how to run the example,

SeekPoint commented 5 years ago

ub16hp@UB16HP:/media/ub16hp/WINDOWS/ub16_prj/py2cytoscape/examples$ python3 samples_for_v0.6.0.py

Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/urllib3/connection.py", line 141, in _new_conn (self.host, self.port), self.timeout, **extra_kw) File "/usr/local/lib/python3.5/dist-packages/urllib3/util/connection.py", line 83, in create_connection raise err File "/usr/local/lib/python3.5/dist-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 111] Connection refused During handling of the above exception, another exception occurred:

jorgeboucas commented 5 years ago

please try updating to python 3.6.

SeekPoint commented 5 years ago

C:\ub16_prj\py2cytoscape\examples>python samples_for_v0.6.0.py To avoid name collision with the igraph project, this visualization library has been renamed to 'jgraph'. Please upgrade when convenient. py2cytoscape: Error importing igraph. You won't be able to import from igraph.

Traceback (most recent call last): File "C:\Users\andyy\AppData\Local\Programs\Python\Python37\lib\site-packages\urllib3\connection.py", line 141, in _new_conn (self.host, self.port), self.timeout, **extra_kw) File "C:\Users\andyy\AppData\Local\Programs\Python\Python37\lib\site-packages\urllib3\util\connection.py", line 83, in create_connection raise err File "C:\Users\andyy\AppData\Local\Programs\Python\Python37\lib\site-packages\urllib3\util\connection.py", line 73, in create_connection sock.connect(sa) ConnectionRefusedError: [WinError 10061] 由于目标计算机积极拒绝，无法连接。

zachary822 commented 5 years ago

Do you have the Cytoscape desktop program running? What version are you using?

jorgeboucas commented 5 years ago

Apart from making sure you have Cytoscape running it might be that the jump to python 3.7 was a bit too much. I would follow @zachary822 recommendation and try it on 3.6.

GlennCGL commented 2 years ago

Why don't you just write a simple example about how to use py2cytoscape? I can not learn any useful getting started about your README.md

matthiaskoenig commented 2 years ago

It seems to me the py2cytoscape project is deprecated and you should have a look at py4cytoscape https://github.com/cytoscape/py4cytoscape With documentation here: https://py4cytoscape.readthedocs.io/en/latest/ and examples here: https://py4cytoscape.readthedocs.io/en/latest/tutorials/index.html

bdemchak commented 2 years ago

Hi ...

With apologies... py2cytoscape has been deprecated. We will put a notice on this report.

In the meantime, would you mind trying py4cytoscape??

https://pypi.org/project/py4cytoscape/

https://github.com/cytoscape/py4cytoscape

... sent from my mobile phone ... please forgive my typos.

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bdemchak commented 2 years ago

Thanks, Matthias … I have added a deprecation message and forwarding link to the py2cytoscape README page.

cytoscape / py2cytoscape

how to run the example, #80