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 [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -129,11 +129,13 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${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
- pip install -r util/readthedocs/requirements.txt
- sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+ cd ..
+ # XXX sphinx build is broken on CI
+ # pip install -r util/readthedocs/requirements.txt
+ # sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
  else
  pytest --pyargs pywt
  fi
@@ -203,7 +205,7 @@ jobs:
  python -m build --sdist
  pip install pywavelets* -v
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -221,7 +223,9 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- python util/refguide_check.py --doctests
+ # doctests docstrings
+ pytest --doctest-modules --pyargs pywt -v --doctest-collect=api
+ pytest --doctest-modules --pyargs pywt.data -v
  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']

pywt/data/_wavelab_signals.py

@@ -70,8 +70,9 @@ def demo_signal(name='Bumps', n=None):
  >>> doppler = pywt.data.demo_signal('doppler', 1024)
  >>> available_signals = pywt.data.demo_signal('list')
  >>> print(available_signals)
-
-
+ ['Blocks', 'Bumps', 'HeaviSine', 'Doppler', 'Ramp', 'HiSine', 'LoSine', 'LinChirp',
+ 'TwoChirp', 'QuadChirp', 'MishMash', 'WernerSorrows', 'HypChirps', 'LinChirps',
+ 'Chirps', 'Gabor', 'sineoneoverx', 'Piece-Regular', 'Piece-Polynomial', 'Riemann']
 
  """
  if name.lower() == 'list':

.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 [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -129,11 +129,13 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${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
- pip install -r util/readthedocs/requirements.txt
- sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+ cd ..
+ # XXX sphinx build is broken on CI
+ # pip install -r util/readthedocs/requirements.txt
+ # sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
  else
  pytest --pyargs pywt
  fi
@@ -203,7 +205,7 @@ jobs:
  python -m build --sdist
  pip install pywavelets* -v
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -221,7 +223,9 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- python util/refguide_check.py --doctests
+ # doctests docstrings
+ pytest --doctest-modules --pyargs pywt -v --doctest-collect=api
+ pytest --doctest-modules --pyargs pywt.data -v
  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']

pywt/data/_wavelab_signals.py

@@ -70,8 +70,9 @@ def demo_signal(name='Bumps', n=None):
  >>> doppler = pywt.data.demo_signal('doppler', 1024)
  >>> available_signals = pywt.data.demo_signal('list')
  >>> print(available_signals)
-
-
+ ['Blocks', 'Bumps', 'HeaviSine', 'Doppler', 'Ramp', 'HiSine', 'LoSine', 'LinChirp',
+ 'TwoChirp', 'QuadChirp', 'MishMash', 'WernerSorrows', 'HypChirps', 'LinChirps',
+ 'Chirps', 'Gabor', 'sineoneoverx', 'Piece-Regular', 'Piece-Polynomial', 'Riemann']
 
  """
  if name.lower() == 'list':

.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 [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -129,11 +129,13 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${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
- pip install -r util/readthedocs/requirements.txt
- sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+ cd ..
+ # XXX sphinx build is broken on CI
+ # pip install -r util/readthedocs/requirements.txt
+ # sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
  else
  pytest --pyargs pywt
  fi
@@ -203,7 +205,7 @@ jobs:
  python -m build --sdist
  pip install pywavelets* -v
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -221,7 +223,9 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- python util/refguide_check.py --doctests
+ # doctests docstrings
+ pytest --doctest-modules --pyargs pywt -v --doctest-collect=api
+ pytest --doctest-modules --pyargs pywt.data -v
  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']

pywt/data/_wavelab_signals.py

@@ -70,8 +70,9 @@ def demo_signal(name='Bumps', n=None):
  >>> doppler = pywt.data.demo_signal('doppler', 1024)
  >>> available_signals = pywt.data.demo_signal('list')
  >>> print(available_signals)
-
-
+ ['Blocks', 'Bumps', 'HeaviSine', 'Doppler', 'Ramp', 'HiSine', 'LoSine', 'LinChirp',
+ 'TwoChirp', 'QuadChirp', 'MishMash', 'WernerSorrows', 'HypChirps', 'LinChirps',
+ 'Chirps', 'Gabor', 'sineoneoverx', 'Piece-Regular', 'Piece-Polynomial', 'Riemann']
 
  """
  if name.lower() == 'list':

.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 [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -129,11 +129,13 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${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
- pip install -r util/readthedocs/requirements.txt
- sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+ cd ..
+ # XXX sphinx build is broken on CI
+ # pip install -r util/readthedocs/requirements.txt
+ # sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
  else
  pytest --pyargs pywt
  fi
@@ -203,7 +205,7 @@ jobs:
  python -m build --sdist
  pip install pywavelets* -v
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -221,7 +223,9 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- python util/refguide_check.py --doctests
+ # doctests docstrings
+ pytest --doctest-modules --pyargs pywt -v --doctest-collect=api
+ pytest --doctest-modules --pyargs pywt.data -v
  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']

pywt/data/_wavelab_signals.py

@@ -70,8 +70,9 @@ def demo_signal(name='Bumps', n=None):
  >>> doppler = pywt.data.demo_signal('doppler', 1024)
  >>> available_signals = pywt.data.demo_signal('list')
  >>> print(available_signals)
-
-
+ ['Blocks', 'Bumps', 'HeaviSine', 'Doppler', 'Ramp', 'HiSine', 'LoSine', 'LinChirp',
+ 'TwoChirp', 'QuadChirp', 'MishMash', 'WernerSorrows', 'HypChirps', 'LinChirps',
+ 'Chirps', 'Gabor', 'sineoneoverx', 'Piece-Regular', 'Piece-Polynomial', 'Riemann']
 
  """
  if name.lower() == 'list':

.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 [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -129,11 +129,13 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${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
- pip install -r util/readthedocs/requirements.txt
- sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+ cd ..
+ # XXX sphinx build is broken on CI
+ # pip install -r util/readthedocs/requirements.txt
+ # sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
  else
  pytest --pyargs pywt
  fi
@@ -203,7 +205,7 @@ jobs:
  python -m build --sdist
  pip install pywavelets* -v
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -221,7 +223,9 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- python util/refguide_check.py --doctests
+ # doctests docstrings
+ pytest --doctest-modules --pyargs pywt -v --doctest-collect=api
+ pytest --doctest-modules --pyargs pywt.data -v
  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']

pywt/data/_wavelab_signals.py

@@ -70,8 +70,9 @@ def demo_signal(name='Bumps', n=None):
  >>> doppler = pywt.data.demo_signal('doppler', 1024)
  >>> available_signals = pywt.data.demo_signal('list')
  >>> print(available_signals)
-
-
+ ['Blocks', 'Bumps', 'HeaviSine', 'Doppler', 'Ramp', 'HiSine', 'LoSine', 'LinChirp',
+ 'TwoChirp', 'QuadChirp', 'MishMash', 'WernerSorrows', 'HypChirps', 'LinChirps',
+ 'Chirps', 'Gabor', 'sineoneoverx', 'Piece-Regular', 'Piece-Polynomial', 'Riemann']
 
  """
  if name.lower() == 'list':

.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 [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -129,11 +129,13 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${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
- pip install -r util/readthedocs/requirements.txt
- sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+ cd ..
+ # XXX sphinx build is broken on CI
+ # pip install -r util/readthedocs/requirements.txt
+ # sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
  else
  pytest --pyargs pywt
  fi
@@ -203,7 +205,7 @@ jobs:
  python -m build --sdist
  pip install pywavelets* -v
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -221,7 +223,9 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- python util/refguide_check.py --doctests
+ # doctests docstrings
+ pytest --doctest-modules --pyargs pywt -v --doctest-collect=api
+ pytest --doctest-modules --pyargs pywt.data -v
  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']

pywt/data/_wavelab_signals.py

@@ -70,8 +70,9 @@ def demo_signal(name='Bumps', n=None):
  >>> doppler = pywt.data.demo_signal('doppler', 1024)
  >>> available_signals = pywt.data.demo_signal('list')
  >>> print(available_signals)
-
-
+ ['Blocks', 'Bumps', 'HeaviSine', 'Doppler', 'Ramp', 'HiSine', 'LoSine', 'LinChirp',
+ 'TwoChirp', 'QuadChirp', 'MishMash', 'WernerSorrows', 'HypChirps', 'LinChirps',
+ 'Chirps', 'Gabor', 'sineoneoverx', 'Piece-Regular', 'Piece-Polynomial', 'Riemann']
 
  """
  if name.lower() == 'list':

.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 [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -129,11 +129,13 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${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
- pip install -r util/readthedocs/requirements.txt
- sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+ cd ..
+ # XXX sphinx build is broken on CI
+ # pip install -r util/readthedocs/requirements.txt
+ # sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
  else
  pytest --pyargs pywt
  fi
@@ -203,7 +205,7 @@ jobs:
  python -m build --sdist
  pip install pywavelets* -v
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -221,7 +223,9 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- python util/refguide_check.py --doctests
+ # doctests docstrings
+ pytest --doctest-modules --pyargs pywt -v --doctest-collect=api
+ pytest --doctest-modules --pyargs pywt.data -v
  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']

pywt/data/_wavelab_signals.py

@@ -70,8 +70,9 @@ def demo_signal(name='Bumps', n=None):
  >>> doppler = pywt.data.demo_signal('doppler', 1024)
  >>> available_signals = pywt.data.demo_signal('list')
  >>> print(available_signals)
-
-
+ ['Blocks', 'Bumps', 'HeaviSine', 'Doppler', 'Ramp', 'HiSine', 'LoSine', 'LinChirp',
+ 'TwoChirp', 'QuadChirp', 'MishMash', 'WernerSorrows', 'HypChirps', 'LinChirps',
+ 'Chirps', 'Gabor', 'sineoneoverx', 'Piece-Regular', 'Piece-Polynomial', 'Riemann']
 
  """
  if name.lower() == 'list':

.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 [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -129,11 +129,13 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${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
- pip install -r util/readthedocs/requirements.txt
- sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+ cd ..
+ # XXX sphinx build is broken on CI
+ # pip install -r util/readthedocs/requirements.txt
+ # sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
  else
  pytest --pyargs pywt
  fi
@@ -203,7 +205,7 @@ jobs:
  python -m build --sdist
  pip install pywavelets* -v
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- pip install sphinx numpydoc
+ pip install sphinx numpydoc scipy-doctest
  pip install . -v
  else
  pip install . -v
@@ -221,7 +223,9 @@ jobs:
  pytest --pyargs pywt
  python ../pywt/tests/test_doc.py
  elif [ "${REFGUIDE_CHECK}" == "1" ]; then
- python util/refguide_check.py --doctests
+ # doctests docstrings
+ pytest --doctest-modules --pyargs pywt -v --doctest-collect=api
+ pytest --doctest-modules --pyargs pywt.data -v
  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']

pywt/data/_wavelab_signals.py

@@ -70,8 +70,9 @@ def demo_signal(name='Bumps', n=None):
  >>> doppler = pywt.data.demo_signal('doppler', 1024)
  >>> available_signals = pywt.data.demo_signal('list')
  >>> print(available_signals)
-
-
+ ['Blocks', 'Bumps', 'HeaviSine', 'Doppler', 'Ramp', 'HiSine', 'LoSine', 'LinChirp',
+ 'TwoChirp', 'QuadChirp', 'MishMash', 'WernerSorrows', 'HypChirps', 'LinChirps',
+ 'Chirps', 'Gabor', 'sineoneoverx', 'Piece-Regular', 'Piece-Polynomial', 'Riemann']
 
  """
  if name.lower() == 'list':