Opened 5 years ago

Closed 4 years ago

#25638 closed enhancement (fixed)

Misc pip upgrades

Reported by: vbraun Owned by:
Priority: major Milestone: sage-8.4
Component: packages: standard Keywords: upgrade, decorator, ipykernel, jupyter_client, notebook, ptyprocess, pyzmq, scandir, send2trash, setuptools, tornado
Cc: embray, jdemeyer, ​slelievre, tmonteil, vbraun Merged in:
Authors: Volker Braun Reviewers: Jeroen Demeyer
Report Upstream: N/A Work issues:
Branch: 61a8ec7 (Commits, GitHub, GitLab) Commit: 61a8ec750d2d90bd1f63714478d280c10a874baa
Dependencies: Stopgaps:

Status badges

Description (last modified by jdemeyer)

In this ticket, we upgrade to:

Change History (23)

comment:1 Changed 5 years ago by vbraun

Branch: u/vbraun/misc_pip_upgrades

comment:2 Changed 5 years ago by vbraun

Cc: ​slelievre added
Commit: d3f883cce0c4c607ecabfa372561722b7793e453
Component: PLEASE CHANGEpackages: standard
Status: newneeds_review
Type: PLEASE CHANGEenhancement

New commits:

d3f883cUpdates of various pip packages

comment:3 Changed 5 years ago by slelievre

Authors: Volker Braun
Description: modified (diff)
Keywords: upgrade decorator ipykernel jupyter_client notebook ptyprocess pyzmq scandir send2trash setuptools tornado added

comment:4 Changed 5 years ago by jdemeyer

Can we postpone this to 8.4?

comment:5 Changed 5 years ago by slelievre

Any particular reason for postponing?

comment:6 in reply to:  5 Changed 5 years ago by jdemeyer

Replying to slelievre:

Any particular reason for postponing?

These kind of packages might introduce subtle failures in the notebook (both Jupyter and sagenb). Given that the correct functioning of the notebook is not tested well, it's better to have more time to test this.

comment:7 Changed 5 years ago by slelievre

By "have more time to test this", do you mean "merge such changes earlier in the beta cycle"?

Sure, why not. By the way, these are preliminaries for making JupyterLab an optional package.

comment:8 in reply to:  7 Changed 5 years ago by jdemeyer

Replying to slelievre:

By "have more time to test this", do you mean "merge such changes earlier in the beta cycle"?

Yes.

comment:9 Changed 5 years ago by jdemeyer

Milestone: sage-8.3sage-pending

comment:10 Changed 5 years ago by slelievre

Cc: embray jdemeyer tmonteil vbraun added
Description: modified (diff)
Milestone: sage-pendingsage-8.4
Status: needs_reviewneeds_work
Summary: Misc pip upgradesMisc pip upgrades, including upgrade to notebook 5.6

New upgrades since this ticket was opened:

  • notebook 5.6
  • pyzmq 17.1.0
  • setuptools 40.0.0
  • tornado 5.1

Note that the notebook 5.6 release includes a security fix, see the notebook 5.6 release announcement. Should we take care of that particular upgrade in another ticket with milestone Sage 8.3?

comment:11 Changed 5 years ago by slelievre

Note: PyZMQ upgrade done in #25906 along with ZeroMQ.

comment:12 Changed 5 years ago by jdemeyer

Description: modified (diff)

comment:13 Changed 4 years ago by slelievre

Description: modified (diff)

New upgrade:

  • scandir 1.8

comment:14 Changed 4 years ago by jdemeyer

See #26008 for setuptools.

comment:15 Changed 4 years ago by jdemeyer

Description: modified (diff)

comment:16 Changed 4 years ago by jdemeyer

Branch: u/vbraun/misc_pip_upgradesu/jdemeyer/misc_pip_upgrades

comment:17 Changed 4 years ago by jdemeyer

Commit: d3f883cce0c4c607ecabfa372561722b7793e453aae198109b1b717b7a878588c13a32b89f4bb00e
Description: modified (diff)
Reviewers: Jeroen Demeyer
Status: needs_workpositive_review
Summary: Misc pip upgrades, including upgrade to notebook 5.6Misc pip upgrades

New commits:

aae1981Updates of various pip packages

comment:18 Changed 4 years ago by vbraun

Branch: u/jdemeyer/misc_pip_upgradesaae198109b1b717b7a878588c13a32b89f4bb00e
Resolution: fixed
Status: positive_reviewclosed

comment:19 Changed 4 years ago by vbraun

Commit: aae198109b1b717b7a878588c13a32b89f4bb00e
Resolution: fixed
Status: closednew

This causes various test failures on OSX, presumably due to ptyprocess:

**********************************************************************
File "src/sage/interfaces/expect.py", line 357, in sage.interfaces.expect.Expect.pid
Failed example:
    gap.quit()
Exception raised:
    Traceback (most recent call last):
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 650, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1061, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.expect.Expect.pid[3]>", line 1, in <module>
        gap.quit()
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 597, in quit
        self._expect.close()
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/pexpect/pty_spawn.py", line 327, in close
        self.ptyproc.close(force=force)
      File "sage/interfaces/sagespawn.pyx", line 202, in sage.interfaces.sagespawn.SagePtyProcess.close (build/cythonized/sage/interfaces/sagespawn.c:3059)
        self.fileobj.close()
    IOError: [Errno 5] Input/output error
**********************************************************************
[...]
**********************************************************************
File "src/sage/interfaces/expect.py", line 858, in sage.interfaces.expect.Expect._eval_line
Failed example:
    singular._eval_line('def a=3;')
Exception raised:
    Traceback (most recent call last):
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 650, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1061, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.expect.Expect._eval_line[0]>", line 1, in <module>
        singular._eval_line('def a=3;')
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 942, in _eval_line
        self._synchronize()
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 1284, in _synchronize
        self._sendstr(cmd)
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 1226, in _sendstr
        self.quit()
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 597, in quit
        self._expect.close()
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/pexpect/pty_spawn.py", line 327, in close
        self.ptyproc.close(force=force)
      File "sage/interfaces/sagespawn.pyx", line 199, in sage.interfaces.sagespawn.SagePtyProcess.close (build/cythonized/sage/interfaces/sagespawn.c:2940)
        self.write(str_to_bytes(self.quit_string))
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/ptyprocess/ptyprocess.py", line 562, in write
        return self._writeb(s, flush=flush)
      File "/Users/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/ptyprocess/ptyprocess.py", line 552, in _writeb
        n = self.fileobj.write(b)
    ValueError: write to closed file
**********************************************************************
[...]
sage -t --long src/sage/interfaces/expect.py  # 29 doctests failed
sage -t --long src/sage/interfaces/gap.py  # 83 doctests failed
sage -t --long src/sage/interfaces/mwrank.py  # 6 doctests failed
sage -t --long src/sage/interfaces/quit.py  # 6 doctests failed

comment:20 Changed 4 years ago by jdemeyer

Branch: aae198109b1b717b7a878588c13a32b89f4bb00eu/jdemeyer/aae198109b1b717b7a878588c13a32b89f4bb00e

comment:21 Changed 4 years ago by jdemeyer

Commit: 61a8ec750d2d90bd1f63714478d280c10a874baa
Description: modified (diff)
Status: newneeds_review

I reverted the ptyprocess upgrade.


New commits:

61a8ec7Updates of various pip packages

comment:22 Changed 4 years ago by jdemeyer

Status: needs_reviewpositive_review

comment:23 Changed 4 years ago by vbraun

Branch: u/jdemeyer/aae198109b1b717b7a878588c13a32b89f4bb00e61a8ec750d2d90bd1f63714478d280c10a874baa
Resolution: fixed
Status: positive_reviewclosed
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