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jklymakjklymak
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MNT: deprecate mlab
.... except for GaussianKDE, which is needed for violinplots
1 parent 04c8107 commit 41f946e

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5 files changed

+58
-12
lines changed

5 files changed

+58
-12
lines changed

‎lib/matplotlib/axes/_axes.py

Lines changed: 22 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1903,7 +1903,7 @@ def acorr(self, x, **kwargs):
19031903
----------
19041904
x : array-like
19051905
1906-
detrend : callable, default: `.mlab.detrend_none` (no detrending)
1906+
detrend : callable, default: no detrending
19071907
A detrending function applied to *x*. It must have the
19081908
signature ::
19091909
@@ -1967,7 +1967,7 @@ def acorr(self, x, **kwargs):
19671967
return self.xcorr(x, x, **kwargs)
19681968

19691969
@_preprocess_data(replace_names=["x", "y"], label_namer="y")
1970-
def xcorr(self, x, y, normed=True, detrend=mlab.detrend_none,
1970+
def xcorr(self, x, y, normed=True, detrend=None,
19711971
usevlines=True, maxlags=10, **kwargs):
19721972
r"""
19731973
Plot the cross correlation between *x* and *y*.
@@ -1980,7 +1980,7 @@ def xcorr(self, x, y, normed=True, detrend=mlab.detrend_none,
19801980
----------
19811981
x, y : array-like of length n
19821982
1983-
detrend : callable, default: `.mlab.detrend_none` (no detrending)
1983+
detrend : callable, default: no detrending
19841984
A detrending function applied to *x* and *y*. It must have the
19851985
signature ::
19861986
@@ -2045,8 +2045,9 @@ def xcorr(self, x, y, normed=True, detrend=mlab.detrend_none,
20452045
if Nx != len(y):
20462046
raise ValueError('x and y must be equal length')
20472047

2048-
x = detrend(np.asarray(x))
2049-
y = detrend(np.asarray(y))
2048+
if detrend is not None:
2049+
x = detrend(np.asarray(x))
2050+
y = detrend(np.asarray(y))
20502051

20512052
correls = np.correlate(x, y, mode="full")
20522053

@@ -7016,6 +7017,7 @@ def hist2d(self, x, y, bins=10, range=None, density=False, weights=None,
70167017

70177018
return h, xedges, yedges, pc
70187019

7020+
@_api.deprecated("3.6", alternative="scipy.signal.psd and ax.loglog")
70197021
@_preprocess_data(replace_names=["x"])
70207022
@_docstring.dedent_interpd
70217023
def psd(self, x, NFFT=None, Fs=None, Fc=None, detrend=None,
@@ -7127,6 +7129,7 @@ def psd(self, x, NFFT=None, Fs=None, Fc=None, detrend=None,
71277129
else:
71287130
return pxx, freqs, line
71297131

7132+
@_api.deprecated("3.6", alternative="scipy.signal.csd and ax.plot")
71307133
@_preprocess_data(replace_names=["x", "y"], label_namer="y")
71317134
@_docstring.dedent_interpd
71327135
def csd(self, x, y, NFFT=None, Fs=None, Fc=None, detrend=None,
@@ -7229,6 +7232,9 @@ def csd(self, x, y, NFFT=None, Fs=None, Fc=None, detrend=None,
72297232
else:
72307233
return pxy, freqs, line
72317234

7235+
@_api.deprecated(
7236+
"3.6",
7237+
alternative="scipy.signal.spectrogram(mode='magnitude') and ax.loglog")
72327238
@_preprocess_data(replace_names=["x"])
72337239
@_docstring.dedent_interpd
72347240
def magnitude_spectrum(self, x, Fs=None, Fc=None, window=None,
@@ -7315,6 +7321,9 @@ def magnitude_spectrum(self, x, Fs=None, Fc=None, window=None,
73157321

73167322
return spec, freqs, line
73177323

7324+
@_api.deprecated("3.6",
7325+
alternative="scipy.signal.spectrogram(mode='angle') and "
7326+
"ax.loglog")
73187327
@_preprocess_data(replace_names=["x"])
73197328
@_docstring.dedent_interpd
73207329
def angle_spectrum(self, x, Fs=None, Fc=None, window=None,
@@ -7384,6 +7393,9 @@ def angle_spectrum(self, x, Fs=None, Fc=None, window=None,
73847393

73857394
return spec, freqs, lines[0]
73867395

7396+
@_api.deprecated("3.6",
7397+
alternative="scipy.signal.spectrogram(mode='phase') and "
7398+
"ax.loglog")
73877399
@_preprocess_data(replace_names=["x"])
73887400
@_docstring.dedent_interpd
73897401
def phase_spectrum(self, x, Fs=None, Fc=None, window=None,
@@ -7453,6 +7465,8 @@ def phase_spectrum(self, x, Fs=None, Fc=None, window=None,
74537465

74547466
return spec, freqs, lines[0]
74557467

7468+
@_api.deprecated("3.6", alternative="scipy.signal.coherence and "
7469+
"ax.semilogx")
74567470
@_preprocess_data(replace_names=["x", "y"])
74577471
@_docstring.dedent_interpd
74587472
def cohere(self, x, y, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none,
@@ -7517,6 +7531,9 @@ def cohere(self, x, y, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none,
75177531

75187532
return cxy, freqs
75197533

7534+
@_api.deprecated("3.6",
7535+
alternative="scipy.signal.spectrogram(mode='psd') and "
7536+
"ax.loglog")
75207537
@_preprocess_data(replace_names=["x"])
75217538
@_docstring.dedent_interpd
75227539
def specgram(self, x, NFFT=None, Fs=None, Fc=None, detrend=None,

‎lib/matplotlib/mlab.py

Lines changed: 12 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,6 @@
11
"""
2-
Numerical Python functions written for compatibility with MATLAB
3-
commands with the same names. Most numerical Python functions can be found in
4-
the `NumPy`_ and `SciPy`_ libraries. What remains here is code for performing
5-
spectral computations and kernel density estimations.
2+
This module is deprecated in favour of modules that can be found in
3+
the `NumPy`_ and `SciPy`_ libraries.
64
75
.. _NumPy: https://numpy.org
86
.. _SciPy: https://www.scipy.org
@@ -58,6 +56,7 @@
5856
from matplotlib import _api, _docstring, cbook
5957

6058

59+
@_api.deprecated("3.6", alternative="np.hanning")
6160
def window_hanning(x):
6261
"""
6362
Return *x* times the Hanning (or Hann) window of len(*x*).
@@ -69,6 +68,7 @@ def window_hanning(x):
6968
return np.hanning(len(x))*x
7069

7170

71+
@_api.deprecated("3.6", alternative="")
7272
def window_none(x):
7373
"""
7474
No window function; simply return *x*.
@@ -80,6 +80,7 @@ def window_none(x):
8080
return x
8181

8282

83+
@_api.deprecated("3.6", alternative="scipy.signal.detrend")
8384
def detrend(x, key=None, axis=None):
8485
"""
8586
Return *x* with its trend removed.
@@ -129,6 +130,7 @@ def detrend(x, key=None, axis=None):
129130
f"'constant', 'mean', 'linear', or a function")
130131

131132

133+
@_api.deprecated("3.6", alternative="scipy.signal.detrend")
132134
def detrend_mean(x, axis=None):
133135
"""
134136
Return *x* minus the mean(*x*).
@@ -157,6 +159,7 @@ def detrend_mean(x, axis=None):
157159
return x - x.mean(axis, keepdims=True)
158160

159161

162+
@_api.deprecated("3.6", alternative="scipy.signal.detrend")
160163
def detrend_none(x, axis=None):
161164
"""
162165
Return *x*: no detrending.
@@ -179,6 +182,7 @@ def detrend_none(x, axis=None):
179182
return x
180183

181184

185+
@_api.deprecated("3.6", alternative="scipy.signal.detrend")
182186
def detrend_linear(y):
183187
"""
184188
Return *x* minus best fit line; 'linear' detrending.
@@ -531,6 +535,7 @@ def _single_spectrum_helper(
531535
MATLAB compatibility.""")
532536

533537

538+
@_api.deprecated("3.6", alternative="scipy.signal.psd")
534539
@_docstring.dedent_interpd
535540
def psd(x, NFFT=None, Fs=None, detrend=None, window=None,
536541
noverlap=None, pad_to=None, sides=None, scale_by_freq=None):
@@ -587,6 +592,7 @@ def psd(x, NFFT=None, Fs=None, detrend=None, window=None,
587592
return Pxx.real, freqs
588593

589594

595+
@_api.deprecated("3.6", alternative="scipy.signal.csd")
590596
@_docstring.dedent_interpd
591597
def csd(x, y, NFFT=None, Fs=None, detrend=None, window=None,
592598
noverlap=None, pad_to=None, sides=None, scale_by_freq=None):
@@ -688,7 +694,6 @@ def csd(x, y, NFFT=None, Fs=None, detrend=None, window=None,
688694
Can return the complex spectrum of segments within the signal.
689695
"""
690696

691-
692697
complex_spectrum = functools.partial(_single_spectrum_helper, "complex")
693698
complex_spectrum.__doc__ = _single_spectrum_docs.format(
694699
quantity="complex-valued frequency spectrum",
@@ -707,6 +712,7 @@ def csd(x, y, NFFT=None, Fs=None, detrend=None, window=None,
707712
**_docstring.interpd.params)
708713

709714

715+
@_api.deprecated("3.6", alternative="scipy.signal.welch")
710716
@_docstring.dedent_interpd
711717
def specgram(x, NFFT=None, Fs=None, detrend=None, window=None,
712718
noverlap=None, pad_to=None, sides=None, scale_by_freq=None,
@@ -790,6 +796,7 @@ def specgram(x, NFFT=None, Fs=None, detrend=None, window=None,
790796
return spec, freqs, t
791797

792798

799+
@_api.deprecated("3.6", alternative="scipy.signal.coherence")
793800
@_docstring.dedent_interpd
794801
def cohere(x, y, NFFT=256, Fs=2, detrend=detrend_none, window=window_hanning,
795802
noverlap=0, pad_to=None, sides='default', scale_by_freq=None):

‎lib/matplotlib/pyplot.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3005,8 +3005,8 @@ def vlines(
30053005
# Autogenerated by boilerplate.py. Do not edit as changes will be lost.
30063006
@_copy_docstring_and_deprecators(Axes.xcorr)
30073007
def xcorr(
3008-
x, y, normed=True, detrend=mlab.detrend_none, usevlines=True,
3009-
maxlags=10, *, data=None, **kwargs):
3008+
x, y, normed=True, detrend=None, usevlines=True, maxlags=10,
3009+
*, data=None, **kwargs):
30103010
return gca().xcorr(
30113011
x, y, normed=normed, detrend=detrend, usevlines=usevlines,
30123012
maxlags=maxlags,

‎lib/matplotlib/tests/test_axes.py

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -4725,6 +4725,8 @@ def test_subplot_key_hash():
47254725
assert ax.get_subplotspec().get_geometry() == (5, 1, 0, 0)
47264726

47274727

4728+
@pytest.mark.filterwarnings(
4729+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
47284730
@image_comparison(
47294731
["specgram_freqs.png", "specgram_freqs_linear.png",
47304732
"specgram_noise.png", "specgram_noise_linear.png"],
@@ -4761,6 +4763,8 @@ def test_specgram():
47614763
scale="linear", norm=matplotlib.colors.LogNorm())
47624764

47634765

4766+
@pytest.mark.filterwarnings(
4767+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
47644768
@image_comparison(
47654769
["specgram_magnitude_freqs.png", "specgram_magnitude_freqs_linear.png",
47664770
"specgram_magnitude_noise.png", "specgram_magnitude_noise_linear.png"],
@@ -4798,6 +4802,8 @@ def test_specgram_magnitude():
47984802
scale="linear", norm=matplotlib.colors.LogNorm())
47994803

48004804

4805+
@pytest.mark.filterwarnings(
4806+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
48014807
@image_comparison(
48024808
["specgram_angle_freqs.png", "specgram_phase_freqs.png",
48034809
"specgram_angle_noise.png", "specgram_phase_noise.png"],
@@ -4836,13 +4842,17 @@ def test_specgram_angle():
48364842
scale="dB")
48374843

48384844

4845+
@pytest.mark.filterwarnings(
4846+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
48394847
def test_specgram_fs_none():
48404848
"""Test axes.specgram when Fs is None, should not throw error."""
48414849
spec, freqs, t, im = plt.specgram(np.ones(300), Fs=None, scale='linear')
48424850
xmin, xmax, freq0, freq1 = im.get_extent()
48434851
assert xmin == 32 and xmax == 96
48444852

48454853

4854+
@pytest.mark.filterwarnings(
4855+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
48464856
@check_figures_equal(extensions=["png"])
48474857
def test_specgram_origin_rcparam(fig_test, fig_ref):
48484858
"""Test specgram ignores image.origin rcParam and uses origin 'upper'."""
@@ -4861,6 +4871,8 @@ def test_specgram_origin_rcparam(fig_test, fig_ref):
48614871
fig_test.subplots().specgram(signal)
48624872

48634873

4874+
@pytest.mark.filterwarnings(
4875+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
48644876
def test_specgram_origin_kwarg():
48654877
"""Ensure passing origin as a kwarg raises a TypeError."""
48664878
t = np.arange(500)
@@ -4870,6 +4882,8 @@ def test_specgram_origin_kwarg():
48704882
plt.specgram(signal, origin='lower')
48714883

48724884

4885+
@pytest.mark.filterwarnings(
4886+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
48734887
@image_comparison(
48744888
["psd_freqs.png", "csd_freqs.png", "psd_noise.png", "csd_noise.png"],
48754889
remove_text=True, tol=0.002)
@@ -4904,6 +4918,8 @@ def test_psd_csd():
49044918
ax.set(xlabel="", ylabel="")
49054919

49064920

4921+
@pytest.mark.filterwarnings(
4922+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
49074923
@image_comparison(
49084924
["magnitude_spectrum_freqs_linear.png",
49094925
"magnitude_spectrum_freqs_dB.png",
@@ -4946,6 +4962,8 @@ def test_spectrum():
49464962
ax.set(xlabel="", ylabel="")
49474963

49484964

4965+
@pytest.mark.filterwarnings(
4966+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
49494967
def test_psd_csd_edge_cases():
49504968
# Inverted yaxis or fully zero inputs used to throw exceptions.
49514969
axs = plt.figure().subplots(2)

‎lib/matplotlib/tests/test_mlab.py

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,10 @@
55

66
from matplotlib import mlab, _api
77

8+
# this module is being deprecated as of 3.6, so...
9+
pytestmark = pytest.mark.filterwarnings(
10+
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
11+
812

913
class TestStride:
1014
def get_base(self, x):

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