Update matplotlib to 3.3 #30176

antonio-rojas · 2020-07-19T20:42:55Z

Brings lots of deprecation warnings on every plot() call, due to OldScalarFormatter deprecation.

Depends on pillow for all image formats now.

Upstream: Fixed upstream, but not in a stable release.

CC: @jhpalmieri @kiwifb @mkoeppe @timokau @egourgoulhon @antonio-rojas @zlscherr

Component: packages: standard

Author: Antonio Rojas

Branch: 73af14a

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/30176

The text was updated successfully, but these errors were encountered:

antonio-rojas · 2020-07-19T20:44:23Z

Branch: u/arojas/update_matplotlib_to_3_3

sagetrac-git · 2020-07-19T20:45:52Z

Commit: cdf20ea

sagetrac-git · 2020-07-19T20:45:52Z

Branch pushed to git repo; I updated commit sha1. New commits:

`cdf20ea`	`Replace deprecated OldScalarFormatter with ScalarFormatter`

sagetrac-git · 2020-07-19T21:03:56Z

Branch pushed to git repo; I updated commit sha1. New commits:

`fee97c7`	`Replace deprecated basex and basey parameters`
`3d41b34`	`Update example`
`80f12fa`	`Update metrics for matplotlib 3.3`

sagetrac-git · 2020-07-19T21:03:56Z

Changed commit from cdf20ea to 80f12fa

antonio-rojas · 2020-07-19T21:10:50Z

Author: Antonio Rojas

antonio-rojas · 2020-07-19T21:13:29Z

comment:5

Still 3 test failures, all looking like

File "/usr/lib/python3.8/site-packages/sage/geometry/polyhedron/plot.py", line 1030, in sage.geometry.polyhedron.plot.Projection.render_2d
Failed example:
    q1.plot() + q2.plot() + q3.plot() + q4.plot()
Expected:
    Graphics object consisting of 17 graphics primitives
Got:
    doctest:warning
      File "/usr/bin/sage-runtests", line 177, in <module>
        err = DC.run()
      File "/usr/lib/python3.8/site-packages/sage/doctest/control.py", line 1196, in run
        self.run_doctests()
      File "/usr/lib/python3.8/site-packages/sage/doctest/control.py", line 897, in run_doctests
        self.dispatcher.dispatch()
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 2038, in dispatch
        self.parallel_dispatch()
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 1933, in parallel_dispatch
        w.start()  # This might take some time
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 2205, in start
        super(DocTestWorker, self).start()
      File "/usr/lib/python3.8/multiprocessing/process.py", line 121, in start
        self._popen = self._Popen(self)
      File "/usr/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/usr/lib/python3.8/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/usr/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
        self._launch(process_obj)
      File "/usr/lib/python3.8/multiprocessing/popen_fork.py", line 75, in _launch
        code = process_obj._bootstrap(parent_sentinel=child_r)
      File "/usr/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
        self.run()
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 2177, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 2506, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 2552, in _run
        result = runner.run(test)
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 905, in run
        return self._run(test, compileflags, out)
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 707, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.8/site-packages/sage/doctest/forker.py", line 1131, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.plot.Projection.render_2d[8]>", line 1, in <module>
        q1.plot() + q2.plot() + q3.plot() + q4.plot()
      File "/usr/lib/python3.8/site-packages/sage/repl/rich_output/display_manager.py", line 811, in displayhook
        plain_text, rich_output = self._rich_output_formatter(obj, dict())
      File "/usr/lib/python3.8/site-packages/sage/repl/rich_output/display_manager.py", line 625, in _rich_output_formatter
        rich_output = self._call_rich_repr(obj, rich_repr_kwds)
      File "/usr/lib/python3.8/site-packages/sage/repl/rich_output/display_manager.py", line 590, in _call_rich_repr
        warnings.warn(
      File "/usr/lib/python3.8/warnings.py", line 109, in _showwarnmsg
        sw(msg.message, msg.category, msg.filename, msg.lineno,
    :
    sage.repl.rich_output.display_manager.RichReprWarning: Exception in _rich_repr_ while displaying object: The first element of 'code' must be equal to 'MOVETO' (1).  Your first code is 79
    Graphics object consisting of 17 graphics primitives
**********************************************************************

antonio-rojas · 2020-07-20T13:09:54Z

Upstream: Reported upstream. No feedback yet.

antonio-rojas · 2020-07-20T13:09:54Z

comment:6

Reported upstream: matplotlib/matplotlib#17975

mkoeppe · 2020-07-22T04:28:43Z

comment:7

Upstream seems to have addressed it in matplotlib/matplotlib#17982

sagetrac-git · 2020-07-22T06:50:36Z

Changed commit from 80f12fa to dbdecd9

sagetrac-git · 2020-07-22T06:50:36Z

Branch pushed to git repo; I updated commit sha1. New commits:

`dbdecd9`	`Backport patch to fix the path of degenerate polygons`

sagetrac-git · 2020-07-22T06:55:08Z

Branch pushed to git repo; I updated commit sha1. New commits:

`fd2a9b8`	`Bump version to account for the added patch`

sagetrac-git · 2020-07-22T06:55:08Z

Changed commit from dbdecd9 to fd2a9b8

antonio-rojas · 2020-07-22T06:56:29Z

comment:10

No more test failures on Arch -> needs review

antonio-rojas · 2020-07-22T06:56:29Z

Changed upstream from Reported upstream. No feedback yet. to Fixed upstream, but not in a stable release.

mkoeppe · 2020-07-22T07:06:22Z

comment:11

Tests run at https://github.com/mkoeppe/sage/actions/runs/178114621

sagetrac-git · 2020-07-22T11:13:09Z

Changed commit from fd2a9b8 to ad67266

sagetrac-git · 2020-07-22T11:13:09Z

Branch pushed to git repo; I updated commit sha1. New commits:

`ad67266`	`Remove merged patch`

mkoeppe · 2020-07-23T05:04:06Z

comment:13

Tests run at https://github.com/mkoeppe/sage/actions/runs/179391787

mkoeppe · 2020-07-24T04:58:20Z

comment:14

Fails on all platforms. For example https://github.com/mkoeppe/sage/runs/901333269

    error: Failed to download FreeType. Please download one of ['https://downloads.sourceforge.net/project/freetype/freetype2/2.6.1/freetype-2.6.1.tar.gz', 'https://download.savannah.gnu.org/releases/freetype/freetype-2.6.1.tar.gz'] and extract it into build/freetype-2.6.1 at the top-level of the source repository.
    Running setup.py install for matplotlib: finished with status 'error'
ERROR: Command errored out with exit status 1: /sage/local/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-_2y953_j/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-_2y953_j/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' --no-user-cfg install --record /tmp/pip-record-v8gxera1/install-record.txt --single-version-externally-managed --root /sage/local/var/tmp/sage/build/matplotlib-3.3.0.p0/inst --compile --install-headers /sage/local/var/tmp/sage/build/matplotlib-3.3.0.p0/inst/sage/local/include/python3.7m/matplotlib Check the logs for full command output.
Exception information:
Traceback (most recent call last):
  File "/sage/local/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 841, in install
    req_description=str(self.req),
  File "/sage/local/lib/python3.7/site-packages/pip/_internal/operations/install/legacy.py", line 86, in install
    raise LegacyInstallFailure

mkoeppe · 2020-07-24T05:04:06Z

comment:16

https://github.com/matplotlib/matplotlib/blob/v3.3.x/INSTALL.rst:
"By default ... Matplotlib downloads and builds its own copy of FreeType ... and uses its own copy of Qhull.
To force Matplotlib to use a copy of FreeType or Qhull already installed in your system, create a setup.cfg file ...."

mkoeppe · 2020-07-25T18:26:01Z

Reviewer: Matthias Koeppe

mkoeppe · 2020-07-25T18:26:01Z

comment:31

Replying to @mkoeppe:

Tests run at https://github.com/mkoeppe/sage/actions/runs/181664763

This looks clean on all platforms.

I think it would be better if the changed multigraphics doctest was adjusted to be more tolerant instead of just updating the result.

Nevertheless, a positive review from my side.

vbraun · 2020-07-27T20:37:16Z

comment:32

There is numerical noise on various buildbots, e.g.

**********************************************************************
File "src/sage/plot/multigraphics.py", line 1297, in sage.plot.multigraphics.GraphicsArray.position
Failed example:
    G.position(0)  # tol 1.0e-13
Expected:
    (0.025045451349937315,
     0.03415488992713045,
     0.4489880779745068,
     0.9345951100728696)
Got:
    (0.02494779509993732,
     0.03415488992713045,
     0.44913456234950677,
     0.9345951100728696)
Tolerance exceeded in 2 of 4:
    0.025045451349937315 vs 0.02494779509993732, tolerance 4e-3 > 1e-13
    0.4489880779745068 vs 0.44913456234950677, tolerance 4e-4 > 1e-13
**********************************************************************
File "src/sage/plot/multigraphics.py", line 1302, in sage.plot.multigraphics.GraphicsArray.position
Failed example:
    G.position(1)  # tol 1.0e-13
Expected:
    (0.5170637412999687,
     0.20212705964722733,
     0.4489880779745068,
     0.5986507706326758)
Got:
    (0.5170149131749686,
     0.20202940339722741,
     0.44913456234950666,
     0.5988460831326756)
Tolerance exceeded in 4 of 4:
    0.5170637412999687 vs 0.5170149131749686, tolerance 1e-4 > 1e-13
    0.20212705964722733 vs 0.20202940339722741, tolerance 5e-4 > 1e-13
    0.4489880779745068 vs 0.44913456234950666, tolerance 4e-4 > 1e-13
    0.5986507706326758 vs 0.5988460831326756, tolerance 4e-4 > 1e-13
**********************************************************************
1 item had failures:
   2 of   6 in sage.plot.multigraphics.GraphicsArray.position
    [192 tests, 2 failures, 20.75 s]
----------------------------------------------------------------------
sage -t --long --random-seed=0 src/sage/plot/multigraphics.py  # 2 doctests failed
----------------------------------------------------------------------

vbraun · 2020-07-27T20:37:54Z

comment:33

**********************************************************************
File "src/sage/plot/multigraphics.py", line 1297, in sage.plot.multigraphics.GraphicsArray.position
Failed example:
    G.position(0)  # tol 1.0e-13
Expected:
    (0.025045451349937315,
     0.03415488992713045,
     0.4489880779745068,
     0.9345951100728696)
Got:
    (0.02494779509993732,
     0.03415488992713045,
     0.44913456234950677,
     0.9345951100728696)
Tolerance exceeded in 2 of 4:
    0.025045451349937315 vs 0.02494779509993732, tolerance 4e-3 > 1e-13
    0.4489880779745068 vs 0.44913456234950677, tolerance 4e-4 > 1e-13
**********************************************************************
File "src/sage/plot/multigraphics.py", line 1302, in sage.plot.multigraphics.GraphicsArray.position
Failed example:
    G.position(1)  # tol 1.0e-13
Expected:
    (0.5170637412999687,
     0.20212705964722733,
     0.4489880779745068,
     0.5986507706326758)
Got:
    (0.5170149131749686,
     0.20202940339722741,
     0.44913456234950666,
     0.5988460831326756)
Tolerance exceeded in 4 of 4:
    0.5170637412999687 vs 0.5170149131749686, tolerance 1e-4 > 1e-13
    0.20212705964722733 vs 0.20202940339722741, tolerance 5e-4 > 1e-13
    0.4489880779745068 vs 0.44913456234950666, tolerance 4e-4 > 1e-13
    0.5986507706326758 vs 0.5988460831326756, tolerance 4e-4 > 1e-13
**********************************************************************
1 item had failures:
   2 of   6 in sage.plot.multigraphics.GraphicsArray.position
    [192 tests, 2 failures, 27.84 s]
----------------------------------------------------------------------
sage -t --long --random-seed=0 src/sage/plot/multigraphics.py  # 2 doctests failed
----------------------------------------------------------------------

sagetrac-git · 2020-08-01T08:24:03Z

Branch pushed to git repo; I updated commit sha1. New commits:

`20ecd18`	`Increase numerical noise tolerance`

sagetrac-git · 2020-08-01T08:24:03Z

Changed commit from 79249f7 to 20ecd18

vbraun · 2020-08-06T21:45:52Z

comment:37

**********************************************************************
File "src/sage/plot/multigraphics.py", line 1297, in sage.plot.multigraphics.GraphicsArray.position
Failed example:
    G.position(0)  # tol 1.0e-3
Expected:
    (0.025045451349937315,
     0.03415488992713045,
     0.4489880779745068,
     0.9345951100728696)
Got:
    (0.02494779509993732,
     0.03415488992713045,
     0.44913456234950677,
     0.9345951100728696)
Tolerance exceeded in 1 of 4:
    0.025045451349937315 vs 0.02494779509993732, tolerance 4e-3 > 1e-3
**********************************************************************
1 item had failures:
   1 of   6 in sage.plot.multigraphics.GraphicsArray.position
    [192 tests, 1 failure, 33.68 s]
----------------------------------------------------------------------
sage -t --long --random-seed=0 src/sage/plot/multigraphics.py  # 1 doctest failed
----------------------------------------------------------------------

sagetrac-git · 2020-08-07T09:15:30Z

Branch pushed to git repo; I updated commit sha1. New commits:

`73af14a`	`Adjust numeric noise tolerance further`

sagetrac-git · 2020-08-07T09:15:30Z

Changed commit from 20ecd18 to 73af14a

vbraun · 2020-08-09T08:47:29Z

Changed branch from u/arojas/update_matplotlib_to_3_3 to 73af14a

kcrisman · 2020-12-15T14:03:48Z

Changed commit from 73af14a to none

kcrisman · 2020-12-15T14:03:48Z

comment:41

Hi! Is it possible that this change is responsible for the difference between the following two images?

Notice that not only is the image slightly narrower, but the labels now all have default of one place beyond the decimal point, which in the past was not desired for the evident reasons we see here. That might be good for scientific plotting, but not for mathematical plotting.

kcrisman · 2020-12-15T14:08:02Z

comment:42

(Note that this explanation of the difference doesn't really seem to have any examples relevant to this situation.)

mkoeppe · 2021-01-02T20:14:50Z

comment:43

Follow-up on qhull in #31148

antonio-rojas added this to the sage-9.2 milestone Jul 19, 2020

antonio-rojas added the p: major / 3 label Jul 19, 2020

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antonio-rojas added c: packages: standard labels Jul 19, 2020

antonio-rojas added the s: needs review label Jul 22, 2020

mkoeppe added s: needs work and removed s: needs review labels Jul 24, 2020

mkoeppe added s: positive review and removed s: needs review labels Jul 25, 2020

vbraun added s: needs work and removed s: positive review labels Jul 27, 2020

antonio-rojas added s: positive review and removed s: needs work labels Aug 1, 2020

vbraun added s: needs work and removed s: positive review labels Aug 6, 2020

antonio-rojas added s: positive review and removed s: needs work labels Aug 7, 2020

vbraun removed the s: positive review label Aug 9, 2020

vbraun closed this as completed in dfdae6f Aug 9, 2020

kliem mentioned this issue May 28, 2021

Make plot doctests ready for random seeds #29986

Closed

mkoeppe mentioned this issue Sep 1, 2020

Update matplotlib to 3.3.1, certifi to 2020.6.20 #30358

Closed

davidlowryduda mentioned this issue Mar 3, 2021

list_plot labels don't indicate exponential notation by default #31447

Closed

mkoeppe mentioned this issue Mar 20, 2021

Updates: pillow 8.1.2, matplotlib 3.3.4, imagesize 1.2.0 #31503

Closed

Update matplotlib to 3.3 #30176

Update matplotlib to 3.3 #30176

Comments

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