Deprecate mlab functions #9151

dstansby · 2017-09-02T13:53:20Z

Here's a catch-all deprecation PR for mlab. The aim is to deprecate or move everything that isn't spectral related.

Non-trival deprecations that are used elsewhere in Matplotlib:

anntzer · 2017-09-02T19:20:39Z

lib/matplotlib/mlab.py

@@ -2115,6 +2118,7 @@ def norm_flat(a, p=2):
        return np.sum(np.abs(a) ** p) ** (1 / p)


+@cbook.deprecated('2.1', alternative='np.linspace(xini, xfin, delta)')


actually the alternative is wrong, but I don't think we really need to bother specifying one

I think it would be worthwhile specifying 'np.linspace' as the alternative without including the arguments. Or specify both: 'np.linspace or np.arange'.

anntzer · 2017-09-02T19:20:50Z

lib/matplotlib/mlab.py

@@ -186,6 +186,8 @@
    long = int


+@cbook.deprecated("2.1",
+                  alternative='np.logspace(np.log(xmin), np.log(xmax), N)')


or geomspace

What? Why? Where is 'geomspace'? The alternative looks fine to me as-is.

https://docs.scipy.org/doc/numpy/reference/generated/numpy.geomspace.html
TBH I don't care enough about mlab to get into a debate of whether we should recommend an old function with a different behavior, or a new function with the same behavior.

So new I wasn't aware of it. Thank you. I guess I would say "np.logspace or np.geomspace (numpy >= 1.13)" and leave the rest to the user to figure out.

@dstansby For the record (more than for another reason as the current suggestions are to avoid specifying the arguments), it should be np.logspace(np.log10(xmin), np.log10(xmax), N) (the default base for np.logspace is 10).

efiring

I think this is fine once the frange alternative is fixed.

efiring · 2017-09-02T20:05:01Z

lib/matplotlib/mlab.py

@@ -2115,6 +2118,7 @@ def norm_flat(a, p=2):
        return np.sum(np.abs(a) ** p) ** (1 / p)


+@cbook.deprecated('2.1', alternative='np.linspace(xini, xfin, delta)')


I think it would be worthwhile specifying 'np.linspace' as the alternative without including the arguments. Or specify both: 'np.linspace or np.arange'.

efiring · 2017-09-02T20:06:25Z

lib/matplotlib/mlab.py

@@ -186,6 +186,8 @@
    long = int


+@cbook.deprecated("2.1",
+                  alternative='np.logspace(np.log(xmin), np.log(xmax), N)')


What? Why? Where is 'geomspace'? The alternative looks fine to me as-is.

anntzer · 2017-09-05T15:48:10Z

(I also think that trying to deprecate mlab one function at a time is a bit a waste of a time, the whole thing should just be dealt with a single shot.)

dstansby · 2017-09-05T16:03:23Z

Fair enough, I'll give it all a go once 2.1 has been released!

dstansby · 2017-09-08T19:48:01Z

Going to carry on with deprecations on this branch. Anyone can feel free to push to it

anntzer · 2017-09-08T20:19:01Z

lib/matplotlib/mlab.py

@@ -194,6 +195,7 @@ def logspace(xmin, xmax, N):
    return np.exp(np.linspace(np.log(xmin), np.log(xmax), N))


+@cbook.deprecated("2.2", alternative='np.sqrt')


just delete it, it's private

comments handled

dstansby · 2017-09-09T11:01:16Z

Okay, I think that's everything that isn't used elsewhere in Matplotlib. I've put a list of everything left at the top of this PR. Some of them are going to need moving somewhere else, or a bit of work to replace.

anntzer · 2017-09-10T19:47:06Z

lib/matplotlib/tests/test_mlab.py

@@ -24,12 +25,21 @@
    HAS_NATGRID = False


+'''


make this a block comment

anntzer · 2017-09-10T19:47:38Z

Probably needs an entry into api_changes, but otherwise lgtm.

anntzer · 2017-09-24T19:54:41Z

lib/matplotlib/cbook/__init__.py

@@ -1578,6 +1578,48 @@ def simple_linear_interpolation(a, steps):
    return result


+def less_simple_linear_interpolation(x, y, xi, extrap=False):


Would https://docs.scipy.org/doc/numpy/reference/generated/numpy.interp.html not be good enough? Sorry to give you more work... :-)

Don't worry, I'm taking this in small steps anyway since it's only going to go in 2.2 anyway. I'll have a go and see if it works.

Not a simple drop in, so I think I'll leave it as is in this PR.

anntzer · 2017-10-01T22:06:25Z

lib/matplotlib/cbook/__init__.py

+    if mask[-1]:
+        idx.append(len(mask))
+
+    return list(zip(idx[::2], idx[1::2]))


I bet the fastest (not that it necessarily matters) is either to return an iterator using itertools.chain and itertools.islice, or to preallocate the result as an appropriately sized array.

This is a function I've just directly copied across from mlab to cbook because it's used in 2 different places in Matplotlib

(sorry, I'm kind of dumping stuff as I work on it here, will remove the WIP bit of the title when I think it's all done)

no worries, I'm also just dumping my thoughts here and there :)

Couldn't get my head around how to make this work so I think I'll leave it for this PR.

np.column_stack([idxs[::2], idxs[1::2]]) should work well.

dstansby · 2017-11-13T11:02:26Z

Apart from the macOS tests not passing, and any changes reviewers request, I'm considering this PR done now.

QuLogic · 2017-11-14T03:27:18Z

Hmm, you only really needed to put the mlab calls in the warns context, which would probably cut down on the changes a bit?

tacaswell · 2017-11-25T20:39:48Z

lib/matplotlib/pylab.py

@@ -240,21 +236,7 @@
 # bring all the symbols in so folks can import them from
 # pylab in one fell swoop

-## We are still importing too many things from mlab; more cleanup is needed.
-
-from matplotlib.mlab import (


These should probably stay but warn?

I've just reverted the changes to pylab - if anyone tries to use the deprecated methods they'll be warned.

issues handled

dstansby · 2018-01-09T10:53:42Z

I've put this as release critical, as I think it would be good to have these deprecations in 2.2 instead of waiting for 3.0.

jklymak

Checked that ll examples and tutorials look good, and they do.

QuLogic · 2018-01-13T01:30:53Z

So you're leaving the remaining unchecked ones for some other PR, right?

dstansby · 2018-01-13T11:18:47Z

Yeah, I have some code sat locally to cover the rest, but don't want to upload it as part of this PR as I think this one's big enough already.

tacaswell · 2018-01-29T20:41:25Z

@dstansby This needs a rebase.

tacaswell · 2018-01-29T20:45:36Z

👍 in principle, will leave detailed review to others

story645 · 2018-02-05T20:17:05Z

lib/matplotlib/contour.py

+def _is_closed_polygon(X):
+    """
+    Tests whether first and last object in a sequence are the same.  These are
+    presumably coordinates on a polygonal curve, in which case this function


These are presumably coordinates on a polygonal curve, in which case this function tests if that curve is closed.

Sort of odd construction?

Since these objects are presumed to be coordinates on a polygonal curve, this function tests if the curve is closed.

tacaswell · 2018-02-05T20:31:45Z

This will need some additional documentation for the final 2.2 release, but merging now to move things along.

dstansby · 2018-02-05T21:30:20Z

🎉 thanks to everyone who left comments or reviewed this!

tacaswell added this to the 2.2 (next next feature release) milestone Sep 2, 2017

anntzer reviewed Sep 2, 2017

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efiring previously requested changes Sep 2, 2017

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dstansby changed the title ~~Deprecate some mlab functions~~ Deprecate mlab functions Sep 8, 2017

dstansby force-pushed the mlab-deprecate branch 2 times, most recently from 9247888 to b4a3430 Compare September 8, 2017 19:47

anntzer reviewed Sep 8, 2017

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dstansby force-pushed the mlab-deprecate branch from 92cc34b to 401373d Compare September 10, 2017 17:12

anntzer reviewed Sep 10, 2017

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lib/matplotlib/tests/test_mlab.py

@@ -24,12 +25,21 @@

HAS_NATGRID = False

'''

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make this a block comment

dstansby force-pushed the mlab-deprecate branch from 401373d to cabc4a3 Compare September 21, 2017 16:36

dstansby mentioned this pull request Sep 21, 2017

Replace mlab functions #9177

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dstansby changed the title ~~Deprecate mlab functions~~ [WIP] Deprecate mlab functions Sep 21, 2017

anntzer reviewed Sep 24, 2017

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dstansby force-pushed the mlab-deprecate branch from 3e41f32 to 860cc4a Compare October 26, 2017 20:48

dstansby force-pushed the mlab-deprecate branch from 860cc4a to 8b54e6b Compare November 5, 2017 12:54

DietBru mentioned this pull request Nov 12, 2017

Factored out spectral analysis functions from mlab into a separate module #9757

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dstansby changed the title ~~[WIP] Deprecate mlab functions~~ Deprecate mlab functions Nov 13, 2017

dstansby force-pushed the mlab-deprecate branch from e92a280 to e9071ef Compare November 25, 2017 12:24

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anntzer mentioned this pull request Nov 26, 2017

Improve less_simple_linear_interpolation. #9859

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dstansby added status: needs review Release critical For bugs that make the library unusable (segfaults, incorrect plots, etc) and major regressions. labels Jan 8, 2018

dstansby force-pushed the mlab-deprecate branch from 72882be to 862ab60 Compare January 9, 2018 10:52

jklymak approved these changes Jan 12, 2018

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jklymak added the status: needs rebase label Jan 29, 2018

dstansby force-pushed the mlab-deprecate branch from 862ab60 to 9bfcec0 Compare January 29, 2018 21:15

dstansby removed the status: needs rebase label Jan 29, 2018

dstansby added 5 commits February 2, 2018 15:32

Deprecate non-spectral mlab methods

e4114e7

Remove bivariate_norm from mpl3d test code

4edc56a

Remove copy of less_simple_linear_interpolation

104e73a

Remove bivariate_norm from examples

32a2f79

Remove more mlab from examples

4c61a1d

dstansby force-pushed the mlab-deprecate branch from 9bfcec0 to 4c61a1d Compare February 2, 2018 15:32

story645 reviewed Feb 5, 2018

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tacaswell merged commit 3e37306 into matplotlib:master Feb 5, 2018

jklymak mentioned this pull request Feb 5, 2018

More documentation mlab deprecation. #10382

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dstansby deleted the mlab-deprecate branch February 5, 2018 21:29

QuLogic mentioned this pull request Feb 10, 2018

Deprecation needed for frange and others? #7555

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QuLogic modified the milestones: needs sorting, v2.2.0 Feb 12, 2018

QuLogic removed the status: needs review label Mar 23, 2018

ImportanceOfBeingErnest mentioned this pull request May 6, 2018

DOC: Revive Irregularly spaced data contour example #11180

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2 tasks

		@@ -2115,6 +2118,7 @@ def norm_flat(a, p=2):
		return np.sum(np.abs(a) p) (1 / p)


		@cbook.deprecated('2.1', alternative='np.linspace(xini, xfin, delta)')

		@@ -194,6 +195,7 @@ def logspace(xmin, xmax, N):
		return np.exp(np.linspace(np.log(xmin), np.log(xmax), N))


		@cbook.deprecated("2.2", alternative='np.sqrt')

		@@ -1578,6 +1578,48 @@ def simple_linear_interpolation(a, steps):
		return result


		def less_simple_linear_interpolation(x, y, xi, extrap=False):

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Deprecate mlab functions #9151

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