Use scipy-doctest instead of refguide-check

.github/workflows/tests.yml

@@ -37,7 +37,7 @@ jobs:
         MINIMUM_REQUIREMENTS: [0]
         USE_SCIPY: [0]
         USE_SDIST: [0]
-        REFGUIDE_CHECK: [0]
+        REFGUIDE_CHECK: [1]
         PIP_FLAGS: [""]
         OPTIONS_NAME: ["default"]
         include:
@@ -105,7 +105,7 @@ jobs:
                 python -m build --sdist
                 pip install dist/pyw*.tar.gz -v
             elif [ "${REFGUIDE_CHECK}" == "1" ]; then
-                pip install sphinx numpydoc
+                pip install sphinx numpydoc scipy-doctest
                 pip install . -v
             else
                 pip install . -v
@@ -129,9 +129,10 @@ jobs:
               pytest --pyargs pywt
               python ../pywt/tests/test_doc.py
           elif [ "${REFGUIDE_CHECK}" == "1" ]; then
-              # Run doctests and check if the refguide contains entries from __all__
-              python util/refguide_check.py --doctests
+              # doctest docstrings
+              pytest --doctest-modules --pyargs pywt -v  --doctest-collect=api
               # Run Sphinx HTML docs builder, converting warnings to errors
+              cd ..
               pip install -r util/readthedocs/requirements.txt
               sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
           else
@@ -203,7 +204,7 @@ jobs:
                 python -m build --sdist
                 pip install pywavelets* -v
             elif [ "${REFGUIDE_CHECK}" == "1" ]; then
-                pip install sphinx numpydoc
+                pip install sphinx numpydoc scipy-doctest
                 pip install . -v
             else
                 pip install . -v
@@ -221,7 +222,8 @@ jobs:
               pytest --pyargs pywt
               python ../pywt/tests/test_doc.py
           elif [ "${REFGUIDE_CHECK}" == "1" ]; then
-              python util/refguide_check.py --doctests
+              # doctests docstrings
+              pytest --doctest-modules --pyargs pywt -v  --doctest-collect=api
           else
               pytest --pyargs pywt
           fi

pywt/_cwt.py

@@ -94,8 +94,8 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
     >>> x = np.arange(512)
     >>> y = np.sin(2*np.pi*x/32)
     >>> coef, freqs=pywt.cwt(y,np.arange(1,129),'gaus1')
-    >>> plt.matshow(coef) # doctest: +SKIP
-    >>> plt.show() # doctest: +SKIP
+    >>> plt.matshow(coef)
+    >>> plt.show()
 
     >>> import pywt
     >>> import numpy as np
@@ -105,8 +105,8 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
     >>> widths = np.arange(1, 31)
     >>> cwtmatr, freqs = pywt.cwt(sig, widths, 'mexh')
     >>> plt.imshow(cwtmatr, extent=[-1, 1, 1, 31], cmap='PRGn', aspect='auto',
-    ...            vmax=abs(cwtmatr).max(), vmin=-abs(cwtmatr).max())  # doctest: +SKIP
-    >>> plt.show() # doctest: +SKIP
+    ...            vmax=abs(cwtmatr).max(), vmin=-abs(cwtmatr).max())
+    >>> plt.show()
     """
 
     # accept array_like input; make a copy to ensure a contiguous array

pywt/_extensions/_pywt.pyx

@@ -85,7 +85,7 @@ class _Modes(object):
     --------
     >>> import pywt
     >>> pywt.Modes.modes
-        ['zero', 'constant', 'symmetric', 'reflect', 'periodic', 'smooth', 'periodization', 'antisymmetric', 'antireflect']
+         ['zero', 'constant', 'symmetric', 'periodic', 'smooth', 'periodization', 'reflect', 'antisymmetric', 'antireflect']
     >>> # The different ways of passing wavelet and mode parameters
     >>> (a, d) = pywt.dwt([1,2,3,4,5,6], 'db2', 'smooth')
     >>> (a, d) = pywt.dwt([1,2,3,4,5,6], pywt.Wavelet('db2'), pywt.Modes.smooth)
@@ -909,34 +909,26 @@ cdef public class ContinuousWavelet [type ContinuousWaveletType, object Continuo
         >>> wavelet.upper_bound = ub
         >>> wavelet.lower_bound = lb
         >>> [psi,xval] = wavelet.wavefun(length=n)
-        >>> plt.plot(xval,psi) # doctest: +ELLIPSIS
-        [<matplotlib.lines.Line2D object at ...>]
-        >>> plt.title("Gaussian Wavelet of order 8") # doctest: +ELLIPSIS
-        <matplotlib.text.Text object at ...>
-        >>> plt.show() # doctest: +SKIP
+        >>> plt.plot(xval,psi)
+        >>> plt.title("Gaussian Wavelet of order 8")
+        >>> plt.show()
 
-        >>> import pywt
+        >>> import numpy as np
         >>> import matplotlib.pyplot as plt
+        >>> import pywt
         >>> lb = -5
         >>> ub = 5
         >>> n = 1000
         >>> wavelet = pywt.ContinuousWavelet("cgau4")
         >>> wavelet.upper_bound = ub
         >>> wavelet.lower_bound = lb
         >>> [psi,xval] = wavelet.wavefun(length=n)
-        >>> plt.subplot(211) # doctest: +ELLIPSIS
-        <matplotlib.axes._subplots.AxesSubplot object at ...>
-        >>> plt.plot(xval,np.real(psi)) # doctest: +ELLIPSIS
-        [<matplotlib.lines.Line2D object at ...>]
-        >>> plt.title("Real part") # doctest: +ELLIPSIS
-        <matplotlib.text.Text object at ...>
-        >>> plt.subplot(212) # doctest: +ELLIPSIS
-        <matplotlib.axes._subplots.AxesSubplot object at ...>
-        >>> plt.plot(xval,np.imag(psi)) # doctest: +ELLIPSIS
-        [<matplotlib.lines.Line2D object at ...>]
-        >>> plt.title("Imaginary part") # doctest: +ELLIPSIS
-        <matplotlib.text.Text object at ...>
-        >>> plt.show() # doctest: +SKIP
+        >>> fix, (ax1, ax2) = plt.subplots(2, 1)
+        >>> ax1.plot(xval,np.real(psi))
+        >>> ax1.set_title("Real part")
+        >>> ax2.plot(xval,np.imag(psi))
+        >>> ax2.set_title("Imaginary part")
+        >>> plt.show()
 
         """
         cdef pywt_index_t output_length "output_length"

pywt/_multilevel.py

@@ -402,7 +402,7 @@ def wavedecn(data, wavelet, mode='symmetric', level=None, axes=None):
     >>> # Levels:
     >>> len(coeffs)-1
     2
-    >>> waverecn(coeffs, 'db1')  # doctest: +NORMALIZE_WHITESPACE
+    >>> waverecn(coeffs, 'db1')
     array([[[ 1.,  1.,  1.,  1.],
             [ 1.,  1.,  1.,  1.],
             [ 1.,  1.,  1.,  1.],
@@ -496,7 +496,7 @@ def waverecn(coeffs, wavelet, mode='symmetric', axes=None):
     >>> # Levels:
     >>> len(coeffs)-1
     2
-    >>> waverecn(coeffs, 'db1')  # doctest: +NORMALIZE_WHITESPACE
+    >>> waverecn(coeffs, 'db1')
     array([[[ 1.,  1.,  1.,  1.],
             [ 1.,  1.,  1.,  1.],
             [ 1.,  1.,  1.,  1.],
@@ -1415,6 +1415,7 @@ def fswavedecn(data, wavelet, mode='symmetric', levels=None, axes=None):
 
     Examples
     --------
+    >>> import numpy as np
     >>> from pywt import fswavedecn
     >>> fs_result = fswavedecn(np.ones((32, 32)), 'sym2', levels=(1, 3))
     >>> print(fs_result.detail_keys())

pywt/data/_readers.py

@@ -36,9 +36,9 @@ def ascent():
 
     >>> import matplotlib.pyplot as plt
     >>> plt.gray()
-    >>> plt.imshow(ascent) # doctest: +ELLIPSIS
+    >>> plt.imshow(ascent
     <matplotlib.image.AxesImage object at ...>
-    >>> plt.show() # doctest: +SKIP
+    >>> plt.show()
 
     """
     with importlib.resources.as_file(_DATADIR.joinpath('ascent.npz')) as f:
@@ -73,9 +73,9 @@ def aero():
 
     >>> import matplotlib.pyplot as plt
     >>> plt.gray()
-    >>> plt.imshow(aero) # doctest: +ELLIPSIS
+    >>> plt.imshow(aero)
     <matplotlib.image.AxesImage object at ...>
-    >>> plt.show() # doctest: +SKIP
+    >>> plt.show()
 
     """
     with importlib.resources.as_file(_DATADIR.joinpath('aero.npz')) as f:
@@ -121,9 +121,9 @@ def camera():
 
     >>> import matplotlib.pyplot as plt
     >>> plt.gray()
-    >>> plt.imshow(camera) # doctest: +ELLIPSIS
+    >>> plt.imshow(camera)
     <matplotlib.image.AxesImage object at ...>
-    >>> plt.show() # doctest: +SKIP
+    >>> plt.show()
 
     """
     with importlib.resources.as_file(_DATADIR.joinpath('camera.npz')) as f:
@@ -154,9 +154,9 @@ def ecg():
     True
 
     >>> import matplotlib.pyplot as plt
-    >>> plt.plot(ecg) # doctest: +ELLIPSIS
+    >>> plt.plot(ecg)
     [<matplotlib.lines.Line2D object at ...>]
-    >>> plt.show() # doctest: +SKIP
+    >>> plt.show()
     """
     with importlib.resources.as_file(_DATADIR.joinpath('ecg.npz')) as f:
         ecg = np.load(f)['data']
@@ -192,9 +192,9 @@ def nino():
     True
 
     >>> import matplotlib.pyplot as plt
-    >>> plt.plot(time,sst) # doctest: +ELLIPSIS
+    >>> plt.plot(time,sst)
     [<matplotlib.lines.Line2D object at ...>]
-    >>> plt.show() # doctest: +SKIP
+    >>> plt.show()
     """
     with importlib.resources.as_file(_DATADIR.joinpath('sst_nino3.npz')) as f:
         sst_csv = np.load(f)['data']