IPython/Jupyter upgrade for Sage 9.5 #31280

mkoeppe · 2021-01-22T04:26:21Z

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

The text was updated successfully, but these errors were encountered:

mkoeppe · 2021-01-22T04:45:29Z

Branch: u/mkoeppe/jupyter_upgrade

mkoeppe · 2021-01-22T04:45:53Z

Commit: ee9317e

mkoeppe · 2021-01-22T04:45:53Z

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 · 2021-01-22T18:26:38Z

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 · 2021-01-22T18:26:38Z

Changed commit from ee9317e to 08e0b83

mkoeppe · 2021-01-22T18:49:45Z

comment:4

importlib_metadata needs toml

mkoeppe · 2021-01-22T18:51:06Z

comment:5

backcall and ptyprocess need flit_core (#29846)

sagetrac-git · 2021-01-22T19:38:37Z

Changed commit from 08e0b83 to 3db1fd3

sagetrac-git · 2021-01-22T19:38:37Z

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 · 2021-01-22T19:44:40Z

Changed commit from 3db1fd3 to 10880b9

sagetrac-git · 2021-01-22T19:44:40Z

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

`10880b9`	`build/pkgs/rst2ipynb: Update`

mkoeppe · 2021-01-22T19:51:48Z

Author: Matthias Koeppe

mkoeppe · 2021-01-22T19:57:32Z

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 · 2021-01-23T08:44:14Z

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 · 2021-01-23T17:42:47Z

comment:11

This ticket is updating 40 packages, including requests

mkoeppe · 2021-02-02T20:16:46Z

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

mkoeppe · 2021-02-02T20:17:02Z

Work Issues: rebase on #31328

mkoeppe · 2021-02-11T23:10:06Z

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

mkoeppe · 2021-02-11T23:10:06Z

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

sagetrac-git · 2021-03-10T02:15:45Z

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 · 2021-03-10T02:15:45Z

Changed commit from 10880b9 to fccddc3

mkoeppe · 2021-03-10T02:16:35Z

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

sagetrac-git · 2021-09-06T23:07:50Z

Changed commit from 0eac2b9 to 7129f85

sagetrac-git · 2021-09-06T23:07:50Z

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

`7129f85`	`build/pkgs/parso: Update to 0.8.2`

mkoeppe · 2021-09-06T23:08:31Z

Changed reviewer from Dima Pasechnik, https://github.com/mkoeppe/sage/actions/runs/1176095684, https://github.com/mkoeppe/sage/actions/runs/1177591365, ... to Dima Pasechnik

mkoeppe · 2021-09-06T23:10:29Z

comment:88

Replying to @mkoeppe:

Dropped parso update, which went outside the version range of another package

Now jedi insisted on parso<0.9.0,>=0.8.0, so I upgraded to latest

sagetrac-git · 2021-09-06T23:41:29Z

Changed commit from 7129f85 to e2fb5ce

sagetrac-git · 2021-09-06T23:41:29Z

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

`e2fb5ce`	`build/pkgs/ipywidgets: Update to 7.6.4`

mkoeppe · 2021-09-06T23:43:35Z

Changed reviewer from Dima Pasechnik to Dima Pasechnik, https://github.com/sagemath/sagetrac-mirror/actions/runs/1207522574

dimpase · 2021-09-07T12:52:33Z

Changed reviewer from Dima Pasechnik, https://github.com/sagemath/sagetrac-mirror/actions/runs/1207522574 to Dima Pasechnik

dimpase · 2021-09-07T12:52:33Z

comment:91

OK, this looks good. I see you're testing cygiwn on GH Actions. Feel free to flip to positive review if these make sense to you.

mkoeppe · 2021-09-07T18:15:27Z

comment:92

Thank you! Yes, the Cygwin test looks fine (in previous runs, the multi-stage CI for Cygwin had revealed some of the missing dependencies).

dimpase · 2021-09-08T13:30:04Z

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 · 2021-09-08T17:36:50Z

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 · 2021-09-08T19:35:41Z

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 · 2021-09-08T19:42:52Z

comment:97

Let's do this in #32493

vbraun · 2021-09-13T22:22:30Z

Changed branch from u/mkoeppe/jupyter_upgrade to e2fb5ce

slel · 2021-11-13T15:24:31Z

Changed keywords from none to upgrade, jupyter

slel · 2021-11-13T15:24:31Z

Changed commit from e2fb5ce to none

dimpase · 2023-09-26T10:22:31Z

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

mkoeppe added this to the sage-9.3 milestone Jan 22, 2021

mkoeppe added c: packages: standard labels Jan 22, 2021

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mkoeppe added s: needs work and removed s: needs review labels Feb 2, 2021

mkoeppe added s: positive review and removed s: needs review labels Sep 7, 2021

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videlec mentioned this issue Jan 7, 2023

reenable jedi #31649

Open

tornaria mentioned this issue Dec 23, 2021

update ipykernel to 6.6.0, make debugpy optional #33020

Closed

dimpase mentioned this issue Sep 25, 2023

allow use of ptyprocess>0.5.1 #36331

Closed

IPython/Jupyter upgrade for Sage 9.5 #31280

IPython/Jupyter upgrade for Sage 9.5 #31280

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