Sagemath won’t run in Linux (No module named ‘sage.repl’)

TLDR: Change #!/usr/bin/env python to #!/usr/bin/env python2 in the file /usr/share/sagemath/bin/sage-ipython

This error happens because the Python environment where Sage is running is set up to use a Python version other than Python 2.7.

If sagemath is installed using the Ubuntu repository (sudo apt-get sagemath) then it will install sagemath under python2.7. We can verify this from the Ubuntu repo

https://packages.ubuntu.com/bionic/amd64/sagemath/filelist

Or if we have already installed sagemath, by going to /usr/lib/python2.7/dist-packages/sage. So trying to run sage from a terminal will only give an error.

$ sage
Traceback (most recent call last):
File "/usr/share/sagemath/bin/sage-ipython", line 7, in
from sage.repl.interpreter import SageTerminalApp
ModuleNotFoundError: No module named 'sage.repl'

This is because sage is trying to run under a python version different than python2.7. We can verify this is the case.

$ which python
/usr/bin/python
$ ls -l /usr/bin/python
lrwxrwxrwx 1 root root 16 Mar 23 12:14 /usr/bin/python -> /usr/bin/python3

So the python environment is python3.6 and not python 2.7 (as required by sage). Sage doesn’t automatically select the right python version.

root@parton:/usr/share/sagemath/bin# cat sage-ipython 
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Sage IPython startup script.
"""

from sage.repl.interpreter import SageTerminalApp

app = SageTerminalApp.instance()
app.initialize()
app.start()

So sage is running ipython with the env set to find python. The env selects python which points to /usr/bin/python3.6. We can see what the current env will select.

$ type -a python
python is /usr/bin/python                   (<- python 3.6)
python is /home/jones/anaconda3/bin/python  (<- python 3.5)

For users running python3.5 with anaconda3 but having python2.7 installed system-wide, temporarily renaming anaconda3 or changing the $PATH variable to move anaconda3 to the end seems to works. I had no success with this and the reason is clear. When anaconda3 is removed from $PATH, the OS python env takes over which is python 3.6. So unless the OS environment is also python2.7, removing anacona3 will not solve the problem of sagemath not running.

There are two options available.

1. Create a new virtual environment with vitrualenv and install python2.7 and sagemath in that environment. This will turn out to be too much work and takes up lot of space.
2. Modify the sage-ipython file to use python2.7

We will modify /usr/share/sagemath/bin/sage-ipython

$ su
$ cd /usr/bin/
$ ls -l python*

Check the python link that points python2.7

lrwxrwxrwx 1 root root 9 Apr 16 2018 python2 -> python2.7

If there is none pointing to python2.7 then create a link

$ ln -s /usr/bin/python2.7 python2

Now let’s modify the sage-ipython file

$ cd /usr/share/sagemath/bin
$ gedit sage-ipython

Change #!/usr/bin/env python to #!/usr/bin/env python2

Save, log out of root, and run sage as a normal user. Sage should work now.

Sagemath jupyter server is crashing

Sagemath Jupyter GUI server crash is fixed by editing
/usr/share/jupyter/kernels/sagemath/kernel.json. See the post Jupyter notebook running the wrong python version.

/usr/share/jupyter/kernels/sagemath had the following kernel declaration for jupyter that was causing the kernel to crash.

{
"display_name": "SageMath 8.1", 
"argv": [
 "/usr/bin/sage",
 "--python",
 "-m",
 "sage.repl.ipython_kernel",
 "-f",
 "{connection_file}"
]
}

When the python was replaced with python2 it started working.

{
"display_name": "SageMath 8.1", 
"argv": [
 "/usr/bin/sage",
 "--python2",
 "-m",
 "sage.repl.ipython_kernel",
 "-f",
 "{connection_file}"
]
}

For Sagemath installed from source this will never happen. However, if Sagemath was installed from the repositories (sudo apt install sagemath sagemath-common) then this error is inevitable due to the dependency of sagemath python 2.