Sage's jupyter doesn't "talk" to a systemwide IRkernel R package

[EmmanuelCharpentier]

TL:DR : Sage's Jupyter cannot use a systemwide R IRkernel (correctly installed and usable from a systemwide jupyter notebook).

Current situation :

• Sage 9.2.beta4 compiled on Linux (Debian testing) from the source tree, configured to use systemwide packages (including R).
• Jupyter : installed from Debian packages
  • jupyter core : 4.6.3
  • jupyter-notebook : 6.0.3
• R: 4.0.2, as obtained from Debian testing.
• IRkernel : 1.1, installed from CRAN

Kernels:

charpent@zen-book-flip:~$ jupyter kernelspec list
Available kernels:
  ir         /usr/local/share/jupyter/kernels/ir
  python3    /usr/share/jupyter/kernels/python3
charpent@zen-book-flip:~$ sage -jupyter kernelspec list
Available kernels:
  python3     /usr/local/sage-9/local/share/jupyter/kernels/python3
  sagemath    /usr/local/sage-9/local/share/jupyter/kernels/sagemath
  ir          /usr/local/share/jupyter/kernels/ir

Symptoms :

• On the systemwide Jupyter notebook (started with jupyter notebook], the R kernel behaves normally :
  • R appears on the list of available kernelsa new tab
  • an R sheet can be created from the relevant menu, behaves normally, and can be saved/reopened.
• On the Sage notebook (sage -n jupyter) :
  • R appears on the list of available kernels
  • when (attempting to) create a new sheet :
    • the browser switches to a new tab, thar remains empty
    • Nothing else happens
    • When closing this new tab and switching back to Jupyter's "directory" tab, a new file ("Untitled.ipynb") is listed as having been created.

Attempts to install the r_jupyter spkg failed :

• As a normal user : because it can't write to the systemwide R library, owned by root
• As root, because Sage can't be built by a privileged user.

The availability of R from Sage's notebook should reduce the need for the systemwide Jupyter(ditto for the other Sage-created Jupyter kernels).

Alternatively, the availability of the Sage kernel from the systemwide notebook would reduce (eliminate ?) the need for Sages's Jupyter (this currently fails, the documentation can't be found during kernel's installation).

//Sidenote :// the r_jupyter spkg downloads the Github version of IRkernel. This is outdated, IRkernel being on CRAN since late 2019 : this version should probably be preferred, if only for stability/availability reasons

Depends on #30124

Component: notebook

Issue created by migration from https://trac.sagemath.org/ticket/30120

[slel]

comment:1

Workaround: install Sage's Jupyter kernel in systemwide Jupyter installation.

$ JUPTER_KERNELS=/path/to/jupyter/kernels

$ SAGE_LOCAL=`$ sage -c "print(SAGE_LOCAL)"`
$ SAGE_KERNEL=$SAGE_LOCAL/share/jupyter/kernels/sagemath

$ ln -s $SAGE_KERNEL $JUPYTER_KERNELS

To find out what to use for /path/to/jupyter/kernels:

$ jupyter kernelspec list

See also:

• sage-devel: Installing sage as a kernel in the system-wide jupyter, tip posted by Nils Bruin
• Stack Overflow: Install SageMath kernel in Jupyter, especially answer by user "Layek"

[EmmanuelCharpentier]

comment:2

Replying to @slel:

Workaround: install Sage's Jupyter kernel in systemwide Jupyter installation.

$ JUPTER_KERNELS=/path/to/jupyter/kernels

$ SAGE_LOCAL=`$ sage -c "print(SAGE_LOCAL)"`
$ SAGE_KERNEL=$SAGE_LOCAL/share/jupyter/kernels/sagemath

$ ln -s $SAGE_KERNEL $JUPYTER_KERNELS

Thanks ! This works.

To find out what to use for /path/to/jupyter/kernels:

$ jupyter kernelspec list

A bashism to find this programatically is :

jupyter kernelspec list| grep python3 | sed -re "s/[ \t]+/ /g" | cut -d " " -f 3 | sed "s/\/python3//"

If this can be generalized to our other supported platforms, this might allow to dispense with Jupyter in sage-the-distribution, in line with the current effort to (be able to) use a maximum of systemwide tools.

See also:

• sage-devel: Installing sage as a kernel in the system-wide jupyter, tip posted by Nils Bruin
• Stack Overflow: Install SageMath kernel in Jupyter, especially answer by user "Layek"

Interesting.

Do you think that this ticket should be :

• Left open to allow someone to work on the use of external kernels with Sage ;
• Closed as invalid (if we move to "external" jupyter
• Be reworked to patch this "external" jupyter solution into Sage itself ?

Thank you again !

[slel]

comment:3

Do you think that this ticket should be:

• Left open to work on using external kernels with Sage
• Closed as invalid (if we move to "external" jupyter)
• Be reworked to patch this "external" jupyter solution into Sage itself?

Document symlinking Jupyter kernels both ways between systemwide Jupyter and Sage's one.

Did you try symlinking the other way, i.e. find the
IRkernel from your systemwide Jupyter and add a symlink
to it in $SAGE_LOCAL/share/jupyter/kernels?

[slel]

comment:4

Related:

• System package information, spkg-configure for Jupyter "notebook" package, "rst2ipynb", and dependencies #30124: spkg-configure.m4 for jupyter

[EmmanuelCharpentier]

comment:5

Replying to @slel:

[ Snip... ]

Did you try symlinking the other way, i.e. find the
IRkernel from your systemwide Jupyter and add a symlink
to it in $SAGE_LOCAL/share/jupyter/kernels?

I tried that (documented in the description), and it doesn't work (same symptoms as with "normal" installation : R appears in the menu for "new sheet", opens a new (blank) tab, that remains totally inactive. No sifgn of life in the cosole where I have done "sagemath -n jupyter" either).

[kiwifb]

comment:6

Have you tried to set JUPYTER_PATH in the sage environment to point to the folder where the system's kernel are located?

https://jupyter-client.readthedocs.io/en/stable/kernels.html

[mkoeppe]

Dependencies: #30124

[mkoeppe]

comment:9

Setting new milestone based on a cursory review of ticket status, priority, and last modification date.