Misc pip upgrades again
Closed this issue · 37 comments
This ticket (similar to #26969) upgrades the following packages:
package before after
----------------------------------
bleach 3.0.2 3.1.0
certifi 2018.11.29 2019.3.9
configparser 3.5.0 3.7.4
cypari 2.1.0.p0 2.1.1
cython 0.29.5.p0 0.29.10
decorator 4.3.0 4.4.0
defusedxml 0.5.0 0.6.0
entrypoints 0.2.3 0.3
Tarballs:
- https://files.pythonhosted.org/packages/78/5a/0df03e8735cd9c75167528299c738702437589b9c71a849489d00ffa82e8/bleach-3.1.0.tar.gz
- https://files.pythonhosted.org/packages/06/b8/d1ea38513c22e8c906275d135818fee16ad8495985956a9b7e2bb21942a1/certifi-2019.3.9.tar.gz
- https://files.pythonhosted.org/packages/e2/1c/83fd53748d8245cb9a3399f705c251d3fc0ce7df04450aac1cfc49dd6a0f/configparser-3.7.4.tar.gz
- https://files.pythonhosted.org/packages/0c/d0/8b868cedd991bbb2098bbc10a0788c7d3ea6bc9dee946e1eb8424cd4b9f6/cypari2-2.1.1.tar.gz
- https://files.pythonhosted.org/packages/e7/2e/aee8dfff93c7f5d20461ddcefd1da3d43bab18e1666a7777f4d9dbe94065/Cython-0.29.10.tar.gz
- https://files.pythonhosted.org/packages/ba/19/1119fe7b1e49b9c8a9f154c930060f37074ea2e8f9f6558efc2eeaa417a2/decorator-4.4.0.tar.gz
- https://files.pythonhosted.org/packages/a4/5f/f8aa58ca0cf01cbcee728abc9d88bfeb74e95e6cb4334cfd5bed5673ea77/defusedxml-0.6.0.tar.gz
- https://files.pythonhosted.org/packages/b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c/entrypoints-0.3.tar.gz
CC: @slel @vbraun @embray @jdemeyer @kiwifb
Component: packages: standard
Keywords: upgrade
Author: Frédéric Chapoton
Branch/Commit: 34aba48
Reviewer: John Palmieri
Issue created by migration from https://trac.sagemath.org/ticket/27886
Some of these are only for Python 3: ipython, ipykernel, matplotlib, Sphinx, rpy2 (?), possibly others. In some cases (matplotlib, rpy2) we may be able to upgrade one or two minor versions and still maintain compatibility with Python 2, but we can't upgrade to the latest version yet.
To take into account py2 / py3, upgrade this:
package upstream version latest wheel py3 spkg name in Sage
official name in Sage py2-ok sdist only if different
-------------------------------------------------------------------------------
Babel 2.6.0 2.7.0 wheel babel
backports.ssl-match-hostname 3.5.0.1 3.7.0.1 sdist backports_ssl_match_hostname
bleach 3.0.2 3.1.0 wheel
certifi 2018.11.29 2019.3.9 wheel
configparser 3.5.0 3.7.4 wheel
cvxopt 1.1.8 1.2.3 wheel
cypari2 2.1.0 2.1.1 sdist
Cython 0.29.5 0.29.8 wheel cython
decorator 4.3.0 4.4.0 wheel
defusedxml 0.5.0 0.6.0 wheel
entrypoints 0.2.3 0.3 wheel
Flask 0.10.1 1.0.3 wheel flask
Flask-AutoIndex 0.6 0.6.2 sdist flask_autoindex
Flask-Babel 0.9 0.12.2 sdist flask_babel
ipykernel 4.8.2 4.10.0 wheel 5+
Jinja2 2.10 2.10.1 wheel jinja2
jsonschema 2.6.0 3.0.1 wheel
kiwisolver 1.0.1 1.1.0 wheel
MarkupSafe 1.1.0 1.1.1 wheel markupsafe
nbconvert 5.4.0 5.5.0 wheel
networkx 2.2 2.3 sdist
notebook 5.7.6 5.7.8 wheel
numpy 1.16.1 1.16.3 wheel
packaging 18.0 19.0 wheel
path.py 7.1 11.5.2 wheel 12+ pathpy
pexpect 4.6.0 4.7.0 wheel
Pillow 5.3.0 6.0.0 wheel pillow
pip 18.1 19.1.1 wheel
pkgconfig 1.4.0 1.5.1 wheel
prometheus-client 0.5.0 0.6.0 sdist prometheus_client
prompt-toolkit 1.0.15 2.0.9 wheel prompt_toolkit
psutil 5.2.0 5.6.2 sdist
ptyprocess 0.5.1 0.6.0 wheel
Pygments 2.3.1 2.4.2 wheel pygments
pyparsing 2.3.0 2.4.0 wheel
python-dateutil 2.5.3 2.8.0 wheel dateutil
pytz 2018.7 2019.1 wheel
pyzmq 17.1.2 18.0.1 wheel
requests 2.13.0 2.22.0 wheel
rpy2 2.8.2 2.8.6 sdist 2.9+
scandir 1.9.0 1.10.0 sdist
scipy 1.2.0 1.2.1 wheel 1.3+
setuptools 40.6.3 41.0.1 wheel
setuptools-scm 3.1.0 3.3.3 wheel setuptools_scm
sphinxcontrib-websupport 1.1.0 1.1.2 wheel sphinxcontrib_websupport
terminado 0.8.1 0.8.2 wheel
tornado 4.5.2 5.1.1 sdist 6+
Twisted 16.3.0 19.2.0 sdist twisted
Werkzeug 0.14.1 0.15.4 wheel werkzeug
Cannot upgrade this until we drop Python 2:
ipython 5.8.0 5.8.0 wheel 6+
matplotlib 2.2.3 2.2.3 wheel 3+
Sphinx 1.8.5 1.8.5 wheel 2+ sphinx
Additional possible PyPI upgrades:
readline 6.3.008.p0 --> gnureadline 6.3.8
pyx 0.12.1.p0 --> 0.14.1
scons 1.2.0 --> 3.0.5
It looks to me as though matplotlib 2.2.4 would be okay for Python 2, but nothing beyond that.
Replying to @jhpalmieri:
It looks to me as though matplotlib 2.2.4 would be okay for Python 2, but nothing beyond that.
Using it in sage-on-gentoo.
as in #26969, we may need to exclude "ptyprocess" and "tornado"
Volker, do you have an easy way to do this kind of batch upgrade, as you did it before ?
Branch: public/27886
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
7d825c3 | some packages upgrade |
ok, maybe this is a good first step. Includes an update of cython.
Author: Frédéric Chapoton
cypari does not build. Should I add back the cython trashcan patch ?
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
e226ab8 | some packages upgrade, including cython |
ok, I have added back the cython patch. Back to needs review.
Updating the ticket description to reflect the actual changes.
Description changed:
---
+++
@@ -1,58 +1,15 @@
-similar to #26969
-
-What could be updated:
+This ticket (similar to #26969) upgrades the following packages:
```
-Babel 2.6.0 2.7.0 wheel
-backports.ssl-match-hostname 3.5.0.1 3.7.0.1 sdist
-bleach 3.0.2 3.1.0 wheel
-certifi 2018.11.29 2019.3.9 wheel
-configparser 3.5.0 3.7.4 wheel
-cvxopt 1.1.8 1.2.3 wheel
-cypari2 2.1.0 2.1.1 sdist
-Cython 0.29.5 0.29.8 wheel
-decorator 4.3.0 4.4.0 wheel
-defusedxml 0.5.0 0.6.0 wheel
-entrypoints 0.2.3 0.3 wheel
-Flask 0.10.1 1.0.3 wheel
-Flask-AutoIndex 0.6 0.6.2 sdist
-Flask-Babel 0.9 0.12.2 sdist
-ipykernel 4.8.2 5.1.1 wheel
-ipython 5.8.0 7.5.0 wheel
-Jinja2 2.10 2.10.1 wheel
-jsonschema 2.6.0 3.0.1 wheel
-kiwisolver 1.0.1 1.1.0 wheel
-MarkupSafe 1.1.0 1.1.1 wheel
-matplotlib 2.2.3 3.1.0 wheel
-nbconvert 5.4.0 5.5.0 wheel
-networkx 2.2 2.3 sdist
-notebook 5.7.6 5.7.8 wheel
-numpy 1.16.1 1.16.3 wheel
-packaging 18.0 19.0 wheel
-path.py 7.1 12.0.1 wheel
-pexpect 4.6.0 4.7.0 wheel
-Pillow 5.3.0 6.0.0 wheel
-pip 18.1 19.1.1 wheel
-pkgconfig 1.4.0 1.5.1 wheel
-prometheus-client 0.5.0 0.6.0 sdist
-prompt-toolkit 1.0.15 2.0.9 wheel
-psutil 5.2.0 5.6.2 sdist
-ptyprocess 0.5.1 0.6.0 wheel
-Pygments 2.3.1 2.4.2 wheel
-pyparsing 2.3.0 2.4.0 wheel
-python-dateutil 2.5.3 2.8.0 wheel
-pytz 2018.7 2019.1 wheel
-pyzmq 17.1.2 18.0.1 wheel
-requests 2.13.0 2.22.0 wheel
-rpy2 2.8.2 3.0.4 sdist
-scandir 1.9.0 1.10.0 sdist
-scipy 1.2.0 1.3.0 wheel
-setuptools 40.6.3 41.0.1 wheel
-setuptools-scm 3.1.0 3.3.3 wheel
-Sphinx 1.8.5 2.0.1 wheel
-sphinxcontrib-websupport 1.1.0 1.1.2 wheel
-terminado 0.8.1 0.8.2 wheel
-tornado 4.5.2 6.0.2 sdist
-Twisted 16.3.0 19.2.0 sdist
-Werkzeug 0.14.1 0.15.4 wheel
+package before after
+----------------------------------
+bleach 3.0.2 3.1.0
+certifi 2018.11.29 2019.3.9
+configparser 3.5.0 3.7.4
+cypari 2.1.0.p0 2.1.1
+cython 0.29.5.p0 0.29.10
+decorator 4.3.0 4.4.0
+defusedxml 0.5.0 0.6.0
+entrypoints 0.2.3 0.3
```
+Changed keywords from none to upgrade
Reviewer: John Palmieri
Description changed:
---
+++
@@ -12,4 +12,13 @@
defusedxml 0.5.0 0.6.0
entrypoints 0.2.3 0.3
```
+Tarballs:
+- https://files.pythonhosted.org/packages/78/5a/0df03e8735cd9c75167528299c738702437589b9c71a849489d00ffa82e8/bleach-3.1.0.tar.gz
+- https://files.pythonhosted.org/packages/06/b8/d1ea38513c22e8c906275d135818fee16ad8495985956a9b7e2bb21942a1/certifi-2019.3.9.tar.gz
+- https://files.pythonhosted.org/packages/e2/1c/83fd53748d8245cb9a3399f705c251d3fc0ce7df04450aac1cfc49dd6a0f/configparser-3.7.4.tar.gz
+- https://files.pythonhosted.org/packages/0c/d0/8b868cedd991bbb2098bbc10a0788c7d3ea6bc9dee946e1eb8424cd4b9f6/cypari2-2.1.1.tar.gz
+- https://files.pythonhosted.org/packages/e7/2e/aee8dfff93c7f5d20461ddcefd1da3d43bab18e1666a7777f4d9dbe94065/Cython-0.29.10.tar.gz
+- https://files.pythonhosted.org/packages/ba/19/1119fe7b1e49b9c8a9f154c930060f37074ea2e8f9f6558efc2eeaa417a2/decorator-4.4.0.tar.gz
+- https://files.pythonhosted.org/packages/a4/5f/f8aa58ca0cf01cbcee728abc9d88bfeb74e95e6cb4334cfd5bed5673ea77/defusedxml-0.6.0.tar.gz
+- https://files.pythonhosted.org/packages/b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c/entrypoints-0.3.tar.gzWorks for me on OS X, both Python 2 and 3. Others should try on other platforms.
Unfortunately it doesn't fix the Python 3 doctest failure in cpython.
Which failure remains in the cpython folder under python3 ? Both of these :
┣ debug.pyx # 1
┗ dict_del_by_value.pyx # 2
or just one ? The upgrade is supposed only to fix the second file. For the first one, see #27964
I still get both failures. I'll try make distclean and then rebuild to see if that helps.
After make distclean, same result: both files have failures.
And Jeroen, who knows about cython and prevented me to fix that in a naive way, seems not to be very active here at the moment.
I see:
test_del_dictitem_by_exact_value(D, ZZ, 2)
fails, but
test_del_dictitem_by_exact_value(D, ZZ, int(2))
works. What was your naive fix? I would be tempted to use
test_del_dictitem_by_exact_value(D, ZZ, hash(2))
This is more robust, since it works in this kind of case:
sage: D = {1230981308409180310928308123: ZZ}
sage: test_del_dictitem_by_exact_value(D, ZZ, hash(1230981308409180310928308123))
while
sage: D = {1230981308409180310928308123: ZZ}
sage: test_del_dictitem_by_exact_value(D, ZZ, 1230981308409180310928308123)
fails with both Python 2 and 3. The current doctest relies on the fact that the hash of the Sage integer 2 is equal to 2, and this doesn't generalize to integers that are too large.
The test_del_dictitem_by_exact_value failure is fixed upstream at cython/cython@2825103
I suggest to just apply that patch instead of "fixing" the doctest.
But this is supposed to be in cython 0.29.3 ??
6 months ago, in #26855 you said : Fixed upstream, but not in a stable release
It's not fixed in a Cython bugfix release it seems, but only in the next major release.
...or maybe it was meant to be fixed in 0.29.x but forgotten.
Branch pushed to git repo; I updated commit sha1. New commits:
34aba48 | Add Cython patch to fix Py_hash_t conversion |
This change does fix the py3 doctest failures in cpython/dict_del_by_value.pyx. I was hoping it would fix some of the doctests in integer.pyx, but it doesn't seem to have done that.
Let's merge this into an early 8.9 beta.
Changed branch from public/27886 to 34aba48