MAINT: remove optional dependence on SciPy for FFT operations#791

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Merged
rgommers merged 9 commits into from
Feb 3, 2025
Merged

MAINT: remove optional dependence on SciPy for FFT operations #791

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e7b80af
DEP: Drop installation of nightly SciPy
agriyakhetarpal Feb 1, 2025
6181b57
MAINT: Move `create_dat.py` to `util/` directory
agriyakhetarpal Feb 1, 2025
c31a47b
MAINT: Remove SciPy ref from manual + installation guide
agriyakhetarpal Feb 1, 2025
d7f52cc
STY: Fix usage of SciPy noun
agriyakhetarpal Feb 1, 2025
e847b6e
DEP, MAINT: Remove optional-dependencies table
agriyakhetarpal Feb 1, 2025
5bcef68
CI, MAINT: Remove SciPy-related CI options
agriyakhetarpal Feb 1, 2025
ed82b68
MAINT: don't opt for SciPy's FFT, use `numpy.fft`
agriyakhetarpal Feb 1, 2025
b8283af
STY: rename noGIL job to `linux-cp313t-default`
agriyakhetarpal Feb 1, 2025
7a692e7
STY: Remove `fftmodule` variable, use `np.fft`
agriyakhetarpal Feb 1, 2025
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1 change: 0 additions & 1 deletion .coveragerc
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@ omit =
*/pywt/_doc_utils.py*
*/pywt/_pytesttester.py*
*/pywt/_pytest.py*
*/pywt/data/create_dat.py
*.pxd
stringsource
plugins = Cython.Coverage
15 changes: 2 additions & 13 deletions .github/workflows/tests.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,6 @@ env:
CYTHONSPEC: cython
NUMPY_MIN: numpy==1.23.0
CYTHON_MIN: cython==3.0.4
SCIPY_MIN: scipy==1.9.0

jobs:
test_pywavelets_linux:
Expand All@@ -36,7 +35,6 @@ jobs:
runs-on: [ubuntu-latest] # Arm runner tested separately, see below
python-version: ["3.10", "3.13"]
MINIMUM_REQUIREMENTS: [0]
USE_SCIPY: [0]
USE_SDIST: [0]
REFGUIDE_CHECK: [1]
PIP_FLAGS: [""]
Expand All@@ -52,8 +50,6 @@ jobs:
OPTIONS_NAME: "minimum-req"
- runs-on: ubuntu-latest
python-version: "3.10"
USE_SCIPY: 1
OPTIONS_NAME: "with-scipy"
- runs-on: ubuntu-latest
python-version: "3.10"
USE_SDIST: 1
Expand DownExpand Up@@ -81,7 +77,6 @@ jobs:
MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
USE_SDIST: ${{ matrix.USE_SDIST }}
USE_SCIPY: ${{ matrix.USE_SCIPY }}
REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }}
run: |
Expand All@@ -97,11 +92,9 @@ jobs:
if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
pip install ${CYTHON_MIN}
pip install ${NUMPY_MIN}
if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
else
pip install ${PIP_FLAGS} cython
pip install ${PIP_FLAGS} numpy
if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
fi
pip install ${PIP_FLAGS} matplotlib pytest

Expand DownExpand Up@@ -147,7 +140,7 @@ jobs:
popd

test_pywavelets_linux_free_threaded:
name: linux-cp313t-with-scipy
name: linux-cp313t-default
runs-on: ubuntu-latest
strategy:
# Ensure that a wheel builder finishes even if another fails
Expand All@@ -169,7 +162,7 @@ jobs:
python --version
pip install --upgrade pip build
# We need nightly wheels for free-threaded support and latest fixes
pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy
pip install pytest meson-python ninja
pip install . -v --no-build-isolation

Expand All@@ -190,7 +183,6 @@ jobs:
matrix:
python-version: ["3.10", "3.13"]
MINIMUM_REQUIREMENTS: [0]
USE_SCIPY: [0]
USE_SDIST: [0]
REFGUIDE_CHECK: [0]
PIP_FLAGS: [""]
Expand DownExpand Up@@ -219,7 +211,6 @@ jobs:
MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
USE_SDIST: ${{ matrix.USE_SDIST }}
USE_SCIPY: ${{ matrix.USE_SCIPY }}
REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
CC: /usr/bin/clang
CXX: /usr/bin/clang++
Expand All@@ -233,10 +224,8 @@ jobs:
# Set numpy version first, other packages link against it
if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
pip install ${CYTHON_MIN} ${NUMPY_MIN}
if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
else
pip install ${PIP_FLAGS} cython numpy
if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
fi
pip install ${PIP_FLAGS} matplotlib pytest

Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/wheel_tests_and_release.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -49,7 +49,7 @@ jobs:
if: ${{ matrix.cibw_python }} == "cp313t"
run: |
PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
pip install numpy pytest meson-python ninja"
NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand DownExpand Up@@ -136,7 +136,7 @@ jobs:
if: ${{ matrix.cibw_python }} == "cp313t"
run: |
PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
pip install numpy pytest meson-python ninja"
NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand Down
4 changes: 1 addition & 3 deletions README.rst
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -67,9 +67,7 @@ Installation

PyWavelets supports `Python`_ >=3.10, and is only dependent on `NumPy`_
(supported versions are currently ``>= 1.23.0``). To pass all of the tests,
`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
present, FFT-based continuous wavelet transforms will use FFTs from SciPy
rather than NumPy.
`Matplotlib`_ is also required.

There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi. If
you are on one of these platforms, you should get a binary (precompiled)
Expand Down
2 changes: 1 addition & 1 deletion doc/source/dev/conduct/code_of_conduct.rst
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -165,7 +165,7 @@ Endnotes
We are thankful to the SciPy developers for creating the code of conduct we
have adapted here.

- `Scipy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_
- `SciPy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_

The SciPy code of conduct was in turn inspired by the following documents:

Expand Down
3 changes: 1 addition & 2 deletions doc/source/install.rst
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -40,8 +40,7 @@ For the requirements needed to build from source are (Python, NumPy and Cython
minimum versions in particular), see ``pyproject.toml``.

To run all the tests for PyWavelets, you will also need to install the
Matplotlib_ package. If SciPy_ is available, FFT-based continuous wavelet
transforms will use the FFT implementation from SciPy instead of NumPy.
Matplotlib_ package.

.. seealso:: The :ref:`Development guide <dev-index>` section contains more
information on building and installing from source code.
Expand Down
3 changes: 0 additions & 3 deletions pyproject.toml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -50,9 +50,6 @@ classifiers = [
"Topic :: Software Development :: Libraries :: Python Modules"
]

[project.optional-dependencies]
optional = ["scipy>=1.9"]

[project.urls]
homepage = "https://github.com/PyWavelets/pywt"
source = "https://github.com/PyWavelets/pywt"
Expand Down
32 changes: 11 additions & 21 deletions pywt/_cwt.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -14,24 +14,14 @@

import numpy as np

try:
import scipy
fftmodule = scipy.fft
next_fast_len = fftmodule.next_fast_len
except ImportError:
fftmodule = np.fft

# provide a fallback so scipy is an optional requirement
# note: numpy.fft in numpy 2.0 is as fast as scipy.fft, so could be used
# unconditionally once the minimum supported numpy version is >=2.0
def next_fast_len(n):
"""Round up size to the nearest power of two.

Given a number of samples `n`, returns the next power of two
following this number to take advantage of FFT speedup.
This fallback is less efficient than `scipy.fftpack.next_fast_len`
"""
return 2**ceil(np.log2(n))

def next_fast_len(n):
"""Round up size to the nearest power of two.

Given a number of samples `n`, returns the next power of two
following this number to take advantage of FFT speedup.
"""
return 2**ceil(np.log2(n))


def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
Expand DownExpand Up@@ -177,10 +167,10 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
)
if size_scale != size_scale0:
# Must recompute fft_data when the padding size changes.
fft_data = fftmodule.fft(data, size_scale, axis=-1)
fft_data = np.fft.fft(data, size_scale, axis=-1)
size_scale0 = size_scale
fft_wav = fftmodule.fft(int_psi_scale, size_scale, axis=-1)
conv = fftmodule.ifft(fft_wav * fft_data, axis=-1)
fft_wav = np.fft.fft(int_psi_scale, size_scale, axis=-1)
conv = np.fft.ifft(fft_wav * fft_data, axis=-1)
conv = conv[..., :data.shape[-1] + int_psi_scale.size - 1]

coef = - np.sqrt(scale) * np.diff(conv, axis=-1)
Expand Down
4 changes: 2 additions & 2 deletions pywt/data/create_dat.py → util/create_dat.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python

"""Helper script for creating image .dat files by numpy.save
"""Helper script for creating image .dat files by numpy.save.

Usage:

Expand All@@ -10,7 +10,7 @@

python create_dat.py aero.png aero.dat

Requires Scipy and PIL.
Requires SciPy and PIL, which need to be installed separately.
"""


Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
MAINT: remove optional dependence on SciPy for FFT operations#791

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to your account

 Merged

rgommers
merged 9 commits into

from

Feb 3, 2025
 Merged


MAINT: remove optional dependence on SciPy for FFT operations
#791
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Commits

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9 commits


Select commit
Hold shift + click to select a range
e7b80af

DEP: Drop installation of nightly SciPy


agriyakhetarpal Feb 1, 2025
6181b57

MAINT: Move `create_dat.py` to `util/` directory


agriyakhetarpal Feb 1, 2025
c31a47b

MAINT: Remove SciPy ref from manual + installation guide


agriyakhetarpal Feb 1, 2025
d7f52cc

STY: Fix usage of SciPy noun


agriyakhetarpal Feb 1, 2025
e847b6e

DEP, MAINT: Remove optional-dependencies table


agriyakhetarpal Feb 1, 2025
5bcef68

CI, MAINT: Remove SciPy-related CI options


agriyakhetarpal Feb 1, 2025
ed82b68

MAINT: don't opt for SciPy's FFT, use `numpy.fft`


agriyakhetarpal Feb 1, 2025
b8283af

STY: rename noGIL job to `linux-cp313t-default`


agriyakhetarpal Feb 1, 2025
7a692e7

STY: Remove `fftmodule` variable, use `np.fft`


agriyakhetarpal Feb 1, 2025

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1 change: 0 additions & 1 deletion
.coveragerc

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@ omit =
 */pywt/_doc_utils.py*
 */pywt/_pytesttester.py*
 */pywt/_pytest.py*
 */pywt/data/create_dat.py
 *.pxd
 stringsource
plugins = Cython.Coverage

15 changes: 2 additions & 13 deletions
.github/workflows/tests.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,6 @@ env:
 CYTHONSPEC: cython
 NUMPY_MIN: numpy==1.23.0
 CYTHON_MIN: cython==3.0.4
 SCIPY_MIN: scipy==1.9.0

jobs:
 test_pywavelets_linux:
Expand All@@ -36,7 +35,6 @@ jobs:
 runs-on: [ubuntu-latest] # Arm runner tested separately, see below
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [1]
 PIP_FLAGS: [""]
Expand All@@ -52,8 +50,6 @@ jobs:
 OPTIONS_NAME: "minimum-req"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SCIPY: 1
 OPTIONS_NAME: "with-scipy"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SDIST: 1
Expand DownExpand Up@@ -81,7 +77,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }}
 run: |
Expand All@@ -97,11 +92,9 @@ jobs:
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN}
 pip install ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython
 pip install ${PIP_FLAGS} numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand DownExpand Up@@ -147,7 +140,7 @@ jobs:
 popd

 test_pywavelets_linux_free_threaded:
 name: linux-cp313t-with-scipy
 name: linux-cp313t-default
 runs-on: ubuntu-latest
 strategy:
 # Ensure that a wheel builder finishes even if another fails
Expand All@@ -169,7 +162,7 @@ jobs:
 python --version
 pip install --upgrade pip build
 # We need nightly wheels for free-threaded support and latest fixes
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy
 pip install pytest meson-python ninja
 pip install . -v --no-build-isolation

Expand All@@ -190,7 +183,6 @@ jobs:
 matrix:
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [0]
 PIP_FLAGS: [""]
Expand DownExpand Up@@ -219,7 +211,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 CC: /usr/bin/clang
 CXX: /usr/bin/clang++
Expand All@@ -233,10 +224,8 @@ jobs:
 # Set numpy version first, other packages link against it
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN} ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand Down

4 changes: 2 additions & 2 deletions
.github/workflows/wheel_tests_and_release.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -49,7 +49,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand DownExpand Up@@ -136,7 +136,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand Down

4 changes: 1 addition & 3 deletions
README.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,9 +67,7 @@ Installation

PyWavelets supports `Python`_ >=3.10, and is only dependent on `NumPy`_
(supported versions are currently ``>= 1.23.0``). To pass all of the tests,
`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
present, FFT-based continuous wavelet transforms will use FFTs from SciPy
rather than NumPy.
`Matplotlib`_ is also required.

There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi. If
you are on one of these platforms, you should get a binary (precompiled)
Expand Down

2 changes: 1 addition & 1 deletion
doc/source/dev/conduct/code_of_conduct.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -165,7 +165,7 @@ Endnotes
We are thankful to the SciPy developers for creating the code of conduct we
have adapted here.

- `Scipy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_
- `SciPy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_

The SciPy code of conduct was in turn inspired by the following documents:

Expand Down

3 changes: 1 addition & 2 deletions
doc/source/install.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -40,8 +40,7 @@ For the requirements needed to build from source are (Python, NumPy and Cython
minimum versions in particular), see ``pyproject.toml``.

To run all the tests for PyWavelets, you will also need to install the
Matplotlib_ package. If SciPy_ is available, FFT-based continuous wavelet
transforms will use the FFT implementation from SciPy instead of NumPy.
Matplotlib_ package.

.. seealso:: The :ref:`Development guide <dev-index>` section contains more
 information on building and installing from source code.
Expand Down

3 changes: 0 additions & 3 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -50,9 +50,6 @@ classifiers = [
 "Topic :: Software Development :: Libraries :: Python Modules"
]

[project.optional-dependencies]
optional = ["scipy>=1.9"]

[project.urls]
homepage = "https://github.com/PyWavelets/pywt"
source = "https://github.com/PyWavelets/pywt"
Expand Down

32 changes: 11 additions & 21 deletions
pywt/_cwt.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,24 +14,14 @@

import numpy as np

try:
 import scipy
 fftmodule = scipy.fft
 next_fast_len = fftmodule.next_fast_len
except ImportError:
 fftmodule = np.fft

 # provide a fallback so scipy is an optional requirement
 # note: numpy.fft in numpy 2.0 is as fast as scipy.fft, so could be used
 # unconditionally once the minimum supported numpy version is >=2.0
 def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 This fallback is less efficient than `scipy.fftpack.next_fast_len`
 """
 return 2**ceil(np.log2(n))

def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 """
 return 2**ceil(np.log2(n))


def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
Expand DownExpand Up@@ -177,10 +167,10 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
 )
 if size_scale != size_scale0:
 # Must recompute fft_data when the padding size changes.
 fft_data = fftmodule.fft(data, size_scale, axis=-1)
 fft_data = np.fft.fft(data, size_scale, axis=-1)
 size_scale0 = size_scale
 fft_wav = fftmodule.fft(int_psi_scale, size_scale, axis=-1)
 conv = fftmodule.ifft(fft_wav * fft_data, axis=-1)
 fft_wav = np.fft.fft(int_psi_scale, size_scale, axis=-1)
 conv = np.fft.ifft(fft_wav * fft_data, axis=-1)
 conv = conv[..., :data.shape[-1] + int_psi_scale.size - 1]

 coef = - np.sqrt(scale) * np.diff(conv, axis=-1)
Expand Down

4 changes: 2 additions & 2 deletions
pywt/data/create_dat.py → util/create_dat.py

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python

"""Helper script for creating image .dat files by numpy.save
"""Helper script for creating image .dat files by numpy.save.

Usage:

Expand All@@ -10,7 +10,7 @@

 python create_dat.py aero.png aero.dat

Requires Scipy and PIL.
Requires SciPy and PIL, which need to be installed separately.
"""


Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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MAINT: remove optional dependence on SciPy for FFT operations#791

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 Merged

rgommers
merged 9 commits into

from

Feb 3, 2025
 Merged


MAINT: remove optional dependence on SciPy for FFT operations
#791
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e7b80af

DEP: Drop installation of nightly SciPy


agriyakhetarpal Feb 1, 2025
6181b57

MAINT: Move `create_dat.py` to `util/` directory


agriyakhetarpal Feb 1, 2025
c31a47b

MAINT: Remove SciPy ref from manual + installation guide


agriyakhetarpal Feb 1, 2025
d7f52cc

STY: Fix usage of SciPy noun


agriyakhetarpal Feb 1, 2025
e847b6e

DEP, MAINT: Remove optional-dependencies table


agriyakhetarpal Feb 1, 2025
5bcef68

CI, MAINT: Remove SciPy-related CI options


agriyakhetarpal Feb 1, 2025
ed82b68

MAINT: don't opt for SciPy's FFT, use `numpy.fft`


agriyakhetarpal Feb 1, 2025
b8283af

STY: rename noGIL job to `linux-cp313t-default`


agriyakhetarpal Feb 1, 2025
7a692e7

STY: Remove `fftmodule` variable, use `np.fft`


agriyakhetarpal Feb 1, 2025

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1 change: 0 additions & 1 deletion
.coveragerc

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Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@ omit =
 */pywt/_doc_utils.py*
 */pywt/_pytesttester.py*
 */pywt/_pytest.py*
 */pywt/data/create_dat.py
 *.pxd
 stringsource
plugins = Cython.Coverage

15 changes: 2 additions & 13 deletions
.github/workflows/tests.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,6 @@ env:
 CYTHONSPEC: cython
 NUMPY_MIN: numpy==1.23.0
 CYTHON_MIN: cython==3.0.4
 SCIPY_MIN: scipy==1.9.0

jobs:
 test_pywavelets_linux:
Expand All@@ -36,7 +35,6 @@ jobs:
 runs-on: [ubuntu-latest] # Arm runner tested separately, see below
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [1]
 PIP_FLAGS: [""]
Expand All@@ -52,8 +50,6 @@ jobs:
 OPTIONS_NAME: "minimum-req"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SCIPY: 1
 OPTIONS_NAME: "with-scipy"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SDIST: 1
Expand DownExpand Up@@ -81,7 +77,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }}
 run: |
Expand All@@ -97,11 +92,9 @@ jobs:
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN}
 pip install ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython
 pip install ${PIP_FLAGS} numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand DownExpand Up@@ -147,7 +140,7 @@ jobs:
 popd

 test_pywavelets_linux_free_threaded:
 name: linux-cp313t-with-scipy
 name: linux-cp313t-default
 runs-on: ubuntu-latest
 strategy:
 # Ensure that a wheel builder finishes even if another fails
Expand All@@ -169,7 +162,7 @@ jobs:
 python --version
 pip install --upgrade pip build
 # We need nightly wheels for free-threaded support and latest fixes
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy
 pip install pytest meson-python ninja
 pip install . -v --no-build-isolation

Expand All@@ -190,7 +183,6 @@ jobs:
 matrix:
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [0]
 PIP_FLAGS: [""]
Expand DownExpand Up@@ -219,7 +211,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 CC: /usr/bin/clang
 CXX: /usr/bin/clang++
Expand All@@ -233,10 +224,8 @@ jobs:
 # Set numpy version first, other packages link against it
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN} ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand Down

4 changes: 2 additions & 2 deletions
.github/workflows/wheel_tests_and_release.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -49,7 +49,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand DownExpand Up@@ -136,7 +136,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand Down

4 changes: 1 addition & 3 deletions
README.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,9 +67,7 @@ Installation

PyWavelets supports `Python`_ >=3.10, and is only dependent on `NumPy`_
(supported versions are currently ``>= 1.23.0``). To pass all of the tests,
`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
present, FFT-based continuous wavelet transforms will use FFTs from SciPy
rather than NumPy.
`Matplotlib`_ is also required.

There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi. If
you are on one of these platforms, you should get a binary (precompiled)
Expand Down

2 changes: 1 addition & 1 deletion
doc/source/dev/conduct/code_of_conduct.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -165,7 +165,7 @@ Endnotes
We are thankful to the SciPy developers for creating the code of conduct we
have adapted here.

- `Scipy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_
- `SciPy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_

The SciPy code of conduct was in turn inspired by the following documents:

Expand Down

3 changes: 1 addition & 2 deletions
doc/source/install.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -40,8 +40,7 @@ For the requirements needed to build from source are (Python, NumPy and Cython
minimum versions in particular), see ``pyproject.toml``.

To run all the tests for PyWavelets, you will also need to install the
Matplotlib_ package. If SciPy_ is available, FFT-based continuous wavelet
transforms will use the FFT implementation from SciPy instead of NumPy.
Matplotlib_ package.

.. seealso:: The :ref:`Development guide <dev-index>` section contains more
 information on building and installing from source code.
Expand Down

3 changes: 0 additions & 3 deletions
pyproject.toml

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -50,9 +50,6 @@ classifiers = [
 "Topic :: Software Development :: Libraries :: Python Modules"
]

[project.optional-dependencies]
optional = ["scipy>=1.9"]

[project.urls]
homepage = "https://github.com/PyWavelets/pywt"
source = "https://github.com/PyWavelets/pywt"
Expand Down

32 changes: 11 additions & 21 deletions
pywt/_cwt.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,24 +14,14 @@

import numpy as np

try:
 import scipy
 fftmodule = scipy.fft
 next_fast_len = fftmodule.next_fast_len
except ImportError:
 fftmodule = np.fft

 # provide a fallback so scipy is an optional requirement
 # note: numpy.fft in numpy 2.0 is as fast as scipy.fft, so could be used
 # unconditionally once the minimum supported numpy version is >=2.0
 def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 This fallback is less efficient than `scipy.fftpack.next_fast_len`
 """
 return 2**ceil(np.log2(n))

def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 """
 return 2**ceil(np.log2(n))


def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
Expand DownExpand Up@@ -177,10 +167,10 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
 )
 if size_scale != size_scale0:
 # Must recompute fft_data when the padding size changes.
 fft_data = fftmodule.fft(data, size_scale, axis=-1)
 fft_data = np.fft.fft(data, size_scale, axis=-1)
 size_scale0 = size_scale
 fft_wav = fftmodule.fft(int_psi_scale, size_scale, axis=-1)
 conv = fftmodule.ifft(fft_wav * fft_data, axis=-1)
 fft_wav = np.fft.fft(int_psi_scale, size_scale, axis=-1)
 conv = np.fft.ifft(fft_wav * fft_data, axis=-1)
 conv = conv[..., :data.shape[-1] + int_psi_scale.size - 1]

 coef = - np.sqrt(scale) * np.diff(conv, axis=-1)
Expand Down

4 changes: 2 additions & 2 deletions
pywt/data/create_dat.py → util/create_dat.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python

"""Helper script for creating image .dat files by numpy.save
"""Helper script for creating image .dat files by numpy.save.

Usage:

Expand All@@ -10,7 +10,7 @@

 python create_dat.py aero.png aero.dat

Requires Scipy and PIL.
Requires SciPy and PIL, which need to be installed separately.
"""


Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
MAINT: remove optional dependence on SciPy for FFT operations#791

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

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to your account

 Merged

rgommers
merged 9 commits into

from

Feb 3, 2025
 Merged


MAINT: remove optional dependence on SciPy for FFT operations
#791
Show file tree
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Hold shift + click to select a range
e7b80af

DEP: Drop installation of nightly SciPy


agriyakhetarpal Feb 1, 2025
6181b57

MAINT: Move `create_dat.py` to `util/` directory


agriyakhetarpal Feb 1, 2025
c31a47b

MAINT: Remove SciPy ref from manual + installation guide


agriyakhetarpal Feb 1, 2025
d7f52cc

STY: Fix usage of SciPy noun


agriyakhetarpal Feb 1, 2025
e847b6e

DEP, MAINT: Remove optional-dependencies table


agriyakhetarpal Feb 1, 2025
5bcef68

CI, MAINT: Remove SciPy-related CI options


agriyakhetarpal Feb 1, 2025
ed82b68

MAINT: don't opt for SciPy's FFT, use `numpy.fft`


agriyakhetarpal Feb 1, 2025
b8283af

STY: rename noGIL job to `linux-cp313t-default`


agriyakhetarpal Feb 1, 2025
7a692e7

STY: Remove `fftmodule` variable, use `np.fft`


agriyakhetarpal Feb 1, 2025

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1 change: 0 additions & 1 deletion
.coveragerc

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@ omit =
 */pywt/_doc_utils.py*
 */pywt/_pytesttester.py*
 */pywt/_pytest.py*
 */pywt/data/create_dat.py
 *.pxd
 stringsource
plugins = Cython.Coverage

15 changes: 2 additions & 13 deletions
.github/workflows/tests.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,6 @@ env:
 CYTHONSPEC: cython
 NUMPY_MIN: numpy==1.23.0
 CYTHON_MIN: cython==3.0.4
 SCIPY_MIN: scipy==1.9.0

jobs:
 test_pywavelets_linux:
Expand All@@ -36,7 +35,6 @@ jobs:
 runs-on: [ubuntu-latest] # Arm runner tested separately, see below
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [1]
 PIP_FLAGS: [""]
Expand All@@ -52,8 +50,6 @@ jobs:
 OPTIONS_NAME: "minimum-req"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SCIPY: 1
 OPTIONS_NAME: "with-scipy"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SDIST: 1
Expand DownExpand Up@@ -81,7 +77,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }}
 run: |
Expand All@@ -97,11 +92,9 @@ jobs:
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN}
 pip install ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython
 pip install ${PIP_FLAGS} numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand DownExpand Up@@ -147,7 +140,7 @@ jobs:
 popd

 test_pywavelets_linux_free_threaded:
 name: linux-cp313t-with-scipy
 name: linux-cp313t-default
 runs-on: ubuntu-latest
 strategy:
 # Ensure that a wheel builder finishes even if another fails
Expand All@@ -169,7 +162,7 @@ jobs:
 python --version
 pip install --upgrade pip build
 # We need nightly wheels for free-threaded support and latest fixes
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy
 pip install pytest meson-python ninja
 pip install . -v --no-build-isolation

Expand All@@ -190,7 +183,6 @@ jobs:
 matrix:
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [0]
 PIP_FLAGS: [""]
Expand DownExpand Up@@ -219,7 +211,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 CC: /usr/bin/clang
 CXX: /usr/bin/clang++
Expand All@@ -233,10 +224,8 @@ jobs:
 # Set numpy version first, other packages link against it
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN} ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand Down

4 changes: 2 additions & 2 deletions
.github/workflows/wheel_tests_and_release.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -49,7 +49,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand DownExpand Up@@ -136,7 +136,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand Down

4 changes: 1 addition & 3 deletions
README.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,9 +67,7 @@ Installation

PyWavelets supports `Python`_ >=3.10, and is only dependent on `NumPy`_
(supported versions are currently ``>= 1.23.0``). To pass all of the tests,
`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
present, FFT-based continuous wavelet transforms will use FFTs from SciPy
rather than NumPy.
`Matplotlib`_ is also required.

There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi. If
you are on one of these platforms, you should get a binary (precompiled)
Expand Down

2 changes: 1 addition & 1 deletion
doc/source/dev/conduct/code_of_conduct.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -165,7 +165,7 @@ Endnotes
We are thankful to the SciPy developers for creating the code of conduct we
have adapted here.

- `Scipy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_
- `SciPy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_

The SciPy code of conduct was in turn inspired by the following documents:

Expand Down

3 changes: 1 addition & 2 deletions
doc/source/install.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -40,8 +40,7 @@ For the requirements needed to build from source are (Python, NumPy and Cython
minimum versions in particular), see ``pyproject.toml``.

To run all the tests for PyWavelets, you will also need to install the
Matplotlib_ package. If SciPy_ is available, FFT-based continuous wavelet
transforms will use the FFT implementation from SciPy instead of NumPy.
Matplotlib_ package.

.. seealso:: The :ref:`Development guide <dev-index>` section contains more
 information on building and installing from source code.
Expand Down

3 changes: 0 additions & 3 deletions
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -50,9 +50,6 @@ classifiers = [
 "Topic :: Software Development :: Libraries :: Python Modules"
]

[project.optional-dependencies]
optional = ["scipy>=1.9"]

[project.urls]
homepage = "https://github.com/PyWavelets/pywt"
source = "https://github.com/PyWavelets/pywt"
Expand Down

32 changes: 11 additions & 21 deletions
pywt/_cwt.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,24 +14,14 @@

import numpy as np

try:
 import scipy
 fftmodule = scipy.fft
 next_fast_len = fftmodule.next_fast_len
except ImportError:
 fftmodule = np.fft

 # provide a fallback so scipy is an optional requirement
 # note: numpy.fft in numpy 2.0 is as fast as scipy.fft, so could be used
 # unconditionally once the minimum supported numpy version is >=2.0
 def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 This fallback is less efficient than `scipy.fftpack.next_fast_len`
 """
 return 2**ceil(np.log2(n))

def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 """
 return 2**ceil(np.log2(n))


def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
Expand DownExpand Up@@ -177,10 +167,10 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
 )
 if size_scale != size_scale0:
 # Must recompute fft_data when the padding size changes.
 fft_data = fftmodule.fft(data, size_scale, axis=-1)
 fft_data = np.fft.fft(data, size_scale, axis=-1)
 size_scale0 = size_scale
 fft_wav = fftmodule.fft(int_psi_scale, size_scale, axis=-1)
 conv = fftmodule.ifft(fft_wav * fft_data, axis=-1)
 fft_wav = np.fft.fft(int_psi_scale, size_scale, axis=-1)
 conv = np.fft.ifft(fft_wav * fft_data, axis=-1)
 conv = conv[..., :data.shape[-1] + int_psi_scale.size - 1]

 coef = - np.sqrt(scale) * np.diff(conv, axis=-1)
Expand Down

4 changes: 2 additions & 2 deletions
pywt/data/create_dat.py → util/create_dat.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python

"""Helper script for creating image .dat files by numpy.save
"""Helper script for creating image .dat files by numpy.save.

Usage:

Expand All@@ -10,7 +10,7 @@

 python create_dat.py aero.png aero.dat

Requires Scipy and PIL.
Requires SciPy and PIL, which need to be installed separately.
"""


Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
MAINT: remove optional dependence on SciPy for FFT operations#791

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 Merged

rgommers
merged 9 commits into

from

Feb 3, 2025
 Merged


MAINT: remove optional dependence on SciPy for FFT operations
#791
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e7b80af

DEP: Drop installation of nightly SciPy


agriyakhetarpal Feb 1, 2025
6181b57

MAINT: Move `create_dat.py` to `util/` directory


agriyakhetarpal Feb 1, 2025
c31a47b

MAINT: Remove SciPy ref from manual + installation guide


agriyakhetarpal Feb 1, 2025
d7f52cc

STY: Fix usage of SciPy noun


agriyakhetarpal Feb 1, 2025
e847b6e

DEP, MAINT: Remove optional-dependencies table


agriyakhetarpal Feb 1, 2025
5bcef68

CI, MAINT: Remove SciPy-related CI options


agriyakhetarpal Feb 1, 2025
ed82b68

MAINT: don't opt for SciPy's FFT, use `numpy.fft`


agriyakhetarpal Feb 1, 2025
b8283af

STY: rename noGIL job to `linux-cp313t-default`


agriyakhetarpal Feb 1, 2025
7a692e7

STY: Remove `fftmodule` variable, use `np.fft`


agriyakhetarpal Feb 1, 2025

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1 change: 0 additions & 1 deletion
.coveragerc

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@ omit =
 */pywt/_doc_utils.py*
 */pywt/_pytesttester.py*
 */pywt/_pytest.py*
 */pywt/data/create_dat.py
 *.pxd
 stringsource
plugins = Cython.Coverage

15 changes: 2 additions & 13 deletions
.github/workflows/tests.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,6 @@ env:
 CYTHONSPEC: cython
 NUMPY_MIN: numpy==1.23.0
 CYTHON_MIN: cython==3.0.4
 SCIPY_MIN: scipy==1.9.0

jobs:
 test_pywavelets_linux:
Expand All@@ -36,7 +35,6 @@ jobs:
 runs-on: [ubuntu-latest] # Arm runner tested separately, see below
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [1]
 PIP_FLAGS: [""]
Expand All@@ -52,8 +50,6 @@ jobs:
 OPTIONS_NAME: "minimum-req"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SCIPY: 1
 OPTIONS_NAME: "with-scipy"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SDIST: 1
Expand DownExpand Up@@ -81,7 +77,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }}
 run: |
Expand All@@ -97,11 +92,9 @@ jobs:
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN}
 pip install ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython
 pip install ${PIP_FLAGS} numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand DownExpand Up@@ -147,7 +140,7 @@ jobs:
 popd

 test_pywavelets_linux_free_threaded:
 name: linux-cp313t-with-scipy
 name: linux-cp313t-default
 runs-on: ubuntu-latest
 strategy:
 # Ensure that a wheel builder finishes even if another fails
Expand All@@ -169,7 +162,7 @@ jobs:
 python --version
 pip install --upgrade pip build
 # We need nightly wheels for free-threaded support and latest fixes
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy
 pip install pytest meson-python ninja
 pip install . -v --no-build-isolation

Expand All@@ -190,7 +183,6 @@ jobs:
 matrix:
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [0]
 PIP_FLAGS: [""]
Expand DownExpand Up@@ -219,7 +211,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 CC: /usr/bin/clang
 CXX: /usr/bin/clang++
Expand All@@ -233,10 +224,8 @@ jobs:
 # Set numpy version first, other packages link against it
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN} ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand Down

4 changes: 2 additions & 2 deletions
.github/workflows/wheel_tests_and_release.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -49,7 +49,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand DownExpand Up@@ -136,7 +136,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand Down

4 changes: 1 addition & 3 deletions
README.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,9 +67,7 @@ Installation

PyWavelets supports `Python`_ >=3.10, and is only dependent on `NumPy`_
(supported versions are currently ``>= 1.23.0``). To pass all of the tests,
`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
present, FFT-based continuous wavelet transforms will use FFTs from SciPy
rather than NumPy.
`Matplotlib`_ is also required.

There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi. If
you are on one of these platforms, you should get a binary (precompiled)
Expand Down

2 changes: 1 addition & 1 deletion
doc/source/dev/conduct/code_of_conduct.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -165,7 +165,7 @@ Endnotes
We are thankful to the SciPy developers for creating the code of conduct we
have adapted here.

- `Scipy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_
- `SciPy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_

The SciPy code of conduct was in turn inspired by the following documents:

Expand Down

3 changes: 1 addition & 2 deletions
doc/source/install.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -40,8 +40,7 @@ For the requirements needed to build from source are (Python, NumPy and Cython
minimum versions in particular), see ``pyproject.toml``.

To run all the tests for PyWavelets, you will also need to install the
Matplotlib_ package. If SciPy_ is available, FFT-based continuous wavelet
transforms will use the FFT implementation from SciPy instead of NumPy.
Matplotlib_ package.

.. seealso:: The :ref:`Development guide <dev-index>` section contains more
 information on building and installing from source code.
Expand Down

3 changes: 0 additions & 3 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -50,9 +50,6 @@ classifiers = [
 "Topic :: Software Development :: Libraries :: Python Modules"
]

[project.optional-dependencies]
optional = ["scipy>=1.9"]

[project.urls]
homepage = "https://github.com/PyWavelets/pywt"
source = "https://github.com/PyWavelets/pywt"
Expand Down

32 changes: 11 additions & 21 deletions
pywt/_cwt.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,24 +14,14 @@

import numpy as np

try:
 import scipy
 fftmodule = scipy.fft
 next_fast_len = fftmodule.next_fast_len
except ImportError:
 fftmodule = np.fft

 # provide a fallback so scipy is an optional requirement
 # note: numpy.fft in numpy 2.0 is as fast as scipy.fft, so could be used
 # unconditionally once the minimum supported numpy version is >=2.0
 def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 This fallback is less efficient than `scipy.fftpack.next_fast_len`
 """
 return 2**ceil(np.log2(n))

def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 """
 return 2**ceil(np.log2(n))


def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
Expand DownExpand Up@@ -177,10 +167,10 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
 )
 if size_scale != size_scale0:
 # Must recompute fft_data when the padding size changes.
 fft_data = fftmodule.fft(data, size_scale, axis=-1)
 fft_data = np.fft.fft(data, size_scale, axis=-1)
 size_scale0 = size_scale
 fft_wav = fftmodule.fft(int_psi_scale, size_scale, axis=-1)
 conv = fftmodule.ifft(fft_wav * fft_data, axis=-1)
 fft_wav = np.fft.fft(int_psi_scale, size_scale, axis=-1)
 conv = np.fft.ifft(fft_wav * fft_data, axis=-1)
 conv = conv[..., :data.shape[-1] + int_psi_scale.size - 1]

 coef = - np.sqrt(scale) * np.diff(conv, axis=-1)
Expand Down

4 changes: 2 additions & 2 deletions
pywt/data/create_dat.py → util/create_dat.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python

"""Helper script for creating image .dat files by numpy.save
"""Helper script for creating image .dat files by numpy.save.

Usage:

Expand All@@ -10,7 +10,7 @@

 python create_dat.py aero.png aero.dat

Requires Scipy and PIL.
Requires SciPy and PIL, which need to be installed separately.
"""


Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
MAINT: remove optional dependence on SciPy for FFT operations#791

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

rgommers
merged 9 commits into

from

Feb 3, 2025
 Merged


MAINT: remove optional dependence on SciPy for FFT operations
#791
Show file tree
Hide file tree
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Commits

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9 commits


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Hold shift + click to select a range
e7b80af

DEP: Drop installation of nightly SciPy


agriyakhetarpal Feb 1, 2025
6181b57

MAINT: Move `create_dat.py` to `util/` directory


agriyakhetarpal Feb 1, 2025
c31a47b

MAINT: Remove SciPy ref from manual + installation guide


agriyakhetarpal Feb 1, 2025
d7f52cc

STY: Fix usage of SciPy noun


agriyakhetarpal Feb 1, 2025
e847b6e

DEP, MAINT: Remove optional-dependencies table


agriyakhetarpal Feb 1, 2025
5bcef68

CI, MAINT: Remove SciPy-related CI options


agriyakhetarpal Feb 1, 2025
ed82b68

MAINT: don't opt for SciPy's FFT, use `numpy.fft`


agriyakhetarpal Feb 1, 2025
b8283af

STY: rename noGIL job to `linux-cp313t-default`


agriyakhetarpal Feb 1, 2025
7a692e7

STY: Remove `fftmodule` variable, use `np.fft`


agriyakhetarpal Feb 1, 2025

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
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1 change: 0 additions & 1 deletion
.coveragerc

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@ omit =
 */pywt/_doc_utils.py*
 */pywt/_pytesttester.py*
 */pywt/_pytest.py*
 */pywt/data/create_dat.py
 *.pxd
 stringsource
plugins = Cython.Coverage

15 changes: 2 additions & 13 deletions
.github/workflows/tests.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,6 @@ env:
 CYTHONSPEC: cython
 NUMPY_MIN: numpy==1.23.0
 CYTHON_MIN: cython==3.0.4
 SCIPY_MIN: scipy==1.9.0

jobs:
 test_pywavelets_linux:
Expand All@@ -36,7 +35,6 @@ jobs:
 runs-on: [ubuntu-latest] # Arm runner tested separately, see below
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [1]
 PIP_FLAGS: [""]
Expand All@@ -52,8 +50,6 @@ jobs:
 OPTIONS_NAME: "minimum-req"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SCIPY: 1
 OPTIONS_NAME: "with-scipy"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SDIST: 1
Expand DownExpand Up@@ -81,7 +77,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }}
 run: |
Expand All@@ -97,11 +92,9 @@ jobs:
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN}
 pip install ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython
 pip install ${PIP_FLAGS} numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand DownExpand Up@@ -147,7 +140,7 @@ jobs:
 popd

 test_pywavelets_linux_free_threaded:
 name: linux-cp313t-with-scipy
 name: linux-cp313t-default
 runs-on: ubuntu-latest
 strategy:
 # Ensure that a wheel builder finishes even if another fails
Expand All@@ -169,7 +162,7 @@ jobs:
 python --version
 pip install --upgrade pip build
 # We need nightly wheels for free-threaded support and latest fixes
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy
 pip install pytest meson-python ninja
 pip install . -v --no-build-isolation

Expand All@@ -190,7 +183,6 @@ jobs:
 matrix:
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [0]
 PIP_FLAGS: [""]
Expand DownExpand Up@@ -219,7 +211,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 CC: /usr/bin/clang
 CXX: /usr/bin/clang++
Expand All@@ -233,10 +224,8 @@ jobs:
 # Set numpy version first, other packages link against it
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN} ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand Down

4 changes: 2 additions & 2 deletions
.github/workflows/wheel_tests_and_release.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -49,7 +49,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand DownExpand Up@@ -136,7 +136,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand Down

4 changes: 1 addition & 3 deletions
README.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,9 +67,7 @@ Installation

PyWavelets supports `Python`_ >=3.10, and is only dependent on `NumPy`_
(supported versions are currently ``>= 1.23.0``). To pass all of the tests,
`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
present, FFT-based continuous wavelet transforms will use FFTs from SciPy
rather than NumPy.
`Matplotlib`_ is also required.

There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi. If
you are on one of these platforms, you should get a binary (precompiled)
Expand Down

2 changes: 1 addition & 1 deletion
doc/source/dev/conduct/code_of_conduct.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -165,7 +165,7 @@ Endnotes
We are thankful to the SciPy developers for creating the code of conduct we
have adapted here.

- `Scipy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_
- `SciPy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_

The SciPy code of conduct was in turn inspired by the following documents:

Expand Down

3 changes: 1 addition & 2 deletions
doc/source/install.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -40,8 +40,7 @@ For the requirements needed to build from source are (Python, NumPy and Cython
minimum versions in particular), see ``pyproject.toml``.

To run all the tests for PyWavelets, you will also need to install the
Matplotlib_ package. If SciPy_ is available, FFT-based continuous wavelet
transforms will use the FFT implementation from SciPy instead of NumPy.
Matplotlib_ package.

.. seealso:: The :ref:`Development guide <dev-index>` section contains more
 information on building and installing from source code.
Expand Down

3 changes: 0 additions & 3 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -50,9 +50,6 @@ classifiers = [
 "Topic :: Software Development :: Libraries :: Python Modules"
]

[project.optional-dependencies]
optional = ["scipy>=1.9"]

[project.urls]
homepage = "https://github.com/PyWavelets/pywt"
source = "https://github.com/PyWavelets/pywt"
Expand Down

32 changes: 11 additions & 21 deletions
pywt/_cwt.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,24 +14,14 @@

import numpy as np

try:
 import scipy
 fftmodule = scipy.fft
 next_fast_len = fftmodule.next_fast_len
except ImportError:
 fftmodule = np.fft

 # provide a fallback so scipy is an optional requirement
 # note: numpy.fft in numpy 2.0 is as fast as scipy.fft, so could be used
 # unconditionally once the minimum supported numpy version is >=2.0
 def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 This fallback is less efficient than `scipy.fftpack.next_fast_len`
 """
 return 2**ceil(np.log2(n))

def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 """
 return 2**ceil(np.log2(n))


def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
Expand DownExpand Up@@ -177,10 +167,10 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
 )
 if size_scale != size_scale0:
 # Must recompute fft_data when the padding size changes.
 fft_data = fftmodule.fft(data, size_scale, axis=-1)
 fft_data = np.fft.fft(data, size_scale, axis=-1)
 size_scale0 = size_scale
 fft_wav = fftmodule.fft(int_psi_scale, size_scale, axis=-1)
 conv = fftmodule.ifft(fft_wav * fft_data, axis=-1)
 fft_wav = np.fft.fft(int_psi_scale, size_scale, axis=-1)
 conv = np.fft.ifft(fft_wav * fft_data, axis=-1)
 conv = conv[..., :data.shape[-1] + int_psi_scale.size - 1]

 coef = - np.sqrt(scale) * np.diff(conv, axis=-1)
Expand Down

4 changes: 2 additions & 2 deletions
pywt/data/create_dat.py → util/create_dat.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python

"""Helper script for creating image .dat files by numpy.save
"""Helper script for creating image .dat files by numpy.save.

Usage:

Expand All@@ -10,7 +10,7 @@

 python create_dat.py aero.png aero.dat

Requires Scipy and PIL.
Requires SciPy and PIL, which need to be installed separately.
"""


Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
MAINT: remove optional dependence on SciPy for FFT operations#791

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 Merged

rgommers
merged 9 commits into

from

Feb 3, 2025
 Merged


MAINT: remove optional dependence on SciPy for FFT operations
#791
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e7b80af

DEP: Drop installation of nightly SciPy


agriyakhetarpal Feb 1, 2025
6181b57

MAINT: Move `create_dat.py` to `util/` directory


agriyakhetarpal Feb 1, 2025
c31a47b

MAINT: Remove SciPy ref from manual + installation guide


agriyakhetarpal Feb 1, 2025
d7f52cc

STY: Fix usage of SciPy noun


agriyakhetarpal Feb 1, 2025
e847b6e

DEP, MAINT: Remove optional-dependencies table


agriyakhetarpal Feb 1, 2025
5bcef68

CI, MAINT: Remove SciPy-related CI options


agriyakhetarpal Feb 1, 2025
ed82b68

MAINT: don't opt for SciPy's FFT, use `numpy.fft`


agriyakhetarpal Feb 1, 2025
b8283af

STY: rename noGIL job to `linux-cp313t-default`


agriyakhetarpal Feb 1, 2025
7a692e7

STY: Remove `fftmodule` variable, use `np.fft`


agriyakhetarpal Feb 1, 2025

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1 change: 0 additions & 1 deletion
.coveragerc

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@ omit =
 */pywt/_doc_utils.py*
 */pywt/_pytesttester.py*
 */pywt/_pytest.py*
 */pywt/data/create_dat.py
 *.pxd
 stringsource
plugins = Cython.Coverage

15 changes: 2 additions & 13 deletions
.github/workflows/tests.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,6 @@ env:
 CYTHONSPEC: cython
 NUMPY_MIN: numpy==1.23.0
 CYTHON_MIN: cython==3.0.4
 SCIPY_MIN: scipy==1.9.0

jobs:
 test_pywavelets_linux:
Expand All@@ -36,7 +35,6 @@ jobs:
 runs-on: [ubuntu-latest] # Arm runner tested separately, see below
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [1]
 PIP_FLAGS: [""]
Expand All@@ -52,8 +50,6 @@ jobs:
 OPTIONS_NAME: "minimum-req"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SCIPY: 1
 OPTIONS_NAME: "with-scipy"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SDIST: 1
Expand DownExpand Up@@ -81,7 +77,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }}
 run: |
Expand All@@ -97,11 +92,9 @@ jobs:
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN}
 pip install ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython
 pip install ${PIP_FLAGS} numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand DownExpand Up@@ -147,7 +140,7 @@ jobs:
 popd

 test_pywavelets_linux_free_threaded:
 name: linux-cp313t-with-scipy
 name: linux-cp313t-default
 runs-on: ubuntu-latest
 strategy:
 # Ensure that a wheel builder finishes even if another fails
Expand All@@ -169,7 +162,7 @@ jobs:
 python --version
 pip install --upgrade pip build
 # We need nightly wheels for free-threaded support and latest fixes
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy
 pip install pytest meson-python ninja
 pip install . -v --no-build-isolation

Expand All@@ -190,7 +183,6 @@ jobs:
 matrix:
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [0]
 PIP_FLAGS: [""]
Expand DownExpand Up@@ -219,7 +211,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 CC: /usr/bin/clang
 CXX: /usr/bin/clang++
Expand All@@ -233,10 +224,8 @@ jobs:
 # Set numpy version first, other packages link against it
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN} ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand Down

4 changes: 2 additions & 2 deletions
.github/workflows/wheel_tests_and_release.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -49,7 +49,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand DownExpand Up@@ -136,7 +136,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand Down

4 changes: 1 addition & 3 deletions
README.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,9 +67,7 @@ Installation

PyWavelets supports `Python`_ >=3.10, and is only dependent on `NumPy`_
(supported versions are currently ``>= 1.23.0``). To pass all of the tests,
`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
present, FFT-based continuous wavelet transforms will use FFTs from SciPy
rather than NumPy.
`Matplotlib`_ is also required.

There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi. If
you are on one of these platforms, you should get a binary (precompiled)
Expand Down

2 changes: 1 addition & 1 deletion
doc/source/dev/conduct/code_of_conduct.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -165,7 +165,7 @@ Endnotes
We are thankful to the SciPy developers for creating the code of conduct we
have adapted here.

- `Scipy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_
- `SciPy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_

The SciPy code of conduct was in turn inspired by the following documents:

Expand Down

3 changes: 1 addition & 2 deletions
doc/source/install.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -40,8 +40,7 @@ For the requirements needed to build from source are (Python, NumPy and Cython
minimum versions in particular), see ``pyproject.toml``.

To run all the tests for PyWavelets, you will also need to install the
Matplotlib_ package. If SciPy_ is available, FFT-based continuous wavelet
transforms will use the FFT implementation from SciPy instead of NumPy.
Matplotlib_ package.

.. seealso:: The :ref:`Development guide <dev-index>` section contains more
 information on building and installing from source code.
Expand Down

3 changes: 0 additions & 3 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -50,9 +50,6 @@ classifiers = [
 "Topic :: Software Development :: Libraries :: Python Modules"
]

[project.optional-dependencies]
optional = ["scipy>=1.9"]

[project.urls]
homepage = "https://github.com/PyWavelets/pywt"
source = "https://github.com/PyWavelets/pywt"
Expand Down

32 changes: 11 additions & 21 deletions
pywt/_cwt.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,24 +14,14 @@

import numpy as np

try:
 import scipy
 fftmodule = scipy.fft
 next_fast_len = fftmodule.next_fast_len
except ImportError:
 fftmodule = np.fft

 # provide a fallback so scipy is an optional requirement
 # note: numpy.fft in numpy 2.0 is as fast as scipy.fft, so could be used
 # unconditionally once the minimum supported numpy version is >=2.0
 def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 This fallback is less efficient than `scipy.fftpack.next_fast_len`
 """
 return 2**ceil(np.log2(n))

def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 """
 return 2**ceil(np.log2(n))


def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
Expand DownExpand Up@@ -177,10 +167,10 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
 )
 if size_scale != size_scale0:
 # Must recompute fft_data when the padding size changes.
 fft_data = fftmodule.fft(data, size_scale, axis=-1)
 fft_data = np.fft.fft(data, size_scale, axis=-1)
 size_scale0 = size_scale
 fft_wav = fftmodule.fft(int_psi_scale, size_scale, axis=-1)
 conv = fftmodule.ifft(fft_wav * fft_data, axis=-1)
 fft_wav = np.fft.fft(int_psi_scale, size_scale, axis=-1)
 conv = np.fft.ifft(fft_wav * fft_data, axis=-1)
 conv = conv[..., :data.shape[-1] + int_psi_scale.size - 1]

 coef = - np.sqrt(scale) * np.diff(conv, axis=-1)
Expand Down

4 changes: 2 additions & 2 deletions
pywt/data/create_dat.py → util/create_dat.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python

"""Helper script for creating image .dat files by numpy.save
"""Helper script for creating image .dat files by numpy.save.

Usage:

Expand All@@ -10,7 +10,7 @@

 python create_dat.py aero.png aero.dat

Requires Scipy and PIL.
Requires SciPy and PIL, which need to be installed separately.
"""


Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
MAINT: remove optional dependence on SciPy for FFT operations#791

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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 Merged

rgommers
merged 9 commits into

from

Feb 3, 2025
 Merged


MAINT: remove optional dependence on SciPy for FFT operations
#791
Show file tree
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9 commits


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Hold shift + click to select a range
e7b80af

DEP: Drop installation of nightly SciPy


agriyakhetarpal Feb 1, 2025
6181b57

MAINT: Move `create_dat.py` to `util/` directory


agriyakhetarpal Feb 1, 2025
c31a47b

MAINT: Remove SciPy ref from manual + installation guide


agriyakhetarpal Feb 1, 2025
d7f52cc

STY: Fix usage of SciPy noun


agriyakhetarpal Feb 1, 2025
e847b6e

DEP, MAINT: Remove optional-dependencies table


agriyakhetarpal Feb 1, 2025
5bcef68

CI, MAINT: Remove SciPy-related CI options


agriyakhetarpal Feb 1, 2025
ed82b68

MAINT: don't opt for SciPy's FFT, use `numpy.fft`


agriyakhetarpal Feb 1, 2025
b8283af

STY: rename noGIL job to `linux-cp313t-default`


agriyakhetarpal Feb 1, 2025
7a692e7

STY: Remove `fftmodule` variable, use `np.fft`


agriyakhetarpal Feb 1, 2025

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1 change: 0 additions & 1 deletion
.coveragerc

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,6 @@ omit =
 */pywt/_doc_utils.py*
 */pywt/_pytesttester.py*
 */pywt/_pytest.py*
 */pywt/data/create_dat.py
 *.pxd
 stringsource
plugins = Cython.Coverage

15 changes: 2 additions & 13 deletions
.github/workflows/tests.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,6 @@ env:
 CYTHONSPEC: cython
 NUMPY_MIN: numpy==1.23.0
 CYTHON_MIN: cython==3.0.4
 SCIPY_MIN: scipy==1.9.0

jobs:
 test_pywavelets_linux:
Expand All@@ -36,7 +35,6 @@ jobs:
 runs-on: [ubuntu-latest] # Arm runner tested separately, see below
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [1]
 PIP_FLAGS: [""]
Expand All@@ -52,8 +50,6 @@ jobs:
 OPTIONS_NAME: "minimum-req"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SCIPY: 1
 OPTIONS_NAME: "with-scipy"
 - runs-on: ubuntu-latest
 python-version: "3.10"
 USE_SDIST: 1
Expand DownExpand Up@@ -81,7 +77,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }}
 run: |
Expand All@@ -97,11 +92,9 @@ jobs:
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN}
 pip install ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython
 pip install ${PIP_FLAGS} numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

Expand DownExpand Up@@ -147,7 +140,7 @@ jobs:
 popd

 test_pywavelets_linux_free_threaded:
 name: linux-cp313t-with-scipy
 name: linux-cp313t-default
 runs-on: ubuntu-latest
 strategy:
 # Ensure that a wheel builder finishes even if another fails
Expand All@@ -169,7 +162,7 @@ jobs:
 python --version
 pip install --upgrade pip build
 # We need nightly wheels for free-threaded support and latest fixes
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
 pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy
 pip install pytest meson-python ninja
 pip install . -v --no-build-isolation

Expand All@@ -190,7 +183,6 @@ jobs:
 matrix:
 python-version: ["3.10", "3.13"]
 MINIMUM_REQUIREMENTS: [0]
 USE_SCIPY: [0]
 USE_SDIST: [0]
 REFGUIDE_CHECK: [0]
 PIP_FLAGS: [""]
Expand DownExpand Up@@ -219,7 +211,6 @@ jobs:
 MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
 PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
 USE_SDIST: ${{ matrix.USE_SDIST }}
 USE_SCIPY: ${{ matrix.USE_SCIPY }}
 REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }}
 CC: /usr/bin/clang
 CXX: /usr/bin/clang++
Expand All@@ -233,10 +224,8 @@ jobs:
 # Set numpy version first, other packages link against it
 if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then
 pip install ${CYTHON_MIN} ${NUMPY_MIN}
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${SCIPY_MIN}; fi
 else
 pip install ${PIP_FLAGS} cython numpy
 if [ "${USE_SCIPY}" == "1" ]; then pip install ${PIP_FLAGS} scipy; fi
 fi
 pip install ${PIP_FLAGS} matplotlib pytest

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4 changes: 2 additions & 2 deletions
.github/workflows/wheel_tests_and_release.yml

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Expand Up@@ -49,7 +49,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
Expand DownExpand Up@@ -136,7 +136,7 @@ jobs:
 if: ${{ matrix.cibw_python }} == "cp313t"
 run: |
 PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
 CIBW_DEPS="pip install --pre -i $PYPI_URL cython &&\
 pip install numpy pytest meson-python ninja"
 NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
 echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
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4 changes: 1 addition & 3 deletions
README.rst

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Expand Up@@ -67,9 +67,7 @@ Installation

PyWavelets supports `Python`_ >=3.10, and is only dependent on `NumPy`_
(supported versions are currently ``>= 1.23.0``). To pass all of the tests,
`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
present, FFT-based continuous wavelet transforms will use FFTs from SciPy
rather than NumPy.
`Matplotlib`_ is also required.

There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi. If
you are on one of these platforms, you should get a binary (precompiled)
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2 changes: 1 addition & 1 deletion
doc/source/dev/conduct/code_of_conduct.rst

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Expand Up@@ -165,7 +165,7 @@ Endnotes
We are thankful to the SciPy developers for creating the code of conduct we
have adapted here.

- `Scipy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_
- `SciPy Code of Conduct <http://scipy.github.io/devdocs/dev/conduct/code_of_conduct.html>`_

The SciPy code of conduct was in turn inspired by the following documents:

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3 changes: 1 addition & 2 deletions
doc/source/install.rst

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Expand Up@@ -40,8 +40,7 @@ For the requirements needed to build from source are (Python, NumPy and Cython
minimum versions in particular), see ``pyproject.toml``.

To run all the tests for PyWavelets, you will also need to install the
Matplotlib_ package. If SciPy_ is available, FFT-based continuous wavelet
transforms will use the FFT implementation from SciPy instead of NumPy.
Matplotlib_ package.

.. seealso:: The :ref:`Development guide <dev-index>` section contains more
 information on building and installing from source code.
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3 changes: 0 additions & 3 deletions
pyproject.toml

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Expand Up@@ -50,9 +50,6 @@ classifiers = [
 "Topic :: Software Development :: Libraries :: Python Modules"
]

[project.optional-dependencies]
optional = ["scipy>=1.9"]

[project.urls]
homepage = "https://github.com/PyWavelets/pywt"
source = "https://github.com/PyWavelets/pywt"
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32 changes: 11 additions & 21 deletions
pywt/_cwt.py

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Expand Up@@ -14,24 +14,14 @@

import numpy as np

try:
 import scipy
 fftmodule = scipy.fft
 next_fast_len = fftmodule.next_fast_len
except ImportError:
 fftmodule = np.fft

 # provide a fallback so scipy is an optional requirement
 # note: numpy.fft in numpy 2.0 is as fast as scipy.fft, so could be used
 # unconditionally once the minimum supported numpy version is >=2.0
 def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 This fallback is less efficient than `scipy.fftpack.next_fast_len`
 """
 return 2**ceil(np.log2(n))

def next_fast_len(n):
 """Round up size to the nearest power of two.

 Given a number of samples `n`, returns the next power of two
 following this number to take advantage of FFT speedup.
 """
 return 2**ceil(np.log2(n))


def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
Expand DownExpand Up@@ -177,10 +167,10 @@ def cwt(data, scales, wavelet, sampling_period=1., method='conv', axis=-1):
 )
 if size_scale != size_scale0:
 # Must recompute fft_data when the padding size changes.
 fft_data = fftmodule.fft(data, size_scale, axis=-1)
 fft_data = np.fft.fft(data, size_scale, axis=-1)
 size_scale0 = size_scale
 fft_wav = fftmodule.fft(int_psi_scale, size_scale, axis=-1)
 conv = fftmodule.ifft(fft_wav * fft_data, axis=-1)
 fft_wav = np.fft.fft(int_psi_scale, size_scale, axis=-1)
 conv = np.fft.ifft(fft_wav * fft_data, axis=-1)
 conv = conv[..., :data.shape[-1] + int_psi_scale.size - 1]

 coef = - np.sqrt(scale) * np.diff(conv, axis=-1)
Expand Down

4 changes: 2 additions & 2 deletions
pywt/data/create_dat.py → util/create_dat.py

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@@ -1,6 +1,6 @@
#!/usr/bin/env python

"""Helper script for creating image .dat files by numpy.save
"""Helper script for creating image .dat files by numpy.save.

Usage:

Expand All@@ -10,7 +10,7 @@

 python create_dat.py aero.png aero.dat

Requires Scipy and PIL.
Requires SciPy and PIL, which need to be installed separately.
"""


Expand Down