Opened 22 months ago

Closed 15 months ago

Last modified 13 months ago

#31280 closed enhancement (fixed)

IPython/Jupyter upgrade for Sage 9.5

Reported by: Matthias Köppe Owned by:
Priority: major Milestone: sage-9.5
Component: packages: standard Keywords: upgrade, jupyter
Cc: Joshua Campbell, Samuel Lelièvre, Karl-Dieter Crisman, Eric Gourgoulhon, François Bissey, Vincent Delecroix, gh-kliem, Antonio Rojas, Isuru Fernando Merged in:
Authors: Matthias Koeppe Reviewers: Dima Pasechnik
Report Upstream: N/A Work issues:
Branch: e2fb5ce (Commits, GitHub, GitLab) Commit:
Dependencies: #32371, #32372 Stopgaps:

Status badges

Description (last modified by Samuel Lelièvre)

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 #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: https://github.com/jupyter/nbclient/pull/154 (merged)

Attachments (1)

piplist.txt (4.0 KB) - added by Dima Pasechnik 16 months ago.
pip list output

Download all attachments as: .zip

Change History (100)

comment:1 Changed 22 months ago by Matthias Köppe

Branch: u/mkoeppe/jupyter_upgrade

comment:2 Changed 22 months ago by Matthias Köppe

Commit: ee9317e50f90b5b35123b5e5c838c001e3d8adc4
Description: modified (diff)

New commits:

9d747fcsage --package update-latest: Distinguish pypi package name and spkg name
256a8f5Merge branch 't/31118/sage___package_update_latest__fix_for_package_names_containing_dashes' into t/31280/jupyter_upgrade
f4273b7build/pkgs/argon2_cffi: New
3cec11bbuild/pkgs/notebook/dependencies: Add argon2_cffi
e51af7eMerge branch 't/31279/add_package_argon2_cffi' into t/31280/jupyter_upgrade
ee9317eUpgrade Jupyter notebook and dependencies to latest

comment:3 Changed 22 months ago by git

Commit: ee9317e50f90b5b35123b5e5c838c001e3d8adc408e0b83be8346a0aeab8de0bfd3f55941397753c

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

f74f66csage --package update-latest: Accept package classes :standard:, :optional: etc., restrict to normal Python packages
aa67103Merge branch 't/31118/sage___package_update_latest__fix_for_package_names_containing_dashes' into t/31280/jupyter_upgrade
08e0b83Update more packages

comment:4 Changed 22 months ago by Matthias Köppe

importlib_metadata needs toml

comment:5 Changed 22 months ago by Matthias Köppe

backcall and ptyprocess need flit_core

Version 0, edited 22 months ago by Matthias Köppe (next)

comment:6 Changed 22 months ago by git

Commit: 08e0b83be8346a0aeab8de0bfd3f55941397753c3db1fd3bc2acb3aaea1fa8eafb250e8f1bc57d2d

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

435f90dbuild/bin/sage-pip-install: For PEP 517 packages, do not try to uninstall first
3db1fd3build/pkgs/{flit_core,pytoml}: New, add as order-only deps of backcall, ptyprocess

comment:7 Changed 22 months ago by git

Commit: 3db1fd3bc2acb3aaea1fa8eafb250e8f1bc57d2d10880b9cff100c769f5e35b6b536aafbd24d0fab

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

10880b9build/pkgs/rst2ipynb: Update

comment:8 Changed 22 months ago by Matthias Köppe

Authors: Matthias Koeppe
Cc: Joshua Campbell Samuel Lelièvre Karl-Dieter Crisman Eric Gourgoulhon François Bissey added
Status: newneeds_review

comment:9 Changed 22 months ago by Matthias Köppe

Cc: Vincent Delecroix added

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

comment:10 Changed 22 months ago by Vincent Delecroix

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.

Last edited 22 months ago by Vincent Delecroix (previous) (diff)

comment:11 Changed 22 months ago by Matthias Köppe

This ticket is updating 40 packages, including requests

comment:12 Changed 22 months ago by Matthias Köppe

Dependencies: #31279, #31118#31279, #31118, #31328

comment:13 Changed 22 months ago by Matthias Köppe

Work issues: rebase on #31328

comment:14 Changed 22 months ago by Matthias Köppe

Status: needs_reviewneeds_work

comment:15 Changed 22 months ago by Matthias Köppe

Cc: gh-kliem added
Dependencies: #31279, #31118, #31328#31279, #31118, #31328, #31373
Work issues: rebase on #31328rebase on #31328, #31373

comment:16 Changed 21 months ago by git

Commit: 10880b9cff100c769f5e35b6b536aafbd24d0fabfccddc33ca384419e70d5a26bfbdc4c59684d216

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

b48a79bMerge #31373
140af6abuild/pkgs/ipython: Downgrade to 7.16.1
e1f9511Merge #31476
a046780build/bin/sage-dist-helpers (sdh_pip_install): Do not give up if sage-pip-uninstall fails
efe7523build/bin/sage-pip-install: For PEP 517 packages, do not try to uninstall first
1f961aaMerge #31423
58895d8Upgrade Jupyter notebook and dependencies to latest
44325beUpdate more packages
6c59cbfbuild/pkgs/{flit_core,pytoml}: New, add as order-only deps of backcall, ptyprocess
fccddc3build/pkgs/rst2ipynb: Update

comment:17 Changed 21 months ago by Matthias Köppe

Dependencies: #31279, #31118, #31328, #31373#31328, #31373, #31476, #31423
Status: needs_workneeds_review
Work issues: rebase on #31328, #31373

comment:18 Changed 21 months ago by Matthias Köppe

Status: needs_reviewneeds_work

comment:19 Changed 21 months ago by Matthias Köppe

Milestone: sage-9.3sage-9.4

comment:20 Changed 20 months ago by Matthias Köppe

Description: modified (diff)
Summary: Jupyter upgradeIPython/Jupyter upgrade for Sage 9.4

comment:21 Changed 20 months ago by Matthias Köppe

Dependencies: #31328, #31373, #31476, #31423#30551

comment:22 Changed 19 months ago by Matthias Köppe

Dependencies: #30551#30551, #31699
Description: modified (diff)

comment:23 Changed 19 months ago by git

Commit: fccddc33ca384419e70d5a26bfbdc4c59684d2164d5eab7b5791bf12509a6a185bfc55091f7903c0

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

fff89bcbuild/pkgs/importlib_metadata: Update to 4.0.1
e14a5edbuild/pkgs/pip: Update to 21.1.1
3386fa1build/pkgs/toml: New
71aeec7build/pkgs/typing_extensions: New
ecdf3e1build/pkgs/importlib_metadata/dependencies: Update
956279dMerge #31699
2bd7643Upgrade Jupyter notebook and dependencies to latest
201d4deUpdate more packages
699dc4fbuild/pkgs/{flit_core,pytoml}: New, add as order-only deps of backcall, ptyprocess
4d5eab7build/pkgs/rst2ipynb: Update

comment:24 Changed 19 months ago by git

Commit: 4d5eab7b5791bf12509a6a185bfc55091f7903c0993406f2c28d54cc79321abff569a8a5dffa0b6a

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

870d23cbuild/pkgs/parso: Update to 0.8.2
f1f172ebuild/pkgs/notebook: Update to 6.3.0
c9fdcd2build/pkgs/nbformat: Update to 5.1.3
1cca2bcbuild/pkgs/jupyter_core: Update to 4.7.1
46805ffbuild/pkgs/jupyter_client: Update to 6.1.12
74e10a0build/pkgs/ipykernel: Update to 5.5.4
025ac8dbuild/pkgs/flit_core: Update to 3.2.0
4c4a967build/pkgs/bleach: Update to 3.3.0
3fd8722build/pkgs/babel: Update to 2.9.1
993406fbuild/pkgs/attrs: Update to 21.2.0

comment:25 Changed 19 months ago by git

Commit: 993406f2c28d54cc79321abff569a8a5dffa0b6a6ffa215121ac9c7c341f3b2de3e5261093986b94

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

1fa5667build/pkgs/babel/checksums.ini: Add upstream_url
6ffa215build/pkgs/pygments/checksums.ini: Add upstream_url

comment:26 Changed 19 months ago by Matthias Köppe

Status: needs_workneeds_review

comment:27 Changed 19 months ago by Matthias Köppe

Status: needs_reviewneeds_work

Upgraded requests has new dependencies:

requires = [
    'chardet>=3.0.2,<5',
    'idna>=2.5,<3',
    'urllib3>=1.21.1,<1.27',
    'certifi>=2017.4.17'
]

comment:28 Changed 19 months ago by Matthias Köppe

(requests unvendored these libraries in 2.16 - https://docs.python-requests.org/en/master/community/updates/#id25)

comment:29 Changed 19 months ago by git

Commit: 6ffa215121ac9c7c341f3b2de3e5261093986b9468efa914e4d26f7e85cc3e7666739f6a5ca0c508

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

b7868b1build/pkgs/chardet: New (unvendored from requests)
b7c39e0build/pkgs/idna: New (unvendored from requests)
68efa91build/pkgs/urllib3: New (unvendored from requests)

comment:30 Changed 19 months ago by git

Commit: 68efa914e4d26f7e85cc3e7666739f6a5ca0c508bacc3a22663268e1ada01106789d9f4521f57583

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

bacc3a2build/pkgs/requests/dependencies: Add unvendored packages

comment:31 Changed 19 months ago by Matthias Köppe

Status: needs_workneeds_review

comment:32 Changed 18 months ago by Matthias Köppe

Dependencies: #30551, #31699#30551, #31699, #31856

comment:33 Changed 18 months ago by git

Commit: bacc3a22663268e1ada01106789d9f4521f57583e0e1489062d5d1017e72d2ad020e10d780298778

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

2a7d940build/pkgs/pyzmq: Update to 22.0.3
e0e1489Merge branch 't/31856/pyzmq__update_to_22_0_3' into t/31280/jupyter_upgrade

comment:34 Changed 18 months ago by git

Commit: e0e1489062d5d1017e72d2ad020e10d780298778d83e2f8b8cdf7b8f46102c86e00d5e99ca1d7060

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

ef12a3ebuild/pkgs/pkgconfig/checksums.ini: Add upstream_url
7a6d0b6build/pkgs/packaging/checksums.ini: Add upstream_url
a2cf107Merge #31699
7c94735build/pkgs/pandocfilters/checksums.ini: Add upstream_url
6079a11build/pkgs/ptyprocess/checksums.ini: Add upstream_url
2694cbfbuild/pkgs/requests/checksums.ini: Add upstream_url
62769f9build/pkgs/rst2ipynb/checksums.ini: Add upstream_url
eb6d3d0build/pkgs/scandir/checksums.ini: Add upstream_url
e2cada9build/pkgs/snowballstemmer/checksums.ini: Add upstream_url
d83e2f8build/pkgs/wcwidth/checksums.ini: Add upstream_url

comment:35 Changed 18 months ago by Dima Pasechnik

Reviewers: Dima Pasechnik
Status: needs_reviewpositive_review

lgtm

comment:36 Changed 18 months ago by Matthias Köppe

Thanks!

comment:37 Changed 18 months ago by Matthias Köppe

Status: positive_reviewneeds_work

comment:38 Changed 18 months ago by git

Commit: d83e2f8b8cdf7b8f46102c86e00d5e99ca1d7060c943913c8551fd1e452f304fe33ca3ec0dff84c4

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

c943913build/pkgs/{backcall,ptyprocess}/dependencies: flit_core switched from pytoml to toml; remove pytoml package

comment:39 Changed 18 months ago by Matthias Köppe

Status: needs_workneeds_review

comment:40 Changed 18 months ago by Dima Pasechnik

Status: needs_reviewpositive_review

OK

comment:41 Changed 18 months ago by Matthias Köppe

Thanks

comment:42 Changed 17 months ago by Volker Braun

Status: positive_reviewneeds_work

On OSX:

sage -t --long --random-seed=0 src/sage/interfaces/expect.py  # 38 doctests failed
sage -t --long --random-seed=0 src/sage/interfaces/gap.py  # 61 doctests failed
sage -t --long --random-seed=0 src/sage/interfaces/mwrank.py  # 6 doctests failed
sage -t --long --random-seed=0 src/sage/interfaces/quit.py  # 6 doctests failed

comment:43 Changed 17 months ago by Matthias Köppe

More detail please

comment:44 Changed 17 months ago by Matthias Köppe

Cc: Antonio Rojas Isuru Fernando added

Indeed, the upgrade of ptyprocess breaks sage.interfaces.expect on macOS.

Does someone already have a fix for this?

comment:45 Changed 17 months ago by Matthias Köppe

Even just upgrading ptyprocess from 0.5.1 to 0.5.2 causes the breakage. All later versions (0.6.0, 0.7.0) are broken.

comment:47 Changed 17 months ago by git

Commit: c943913c8551fd1e452f304fe33ca3ec0dff84c445cf01395aa1f4c7145cf6450e6ba1102a0c8d6f

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

b348305Merge tag '9.4.beta4' into t/31280/jupyter_upgrade
2582707build/pkgs/ptyprocess: Revert upgrade to 0.7.0; pin version to 0.5.1
45cf013build/pkgs/rst2ipynb/patches: Remove

comment:48 Changed 17 months ago by Matthias Köppe

I have opened #32147 (Make sage.interfaces.expect compatible with ptyprocess >= 0.5.2). I don't think we need it for this ticket.

comment:49 Changed 17 months ago by Matthias Köppe

Cherry-picked the single fix-up commit for rst2ipynb from #31967.

comment:50 Changed 17 months ago by Matthias Köppe

Dependencies: #30551, #31699, #31856
Status: needs_workneeds_review

comment:51 Changed 17 months ago by Dima Pasechnik

starting ./sage -n and attempting to create a Sage notebook from browser leads to 500 Internal Server Error and on console I see

ModuleNotFoundError: No module named 'jupyterlab_pygments'

the full log (I killed the session with Ctrl-C in the end)

Please wait while the Sage Jupyter Notebook server starts...
[I 19:04:20.346 NotebookApp] Serving notebooks from local directory: /mnt/opt/Sage/sage-dev
[I 19:04:20.346 NotebookApp] Jupyter Notebook 6.3.0 is running at:
[I 19:04:20.347 NotebookApp] http://localhost:8888/?token=0d3f0cbd61c7d818de2b8399e051f51dc2fdf23481edb381
[I 19:04:20.347 NotebookApp]  or http://127.0.0.1:8888/?token=0d3f0cbd61c7d818de2b8399e051f51dc2fdf23481edb381
[I 19:04:20.347 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 19:04:20.394 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///home/dima/.local/share/jupyter/runtime/nbserver-11985-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/?token=0d3f0cbd61c7d818de2b8399e051f51dc2fdf23481edb381
     or http://127.0.0.1:8888/?token=0d3f0cbd61c7d818de2b8399e051f51dc2fdf23481edb381
[I 19:04:31.562 NotebookApp] Creating new notebook in 
[E 19:04:31.729 NotebookApp] Uncaught exception GET /notebooks/Untitled1.ipynb?kernel_name=sagemath (127.0.0.1)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/notebooks/Untitled1.ipynb?kernel_name=sagemath', version='HTTP/1.1', remote_ip='127.0.0.1')
    Traceback (most recent call last):
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/tornado/web.py", line 1704, in _execute
        result = await result
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/tornado/gen.py", line 775, in run
        yielded = self.gen.send(value)
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/notebook/notebook/handlers.py", line 95, in get
        self.write(self.render_template('notebook.html',
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/notebook/base/handlers.py", line 516, in render_template
        return template.render(**ns)
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/jinja2/environment.py", line 1090, in render
        self.environment.handle_exception()
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/jinja2/environment.py", line 832, in handle_exception
        reraise(*rewrite_traceback_stack(source=source))
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/jinja2/_compat.py", line 28, in reraise
        raise value.with_traceback(tb)
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/notebook/templates/notebook.html", line 1, in top-level template code
        {% extends "page.html" %}
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/notebook/templates/page.html", line 154, in top-level template code
        {% block header %}
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/notebook/templates/notebook.html", line 115, in block "header"
        {% for exporter in get_frontend_exporters() %}
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/notebook/notebook/handlers.py", line 23, in get_frontend_exporters
        from nbconvert.exporters.base import get_export_names, get_exporter
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/nbconvert/__init__.py", line 4, in <module>
        from .exporters import *
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/nbconvert/exporters/__init__.py", line 4, in <module>
        from .slides import SlidesExporter
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/nbconvert/exporters/slides.py", line 12, in <module>
        from ..preprocessors.base import Preprocessor
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/nbconvert/preprocessors/__init__.py", line 7, in <module>
        from .csshtmlheader import CSSHTMLHeaderPreprocessor
      File "/mnt/opt/Sage/sage-dev/local/lib/python3.8/site-packages/nbconvert/preprocessors/csshtmlheader.py", line 14, in <module>
        from jupyterlab_pygments import JupyterStyle
    ModuleNotFoundError: No module named 'jupyterlab_pygments'
[E 19:04:31.737 NotebookApp] {
      "Host": "localhost:8888",
      "User-Agent": "Mozilla/5.0 (X11; Linux x86_64; rv:87.0) Gecko/20100101 Firefox/87.0",
      "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8",
      "Accept-Language": "en-US,en;q=0.5",
      "Accept-Encoding": "gzip, deflate",
      "Dnt": "1",
      "Connection": "keep-alive",
      "Referer": "http://localhost:8888/tree",
      "Cookie": "username-localhost-8888=\"2|1:0|10:1625681061|23:username-localhost-8888|44:Yzk3OTE4MGZmZDk0NGIwZWE3OGJhN2U2ZWRlZjM2MjQ=|1dece02d459d6cbd9afa3010954d3af0225ea32fc03d6fb8a2c97d06acb77c3b\"; _xsrf=2|32f2db10|41bba910a8914a43d015ffbce18afe72|1625680821",
      "Upgrade-Insecure-Requests": "1"
    }
[E 19:04:31.737 NotebookApp] 500 GET /notebooks/Untitled1.ipynb?kernel_name=sagemath (127.0.0.1) 94.570000ms referer=http://localhost:8888/tree
^C[I 19:04:51.095 NotebookApp] interrupted
Serving notebooks from local directory: /mnt/opt/Sage/sage-dev
0 active kernels
Jupyter Notebook 6.3.0 is running at:
http://localhost:8888/?token=0d3f0cbd61c7d818de2b8399e051f51dc2fdf23481edb381
 or http://127.0.0.1:8888/?token=0d3f0cbd61c7d818de2b8399e051f51dc2fdf23481edb381
Shutdown this notebook server (y/[n])? y

comment:52 Changed 17 months ago by Dima Pasechnik

To make it work, I tried

$ ./sage --pip3 install jupyterlab_pygments

and got

Collecting jupyterlab_pygments
  Using cached jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB)
Requirement already satisfied: pygments<3,>=2.4.1 in ./local/lib/python3.8/site-packages (from jupyterlab_pygments) (2.9.0)
Installing collected packages: jupyterlab-pygments
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
nbconvert 6.0.7 requires nbclient<0.6.0,>=0.5.0, which is not installed.
Successfully installed jupyterlab-pygments-0.1.2

Then I did

./sage --pip3 uninstall jupyterlab_pygments
./sage --pip3 install nbclient
./sage --pip3 install jupyterlab_pygments

and this fixed this issue.

comment:53 Changed 17 months ago by Matthias Köppe

Status: needs_reviewneeds_work

Thanks for testing!

comment:54 Changed 17 months ago by git

Commit: 45cf01395aa1f4c7145cf6450e6ba1102a0c8d6f285c758f4fa2b8a54dfaaf6976ed06dfc07654d2

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

285c758Merge tag '9.4.beta5' into t/31280/jupyter_upgrade

comment:55 Changed 17 months ago by Matthias Köppe

Status: needs_workneeds_review

I can't reproduce this error... Another try on top of the current beta?

comment:56 Changed 16 months ago by Dima Pasechnik

still the same error as in comment:51

comment:57 Changed 16 months ago by Matthias Köppe

What does ./sage -pip list say on this installation?

Changed 16 months ago by Dima Pasechnik

Attachment: piplist.txt added

pip list output

comment:58 in reply to:  57 Changed 16 months ago by Dima Pasechnik

Replying to mkoeppe:

What does ./sage -pip list say on this installation?

attached.

comment:59 Changed 16 months ago by Matthias Köppe

Milestone: sage-9.4sage-9.5

comment:60 Changed 16 months ago by Matthias Köppe

Summary: IPython/Jupyter upgrade for Sage 9.4IPython/Jupyter upgrade for Sage 9.5

comment:61 Changed 16 months ago by git

Commit: 285c758f4fa2b8a54dfaaf6976ed06dfc07654d238e3bae0ea2c9786fde8a159fbcf40d6eb8a3e42

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

38e3baeMerge tag '9.4.rc1' into t/31280/jupyter_upgrade

comment:62 Changed 16 months ago by git

Commit: 38e3bae0ea2c9786fde8a159fbcf40d6eb8a3e4281ec362884c8760351a7e0c81e9db5461dec7c3e

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

605fb85build/pkgs/ipykernel: Update to 6.0.3
2a07328build/pkgs/nbconvert: Update to 6.1.0
5fed892build/pkgs/notebook: Update to 6.4.3
ca9c79ebuild/pkgs/prometheus_client: Update to 0.11.0
65266ebbuild/pkgs/prompt_toolkit: Update to 3.0.19
6ec0526build/pkgs/pybind11: Update to 2.7.1
c74a4d1build/pkgs/pyrsistent: Update to 0.18.0
1f08806build/pkgs/requests: Update to 2.26.0
f4fad01build/pkgs/terminado: Update to 0.10.1
81ec362build/pkgs/urllib3: Update to 1.26.6

comment:63 Changed 16 months ago by git

Commit: 81ec362884c8760351a7e0c81e9db5461dec7c3e997611e76fd4c3f0823d91564421bcf6be9a0376

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

6508c8bbuild/pkgs/jupyterlab_pygments: New (nbformat dependency)
057c67abuild/pkgs/nbclient: Mew (nbformat dependency)
8f408d4build/pkgs/nest_asyncio: New (nbformat dependency)
a267479build/pkgs/async_generator: New (backport package, dependency of nbclient)
997611ebuild/pkgs/ipython: Update to 7.26.0

comment:64 Changed 16 months ago by Matthias Köppe

OK... jupyterlab_pygments is a new dependency of nbconvert. Some more dependencies also came in.

comment:65 Changed 16 months ago by Frédéric Chapoton

Note: update of requests should help for #30768

comment:66 Changed 16 months ago by Matthias Köppe

Dependencies: #32371, #32372

comment:67 Changed 16 months ago by git

Commit: 997611e76fd4c3f0823d91564421bcf6be9a037614b88fd20d0152ceafb2cb378c2034630eeb9e5d

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

d9214f7build/pkgs/prometheus_client: Update to 0.11.0
10db3b9build/pkgs/prompt_toolkit: Update to 3.0.19
1f846cabuild/pkgs/pybind11: Update to 2.7.1
8ab444ebuild/pkgs/pyrsistent: Update to 0.18.0
f598c25build/pkgs/terminado: Update to 0.10.1
7a3ce68build/pkgs/jupyterlab_pygments: New (nbformat dependency)
1d8a335build/pkgs/nbclient: Mew (nbformat dependency)
3c52d9ebuild/pkgs/nest_asyncio: New (nbformat dependency)
2bd96a7build/pkgs/async_generator: New (backport package, dependency of nbclient)
14b88fdbuild/pkgs/ipython: Update to 7.26.0

comment:68 Changed 16 months ago by Matthias Köppe

Rebased onto 9.4.rc1 + #32371, #32372. Dropped parso update, which went outside the version range of another package

comment:69 Changed 16 months ago by git

Commit: 14b88fd20d0152ceafb2cb378c2034630eeb9e5de19e1d1bd8d9c2d30cadd5dc8d44cfc8d503255a

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

1e48ab9build/pkgs/tornado: Update to 6.1
e19e1d1build/pkgs/traitlets: Update to 5.0.5

comment:70 Changed 16 months ago by Matthias Köppe

Description: modified (diff)

comment:71 Changed 16 months ago by git

Commit: e19e1d1bd8d9c2d30cadd5dc8d44cfc8d503255aaafc4966652133273889072c7f1d6cb70127b731

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

8c8a766build/pkgs/charset_normalizer: New, use it instead of chardet as a dependency of requests
8cc62debuild/pkgs/chardet: Remove
aafc496Merge #32372

comment:72 Changed 16 months ago by Matthias Köppe

Description: modified (diff)

comment:73 Changed 16 months ago by git

Commit: aafc4966652133273889072c7f1d6cb70127b7311bb7e0cb8a4e639270b0122179eb72b58257b318

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

1bb7e0cbuild/pkgs/nbclient: Patch out dep on backport package async_generator, remove that package

comment:74 Changed 16 months ago by Matthias Köppe

The upgraded ipykernel declares two new install_requires: https://pypi.org/project/debugpy/, https://pypi.org/project/matplotlib-inline/

comment:75 Changed 16 months ago by git

Commit: 1bb7e0cb8a4e639270b0122179eb72b58257b318f4b68c78e8e4ed16d5c03b53f66d918d0fe6c43f

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

29acde8build/pkgs/parso: Update to 0.7.1
fb9dc01build/pkgs/matplotlib_inline: New (ipython dependency)
f4b68c7build/pkgs/debugpy: New (ipykernel dependency)

comment:76 Changed 16 months ago by git

Commit: f4b68c78e8e4ed16d5c03b53f66d918d0fe6c43f0050b78ea8ef098e6665c77e37417f7db79d7544

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

0050b78build/pkgs/send2trash: Update to 1.8.0

comment:77 Changed 15 months ago by git

Commit: 0050b78ea8ef098e6665c77e37417f7db79d754435c812c901056d10e757315f5fbf66d256ed01e1

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

a69861abuild/pkgs/pandocfilters: Update to 1.4.3
0592af4build/pkgs/prompt_toolkit: Update to 3.0.20
fcfefe7build/pkgs/pygments: Update to 2.10.0
7f72f20build/pkgs/pyzmq: Update to 22.2.1
12b8a77build/pkgs/scandir: Update to 1.10.0
2f0edacbuild/pkgs/snowballstemmer: Update to 2.1.0
85420b1build/pkgs/terminado: Update to 0.11.1
319aacdbuild/pkgs/testpath: Update to 0.5.0
c73c32fbuild/pkgs/wcwidth: Update to 0.2.5
35c812cMerge tag '9.4' into t/31280/jupyter_upgrade

comment:78 Changed 15 months ago by Matthias Köppe

Reviewers: Dima PasechnikDima Pasechnik, https://github.com/mkoeppe/sage/actions/runs/1175727870, https://github.com/mkoeppe/sage/actions/runs/1175727869, ...

comment:79 Changed 15 months ago by git

Commit: 35c812c901056d10e757315f5fbf66d256ed01e1c0b99879e77a86fdc66f92acb74230cbf6c89dd1

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

c0b9987build/pkgs/send2trash/checksums.ini: Add upstream_url

comment:80 Changed 15 months ago by Matthias Köppe

Reviewers: Dima Pasechnik, https://github.com/mkoeppe/sage/actions/runs/1175727870, https://github.com/mkoeppe/sage/actions/runs/1175727869, ...Dima Pasechnik, https://github.com/mkoeppe/sage/actions/runs/1176095684, https://github.com/mkoeppe/sage/actions/runs/1175727875, ...

comment:81 Changed 15 months ago by Matthias Köppe

Some dependencies need to be declared:

   File "/opt/sage-5e2cde910e349f3b257feb1bbcf1c5a3f83d122b/lib/python3.8/site-packages/jupyter_client/provisioning/factory.py", line 9, in <module>
      from entrypoints import EntryPoint  # type: ignore
  ModuleNotFoundError: No module named 'entrypoints'
  Building wheel for ipykernel (PEP 517): finished with status 'error'
  ERROR: Failed building wheel for ipykernel
Failed to build ipykernel
ERROR: Failed to build one or more wheels

https://github.com/mkoeppe/sage/runs/3449969195

comment:82 Changed 15 months ago by git

Commit: c0b99879e77a86fdc66f92acb74230cbf6c89dd15476f6fc107e583d59db25c15e34b3d9b0462257

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

5476f6fbuild/pkgs/jupyter_client/dependencies: Add new deps

comment:83 Changed 15 months ago by Matthias Köppe

Reviewers: Dima Pasechnik, https://github.com/mkoeppe/sage/actions/runs/1176095684, https://github.com/mkoeppe/sage/actions/runs/1175727875, ...Dima Pasechnik, https://github.com/mkoeppe/sage/actions/runs/1176095684, https://github.com/mkoeppe/sage/actions/runs/1177591365, ...

comment:84 Changed 15 months ago by Matthias Köppe

https://github.com/mkoeppe/sage/actions/runs/1177591365 still indicates dependency trouble

  [ipykernel-6.2.0] error installing, exit status 1. End of log file:
  [ipykernel-6.2.0]       File "/opt/sage-7bc14322e3a24f69b4bf3741c25d26d20a26f47c/lib/python3.8/site-packages/jupyter_client/provisioning/factory.py", line 9, in <module>
  [ipykernel-6.2.0]         from entrypoints import EntryPoint  # type: ignore
  [ipykernel-6.2.0]     ModuleNotFoundError: No module named 'entrypoints'
  [ipykernel-6.2.0]     Building wheel for ipykernel (PEP 517): finished with status 'error'
  [ipykernel-6.2.0]     ERROR: Failed building wheel for ipykernel

comment:85 Changed 15 months ago by git

Commit: 5476f6fc107e583d59db25c15e34b3d9b04622570eac2b93997e5b2725c2dff5cf9816eac8b08d9d

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

5dab021build/pkgs/jupyter_client/dependencies: Add entrypoints
7eb450fMerge tag '9.5.beta0' into t/31280/jupyter_upgrade
76be564build/pkgs/ipykernel: Update to 6.3.1
4356908build/pkgs/ipython: Update to 7.27.0
8deb371build/pkgs/jupyter_client: Update to 7.0.2
0eac2b9build/pkgs/traitlets: Update to 5.1.0

comment:86 Changed 15 months ago by git

Commit: 0eac2b93997e5b2725c2dff5cf9816eac8b08d9d7129f8589ab27dcf424e1707cd39801587446ff3

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

7129f85build/pkgs/parso: Update to 0.8.2

comment:87 Changed 15 months ago by Matthias Köppe

Reviewers: Dima Pasechnik, https://github.com/mkoeppe/sage/actions/runs/1176095684, https://github.com/mkoeppe/sage/actions/runs/1177591365, ...Dima Pasechnik

comment:88 in reply to:  68 Changed 15 months ago by Matthias Köppe

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

comment:89 Changed 15 months ago by git

Commit: 7129f8589ab27dcf424e1707cd39801587446ff3e2fb5ce1ef66a735708d8f6546410b7753b31aa7

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

e2fb5cebuild/pkgs/ipywidgets: Update to 7.6.4

comment:90 Changed 15 months ago by Matthias Köppe

Reviewers: Dima PasechnikDima Pasechnik, https://github.com/sagemath/sagetrac-mirror/actions/runs/1207522574

comment:91 Changed 15 months ago by Dima Pasechnik

Reviewers: Dima Pasechnik, https://github.com/sagemath/sagetrac-mirror/actions/runs/1207522574Dima Pasechnik

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.

comment:92 Changed 15 months ago by Matthias Köppe

Status: needs_reviewpositive_review

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

comment:93 Changed 15 months ago by Dima Pasechnik

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.

comment:94 Changed 15 months ago by Dima Pasechnik

Status: positive_reviewneeds_info

comment:95 Changed 15 months ago by Matthias Köppe

Status: needs_infopositive_review

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

comment:96 Changed 15 months ago by Dima Pasechnik

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.

comment:97 Changed 15 months ago by Matthias Köppe

Let's do this in #32493

comment:98 Changed 15 months ago by Volker Braun

Branch: u/mkoeppe/jupyter_upgradee2fb5ce1ef66a735708d8f6546410b7753b31aa7
Resolution: fixed
Status: positive_reviewclosed

comment:99 Changed 13 months ago by Samuel Lelièvre

Commit: e2fb5ce1ef66a735708d8f6546410b7753b31aa7
Description: modified (diff)
Keywords: upgrade jupyter added
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