difficulty importing nxviz in Python 3.6.5

[ghost]

• nxviz version: (unsure)
• Python version: 3.6.5
• Operating System: Windows 7 (using Jupyter Notebook through Anaconda)

Description

I am trying to visualize my data in a network, and so began working with the networkx module in Python 3.6.5. The import of networkx worked just fine, but when I attempted to import the nxviz module as well, I received an error message (see below).

What I Did

import nxviz as nv

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-2-870a416d29dd> in <module>()
----> 1 import nxviz as nv

ModuleNotFoundError: No module named 'nxviz'

Any help would be greatly appreciated!

[ericmjl]

Hi @hansenzoe! Thanks for pinging in.

My first hunch is to check that nxviz has been installed into the correct environment. Can you paste the result of the following command in Jupyter?

import sys
sys.path

This will tell me where your Jupyter kernel is looking for packages.

[ghost]

Hi Eric! Thank you for getting back to me! Here is the output of the command:

import sys
sys.path

['',
'C:\Users\Zoe\Anaconda3\python36.zip',
'C:\Users\Zoe\Anaconda3\DLLs',
'C:\Users\Zoe\Anaconda3\lib',
'C:\Users\Zoe\Anaconda3',
'C:\Users\Zoe\Anaconda3\lib\site-packages',
'C:\Users\Zoe\Anaconda3\lib\site-packages\win32',
'C:\Users\Zoe\Anaconda3\lib\site-packages\win32\lib',
'C:\Users\Zoe\Anaconda3\lib\site-packages\Pythonwin',
'C:\Users\Zoe\Anaconda3\lib\site-packages\IPython\extensions',
'C:\Users\Zoe\.ipython']

[ericmjl]

And just to check, are you working out of the "base" Anaconda environment, or are you using a separate conda environment?

[ghost]

I am using Anaconda Navigator to launch Jupyter Notebook on a server. (I'm not sure if that answers your question -- I'm fairly new to Python and programming, so I'm sorry for my ignorance!).

[ericmjl]

@hansenzoe no worries! Welcome to the Python world 😄.

In a Jupyter cell, you can execute bash commands by prefixing them with an exclamation mark. The next command I'd like to see the output for is:

! conda list | grep nxviz  # this one if you installed nxviz by using conda.

As well as:

! pip list | grep nxviz  # this one if you installed nxviz by using pip

[ghost]

Thanks, Eric! Here is the output I receive (it seems that my Jupyter isn't recognizing the bash commands...).

! conda list | grep nxviz

'grep' is not recognized as an internal or external command,
operable program or batch file.

! pip list | grep nxviz

'grep' is not recognized as an internal or external command,
operable program or batch file.

[ericmjl]

Oh yes, that's right, my bad -- grep is a Linux command.

Can you do:

! conda list

and see if "nxviz" is listed in the long list of things that comes out?

[ghost]

Running '! conda list' did not display "nxviz". Does this mean that it still needs to be installed somehow?

[ericmjl]

Yes, that is right!

In your Jupyter notebook, you can do the following to install nxviz:

! conda install nxviz

Then try importing. If import nxviz as nv works, then make sure to delete the cell that contains the ! conda install nxviz command.

[ghost]

When I try running the "! conda install" command, I receive the following error:

Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

• nxviz

Current channels:

• https://repo.continuum.io/pkgs/main/win-64
• https://repo.continuum.io/pkgs/main/noarch
• https://repo.continuum.io/pkgs/free/win-64
• https://repo.continuum.io/pkgs/free/noarch
• https://repo.continuum.io/pkgs/r/win-64
• https://repo.continuum.io/pkgs/r/noarch
• https://repo.continuum.io/pkgs/pro/win-64
• https://repo.continuum.io/pkgs/pro/noarch
• https://repo.continuum.io/pkgs/msys2/win-64
• https://repo.continuum.io/pkgs/msys2/noarch

Does this indicate that I need to access a different "channel" in order to find the correct package?

[ericmjl]

Ah yes, that is right! Apologies, I had taken some settings for granted - I have configured my conda to automatically search conda-forge, which is where nxviz is located.

To get nxviz from conda-forge, use:

! conda install -c conda-forge nxviz

The -c flag tells conda to search the channel that is specified, in this case, conda-forge.

[ericmjl]

Do let me know if it works, and if it does, don't forget to close the issue!

[ghost]

Hi Eric,
The install command has been running for quite some time (multiple hours), and my Kernel is still "busy". Does the install typically take this long? Luckily an error has not shown up yet, though!

[ericmjl]

That definitely looks weird. What if you tried restarting your jupyter notebook server? That would mean closing everything, and shutting down the server in Anaconda Navigator.

[ericmjl]

@hansenzoe do let me know how things are!

[ghost]

Hi Eric!
I haven't had any luck yet, but I will keep trying! Again, the kernel has been 'busy' trying to install nxviz for a number of hours. I'm not sure what the issue is?

[ericmjl]

@hansenzoe this is beginning to look like an issue unrelated to nxviz, but for which I don't have a clear hypothesis. Installation for nxviz usually should take at most a few minutes on a reasonably modern computer; my experience in new environments is that it's been seconds to install. Windows users in my tutorials also have had few issues. I have also not used a Windows machine regularly for more than 13 years now, so I'm very out-of-date w.r.t. how to debug on Windows machines.

The hypotheses that I have below may be helpful for you to debug generally, but I doubt I'll be able to do more than list them out below. Hopefully, you have colleagues around you who might be more knowledgeable about your specific circumstances.

Hypothesis 1: Running the installation inside a Jupyter notebook doesn't work.

Proposed solution: run the installation command using the command prompt.

Hypothesis 2: Jupyter is hanging

Proposed solution: Kill the Jupyter server, and restart it. Failing that, restart computer.

Hypothesis 3: Jupyter and/or Anaconda installation is faulty (highly unlikely, but still a hypothesis)

Proposed solution: Remove Anaconda and reinstall it.

[ghost]

Thank you for the information, Eric! I appreciate you taking the time to help me, despite being unable to figure out the problem!

[ericmjl]

My pleasure, @hansenzoe! All the best in your debugging journeys.

[stonegz]

it's really strange, "import nxviz as nz" works fine in python command interface, but not in jupyter notebook.

Python 3.6.5 |Anaconda, Inc.| (default, Mar 29 2018, 13:32:41) [MSC v.1900 64 bit (AMD64)]

[ericmjl]

@stonegz welcome to the nxviz issue tracker!

From what I know, it's possibly because you don't have a Python kernel that Jupyter can recognize. To do this, you have to install the kernel:

$ conda activate <your_env_name_no_brackets>
$ python -m ipykernel install --user --name <your_env_name_no_brackets>

[stonegz]

Thanks, Eric. Yup, as you guess, the problem is i have two python installations, the default to jupyter is not the one i installed nxviz.
It's been fixed by
conda install jupyter.

[PyMap]

Hi Eric. I´m having the same issue as @hansenzoe! . I´m trying to install nxviz with python 3.6 on jupyter notebook (Windows 10). This is a virtual environment (the root is python 2.7). Using "!pip install nxviz" on jupyter I get the following error:

ERROR: Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

When I try with "! conda install nxviz" or "! conda install -c conda-forge nxviz" (from notebook or the anaconda prompt of the virtual environment) the instalation process never ends.

Do you any idea?

Thanks!

[saurabhiitg]

Hi Eric. I´m having the same issue as @hansenzoe! . I´m trying to install nxviz with python 3.6 on jupyter notebook (Windows 10). This is a virtual environment (the root is python 2.7). Using "!pip install nxviz" on jupyter I get the following error:

ERROR: Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

When I try with "! conda install nxviz" or "! conda install -c conda-forge nxviz" (from notebook or the anaconda prompt of the virtual environment) the instalation process never ends.

Do you any idea?

Thanks!

Try
pip install nxviz--ignore-installed PyYAML
Reference and real problem: pypa/pip#5247 (comment)

[Mafaldim]

Hi @ericmjl, @saurabhiitg

I had the same problem with @hansenzoe, I managed to overcome the problem after updating Anaconda navigator and trying conda install nxviz or conda install -c conda-forge nxviz .