Opened 5 years ago
Closed 4 years ago
#25638 closed enhancement (fixed)
Misc pip upgrades
Reported by:  vbraun  Owned by:  

Priority:  major  Milestone:  sage8.4 
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: 
Description (last modified by )
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)
Change History (23)
comment:1 Changed 5 years ago by
Branch:  → u/vbraun/misc_pip_upgrades 

comment:2 Changed 5 years ago by
Cc:  slelievre added 

Commit:  → d3f883cce0c4c607ecabfa372561722b7793e453 
Component:  PLEASE CHANGE → packages: standard 
Status:  new → needs_review 
Type:  PLEASE CHANGE → enhancement 
comment:3 Changed 5 years ago by
Authors:  → Volker Braun 

Description:  modified (diff) 
Keywords:  upgrade decorator ipykernel jupyter_client notebook ptyprocess pyzmq scandir send2trash setuptools tornado added 
comment:6 Changed 5 years ago by
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 followup: 8 Changed 5 years ago by
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 Changed 5 years ago by
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
Milestone:  sage8.3 → sagepending 

comment:10 Changed 5 years ago by
Cc:  embray jdemeyer tmonteil vbraun added 

Description:  modified (diff) 
Milestone:  sagepending → sage8.4 
Status:  needs_review → needs_work 
Summary:  Misc pip upgrades → Misc 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:12 Changed 5 years ago by
Description:  modified (diff) 

comment:15 Changed 4 years ago by
Description:  modified (diff) 

comment:16 Changed 4 years ago by
Branch:  u/vbraun/misc_pip_upgrades → u/jdemeyer/misc_pip_upgrades 

comment:17 Changed 4 years ago by
Commit:  d3f883cce0c4c607ecabfa372561722b7793e453 → aae198109b1b717b7a878588c13a32b89f4bb00e 

Description:  modified (diff) 
Reviewers:  → Jeroen Demeyer 
Status:  needs_work → positive_review 
Summary:  Misc pip upgrades, including upgrade to notebook 5.6 → Misc pip upgrades 
New commits:
aae1981  Updates of various pip packages

comment:18 Changed 4 years ago by
Branch:  u/jdemeyer/misc_pip_upgrades → aae198109b1b717b7a878588c13a32b89f4bb00e 

Resolution:  → fixed 
Status:  positive_review → closed 
comment:19 Changed 4 years ago by
Commit:  aae198109b1b717b7a878588c13a32b89f4bb00e 

Resolution:  fixed 
Status:  closed → new 
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/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 650, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/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/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/interfaces/expect.py", line 597, in quit self._expect.close() File "/Users/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/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/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 650, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/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/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/interfaces/expect.py", line 942, in _eval_line self._synchronize() File "/Users/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/interfaces/expect.py", line 1284, in _synchronize self._sendstr(cmd) File "/Users/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/interfaces/expect.py", line 1226, in _sendstr self.quit() File "/Users/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/interfaces/expect.py", line 597, in quit self._expect.close() File "/Users/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/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/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/ptyprocess/ptyprocess.py", line 562, in write return self._writeb(s, flush=flush) File "/Users/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/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
Branch:  aae198109b1b717b7a878588c13a32b89f4bb00e → u/jdemeyer/aae198109b1b717b7a878588c13a32b89f4bb00e 

comment:21 Changed 4 years ago by
Commit:  → 61a8ec750d2d90bd1f63714478d280c10a874baa 

Description:  modified (diff) 
Status:  new → needs_review 
comment:22 Changed 4 years ago by
Status:  needs_review → positive_review 

comment:23 Changed 4 years ago by
Branch:  u/jdemeyer/aae198109b1b717b7a878588c13a32b89f4bb00e → 61a8ec750d2d90bd1f63714478d280c10a874baa 

Resolution:  → fixed 
Status:  positive_review → closed 
New commits:
Updates of various pip packages