Does anyone know how to get IPython to ignore site-packages in the context of a virtualenv that was created with the --no-site-packages flag?
ipython is not virtualenv aware. There are several examples on the web of how to make ipython understand virtualenvs: for instance here and here. That said, you may need to manipulate the environment a little more than these examples to remove the global site-packages dir(s) from the ipython's path.
Related
I could use Python Kernel with Jupyter. I am looking for a way to use sagemath inside Jupyter.I couldnt see a way for installing it. How to do that?
I have just installed SageMath kernel on my existing Jupyter installation. It's super easy.
$ sudo jupyter kernelspec install ./SageMath/local/share/jupyter/kernels/sagemath
Where SageMath is your root sagemath directory. Hope this will help someone.
If you don't have sudo rights you won't be able to install system-wide,
but you can still install for yourself using the --user flag:
$ jupyter kernelspec install --user ./SageMath/local/share/jupyter/kernels/sagemath
The answer suggesting
$ jupyter kernelspec install --user <path to SageMath/local/share/jupyter/kernels/sagemath>
works only if you provide the environment variable SAGE_ROOT in the kernel spec. This requires adding an "env" item to the kernel.json. The line that must be added is:
"env":{"SAGE_ROOT":"<Path to sage root>"}
An example specific to an installed mac app for version 8.7 is:
"env":{"SAGE_ROOT":"/Applications/SageMath-8.7.app/Contents/Resources/sage"}
See this question for general information and a complete example.
You are going about it backwards; Sage includes the Jupyter notebook inside of it, and you can use it with that kernel that way. (As well as others.) Use
$ sage --notebook ipython
I believe. See also here.
(I think there are also some people who have had success redirecting their Jupyter to "see" the Sage kernel by editing some file or configuration. On Arch Linux this is apparently supported ... ?)
I know this is an old question, but I stumbled onto it and ended up making a docker container to accomplish this for anyone who is interested.
https://hub.docker.com/r/sharptrick/sage-notebook
The dockerfile may be of interest as it has explicit instructions which install the kernel to the official "jupyter/minimal-notebook".
https://github.com/sharpTrick/sage-notebook/blob/master/Dockerfile
I'm trying to import a self-defined module in a Jupyter notebook using PyCharm (2016.1). However, I always get "ImportError: No module named xxx". Importing packages like NumPy or Matplotlib works fine. The self-defined module and the notebook are in the same directory and I've tried to set the directory as sources root. How can I fix this? Thanks a lot!
If you run the following in your notebook...
import sys
sys.path
...and you don't see the path to the directory containing the packages/modules, there are a couple ways around it. I can't speculate why this might happen in this example. I have seen some discrepancies in the results of sys.path when running Jupyter locally from PyCharm on OS X vs. on a managed Linux service.
An easy if hacky workaround is to set the sys path in your notebook to reflect where the packages/modules are rooted. For example, if your notebook was in a subdirectory from where the packages or modules are and sys.path only reflects that subdirectory:
import sys
sys.path.append("../")
The point is that sys.path must include the the directory the packages and modules are rooted in so the path you append will depend on the circumstances.
Perhaps a more proper solution, if you are using a virtualenv as your project interpreter, is to create a setup.py for your project and install the project as an editable package with pip. E.g. pip install -e . Then as long as Jupyter is running from that virtualenv there shouldn't be any issues with imports.
One ugly gotcha I ran into on OS X was Jupyter referencing the wrong virtualenv when started. This should also be apparent by inspecting the results of sys.path. I don't really know how I unintentionally managed set this but presume it was due to futzing around my first time getting Jupyter working in PyCharm. Instead of starting Jupyter with the local virtual env it would run with the one defined in ~/Library/Jupyter/kernels/.python/kernel.json. I was able to clear it by cleaning out that directory, e.g. rm -r ~/Library/Jupyter/kernels/.python.
As stated by Thomas in the comments make sure that your notebook serving path and project path are same. When you start your notebook in pycharm you should get something like this :
Serving notebooks from local directory: <path to your project root folder>
I am running IPython Notebook on Enthought's Canopy 64 bit distribution, Ubuntu 14.04.
I've tried install libtiff, but when I import it in IPython Notebook, the kernel always dies at the import statement. What could possibly be causing this? Canopy is my default Python distribution, my paths all seem like they're set up appropriately, although I'm convinced that something in my Python setup is borked.
Any advice is appreciated.
EDIT: I'll be more specific. Output of sys.path:
['',
'/home/joe/Enthought/Canopy_64bit/User/src/svn',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python27.zip',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/plat-linux2',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/lib-tk',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/lib-old',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/lib-dynload',
'/home/joe/Enthought/Canopy_64bit/User/lib/python2.7/site-packages',
'/home/joe/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/PIL',
'/home/joe/opencv-2.4.9',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/site-packages',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/site-packages/IPython/extensions']
As for how to install Python packages, I assume I go to ~/Enthought/Canopy_64bit/User/lib/python2.7/site-packages and run pip, setup.py, or a shell script, per the specific package's instructions. Is that correct? The article that I linked has the following line: "To install a package which is not available in the Canopy / EPD repository, follow standard Python installation procedures from the OS command line.", which seems to imply that I install per package instructions.
In .bashrc, I have the following:
VIRTUAL_ENV_DISABLE_PROMPT=1 source /home/joe/Enthought/Canopy_64bit/User/bin/activate
export PYTHONHOME=/home/joe/Enthought/Canopy_64bit/User/bin
export PATH=/home/joe/Enthought/Canopy_64bit/User/bin
export PYTHONPATH=/home/joe/Enthought/Canopy_64bit/User/bin
From what I understand of the linked articles, this means I'm setting Canopy User as my default Python distribution. I'm sure I'm doing something a bit over my head here, but I can't understand what else I need to do to fix this issue.
Worse yet, now I'm getting an "ImportError: No module named site" with these .bashrc settings, when trying to start IPython notebook or python from the command line. I can run only from the Canopy GUI.
Closing this. I made it harder than necessary.
It turns out, the PYTHONHOME and PYTHONPATH .bashrc variables were causing some conflicts. Commenting them out seems to have resolved the issue.
Installing outside packages does, indeed, happen from the home (~) directory.
Background
I use Anaconda's IPython on my mac and it's a great tool for data exploration and debugging. However, when I wish to use IPython for my programs that require virtualenv (e.g. a Django web app), I don't want to have to reinstall IPython every time.
Question
Is there a way to use my local IPython while also using the rest of my virtualenv packages? (i.e. just make IPython the exception to virtualenv packages so that the local IPython setup is available no matter what) If so, how would you do this on a mac? My guess is that it would be some nifty .bash_profile changes, but my limited knowledge with it hasn't been fruitful. Thanks.
Example Usage
Right now if I'm debugging a program, I'd use the following:
import pdb
pdb.set_trace() # insert this to pause program and explore at command line
This would bring it to the command line (that I wish was IPython)
If you have a module in your local Python and not in the virtualenv, it will still be available in the virtualenv. Unless you shadow it with another virtualenv version. Did you try to launch your local IPython from a running virtualenv that didn't have an IPython? It should work.
Will, I assume you are using Anaconda's "conda" package manager? (Which combines the features of pip and virtualenv). If so you should be aware that many parts of it does not work completely like the tools it is replacing. E.g. if you are using conda create -n myenv to create your virtual environment, this is different from the "normal" virtualenv in a number of ways. In particular, there is no "global/default" packages: Even the default installation is essentially an environment ("root") like all other environments.
To obtain the usual virtualenv behavior, you can create your environments by cloning the root environment: conda create -n myenv --clone root. However, unlike for regular virtualenv, if you make changes to the default installation (the "root" environment in conda) these changes are not reflected in the environments that were created by cloning the root environment.
An alternative to cloning the root is to keep an updated list of "default packages" that you want to be available in new environments. This is managed by the create_default_packages option in the condarc file.
In summary: Don't treat your conda environments like regular python virtualenvs - even though they appear deceptively similar in many regards. Hopefully at some point the two implementations will converge.
I want to be able to start an ipython session with it importing some modules. On Windows this would be simple - I had a global installation of ipython and I used .pythonrc I think it was.
However, in Ubuntu 13 I have ipython installed in a virtualenv (but not installed globally).
In my .bashrc is:
alias ipy="python -c 'import IPython; IPython.terminal.ipapp.launch_new_instance()'"
I am wondering if it's possible to run similar startup commands in ipython. Or if that's not possible with my current setup - then what is the best way to achieve what I want in Ubuntu.
Hopefully some combination of PYTHONSTARTUP or IPYTHONDIR environment variables in your .bashrc can accomplish what you want.