Upgrade Jupyter notebook to latest (6.1.1) and its dependencies to latest

[slel]

Upgrade:

• https://pypi.org/project/notebook/ 6.1.1 (current as of 2020-08-07, supports python >= 3.5)

New dependencies:

• argon2-cffi (?)
• pyrsistent, attrs, importlib_metadata, zipp

Upgrade of its dependencies:

• https://pypi.org/project/nbformat/ 5.0.7 (released 2020-06-09, current as of 2020-08-07, supports python >= 3.5)
• https://pypi.org/project/nbconvert/ 5.6.1 (released 2019-10-24, current as of 2020-08-07, supports python >= 3.5)
• https://pypi.org/project/jupyter-client/ 6.1.6 (released 2020-07-13, current as of 2020-08-07, supports python >= 3.5)
• https://pypi.org/project/jupyter-core/ 4.6.3 (released 2020-02-18, current as of 2020-08-07, supports python >= 3.5)
• https://pypi.org/project/Jinja2/ 2.11.2 (released 2020-04-13, current as of 2020-08-07, supports python >= 3.5)
• https://pypi.org/project/tornado/ 6.0.4 (released 2020-03-03, current as of 2020-08-07, supports python >= 3.5)
• https://pypi.org/project/terminado/ 0.8.3 (released 2019-11-12, current as of 2020-08-07, supports python >= 3.4)
• https://pypi.org/project/prometheus-client/ 0.8.0 (released 2020-05-25, current as of 2020-08-07, supports python >= 3.4)
• https://pypi.org/project/pyzmq/ 19.0.2 (released 2020-07-31, current as of 2020-08-07, supports python >= 3.3)

Recursive dependencies:

• https://pypi.org/project/jsonschema/ 3.2.0 (released 2019-11-18, current as of 2020-08-07, supports python >= 2.7)
• bleach 3.1.5
• testpath 0.4.4

Upgrade of a reverse dependency:

• https://pypi.org/project/widgetsnbextension/ 3.5.1 (released 2019-07-29, supports python >= 2.7)
• ipywidgets 7.5.1

(tarball URLs: see checksums.ini; use ./configure --enable-download-from-upstream-url to enable automatic downloads of the new versions)

Previous upgrades:

• notebook 5.7.6 in Sage cannot open a Jupyter notebook directly #27463
• notebook 5.7.1, in Upgrade to jupyter notebook 5.7.1 #26709, merged in Sage 8.5.beta5.

See also:

• System package information, spkg-configure for Jupyter "notebook" package, "rst2ipynb", and dependencies #30124 System package information, spkg-configure for Jupyter "notebook" package and dependencies
• Meta-ticket: Use system Jupyter notebook / JupyterLab #30306 Meta-ticket: Use system Jupyter

Depends on #28197
Depends on #30299
Depends on #25363

CC: @antonio-rojas @kiwifb @bryangingechen @timokau @infinity0 @jdemeyer @slel @tobihan @egourgoulhon

Component: packages: standard

Keywords: upgrade, jupyter, notebook

Author: Matthias Koeppe, Joshua Campbell

Branch/Commit: 445c1d7

Reviewer: Joshua Campbell, Matthias Koeppe, Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/26919

[embray]

comment:1

Retarging tickets optimistically to the next milestone. If you are responsible for this ticket (either its reporter or owner) and don't believe you are likely to complete this ticket before the next release (8.7) please retarget this ticket's milestone to sage-pending or sage-wishlist.

[embray]

comment:2

Moving all blocker/critical issues from 8.7 to 8.8.

[slel]

Branch: u/slelievre/notebook-5.7.8

[slel]

New commits:

b1a4b7f

Upgrade to notebook 5.7.8

[slel]

Commit: b1a4b7f

[embray]

comment:7

Note, this would conflict slightly with #27715. As this ticket came first I'd be happy to rebase onto it so long as do intend to move forward on this ticket (I don't see why we shouldn't, though I haven't tested it yet...)

[embray]

comment:8

Moving tickets from the Sage 8.8 milestone that have been actively worked on in the last six months to the next release milestone (optimistically).

[fchapoton]

comment:9

branch is red

[embray]

comment:11

Ticket retargeted after milestone closed

[sagetrac-git]

Changed commit from 0a6487c to af85282

[mkoeppe]

comment:43

I've merged your commit. Please test again...

[mkoeppe]

comment:45

A build test is running at https://github.com/mkoeppe/sage/actions/runs/201573039

[jcamp0x2a]

comment:46

Replying to @mkoeppe:

Yes, runtime dependencies should be added in the dependencies file. We do not really distinguish build dependencies and runtime dependencies in the Sage distribution. (There is a notion of order-only dependencies, which are listed after the vertical-bar symbol (|), but it's OK to ignore.)

Ok, I've added dependencies on attrs, importlib_metadata, and pyrsistent to jsonschema and a dependency on zipp to importlib_metadata. (I mispoke earlier that it was required by pyrsistent.) I will update the ticket with the branch.

Also, I want to mention that the latest version of zipp (3.1.0) did not build correctly in the Sage environment, and I didn't do much troubleshooting on it, falling back instead to the specific major and minor version called out by importlib_metadata (0.5, so I used 0.5.2). Just in case that comes up in the future.

[jcamp0x2a]

comment:47

Replying to @mkoeppe:

Replying to @jcamp0x2a:

I see 404 status codes for /nbextensions/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML-full,Safe&delayStartupUntil=configured and /nbextensions/jsmol/JSmol.min.js, which are perhaps related to some of the other outstanding Jupyter tickets.

OK, I forgot to push the merge with #30299 -- sorry about that

I've tested this again following your merge and both JSmol and MathJax are now working correctly.

[jcamp0x2a]

Changed branch from u/mkoeppe/notebook-5.7.8 to u/gh-jcamp0x2a/notebook-5.7.8

[jcamp0x2a]

Changed commit from af85282 to d7d995d

[mkoeppe]

Changed author from Matthias Koeppe to Matthias Koeppe, Joshua Campbell

[mkoeppe]

comment:49

Thanks very much! Looking great.

I have restarted the build tests, now at https://github.com/mkoeppe/sage/actions/runs/201611495

[mkoeppe]

Reviewer: ​https://github.com/mkoeppe/sage/actions/runs/201611495

[mkoeppe]

Changed reviewer from ​https://github.com/mkoeppe/sage/actions/runs/201611495 to Joshua Campbell, ​https://github.com/mkoeppe/sage/actions/runs/201611495

[mkoeppe]

Changed reviewer from Joshua Campbell, ​https://github.com/mkoeppe/sage/actions/runs/201611495 to Joshua Campbell, ​github.com/mkoeppe/sage/actions/runs/201611495, ...

[mkoeppe]

comment:52

Clean tests for slackware-14.2-standard (https://github.com/mkoeppe/sage/runs/964353866), gentoo-standard (https://github.com/mkoeppe/sage/runs/964353835), fedora-32-standard (https://github.com/mkoeppe/sage/runs/964353804). (Tests on many other platforms did not go through because of current reliability issues of GH Action - unrelated to this ticket.)

[mkoeppe]

Changed reviewer from Joshua Campbell, ​github.com/mkoeppe/sage/actions/runs/201611495, ... to Joshua Campbell, Matthias Koeppe, ​github.com/mkoeppe/sage/actions/runs/201611495, ...

[mkoeppe]

Changed branch from u/gh-jcamp0x2a/notebook-5.7.8 to u/mkoeppe/notebook-5.7.8

[mkoeppe]

Changed dependencies from #28197, #30299 to #28197, #30299, #25363

[mkoeppe]

Changed commit from d7d995d to 445c1d7

[mkoeppe]

comment:55

Merged #25363 (and 9.2.beta8) to facilitate testing

---

New commits:

3b8b2bd	trac 25363: implement "sage --simple-prompt"
445c1d7	Merge branch 'u/jhpalmieri/ticket-25363' of git://trac.sagemath.org/sage into t/26919/jupyter-notebook-6.1.1

[dimpase]

comment:56

Great!

[dimpase]

Changed reviewer from Joshua Campbell, Matthias Koeppe, ​github.com/mkoeppe/sage/actions/runs/201611495, ... to Joshua Campbell, Matthias Koeppe, ​github.com/mkoeppe/sage/actions/runs/201611495, Dima Pasechnik

[mkoeppe]

comment:57

Thank you!

[mkoeppe]

Changed reviewer from Joshua Campbell, Matthias Koeppe, ​github.com/mkoeppe/sage/actions/runs/201611495, Dima Pasechnik to Joshua Campbell, Matthias Koeppe, Dima Pasechnik

[vbraun]

Changed branch from u/mkoeppe/notebook-5.7.8 to 445c1d7