Closed SalvatoreRa closed 4 years ago
Hi @SalvatoreRa , Thanks for spotting this out the call to netzoo is
from netZooPy.panda.panda import Panda
from netZooPy.puma.puma import Puma
from netZooPy.lioness.lioness import Lioness
Let me know how it goes, I will update the readme file.
And to install netZooPy
, please follow the updated guide here
https://netzoopy.readthedocs.io/en/latest/install/index.html
Actually, you can follow this Jupyter notebook to get started
https://github.com/netZoo/netZooPy/tree/master/tutorial/panda
thank you for your answer
I have downloaded the ipynb and imported in Jupyter.
I used the installation with conda:
source activate myenv
conda install git pip
pip install git+git://github.com/netZoo/netZooPy.git
the source comand was not recognized and gave issued. Indeed, I use the anacond powershell prompt to install :
conda install git pip
pip install git+git://github.com/netZoo/netZooPy.git
no error arose during this process.
I restarted the kernel in Jupyter and then executed the following cells:
import os
# os.getcwd()
# os.chdir("~/")
os.getcwd()
when I executed:
from netZooPy.panda.panda import Panda
import pandas as pd
import matplotlib.pyplot as plt
I received this error:
ImportError Traceback (most recent call last)
in ----> 1 from netZooPy.panda.panda import Panda 2 import pandas as pd 3 import matplotlib.pyplot as plt ~\Anaconda3\lib\site-packages\netZooPy\__init__.py in 1 from __future__ import absolute_import 2 ----> 3 from netZooPy import panda 4 from netZooPy import puma 5 fromz netZooPy import lioness ImportError: cannot import name 'panda' from 'netZooPy' (C:\Users\Bio03\Anaconda3\lib\site-packages\netZooPy\__init__.py)
Hi @SalvatoreRa ,
The installation with conda
is untested.
Could you please try installing with pip3
as suggested here https://netzoopy.readthedocs.io/en/latest/install/index.html
Please let me know how it goes!
I installed ubuntu for windows, and after reinstalling different packages, and then I have installed through pip3
but I received this error:
ImportError Traceback (most recent call last)
So the error points to your distribution of conda ~\Anaconda3\lib\site-packages\netZooPy_init_.py
, which means that you are not using the pip installation.
Could you please
conda remove netZooPy
Then in netZooPy root
pip3 install -e .
and let me know how it goes!
Thanks @SalvatoreRa
thank you for your quick reply and your help, I tried different things before replying
I used conda remove netZooPy in the terminal:
Solving environment: failed
PackagesNotFoundError: The following packages are missing from the target environment:
- netzoopy
when I check using pip list I found netZooPy 0.1.1 present.
pip uninstall netZooPy
Instead it works and successfully unistalls netzoopy I have run again the jupyter code:
%%bash
cd ~
git clone https://github.com/netZoo/netZooPy.git
cd netZooPy
pip3 install -e .
and then:
from netZooPy.panda.panda import Panda
import pandas as pd
import matplotlib.pyplot as plt
but this lead to an error:
ModuleNotFoundError Traceback (most recent call last)
Hi @SalvatoreRa , Here is my Skype: marouenbg Can you meet today at 6 pm CET time? Otherwise what time works for you best? See you
HI thank you, I just noticed.
I cannot at 6 PM, but tomorrow I am available at any time after 9:30 CET am let me know
How about tomorrow at 6pm CET time?
thank you for your quick reply and your help, I tried different things before replying
I used conda remove netZooPy in the terminal:
Solving environment: failed PackagesNotFoundError: The following packages are missing from the target environment:
- netzoopy
when I check using pip list I found netZooPy 0.1.1 present.
pip uninstall netZooPy
Instead it works and successfully unistalls netzoopy I have run again the jupyter code:
%%bash cd ~ git clone https://github.com/netZoo/netZooPy.git cd netZooPy pip3 install -e .
and then:
from netZooPy.panda.panda import Panda import pandas as pd import matplotlib.pyplot as plt
but this lead to an error:
ModuleNotFoundError Traceback (most recent call last) in ----> 1 from netZooPy.panda.panda import Panda 2 import pandas as pd 3 import matplotlib.pyplot as plt
ModuleNotFoundError: No module named 'netZooPy.panda'
actually using pip list was not showing netZooPy installed.
I tried also:
pip install git+https://github.com/netZoo/netZooPy.git
which actually is creating a folder in the anaconda site package and I see is installed using pip list.
I tried to dig a bit more.
what I noticed:
conda, pip + git are all creating a folder in
C:\Users\Bio03\Anaconda3\lib\site-packages\
could you check if the files are actually .py files are copied here, or if the folder is empty?
while actually the bash approach is creating a folder in
C:\Users\Bio03\AppData\Local\Packages\CanonicalGroupLimited.Ubuntu18.04onWindows_79rhkp1fndgsc\LocalState\rootfs\home\Bio03
same here
the two folder have identical name but the folder generated in the anaconda folder but they are slightly different.
@marouenbg it is fine for me, thank you
@dcolinmorgan this is what there is the folder:
C:\Users\Bio03\Anaconda3\lib\site-packages\
instead this what is in the folder:
C:\Users\Bio03\AppData\Local\Packages\CanonicalGroupLimited.Ubuntu18.04onWindows_79rhkp1fndgsc\LocalState\rootfs\home\Bio03
@SalvatoreRa please add me in skype
@marouenbg I wrote you on skype
problem solved through using python3
in Ubuntu. NetZooPy does not currently support conda
installation from Windows.
Hi,
I have anaconda, python 3.7, and windows 10.
I installed netzoopy through conda:
I followed the vignette to test the library: https://github.com/netZoo/netZooPy/blob/master/UserGuide.md
I used py -3 instead python3, since it not recognized python 3 (but up to my knowledge should be the same).
I encoutered an error trying to import Puma:
panda and Lioness were imported without issues.
then:
panda_obj = Panda('../../tests/ToyData/ToyExpressionData.txt', '../../tests/ToyData/ToyMotifData.txt', '../../tests/ToyData/ToyPPIData.txt', remove_missing=False)
generated issues with the file localization. I updated the localization:
this is resulting in the following error:
I read online that this issue can arise from the fact the files are not in the correct but If I use pd.read_csv I can load the individual files.
how I can salve it?
Thank you very much for your help