Develop Reference

Multiple issues with Python's code from Time Varying Graphical Lasso by David Hallac

Premise: I use Python 3.9.0 on a MacOS with Mojave (version 10.14.5).
The paper "Network Inference via the Time-Varying Graphical Lasso" by David Hallac, Youngsuk Park, Stephen Boyd, Jure Leskovec comes with a Python code which can be found at https://github.com/davidhallac/TVGL. I tried to run the file exampleTVGL.py with Python IDLE but I have the following issues:
It seems to be written in Python2 language, so I converted it in Python3 language with 2to3 command in the terminal;
Then, when running exampleTVGL.py I got the error:
"SyntaxError: import * only allowed at module level"
which I tried to solve by replacing:
from <modulename> import *
with
import <modulename>
*** update: not even this point is working, cannot substitute like this in order to import all from a module; How, so?
Then two modules were missing (snap and cvxpy), so I installed them in the terminal;
Last I got the error:
NameError: name 'TUNGraph' is not defined
I see that David Hallac himself on GitHub issues page suggests to solve the error by installing snap package, but on my computer the requirement is already satisfied and still not working.
What am I doing wrong? I tried use Python2, but was not able to install it, although not sure this would be sufficient to solve all issues. How can I solve the NameError 'TUNGraph" problem? Do you have any suggestion on how could I run more efficiently the code without experimenting issues?
Thank you

Importing a module works in IDE but doesn't work in windows command line (edited)

I am new to Python so this may be a stupid question, sorry in advance if it is so!
The paths Python searches for modules using Spyder 4.1.4.:
[.., 'D:\Users\Martin\Anaconda3\lib\site-packages', ..]
The paths Python searches for when used via command line in windows:
[.., 'D:\Users\Martin\Anaconda3\lib\site-packages', ..]
Thus, both include path to
'D:\Users\Martin\Anaconda3\lib\site-packages'
where I store my cv2 module installed. Yet, Spyder can import cv2 and to my surprise cmd cannot import cv2 with an error No module named 'cv2'. What am I missing please? Can anyone verify if it works for him in command line please? (I changed/edited the question again to cut unneccessary long talk, though the essence stayed the same, in hope someone could answer).

I solved it. If you have a similar problem, you can check if your case is similar to mine and follow the steps.
I use Spyder and everything works fine. However my goal is to use Python via cmd. This could not be done because Python via cmd could not find my modules.
What I did: After typing python in cmd, Python worked and output its version by default. However, I noticed the version was different than version running in Spyder - I had two Python installations (one of which I didn't know about). I found the installation cmd uses by import sys and print(sys.executable). I uninstalled that Python installation.
Now, typing python in cmd does not do anything, it is an unknown command. Then I followed this guide to add my Python installation to Path (using Windows) by:
My Computer > Properties > Advanced System Settings > Environment Variables >
in System variables, I found "Path", clicked Edit, New, then input my Python installation path D:\Users\Martin\Anaconda3 as well as D:\Users\Martin\Anaconda3\Scripts and D:\Users\Martin\Anaconda3\Library\bin. This solved it for me.

Why does importing a Python library throw a syntax error?

I have a Windows machine in which some Python code works, but now needs to work on new machine.
I have installed the same Python version 3.6.5.
First issue was that when I run the code, it can not find a re.py library, which is in fact in Python's Lib folder. So I have added sys.path.append('C:\Python\Lib') and now it can find it.
But now I get the syntax error from that library, where I say import re, that lines throws an error regarding some line in re.py library. If I import getopt, I also get syntax error on some line.
How is that even possible? Syntax error in pythons Lib files which came with installation?
And the thing is that on machine 1 it works, same file contents, same python version. I am under impression that I have wrong in python.exe version for this version of libraries, but I have simply downloaded Windows installer and installed it.
I don't even know what to google for, does someone has any idea? I am importing re in WeblogicAuto.py on line 5.
D:\Jenkins\workspace\weblogic-full-deployment-copy\weblogic-deployment>MainAutoDeployment.py -f DEV -v 2.61.0.12
Initializing WebLogic Scripting Tool (WLST) ...
Welcome to WebLogic Server Administration Scripting Shell
Type help() for help on available commands
Problem invoking WLST - Traceback (innermost last):
File "D:\Jenkins\workspace\weblogic-full-deployment-copy\weblogic-deployment\WeblogicAuto.py", line 5, in ?
File "C:\Python\Lib\re.py", line 247
b"_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ01234567890")
^
SyntaxError: invalid syntax

You are using WLST (WebLogic Scripting Tool).
WLST is very specific distribution of python:
it's jython
it roughly corresponds with python 2.7
And you trying to import libs from your CPython 3.6.5 distribution.
You need to:
remove your sys.path.append that you added earlier
check python libraries in jython library path. Which could be $HOME/.jython or WLST-specific path (look in WebLogic documentation)

OK many thanks to ya all, I've found the solution, it was about Jython libraries. I will try to elaborate a bit if someone stumbles upon this issue.
What I do here is that I deploy java modules to Oracle Weblogic application server. So this answer will also help someone trying to deploy to Weblogic from python.
From the start I was avoiding to install Webloglogic software on a machine from where I do the deploy (and that is a Jenkins slave which runs these python file, simple job).
I noticed that first machine (first Jenkins slave) has Weblogic installed, but I like to keep it minimal :)
What you do need is weblogic.jar and (not sure at this moment) wlfullclient.jar which is generated on Weblogic server (google how if needed or you may already have it).
The thing is that even though I have pure python code, when you call another python code with java weblogic.WLST pythonCode.py, it will be run with jython application! And it needs its libraries in its sys path.
In jython file I've added print(sys.path) then run in on both machines (slaves). I've noticed that path is different on those machines, even though if you type it in command prompt you get the same, but different then when Jenkins runs it.
So instead of looking how to fix those paths and copy files to them, I have created folders where it expects them, and copied them from first machine (easy fix, I may look into it later).
These are the sys.path and files that were needed, present on first machine:
['D:\\Jenkins\\weblogic\\Lib', '__classpath__', 'C:/bea10/wlserver_10.3/server/lib/weblogic.jar', 'C:/bea10/wlserver_10.3/common/wlst/modules/jython-modules.jar/Lib', 'C:/bea10/wlserver_10.3/common/wlst', 'C:/bea10/wlserver_10.3/common/wlst/lib', 'C:/bea10/wlserver_10.3/common/wlst/modules', '.']
This was sys.path on second machine, so I simply copied there:
['D:\\Jenkins\\weblogic\\Lib', '__classpath__', 'D:/Jenkins/server/lib/weblogic.jar', 'D:/Jenkins/common/wlst/modules/jython-modules.jar/Lib', 'D:/Jenkins/common/wlst', 'D:/Jenkins/common/wlst/lib', 'D:/Jenkins/common/wlst/modules', '.']
Note that jython-modules.jar is a file, so /Lib should be from that file if I get how java works.
Feel free to contact me for more details.

Error in launching Stanford corenlp server

I want to use Stanford parser in order to get typed dependency of a text. I was trying to follow the instructions provided in https://bitbucket.org/torotoki/corenlp-python, however, I got an error, both while launching the server and using the python library:
from corenlp import *
corenlp = StanfordCoreNLP("./stanford-corenlp-full-2014-08-27/")
This is the error:
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/
pexpect/__init__.py", line 1554, in expect_loopraise EOF(str(err) + '\n' + str(self))
pexpect.EOF: End Of File (EOF). Empty string style platform.
It seems the problem is about pexpect package. I already installed it as it is explained in the insturctuion. I saw similiar problem here(EOF when using pexpect and pxssh), but it is different from my case. I am using Mac and Python 2.7.
Could you please help me!

This is not the solution you wanted.
Are you sure that it is the same error if you use corenlp using the package implementation ?
pexpect is required only when there is interaction with the interactive shell of corenlp, which is present in the server implementation. In the package implementation, a file containing a list of input files is given to the parser. (using batch_parse)
In the server implementation, there is a JSON-RPC server created by the wrapper. If you want to use the server implementation, you have to remotely call one of the procedures and you don't need the package on the client end. I guess, you have mistaken in putting the right code here.
PS:
I, myself is one of the corenlp users but i used a different wrapper.

I hit the same issue while on mac. For posterity, just follow verbatim the instructions at https://bitbucket.org/torotoki/corenlp-python to use python wrapper around Stanford-corenlp. This package gets around the "End Of File (EOF). Empty string style platform." error that throws up on the some mac (or other OS, didnt check though but I know someone who also got it on windows) versions.
Also don't forget to download the stanford-corenlp-full-2014-08-27.zip instead of the latest version.
The solution of using expect(pexpect.EOF) didn't work for me (https://github.com/pexpect/pexpect/blob/master/doc/overview.rst) as the Stanford-corenlp jar was not loading properly in this case.
I also tried https://github.com/dasmith/stanford-corenlp-python as well as https://github.com/Wordseer/stanford-corenlp-python but neither of them worked. Both threw up the EOF error

Using Pexpect with Python 3

After hours of research I have broken down to posting. I am trying to use the Pexpect module with python 3, which I am led to believe is possible from the document page which does say it will run with python 3.2.
Things I have tried: I have tried many different ways of installing including downloading the source and running the command sudo python3 setup.py install. I have also tried installing it with pip and *easy_install* which is what the documentation suggest. It seems that everything goes off with out a hitch until I attempt to import the module in the pyshell. When I type import pexpect I get the error:
class spawn(object):
File "/usr/local/lib/python3.2/dist-packages/pexpect/init.py", line 286, in spawn
write_to_stdout = sys.stdout.buffer.write
AttributeError: 'PseudoFile' object has no attribute 'buffer'
I have also tried googleing the error with no luck. And I have tried using python 2.7 and it works fine. I have tried on multiple debian based operating systems: Ubuntu 12.04 and Kali with the same results.
I feel like there is something obvious I am missing, but I just don't see it. Any points in the right direction Or helping me understand the error message would be much appreciated!

There was a bug in Pexpect 3.0 which stopped it working if sys.stdout was replaced before it was imported. It looks like IDLE replaces stdout, so as you've found, it doesn't work in IDLE & Python 3.
The bug has now been fixed. I'll try to get a new version of Pexpect out in the next few days, and then you'll be able to use it from IDLE.