Unpin matplotlib to support >=2.0 #3019

bjlittle · 2018-05-17T06:31:33Z

This PR is attempting to unpin mpl. As a result of unpinning mpl from 1.5.3 to 2.2.2 it releases the implicit dependency pin on numpy, which moves from 1.13.3 to 1.14.3.

This causes royal carnage, pepper sprayed pretty much everywhere...

Can't see quite how to not make this PR wide ranging, so I'm going to adopt the strategy of fixing individual tests per commit.

The main culprit for causing so much noise (so far) is numpy changing the implementation of its np.core.arrayprint._formatArray functionality, which we tap into via iris.util.format_array for printing numpy arrays... hence the CML armageddon. I've tried best I can to replicate legacy numpy 1.13 array printing for 1.14, but there are (unavoidable) minor differences that are causing us great pain. C'est la vive!

I'm going to keep drip feeding commits into this PR until I nail all the test failures... then I'm going to sit in a dark, quiet room for a while.

Outstanding Actions:

Fix CellMeasures tests
Fix graphic test_plot errors for test_zx and test_tx
Create new citation graphic test
~~Fix NetCDF/HDF tmp file error~~
- legitimate HDF error output from test_netcdf.SavePermissions tests.
Add iris-grib example graphic test hash
Investigate example test TestPolynomialFit mpl UserWarning
- raised Iris documentation - example test mpl UserWarning #3032 to cover this
Investigate example test_COP_maps usage of linewidth
Fix unit test axes tick labels failures
Merge companion test-iris-imagehash PR WIP: unpin mpl test-iris-imagehash#15

pp-mo · 2018-05-17T09:08:22Z

IMO CML is not really fit for purpose, and actually never has been.
Seriously, could we not at this point work to retire CML instead ??

bjlittle · 2018-05-17T09:13:07Z

@pp-mo 👍 For retiring / replacing CML, but not at the point when we're making major changes.

It would just be totally impossible to track the differences. It's hard enough as it is, so I'd say not now and not in this PR. But definitely in a separate, focused PR for that purpose.

bjlittle · 2018-05-17T09:52:50Z

@pp-mo Actually, github has changed (again) for the better, and you can now do diffs but with whitespace differences hidden, see this as an example... it makes this PR a lot easier to review 😺

pp-mo · 2018-05-17T10:44:09Z

you can now do diffs but with whitespace differences hidden, see this as an example...

Oh yeah, great spot -- that really is progress ! 😮 😹

pp-mo · 2018-05-17T10:52:04Z

lib/iris/util.py

+    if arr.size > summary_threshold:
+        summary_insert = '...'
+    options = np.get_printoptions()
+    options['legacy'] = legacy


Do we really need to do this, if virtually every CML is changing anyway ??

N.B. I have no idea how much more carnage that might be !!
So far (https://github.com/bjlittle/iris/tree/d910238b43bf3e5b57ff35c4ac813d7a077626c9/ ~= 9am Thu 17 May) we have 77 CML files changed out of 569 ???

Yes, we really need to do this.

You'll need to open the hood on numpy 1.13 vs 1.14 to see the changes that they've made. The legacy support is the way to get close to 1.13 output from 1.14.

To put this in context... I'm down to my last 17 test failures and 1 error (excluding graphical tests), so I'm in the home straight. I don't expect another ~500 CML file changes 🙏

The graphical tests will be a different can of worms...

I agree with merging this as it is. I'd like to follow it up with another PR though and change all ~500 CML to modern numpy.

pp-mo · 2018-05-17T10:54:32Z

I think you may need to rebase, there is still a check_graphic action failure :

FAIL: test_cube_animation (iris.tests.experimental.test_animate.IntegrationTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/test-environment/lib/python2.7/site-packages/scitools_iris-2.1.0.dev0-py2.7.egg/iris/tests/experimental/test_animate.py", line 82, in test_cube_animation
    self.check_graphic()
  File "/home/travis/miniconda/envs/test-environment/lib/python2.7/site-packages/scitools_iris-2.1.0.dev0-py2.7.egg/iris/tests/__init__.py", line 842, in check_graphic
    raise AssertionError(emsg.format(msg))
AssertionError: Image comparison failed: Bad phash fe81c17e817e3e81817e7e81857e7a817e81c17e7e81c17e7a81817e817e842e with hamming distance [44] for test iris.tests.experimental.test_animate.IntegrationTest.test_cube_animation.0.
-------------------- >> begin captured logging << --------------------
PIL.PngImagePlugin: DEBUG: STREAM 'IHDR' 16 13
PIL.PngImagePlugin: DEBUG: STREAM 'sBIT' 41 4
PIL.PngImagePlugin: DEBUG: 'sBIT' 41 4 (unknown)
PIL.PngImagePlugin: DEBUG: STREAM 'pHYs' 57 9
PIL.PngImagePlugin: DEBUG: STREAM 'tEXt' 78 57
PIL.PngImagePlugin: DEBUG: STREAM 'IDAT' 147 4821
--------------------- >> end captured logging << ---------------------

We fixed this? ...

pp-mo · 2018-05-17T11:03:40Z

Just did a quick scan of the test output log.

Do we really need to do this, if virtually every CML is changing anyway ?? ...N.B. I have no idea how much more carnage that might be !!

Status update:
Looks like we only have 2-3 CML mismatches outstanding (but in many cases more errors may emerge when those are fixed)

Then there are a bunch of about 125 image failures, most of which are reporting just "Image sizes do not match expected size"
Is that a limitation of imagehash ??

Also we currently have ~13 PP file mismatches.
~~I'm a bit concerned about that.~~
It's just because it uses string reprs of PPfields

bjlittle · 2018-05-17T11:08:46Z

@pp-mo mpl 2.0 is quite different to 1.5.3... infact it's very different. I'm expecting to see pretty much all the graphical tests fail, even with perceptual image hashing. For a starter the mpl default png sizes are different... it would be nice if we were invariant to that. I'm not too concerned at the moment.

Let me get to the point where everything is passing apart from the graphical tests... I'm pretty close to that point. Then it'll be time to pause and work out what to do with the graphical tests.

pp-mo · 2018-05-17T11:10:28Z

Let me get to the point where everything is passing apart from the graphical tests... I'm pretty close to that point.

👍

pelson · 2018-05-22T09:41:11Z

lib/iris/tests/__init__.py

@@ -1174,7 +1174,7 @@ class MyPlotTests(test.GraphicsTest):


 skip_sample_data = unittest.skipIf(not SAMPLE_DATA_AVAILABLE,
-                                   ('Test(s) require "iris_sample_data", '
+                                   ('Test(s) require "iris-sample-data", '


bjlittle · 2018-05-22T10:46:59Z

lib/iris/experimental/regrid.py

@@ -390,7 +390,7 @@ def _weighted_mean_with_mdtol(data, weights, axis=None, mdtol=0):
            weights_sum = weights.sum(axis=axis)
            frac_masked = 1 - np.true_divide(unmasked_weights_sum, weights_sum)
            mask_pt = frac_masked > mdtol
-            if np.any(mask_pt):


A slight behaviour change between numpy versions 1.13.3 and 1.14.3 - you can no longer change the mask of a MaskedConstant. This makes total sense, and numpy have quite rightly made this stricter.

Our test was abusing this convenience prior to 1.14.3...

>>> import numpy as np >>> np.__version__ '1.14.3' >>> import numpy.ma as ma >>> a = ma.array([1.0], mask=True) >>> m = a[0] >>> type(m) <class 'numpy.ma.core.MaskedConstant'> >>> m.mask |= True Traceback (most recent call last): File "<stdin>", line 1, in <module> ValueError: output array is read-only

as opposed to

>>> import numpy as np >>> np.__version__ '1.13.3' >>> import numpy.ma as ma >>> a = ma.array([1.0], mask=True) >>> m = a[0] >>> type(m) <class 'numpy.ma.core.MaskedConstant'> >>> m.mask |= True >>> m masked >>> m.mask |= False >>> m masked

stickler-ci · 2018-05-25T12:36:24Z

lib/iris/tests/idiff.py

+# command-line argument as idiff is an interactive tool that requires a
+# gui interface.
+sys.argv.append('-d')
+import iris.tests


E402 module level import not at top of file

bjlittle · 2018-05-30T11:49:10Z

@pp-mo and @pelson

Okay, so I'm pretty much done here...finally 😄

All the tests are passing, apart from one final failure!

This simply requires the companion test-iris-imagehash PR SciTools/test-iris-imagehash#15 to be merged in order to support the perceptual image hash changes check of the imagerepo.json in the iris.tests.test_image_json.TestImageFile.test_resolve test.

If you're happy to merge that PR, I'll rerun the default tests on travis for 2.7 and 3.6 to see if all the tests light up green...

bjlittle · 2018-05-30T14:26:01Z

@pp-mo and @pelson

Holy moly... the tests are all passing

pp-mo · 2018-05-30T14:42:26Z

Plugging away at these with #1 eyeball.
. . .

pp-mo · 2018-05-30T14:42:33Z

IMO CML is not really fit for purpose, and actually never has been.

Even if you exclude problems due to small numeric differences ...
... and numeric representation differences ...
There are still a lot of "no real change changes" due to comparing strings here
(i.e. whitespace + layout differences).
E.G. everything in tests/results/unit/analysis/maths : all have whitespace changes.

There's really no excuse for that in an XML (structural) comparison (!!)

JSON would probably be a better solution anyway.

pp-mo · 2018-05-30T15:00:28Z

plugging away at these with #1 eyeball.

Happy that everything inside tests/results is good to go.

pp-mo · 2018-05-30T15:03:52Z

I still think we can improve on the methods that makes this stuff so hard ...

pelson · 2018-05-31T11:36:28Z

docs/iris/example_code/Meteorology/COP_maps.py

@@ -114,7 +113,7 @@ def main():
        plt.subplot(122)
        plt.title('HadGEM2 A1B-Image Scenario',  fontsize=10)
        contour_result = iplt.contourf(delta_a1b, levels, colors=colors,
-                                       linewidth=0, extend='both')


Would be interested to see that this is the right thing to do. Will dig a little.

pelson · 2018-05-31T11:40:22Z

lib/iris/tests/test_plot.py

@@ -938,5 +938,28 @@ def test_plot_tmerc(self):
        self.check_graphic()


+@tests.skip_plot


Hello hello... What's the deal here then? How come this is done in this PR? 😄

@corinnebosley

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Added a what's new to help reduce possible impact for users. * Use ConfigParser for py>=3.2 (SciTools#3025) * WIP: Unpin mpl (SciTools#3019) * unpin mpl * Add _repr_html_ for Iris cubes (SciTools#2918) Add cube _repr_html_ functionality * Partial collapse of multi-dimensional coordinates (SciTools#3028) Adding support for partial collapse of multi-dimensional coordinates * Tidy up the root of the repository for v2.1 (SciTools#3034) A bunch of miscellaneous changes in preparation for the v2.1 release: * Move CONTRIBUTING.md to a .github/ folder. See also: https://help.github.com/articles/setting-guidelines-for-repository-contributors/ * Updated the .gitignore to reflect what gets produce in day-to-day iris development * Reduced the amount of redundancy in INSTALL. 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(SciTools#3037) * Fixed the intermittent test in SciTools#3035. The problem was that iris.util.format_array was stateful (via np.set_printoptions). * Fix stateful tests (SciTools#26) * Add dask-array as a requirement when pip installing. (SciTools#3033) * Unpin netcdf4 (SciTools#3031) * unpin netcdf4 * adapt for netcdf4 >=1.4 * fix userguide doctests * Metarelate updates in the UM 2 CF mapping (SciTools#3043) * Updated the README, and copied that over to the iris docs homepage. (SciTools#3045) * Added the what's new for iris 2.1 (SciTools#3044) Added the what's new for iris 2.1 * Updated the cf-standard names to v54. (SciTools#3046) Achieved with: $ wget http://cfconventions.org/Data/cf-standard-names/54/src/cf-standard-name-table.xml -O etc/cf-standard-name-table.xml ... --2018-06-02 06:32:17-- http://cfconventions.org/Data/cf-standard-names/54/src/cf-standard-name-table.xml ... * iris.quickplot: Ensure labels and plot use the same axes Allow iris.quickplot to accept an axes kwarg to which title and axes labels can be attached. This is done without using the matplotlib state machine. Closes SciTools#2946 * sticklering * Full-featured Mercator coord system (SciTools#3041) Add ``standard_parallel`` to the Mercator Coord System * Updated the branding and execution of Iris docs (SciTools#3050) * Updated the branding and execution of Iris This includes: * removing the "easy-to-use" statement in Iris' strapline. Let's let users be the judge of that. * improved the styling of the homepage, including re-instating the search bar. * Added a what's new for SciTools#3010. * Added a extlinks section for convenient linking to github issues with :issue:`number` and :pr:`number`. * Added a favicon for the docs. * Improve strapline style, content (SciTools#27) * Further improvements to Iris docs * Improved font (noto-sans) * Removed old CSS * Fixed a few what's new entries * [DOC] Iris Introduction updates (SciTools#3052) Update the introduction of Iris content. * Updated to v2.1.0. (SciTools#3051) * Move into development mode for v2.1.1 * Move into development mode for v2.2.0 * remove first 'and' from tagline to make it read easier * Notebook repr whatsnew update * remove first 'and' from tagline to make it read easier * minor requirements tidy * http -> https for copybutton.js (SciTools#3066) * Explain use of saver='string' in iris.save (SciTools#3062) * Fix reStructuredText warnings in documentation (SciTools#3069) * Add information about comparing STASH objects with strings (SciTools#3072) * Doc: Fallback to no syntax hightlighting without warning. (SciTools#3071) Fixes: iris/docs/iris/src/developers_guide/gitwash/development_workflow.rst:317: WARNING: Could not lex literal_block as "python". Highlighting skipped. http://www.sphinx-doc.org/en/stable/config.html#confval-highlight_language * Quick fix to get tests passing by pinning dask version (SciTools#3086) * ENH: Working zonal mean linear regridding for circular sources or with use of extrapolation (SciTools#3085) * Working zonal mean from circular/extrapolated source to target * MAINT: Refactor of zonal mean testing * MAINT: Documentation changes from review * Avoid pandas deprecation warning. (SciTools#3079) Avoid pandas deprecation warning. This also simplifies code by being explicit about usage of "base" and "values" for numpy and pandas objects, and removes legacy code that may no longer be valid. * Workaround for dask array copy bug (SciTools#3088) * add contact options to README * Add stash mapping changes to v2.1.0 changelog * Pin Dask for avoid 0.18.2 bug with masked arrays. * Tiny fix for dask, Python3 only? * Disable doctests for Python 2. * Ignore warnings and update array printouts. * Better way to disable Python2 doctests. * Support plotting 2D bounded coords * Add gridcell_angles and rotate_grid_vectors to iris.analysis.cartography, with tests: INCOMPLETE WIP * Roughly working, snapshotted with complex test plot code, to be reduced. * Small improvements. * First working quiver+streamplot. * Handle custom coords correctly * some words for docs, WIP probably * suggested tweaks and corrections * Update docs to included 2.2 versions (SciTools#3110) * Provide a test skipper for 2d coords WIP. (SciTools#3099) * Change version number (SciTools#3118) * re-added bounds definition for contiguity check, removed unnecessary test * Ensure Sphinx autodocs for grid_angles routines. * Codestyle fixes. * Whatsnew entries for 2d vector support. * Pin Dask to avoid 0.18.2 bug with masked arrays. (SciTools#3127) * Put orca_util routines in subpackage of iris.test.stock, to get existing iris.tests.unit.plot.test_2d_coords working. * Disable broken misused testcode in test_gridcell_angles. * Ditch test_gridcell_angles, none of it is functional. * Further style fixes. * Skip tests using iris-test-data, for Travis TEST_MINIMAL phases. * Codestyle fix (though this code obsolete anyway). * Fix unused imports. * Made-up test cube replaces use of iris-test-data. * Renamed keyword; improved docstring. * Change 'co' to 'coord' for clarity. * Review changes. * Update pp save rules to handle time means (SciTools#3132) * Vector plots 2 (SciTools#3120) * Small improvements; first sensible tests. * Enhanced testing; better checking and crs awareness in grid_angles routine. * Remove crud from test_gridcell_angles. * Use degree units for everything in _grid_angles. * Make assertArrayAllClose print details when it fails. * Rework and extend testing for gridcell_angles. * Fix assertArrayAllClose; remove debug code from test_gridcell_angles. * Remove obsolete assignments. * Remove obsolete code. * Small comment improvements. * Attempt to clarify docstrings of low-level routines. * More tests, and some functional fixes. * Codestyle fixes. * Review changes + fixes. * Avoid using sample data. * Temporary pin to avoid problems caused by Proj4 v5.1. (SciTools#3150) * Extending ORCA blockplotting (w/ tests) (SciTools#3135) * Tests for rotate_grid_vectors (SciTools#3148) * Tests for rotate_grid_vectors. * Small fix to assertArrayAllClose for values near 0. * Small tweaks. * Fix test method. * Fix 1 test for 'equal_nans' no longer the default. * Review changes. * Remove 'skip_2d' test decorator. (SciTools#3156) * Add integration graphics tests for pcolormesh with 2d coords (SciTools#3149) * Vector plots 4 (SciTools#3158) * Fix contig_ tolerance kwarg bug (SciTools#3162) * Add simple lazy aggregations * Lazy SUM and COUNT, tests improved * Add tests for MAX and MIN * Update tests for STD_DEV * Use NetCDF variable's chunks on load (SciTools#3131) Preserve NetCDF chunks on dataset load * Iteration and less duplication * Attempt to fix Matplotlib issue by resticting to 2.x * Non-test review actions * Make COUNT tests truer unit tests * Convert MAX and MIN tests to truer unit tests * Convert COUNT and SUM agg tests to truer unit tests * Tests for new _lazy_data function * Fix for netCDF4 1.4 behaviour change. (SciTools#3177) * Improve gracefully filling warning (SciTools#3171) * Realise that running the tests is simpler than I thought * Make Gracefully warning only appear when filling is required * Add tests of warnings * Get rid of install changes, they are in SciTools#3170 * Update after review * Add whatsnew entry * Minor clarification to entry via a little more punctuation * Revert nc vars masking fix (temporarily). (SciTools#3178) * fix for pandas column object bug (SciTools#3176) * turn columns object into pandas array, plus test included cml this time * made things the way pandas like it; bambooish * regenerated cml to match output * Update module headers and installation instructions (SciTools#3170) * Update module headers and installation instructions * Realise that running the tests is simpler than I thought * Update install instructions for developers * Update INSTALL to be consistent * Correct some failing tests * Update tests.rst (SciTools#3082) Added one line on how to test. This is mentioned in the Iris Check List in pulls.rst list, but would be good to have it here as well (useful for new contributors like me). * Add link to developer guide. (SciTools#3093) * Combine identical test routines for pcolor + pcolormesh. * Test 'contiguity_tolerance' use in iris.plot.pcolor and pcolormesh. * Unpin dask * Handle printing bounds of long time interval coords (SciTools#3140) * Handle printing time bounds * Whatsnew, whitespace fix for test result * iris.util.reverse on cubes (SciTools#3155) * make cube reversing official * review: test conventions, etc. * review: enable coord specification * add whatsnew * review: AssertRaises --> AssertRaisesRegexp * cube error handling * Improved Aux factory error handling: better message, delivered earlier (SciTools#3182) * Tests for expected behaviour * Raise error if aux factory relies on a coordinate external to cube * Include coordinate name in error message * Don't check whether dependencies that are "None" are in the coords. * Review changes: check cube name in error and variable rename * Truncated variable for flake8 * Correct cube collapse code * Provide info on pp-field indices in the file for structured um loads. (SciTools#2977) * Field locations for structured um loads. * Remove unused import. * Fix test for new implementation. * Added whatsnew. * Review changes. * simplify dev guide * Integration test for iris.plot.contour with 2d coords. (SciTools#3189) * Integration test for iris.plot.contour with 2d coords. * Review changes. * pinned numpy to not 1.15.2 in core requirements * Public contiguity checking (SciTools#3144) :champagne: :1st_place_medal: for sticking with it @corinnebosley * Populate whatsnew 2.2 (SciTools#3192) * started adding entries to whatsnew * more updates to whatsnew * first complete draft of 2.2 whatsnew * some small corrections * made corrections suggested in review * Update version str * Update CF standard name table to v59 * Fix docstring re structured text warnings (SciTools#3073) (SciTools#3197) * updated version string to 2.3.0dev0 * add contact options to README removed gitter from contact list * Add stash mapping changes to v2.1.0 changelog replaced list with link of stash mappings * expanded name of dev group * added an n for better flow * Fix broken link to dask docs (SciTools#3204)

bjlittle added Type: Enhancement Status: Work in Progress Release: Minor Type: Infrastructure labels May 17, 2018

pp-mo reviewed May 17, 2018

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bjlittle mentioned this pull request May 22, 2018

WIP: Unpin the numpy version in our CI testing. #3024

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pelson reviewed May 22, 2018

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bjlittle commented May 22, 2018

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bjlittle force-pushed the unpin-mpl branch 3 times, most recently from 7eb7ecc to 390066e Compare May 22, 2018 12:17

stickler-ci reviewed May 25, 2018

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bjlittle force-pushed the unpin-mpl branch 2 times, most recently from a8e28a2 to bd4bf06 Compare May 26, 2018 19:58

bjlittle added 8 commits May 27, 2018 00:55

unpin mpl

d374f01

fix format_array

8c2e6fb

correct skip test skip message

e4e17f1

tidy format_array

330f78e

test_collapsed cml

ff88152

test_hybrid_height cml

83845e8

test_hybrid_height_cubes cml

4edea6b

test_hybrid_height cml

94fa447

fix default images

fdeeeb7

bjlittle force-pushed the unpin-mpl branch from 04a6565 to 938fc76 Compare May 27, 2018 02:26

bjlittle mentioned this pull request May 27, 2018

WIP: unpin mpl SciTools/test-iris-imagehash#15

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fix example tests

eaeda68

bjlittle force-pushed the unpin-mpl branch from 938fc76 to eaeda68 Compare May 27, 2018 14:16

add citation graphic test

1d9999f

bjlittle force-pushed the unpin-mpl branch from 3bc70b1 to 1d9999f Compare May 28, 2018 13:16

bjlittle added 3 commits May 29, 2018 13:14

fix string coord ticks

65087d8

fix test_zx and test_tx scatter

bb733c1

fix test_CellMeasure

a468646

bjlittle force-pushed the unpin-mpl branch from 99321f4 to a468646 Compare May 30, 2018 09:02

bjlittle added 2 commits May 30, 2018 10:54

remove ignored contourf linewidth kwarg

1e43862

travis explicit conda env install

d97dfd0

bjlittle removed the Status: Work in Progress label May 30, 2018

pp-mo merged commit 2b4f1b3 into SciTools:master May 30, 2018

bjlittle mentioned this pull request May 30, 2018

Unpin mpl SciTools/nc-time-axis#34

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pelson changed the title ~~WIP: Unpin mpl~~ Unpin matplotlib to support >=2.0 May 31, 2018

pelson mentioned this pull request May 31, 2018

Failing tests #3035

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pelson reviewed May 31, 2018

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pelson mentioned this pull request May 31, 2018

Fixed the intermittent test in #3035. #3037

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bjlittle deleted the unpin-mpl branch June 2, 2018 06:19

pp-mo mentioned this pull request Aug 13, 2018

Review use of numpy array print formats, and Python2/3 variation #3138

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Unpin matplotlib to support >=2.0 #3019

Unpin matplotlib to support >=2.0 #3019

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		@@ -938,5 +938,28 @@ def test_plot_tmerc(self):
		self.check_graphic()


		@tests.skip_plot

Unpin matplotlib to support >=2.0 #3019

Unpin matplotlib to support >=2.0 #3019

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