucas]

we will work on it but don't yet have a timeline.

I would advise you against using conda and to run your work from an official python docker container - https://hub.docker.com/_/python - if you want to have controlled environments.

[zachary822]

What functions are you finding problematic on python 3.7.1?

[empet]

@zachary822 Since py2cytoscape is not yet compatible with Python 3.7+, it stops working just after the following imports and setting the CyRestClient():

from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape import cyrest

cy = CyRestClient()
JSONDecodeError                           Traceback (most recent call last)
<ipython-input-13-8c8d322c11ec> in <module>
----> 1 cy = CyRestClient()
      2 cy.session.delete()
      3 cytoscape=cyrest.cyclient()

~/Miniconda2/envs/.../py2cytoscape/data/cyrest_client.py in __init__(self, ip, port, version)
     17 
     18         self.network = NetworkClient(self.__url)
---> 19         self.style = StyleClient(self.__url)
     20         self.layout = LayoutClient(self.__url)
     21         self.edgebundling = EdgeBundlingClient(self.__url)

~/Miniconda2/envs/.../py2cytoscape/data/style_client.py in __init__(self, url)
     14         self.__url_apply = url + 'apply/styles/'
     15 
---> 16         self.vps = VisualProperties(url)
     17 
     18     def create(self, name=None, original_style=None):

~/Miniconda2/envs/.../py2cytoscape/data/style_client.py in __init__(self, url)
     75     def __init__(self, url):
     76         self.__url = url + 'styles/visualproperties'
---> 77         self.__convert_to_dict()
     78 
     79     def __convert_to_dict(self):

~/Miniconda2/envs/.../py2cytoscape/data/style_client.py in __convert_to_dict(self)
     78 
     79     def __convert_to_dict(self):
---> 80         vps = requests.get(self.__url).json()
     81         vp_dict = {}
     82         node_vps = []

~/Miniconda2/envs/..../requests/models.py in json(self, **kwargs)
    894                     # used.
    895                     pass
--> 896         return complexjson.loads(self.text, **kwargs)
    897 
    898     @property

~/Miniconda2/envs/... /json/__init__.py in loads(s, encoding, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
    346             parse_int is None and parse_float is None and
    347             parse_constant is None and object_pairs_hook is None and not kw):
--> 348         return _default_decoder.decode(s)
    349     if cls is None:
    350         cls = JSONDecoder

~/Miniconda2/envs/..../lib/json/decoder.py in decode(self, s, _w)
    335 
    336         """
--> 337         obj, end = self.raw_decode(s, idx=_w(s, 0).end())
    338         end = _w(s, end).end()
    339         if end != len(s):

~/Miniconda2/envs/.../lib/json/decoder.py in raw_decode(self, s, idx)
    353             obj, end = self.scan_once(s, idx)
    354         except StopIteration as err:
--> 355             raise JSONDecodeError("Expecting value", s, err.value) from None
    356         return obj, end

JSONDecodeError: Expecting value: line 1 column 1 (char 0)

After installing Python 3.7.1 almost all Python packages stopped: pandas, igraph, scikit-learn, matplotlib, and more. But after upgrading to the version compatible with the Python version they worked.

[zachary822]

Same issue as #79.

#84 This pull request should fix that. It has to do with the usage of the json.load function. It only excepts strings prior to python 3.5, but excepts strings and bytes after python 3.6.

My mistake. I misread. This is another issue. I am currently fixing an unrelated issue that might solve this problem. It has to do with PUT requests to the api don't have a response body. #84 might fix that issue (02992bb).

For posterity, this is the same underlying issue as #82.

[zachary822]

The newest version on pypi should fix this issue. Closed.