Add jupyter-kernel-gap package

[jdemeyer]

This package provides the GAP kernel for the Jupyter notebook,
making it available from the Sage's Jupyter notebook .

The source repository is at

• https://github.com/gap-packages/jupyter-kernel-gap

Demo notebook

• https://github.com/OpenDreamKit/OpenDreamKit/blob/master/WP4/D4.4/demo-gap.ipynb

Tarball

• https://pypi.python.org/packages/6d/02/2c88024c5851d8fc2a1340d1ffe9a2daf7d2fb0b72468e88348809d19ecd/jupyter-kernel-gap-0.9.tar.gz

Note. This is an optional package. To make it available to an existing Sage installation,
run the following command in a terminal:

sage -i gap_jupyter

Upstream: Reported upstream. Developers acknowledge bug.

CC: @nthiery @dimpase

Component: packages: optional

Author: Jeroen Demeyer

Branch: 33e27fd

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/21416

[jdemeyer]

Branch: u/jdemeyer/add_jupyter_gap_wrapper_package

[jdemeyer]

Commit: 9a6b076

[jdemeyer]

New commits:

9a6b076

Package jupyter_gap_wrapper

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

33e27fd

Package jupyter-kernel-gap-0.9

[sagetrac-git]

Changed commit from 9a6b076 to 33e27fd

[dimpase]

comment:9

I wonder why this cannot be a package of type pip.

[dimpase]

comment:10

Anyhow, this appears to work. I'll check this on OSX, too.

[dimpase]

comment:11

for some reason, the log is very chatty (on OSX):

[IPKernelApp] ERROR | (u'json part: {"result" : {"data" : {"text/html" : "Reference: <a target=\\"_blank\\" href=\\"https://cloud.gap-system.org/doc/ref/chap40.html#X87677B0787B4461A\\">AutomorphismGroup</a><br/>AutPGrp (not loaded): <a target=\\"_blank\\" href=\\"https://cloud.gap-system.org/pkg/autpgrp/htm/CHAP002.htm\\">AutomorphismGroup</a><br/>GUAVA (not loaded): <a target=\\"_blank\\" href=\\"https://cloud.gap-system.org/pkg/guava-3.13/doc/chap4.html#X87677B0787B4461A\\">AutomorphismGroup</a><br/>Reference: <a target=\\"_blank\\" href=\\"https://cloud.gap-system.org/doc/ref/chap45.html#X7A19DF1E7E841074\\">AutomorphismGroup for groups with pcgs</a><br/>AutPGrp (not loaded): <a target=\\"_blank\\" href=\\"https://cloud.gap-system.org/pkg/autpgrp/htm/CHAP003.htm\\">AutomorphismGroupPGroup</a><br/>HAP (not loaded): <a target=\\"_blank\\" href=\\"https://cloud.gap-system.org/pkg/Hap1.11/doc/chap23.html#X7B54B8CA841C517B\\">AutomorphismGroupAsCatOneGroup</a><br/>"},"source" : "gap","json" : true},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'rest part: ',)
[IPKernelApp] ERROR | (u'command JUPYTER_RunCommand("a := AutomorphismGroup(G); ;");',)
[IPKernelApp] ERROR | (u'reply {"result" : {"name" : "stdout","text" : "<group with 4 generators>"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'json part: {"result" : {"name" : "stdout","text" : "<group with 4 generators>"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'rest part: ',)
[IPKernelApp] ERROR | (u'command JUPYTER_RunCommand("SylowSubgroup(a,2); ;");',)
[IPKernelApp] ERROR | (u'reply {"result" : {"name" : "stdout","text" : "<group>"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'json part: {"result" : {"name" : "stdout","text" : "<group>"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'rest part: ',)
[IPKernelApp] ERROR | (u'command JUPYTER_RunCommand("s := SylowSubgroup(a,2); ;");',)
[IPKernelApp] ERROR | (u'reply {"result" : {"name" : "stdout","text" : "<group>"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'json part: {"result" : {"name" : "stdout","text" : "<group>"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'rest part: ',)
[IPKernelApp] ERROR | (u'command JUPYTER_RunCommand("Order(s); ;");',)
[IPKernelApp] ERROR | (u'reply {"result" : {"name" : "stdout","text" : "32"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'json part: {"result" : {"name" : "stdout","text" : "32"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'rest part: ',)
[IPKernelApp] ERROR | (u'command JUPYTER_RunCommand("IdGroup(s); ;");',)
[IPKernelApp] ERROR | (u'reply {"result" : {"name" : "stdout","text" : "[ 32, 43 ]"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'json part: {"result" : {"name" : "stdout","text" : "[ 32, 43 ]"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'rest part: ',)
[IPKernelApp] ERROR | (u'command JUPYTER_RunCommand("List(LowerCentralSeries(s), Order); ;");',)
[IPKernelApp] ERROR | (u'reply {"result" : {"name" : "stdout","text" : "[ 32, 4, 2, 1 ]"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'json part: {"result" : {"name" : "stdout","text" : "[ 32, 4, 2, 1 ]"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'rest part: ',)

it still all seems to work, but it's good to understand how harmless this is.

[dimpase]

comment:12

same picture on Linux; here I open a new jupyter notebook and evaluate g:=SymmetricGroup(6);

        http://localhost:8888/?token=301f73a3b3d0dc134012907a7430e55612e3049b811f07b2
[19710:19710:0224/145625.946823:ERROR:child_thread_impl.cc(762)] Request for unknown Channel-associated interface: ui::mojom::GpuMain
Created new window in existing browser session.
[I 14:56:29.795 NotebookApp] Accepting one-time-token-authenticated connection from ::1
[I 14:56:36.234 NotebookApp] Creating new notebook in 
[I 14:56:36.760 NotebookApp] Kernel started: 17affbdf-63c3-49fa-ac3e-2e9dd3d2e64f
[IPKernelApp] ERROR | ('starting GAP: gap',)
[IPKernelApp] ERROR | UNKNOWN MESSAGE TYPE: u'comm_open'
[IPKernelApp] ERROR | UNKNOWN MESSAGE TYPE: u'comm_open'
[W 14:56:38.367 NotebookApp] 404 GET /static/components/codemirror/mode/gap/gap.js (::1) 9.64ms referer=http://localhost:8888/notebooks/Untitled1.ipynb?kernel_name=gap
[IPKernelApp] ERROR | (u'command JUPYTER_RunCommand("g:=SymmetricGroup(6); ;");',)
[IPKernelApp] ERROR | (u'reply {"result" : {"name" : "stdout","text" : "Sym( [ 1 .. 6 ] )"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'json part: {"result" : {"name" : "stdout","text" : "Sym( [ 1 .. 6 ] )"},"status" : "ok"}',)
[IPKernelApp] ERROR | (u'rest part: ',)

it looks as if json parsing is a problem here. Wrong json or wrong parser?

[jdemeyer]

Upstream: Reported upstream. Developers acknowledge bug.

[jdemeyer]

comment:13

Upstream acknowledges bug but doesn't care...

[dimpase]

comment:14

according to https://github.com/gap-packages/jupyter-kernel-gap/issues/36
this kernel is abandoned by upstream. Apparenly upstream has or is working on another way to hook GAP onto jupyter.

[jdemeyer]

comment:15

Replying to @dimpase:

according to https://github.com/gap-packages/jupyter-kernel-gap/issues/36
this kernel is abandoned by upstream.

True, but I don't see why that means that we shouldn't merge it in Sage. There are several abandoned projects in Sage already, even as standard packages.

[nthiery]

comment:16

+1. What would be bad would be to introduce the feature, and then later have to remove it because it does not work anymore. Here upstream is very motivated by the feature, and has gone a long way toward the newer implementation with libgap being planned for next GAP release.

So we can expect the new implementation to come along in the coming months. And for now the current implementation works and is useful.

I'll double check with Markus that he is ok to expose the current implementation.

[nthiery]

comment:17

Markus's answer: absolutely, its available, it should be used. I'm not keen to spend a lot of time on maintenance, since I'd rather get the new kernel to work.

[jdemeyer]

comment:18

So please review this ticket then :-)

[dimpase]

Reviewer: Dima Pasechnik

[vbraun]

Changed branch from u/jdemeyer/add_jupyter_gap_wrapper_package to 33e27fd

[slel]

Changed commit from 33e27fd to none

[slel]

comment:21

Instruction of how to install the optional package:

sage -i gap_jupyter