Misc pip upgrades again

[fchapoton]

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

[jhpalmieri]

comment:1

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.

[slel]

comment:2

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

[jhpalmieri]

comment:4

It looks to me as though matplotlib 2.2.4 would be okay for Python 2, but nothing beyond that.

[kiwifb]

comment:5

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.

[fchapoton]

comment:6

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 ?

[fchapoton]

New commits:

1f1ec27

some packages upgrade

[fchapoton]

Branch: public/27886

[fchapoton]

Commit: 1f1ec27

[sagetrac-git]

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

7d825c3

some packages upgrade

[sagetrac-git]

Changed commit from 1f1ec27 to 7d825c3

[fchapoton]

comment:9

ok, maybe this is a good first step. Includes an update of cython.