IPython/Jupyter upgrade for Sage 9.5

[mkoeppe]

https://repology.org/projects/p/?inrepo=sagemath

We upgrade the following packages
(updating some SPKG.rst as needed):

• appnope 0.1.2, from 0.1.0.p0
• attrs 21.2.0, from 19.3.0
• backcall 0.2.0, from 0.1.0
• bleach 4.1.0, from 3.1.5
• certifi 2021.5.30, from 2020.11.8
• cffi 1.14.6, from 1.14.5
• debugpy 1.4.1, new standard spkg
• flit_core 3.3.0, new standard spkg
• html5lib 1.1, from 1.0.1
• ipykernel 6.3.1, from 5.2.1
• ipympl 0.7.0, from 0.6.3
• ipython 7.27.0, from 7.16.1
• ipywidgets 7.6.4.p0, from 7.6.3.p0
• jedi 0.18.0, from 0.17.2
• jupyter_client 7.0.2, from 6.1.6
• jupyter_core 4.7.1, from 4.6.3
• jupyterlab_pygments 0.1.2, new standard spkg
• matplotlib_inline 0.1.2, new standard spkg
• nbclient 0.5.4, new standard spkg
• nbconvert 6.1.0, from 5.6.1
• nbformat 5.1.3, from 5.0.7
• nest_asyncio 1.5.1, new standard spkg
• notebook 6.4.3, from 6.1.1
• pandocfilters 1.4.3, from 1.4.2
• parso 0.8.2, from 0.7.0
• prometheus_client 0.11.0, from 0.8.0
• prompt_toolkit 3.0.20, from 3.0.5
• pybind11 2.7.1, from 2.6.0
• pygments 2.10.0, from 2.3.1.p0
• pyrsistent 0.18.0, from 0.16.0
• pytz 2021.1, from 2020.4
• pyzmq 22.2.1, from 22.0.3
• rst2ipynb 0.2.3, from 0.2.2.p0
• scandir 1.10.0, from 1.9.0 (NB: later removed in ipykernel: Missing dependency argcomplete for Python 3.7; remove obsolete scandir package #32626)
• send2trash 1.8.0, from 1.5.0
• snowballstemmer 2.1.0, from 1.2.1.p0
• terminado 0.11.1, from 0.8.3
• testpath 0.5.0, from 0.4.4
• tornado 6.1, from 6.0.4
• traitlets 5.1.0, from 4.3.3
• wcwidth 0.2.5, from 0.1.7.p0

Previous updates: #26919, #31373, #31476, #31648.

PR to avoid pulling in a backport package: jupyter/nbclient#154 (merged)

Depends on #32371
Depends on #32372

CC: @jcamp0x2a @slel @kcrisman @egourgoulhon @kiwifb @videlec @kliem @antonio-rojas @isuruf

Component: packages: standard

Keywords: upgrade, jupyter

Author: Matthias Koeppe

Branch: e2fb5ce

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/31280

[mkoeppe]

Branch: u/mkoeppe/jupyter_upgrade

[mkoeppe]

Commit: ee9317e

[mkoeppe]

New commits:

9d747fc	sage --package update-latest: Distinguish pypi package name and spkg name
256a8f5	Merge branch 't/31118/sage___package_update_latest__fix_for_package_names_containing_dashes' into t/31280/jupyter_upgrade
f4273b7	build/pkgs/argon2_cffi: New
3cec11b	build/pkgs/notebook/dependencies: Add argon2_cffi
e51af7e	Merge branch 't/31279/add_package_argon2_cffi' into t/31280/jupyter_upgrade
ee9317e	Upgrade Jupyter notebook and dependencies to latest

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

f74f66c	sage --package update-latest: Accept package classes :standard:, :optional: etc., restrict to normal Python packages
aa67103	Merge branch 't/31118/sage___package_update_latest__fix_for_package_names_containing_dashes' into t/31280/jupyter_upgrade
08e0b83	Update more packages

[sagetrac-git]

Changed commit from ee9317e to 08e0b83

[mkoeppe]

comment:4

importlib_metadata needs toml

[mkoeppe]

comment:5

backcall and ptyprocess need flit_core (#29846)

[sagetrac-git]

Changed commit from 08e0b83 to 3db1fd3

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

435f90d	build/bin/sage-pip-install: For PEP 517 packages, do not try to uninstall first
3db1fd3	build/pkgs/{flit_core,pytoml}: New, add as order-only deps of backcall, ptyprocess

[sagetrac-git]

Changed commit from 3db1fd3 to 10880b9

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

10880b9

build/pkgs/rst2ipynb: Update

[mkoeppe]

Author: Matthias Koeppe

[mkoeppe]

comment:9

With this update I seem to be running into:

  [pplpy-0.8.6]   Extension error:
  [pplpy-0.8.6]   Could not import extension sphinx.builders.linkcheck (exception: No module named 'urllib3')
  [pplpy-0.8.6]   make[5]: *** [html] Error 2
  [pplpy-0.8.6]   cp: build/html/*: No such file or directory

[videlec]

comment:10

I don't see why this would have anything to do with Jupyter. The problem seems to happen during the build of the pplpy documentation with sphinx. Probably to make cross linking, sphinx requires urllib3... though this problem never occured to me.

[mkoeppe]

comment:11

This ticket is updating 40 packages, including requests

[mkoeppe]

Changed dependencies from #31279, #31118 to #31279, #31118, #31328

[mkoeppe]

Work Issues: rebase on #31328

[mkoeppe]

Changed work issues from rebase on #31328 to rebase on #31328, #31373

[mkoeppe]

Changed dependencies from #31279, #31118, #31328 to #31279, #31118, #31328, #31373

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

b48a79b	Merge #31373
140af6a	build/pkgs/ipython: Downgrade to 7.16.1
e1f9511	Merge #31476
a046780	build/bin/sage-dist-helpers (sdh_pip_install): Do not give up if sage-pip-uninstall fails
efe7523	build/bin/sage-pip-install: For PEP 517 packages, do not try to uninstall first
1f961aa	Merge #31423
58895d8	Upgrade Jupyter notebook and dependencies to latest
44325be	Update more packages
6c59cbf	build/pkgs/{flit_core,pytoml}: New, add as order-only deps of backcall, ptyprocess
fccddc3	build/pkgs/rst2ipynb: Update

[sagetrac-git]

Changed commit from 10880b9 to fccddc3

[mkoeppe]

Changed dependencies from #31279, #31118, #31328, #31373 to #31328, #31373, #31476, #31423

[dimpase]

comment:93

debugpy is introduced here, but not listed as a dependency anywhere. Seems to be a bug.
(I got an error importing debugpy while working on new matplotlib with this ticket merged).

Should be a dependency of ipykernel as far as I can tell.

[mkoeppe]

comment:95

It is only needed at runtime. Being a standard package, debugpy is installed whenever make build is used.

Since this is already on Volker's branch, let's keep it on "positive review" and add the dependency in a follow-up ticket

[dimpase]

comment:96

I think I got the error after I typed make, and it was building docs. So I am not 100% sure that it would be built without declared a dependency of sagelib.

[mkoeppe]

comment:97

Let's do this in #32493

[vbraun]

Changed branch from u/mkoeppe/jupyter_upgrade to e2fb5ce

[slel]

Changed keywords from none to upgrade, jupyter

[slel]

Changed commit from e2fb5ce to none

[dimpase]

ptyprocess issue, see comment:42 and later, is handled on #32147