Misc pip upgrades

[vbraun]

In this ticket, we upgrade to:

• ​decorator 4.3.0 (from 4.0.6.p0)
• ​ipykernel 4.8.2 (from 4.7.0)
• ​jupyter_client 5.2.3 (from 5.2.2)
• ​notebook 5.5.0 (from 5.3.1)
• ​scandir 1.7 (from 1.6)
• ​send2trash 1.5.0 (from 1.4.2) (Send2Trash on PyPI)

[vbraun]

New commits:

​d3f883c

Updates of various pip packages

[jdemeyer]

Can we postpone this to 8.4?

[slelievre]

Any particular reason for postponing?

[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.

[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.

[jdemeyer]

Replying to slelievre:

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

Yes.

[slelievre]

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?

[slelievre]

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

[slelievre]

New upgrade:

• scandir 1.8

[jdemeyer]

See #26008 for setuptools.

[jdemeyer]

New commits:

​aae1981

Updates of various pip packages

[vbraun]

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

[jdemeyer]

I reverted the ptyprocess upgrade.

---

New commits:

​61a8ec7

Updates of various pip packages