DEP: deprecate scipy.signal wavelets (scipy#19340)

* DEP: deprecate scipy.signal wavelets

* MAINT: signal: add deprecated wavelets to the deprecated list in doc/conf.py

* TST: use pytest.deprecated_call instead of filtering warnings

---------

Co-authored-by: Jake Bowhay <[email protected]>

Author: ev-br

doc/source/conf.py

@@ -328,12 +328,20 @@
         'interp2d` is deprecated',  # Deprecation of scipy.interpolate.interp2d
         'scipy.misc',  # scipy.misc deprecated in v1.10.0; use scipy.datasets
         'kurtosistest only valid',  # intentionally "bad" excample in docstring
+        'scipy.signal.daub is deprecated',
+        'scipy.signal.qmf is deprecated',
+        'scipy.signal.cascade is deprecated',
+        'scipy.signal.morlet is deprecated',
+        'scipy.signal.morlet2 is deprecated',
+        'scipy.signal.ricker is deprecated',
+        'scipy.signal.cwt is deprecated',
         ):
     warnings.filterwarnings(action='ignore', message='.*' + key + '.*')
 
 import numpy as np
 np.random.seed(123)
 """
+
 plot_include_source = True
 plot_formats = [('png', 96)]
 plot_html_show_formats = False

scipy/signal/_peak_finding.py

@@ -4,7 +4,7 @@
 import math
 import numpy as np
 
-from scipy.signal._wavelets import cwt, ricker
+from scipy.signal._wavelets import _cwt, _ricker
 from scipy.stats import scoreatpercentile
 
 from ._peak_finding_utils import (
@@ -1300,9 +1300,9 @@ def find_peaks_cwt(vector, widths, wavelet=None, max_distances=None,
     if max_distances is None:
         max_distances = widths / 4.0
     if wavelet is None:
-        wavelet = ricker
+        wavelet = _ricker
 
-    cwt_dat = cwt(vector, wavelet, widths)
+    cwt_dat = _cwt(vector, wavelet, widths)
     ridge_lines = _identify_ridge_lines(cwt_dat, max_distances, gap_thresh)
     filtered = _filter_ridge_lines(cwt_dat, ridge_lines, min_length=min_length,
                                    window_size=window_size, min_snr=min_snr,

scipy/signal/_wavelets.py

@@ -1,3 +1,5 @@
+import warnings
+
 import numpy as np
 from scipy.linalg import eig
 from scipy.special import comb
@@ -6,8 +8,18 @@
 __all__ = ['daub', 'qmf', 'cascade', 'morlet', 'ricker', 'morlet2', 'cwt']
 
 
+_msg="""scipy.signal.%s is deprecated in SciPy 1.12 and will be removed
+in SciPy 1.14. We recommend using PyWavelets instead.
+"""
+
+
 def daub(p):
     """
+    .. deprecated:: 1.12.0
+
+        scipy.signal.daub is deprecated in SciPy 1.12 and will be removed
+        in SciPy 1.14. We recommend using PyWavelets instead.
+
     The coefficients for the FIR low-pass filter producing Daubechies wavelets.
 
     p>=1 gives the order of the zero at f=1/2.
@@ -24,6 +36,8 @@ def daub(p):
         Return
 
     """
+    warnings.warn(_msg % 'daub', DeprecationWarning, stacklevel=2)
+
     sqrt = np.sqrt
     if p < 1:
         raise ValueError("p must be at least 1.")
@@ -77,6 +91,12 @@ def daub(p):
 
 def qmf(hk):
     """
+    .. deprecated:: 1.12.0
+
+        scipy.signal.qmf is deprecated in SciPy 1.12 and will be removed
+        in SciPy 1.14. We recommend using PyWavelets instead.
+
+
     Return high-pass qmf filter from low-pass
 
     Parameters
@@ -90,13 +110,21 @@ def qmf(hk):
         High-pass filter coefficients.
 
     """
+    warnings.warn(_msg % 'qmf', DeprecationWarning, stacklevel=2)
+
     N = len(hk) - 1
     asgn = [{0: 1, 1: -1}[k % 2] for k in range(N + 1)]
     return hk[::-1] * np.array(asgn)
 
 
 def cascade(hk, J=7):
     """
+    .. deprecated:: 1.12.0
+
+        scipy.signal.cascade is deprecated in SciPy 1.12 and will be removed
+        in SciPy 1.14. We recommend using PyWavelets instead.
+
+
     Return (x, phi, psi) at dyadic points ``K/2**J`` from filter coefficients.
 
     Parameters
@@ -127,6 +155,8 @@ def cascade(hk, J=7):
     end.
 
     """
+    warnings.warn(_msg % 'cascade', DeprecationWarning, stacklevel=2)
+
     N = len(hk) - 1
 
     if (J > 30 - np.log2(N + 1)):
@@ -203,6 +233,11 @@ def cascade(hk, J=7):
 
 def morlet(M, w=5.0, s=1.0, complete=True):
     """
+    .. deprecated:: 1.12.0
+
+        scipy.signal.morlet is deprecated in SciPy 1.12 and will be removed
+        in SciPy 1.14. We recommend using PyWavelets instead.
+
     Complex Morlet wavelet.
 
     Parameters
@@ -267,6 +302,8 @@ def morlet(M, w=5.0, s=1.0, complete=True):
     >>> plt.show()
 
     """
+    warnings.warn(_msg % 'morlet', DeprecationWarning, stacklevel=2)
+
     x = np.linspace(-s * 2 * np.pi, s * 2 * np.pi, M)
     output = np.exp(1j * w * x)
 
@@ -280,6 +317,12 @@ def morlet(M, w=5.0, s=1.0, complete=True):
 
 def ricker(points, a):
     """
+    .. deprecated:: 1.12.0
+
+        scipy.signal.ricker is deprecated in SciPy 1.12 and will be removed
+        in SciPy 1.14. We recommend using PyWavelets instead.
+
+
     Return a Ricker wavelet, also known as the "Mexican hat wavelet".
 
     It models the function:
@@ -315,6 +358,11 @@ def ricker(points, a):
     >>> plt.show()
 
     """
+    warnings.warn(_msg % 'ricker', DeprecationWarning, stacklevel=2)
+    return _ricker(points, a)
+
+
+def _ricker(points, a):
     A = 2 / (np.sqrt(3 * a) * (np.pi**0.25))
     wsq = a**2
     vec = np.arange(0, points) - (points - 1.0) / 2
@@ -327,6 +375,12 @@ def ricker(points, a):
 
 def morlet2(M, s, w=5):
     """
+    .. deprecated:: 1.12.0
+
+        scipy.signal.morlet2 is deprecated in SciPy 1.12 and will be removed
+        in SciPy 1.14. We recommend using PyWavelets instead.
+
+
     Complex Morlet wavelet, designed to work with `cwt`.
 
     Returns the complete version of morlet wavelet, normalised
@@ -397,6 +451,8 @@ def morlet2(M, s, w=5):
     >>> plt.show()
 
     """
+    warnings.warn(_msg % 'morlet2', DeprecationWarning, stacklevel=2)
+
     x = np.arange(0, M) - (M - 1.0) / 2
     x = x / s
     wavelet = np.exp(1j * w * x) * np.exp(-0.5 * x**2) * np.pi**(-0.25)
@@ -406,6 +462,12 @@ def morlet2(M, s, w=5):
 
 def cwt(data, wavelet, widths, dtype=None, **kwargs):
     """
+    .. deprecated:: 1.12.0
+
+        scipy.signal.cwt is deprecated in SciPy 1.12 and will be removed
+        in SciPy 1.14. We recommend using PyWavelets instead.
+
+
     Continuous wavelet transform.
 
     Performs a continuous wavelet transform on `data`,
@@ -479,6 +541,11 @@ def cwt(data, wavelet, widths, dtype=None, **kwargs):
     ...            vmax=abs(cwtmatr).max(), vmin=-abs(cwtmatr).max())
     >>> plt.show()
     """
+    warnings.warn(_msg % 'cwt', DeprecationWarning, stacklevel=2)
+    return _cwt(data, wavelet, widths, dtype, **kwargs)
+
+
+def _cwt(data, wavelet, widths, dtype=None, **kwargs):
     # Determine output type
     if dtype is None:
         if np.asarray(wavelet(1, widths[0], **kwargs)).dtype.char in 'FDG':