From 512e7ec0a7d536d66dac37e1dd1cbe097bbb2e7d Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Sat, 7 Jan 2023 21:32:54 -0500
Subject: [PATCH 01/20] github ci updates
---
.github/workflows/main.yml | 6 +++---
.github/workflows/python-publish.yml | 26 +++++++++++++-------------
2 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9e0a57df..91da142d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -60,9 +60,9 @@ jobs:
toxenv: build_docs
steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v2
+ uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install testing dependencies
@@ -71,6 +71,6 @@ jobs:
run: tox -v -e ${{ matrix.toxenv }}
- name: Upload coverage to codecov
if: ${{ contains(matrix.toxenv,'-cov') }}
- uses: codecov/codecov-action@v1.0.13
+ uses: codecov/codecov-action@v3
with:
file: ./coverage.xml
\ No newline at end of file
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 4fe8c22b..377f4c0d 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -10,8 +10,8 @@ jobs:
matrix:
os: [ubuntu-latest]
steps:
- - uses: actions/checkout@v2
- - uses: actions/setup-python@v2
+ - uses: actions/checkout@v3
+ - uses: actions/setup-python@v4
name: Install Python
with:
python-version: '3.9'
@@ -25,7 +25,7 @@ jobs:
CIBW_BUILD: cp37-manylinux_x86_64 cp38-manylinux_x86_64 cp39-manylinux_x86_64 cp310-manylinux_x86_64
CIBW_TEST_EXTRAS: test
CIBW_TEST_COMMAND: pytest --pyargs turbustat
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
with:
path: ./wheelhouse/*.whl
@@ -37,8 +37,8 @@ jobs:
matrix:
os: [macos-latest]
steps:
- - uses: actions/checkout@v2
- - uses: actions/setup-python@v2
+ - uses: actions/checkout@v3
+ - uses: actions/setup-python@v4
name: Install Python
with:
python-version: '3.9'
@@ -52,7 +52,7 @@ jobs:
CIBW_BUILD: cp37-* cp38-* cp39-* cp310-*
CIBW_TEST_EXTRAS: test
CIBW_TEST_COMMAND: pytest --pyargs turbustat
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
with:
path: ./wheelhouse/*.whl
@@ -64,8 +64,8 @@ jobs:
matrix:
os: [windows-latest]
steps:
- - uses: actions/checkout@v2
- - uses: actions/setup-python@v2
+ - uses: actions/checkout@v3
+ - uses: actions/setup-python@v4
name: Install Python
with:
python-version: '3.9'
@@ -79,7 +79,7 @@ jobs:
CIBW_BUILD: cp37-* cp38-* cp39-*
CIBW_TEST_EXTRAS: test
CIBW_TEST_COMMAND: pytest --pyargs turbustat
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
with:
path: ./wheelhouse/*.whl
@@ -87,8 +87,8 @@ jobs:
name: Build source distribution
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v2
- - uses: actions/setup-python@v2
+ - uses: actions/checkout@v3
+ - uses: actions/setup-python@v4
name: Install Python
with:
python-version: '3.9'
@@ -98,7 +98,7 @@ jobs:
python -m pip install build
- name: Build sdist
run: python -m build --sdist --outdir dist/ .
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
with:
path: dist/*.tar.gz
@@ -108,7 +108,7 @@ jobs:
runs-on: ubuntu-latest
if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
steps:
- - uses: actions/download-artifact@v2
+ - uses: actions/download-artifact@v3
with:
name: artifact
path: dist
From d0fc13a6576b73265930f245853a0051984df81c Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Sat, 7 Jan 2023 21:39:43 -0500
Subject: [PATCH 02/20] Fix for numpy=1.24
---
turbustat/moments/_moment_errs.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/turbustat/moments/_moment_errs.py b/turbustat/moments/_moment_errs.py
index fcffaeb2..679eb22f 100644
--- a/turbustat/moments/_moment_errs.py
+++ b/turbustat/moments/_moment_errs.py
@@ -238,7 +238,7 @@ def _slice0(cube, axis, scale):
result = np.zeros(shp) * cube.unit ** 2
view = [slice(None)] * 3
- valid = np.zeros(shp, dtype=np.bool)
+ valid = np.zeros(shp, dtype=bool)
for i in range(cube.shape[axis]):
view[axis] = i
From 303ca8327825e20d270c88aa69bb2bff2722343e Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Sat, 7 Jan 2023 21:43:08 -0500
Subject: [PATCH 03/20] Ignore warnings
---
setup.cfg | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/setup.cfg b/setup.cfg
index 52cfa8f3..1586d47d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -48,7 +48,7 @@ testpaths = "turbustat" "docs"
astropy_header = true
doctest_plus = enabled
text_file_format = rst
-addopts = --doctest-rst
+addopts = --doctest-rst -p no:warnings
[coverage:run]
omit =
From cc46364fed76415f582583f2fe1282a89941a885 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Sat, 7 Jan 2023 21:55:57 -0500
Subject: [PATCH 04/20] More fixes for changes in numpy=1.24
---
turbustat/statistics/pspec_bispec/bispec.py | 4 ++--
turbustat/statistics/wavelets/wavelet_transform.py | 2 +-
turbustat/tests/test_wavelet.py | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/turbustat/statistics/pspec_bispec/bispec.py b/turbustat/statistics/pspec_bispec/bispec.py
index 990443bd..b02256ef 100644
--- a/turbustat/statistics/pspec_bispec/bispec.py
+++ b/turbustat/statistics/pspec_bispec/bispec.py
@@ -114,8 +114,8 @@ def compute_bispectrum(self, show_progress=True, use_pyfftw=False,
bispec_shape = (int(self.shape[0] / 2.), int(self.shape[1] / 2.))
- self._bispectrum = np.zeros(bispec_shape, dtype=np.complex)
- self._bicoherence = np.zeros(bispec_shape, dtype=np.float)
+ self._bispectrum = np.zeros(bispec_shape, dtype=complex)
+ self._bicoherence = np.zeros(bispec_shape, dtype=float)
self._tracker = np.zeros(self.shape, dtype=np.int16)
biconorm = np.ones_like(self.bispectrum, dtype=float)
diff --git a/turbustat/statistics/wavelets/wavelet_transform.py b/turbustat/statistics/wavelets/wavelet_transform.py
index 9efb3826..b518e702 100644
--- a/turbustat/statistics/wavelets/wavelet_transform.py
+++ b/turbustat/statistics/wavelets/wavelet_transform.py
@@ -152,7 +152,7 @@ def compute_transform(self, show_progress=True, scale_normalization=True,
A = len(self.scales)
if keep_convolved_arrays:
- self._Wf = np.zeros((A, n0, m0), dtype=np.float)
+ self._Wf = np.zeros((A, n0, m0), dtype=float)
else:
self._Wf = None
diff --git a/turbustat/tests/test_wavelet.py b/turbustat/tests/test_wavelet.py
index 6b11c021..d5bc39da 100644
--- a/turbustat/tests/test_wavelet.py
+++ b/turbustat/tests/test_wavelet.py
@@ -67,7 +67,7 @@ def test_Wavelet_method_failbreak():
# No break and only 1 slope
assert tester.brk is None
- assert isinstance(tester.slope, np.float)
+ assert isinstance(tester.slope, float)
def test_Wavelet_method_fitlimits():
From f28b20622bfb3e0cf9c8f0a2ec976a131c8db931 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Sat, 7 Jan 2023 22:07:49 -0500
Subject: [PATCH 05/20] Temporarily use dev version of spectral-cube for
testing
---
setup.cfg | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/setup.cfg b/setup.cfg
index 1586d47d..d8cd5bcc 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -21,7 +21,8 @@ install_requires =
scikit-learn>=0.13
statsmodels>=0.4.0
scikit-image>=0.12
- spectral_cube
+ # spectral_cube # Temporarily remove pip version until tag with numpy 1.24 is pushed
+ pip+https://github.com/radio-astro-tools/spectral-cube.git
[extension-helpers]
use_extension_helpers = true
From 1255c6f75114785d887ed1d37321438cb0273e6b Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Sat, 7 Jan 2023 22:15:14 -0500
Subject: [PATCH 06/20] Wrong syntax
---
setup.cfg | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/setup.cfg b/setup.cfg
index d8cd5bcc..b617aa41 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,7 +22,7 @@ install_requires =
statsmodels>=0.4.0
scikit-image>=0.12
# spectral_cube # Temporarily remove pip version until tag with numpy 1.24 is pushed
- pip+https://github.com/radio-astro-tools/spectral-cube.git
+ git+https://github.com/radio-astro-tools/radio-beam#egg=radio-beam
[extension-helpers]
use_extension_helpers = true
From 2279a6d1632a4e60f18bdeafad759d78b3b09c77 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Sat, 7 Jan 2023 22:18:37 -0500
Subject: [PATCH 07/20] Revert: this doesn't work
---
setup.cfg | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/setup.cfg b/setup.cfg
index b617aa41..1586d47d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -21,8 +21,7 @@ install_requires =
scikit-learn>=0.13
statsmodels>=0.4.0
scikit-image>=0.12
- # spectral_cube # Temporarily remove pip version until tag with numpy 1.24 is pushed
- git+https://github.com/radio-astro-tools/radio-beam#egg=radio-beam
+ spectral_cube
[extension-helpers]
use_extension_helpers = true
From 37d185f3431dd31e4b7cf0b1f72e8b3b2db3eb55 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Thu, 5 Oct 2023 13:44:16 -0400
Subject: [PATCH 08/20] Non-working version of analytic deriv for
LogEllipticalPowerLaw2D
---
turbustat/statistics/elliptical_powerlaw.py | 56 ++++++++++++++++++---
1 file changed, 50 insertions(+), 6 deletions(-)
diff --git a/turbustat/statistics/elliptical_powerlaw.py b/turbustat/statistics/elliptical_powerlaw.py
index fe72dc90..0779b031 100644
--- a/turbustat/statistics/elliptical_powerlaw.py
+++ b/turbustat/statistics/elliptical_powerlaw.py
@@ -5,6 +5,8 @@
from astropy.modeling import Fittable2DModel, Parameter, fitting
from warnings import warn
+log_ten = 2.302585092994046
+
def fit_elliptical_powerlaw(values, x, y, p0, fit_method='LevMarq',
bootstrap=False, niters=100, alpha=0.6827,
@@ -99,7 +101,8 @@ def fit_elliptical_powerlaw(values, x, y, p0, fit_method='LevMarq',
model.theta.fixed = True
fitter = fitting.LevMarLSQFitter()
- fit_model = fitter(model, x, y, values, weights=weights)
+ fit_model = fitter(model, x, y, values, weights=weights,
+ estimate_jacobian=True)
resids = np.sum(np.abs(values - fit_model(x, y)))
@@ -111,7 +114,8 @@ def fit_elliptical_powerlaw(values, x, y, p0, fit_method='LevMarq',
model_f = LogEllipticalPowerLaw2D(*p0_f)
fitter_f = fitting.LevMarLSQFitter()
- fit_model_f = fitter(model_f, x, y, values, weights=weights)
+ fit_model_f = fitter(model_f, x, y, values, weights=weights,
+ estimate_jacobian=True)
resids_f = np.sum(np.abs(values - fit_model_f(x, y)))
@@ -225,10 +229,10 @@ class LogEllipticalPowerLaw2D(Fittable2DModel):
Power-law index.
"""
- logamplitude = Parameter(default=0, bounds=(-10, None))
- ellip_transf = Parameter(default=1)
- theta = Parameter(default=0)
- gamma = Parameter(default=-1)
+ logamplitude = Parameter(default=0., bounds=(-10, None))
+ ellip_transf = Parameter(default=1, bounds=(-50, 50))
+ theta = Parameter(default=0, bounds=(-np.pi, np.pi))
+ gamma = Parameter(default=-1, bounds=(-20., 20.))
@classmethod
def evaluate(cls, x, y, logamplitude, ellip_transf, theta, gamma):
@@ -255,6 +259,46 @@ def evaluate(cls, x, y, logamplitude, ellip_transf, theta, gamma):
return model
+ # Attempt at numerical implementation for the gradient.
+ # Implementation is not currently stable.
+
+ # def fit_deriv(self, x, y, logamplitude, ellip_transf, theta, gamma):
+ # """
+ # Derivatives of the model with respect to parameters
+ # """
+
+ # ellip = 1.0 / (1 + np.exp(-ellip_transf))
+
+ # costhet = np.cos(theta)
+ # sinthet = np.sin(theta)
+
+ # q = ellip
+
+ # term1 = (q * costhet)**2 + sinthet**2
+ # term2 = 2 * (1 - q**2) * sinthet * costhet
+ # term3 = (q * sinthet)**2 + costhet**2
+
+ # r2 = x**2 * term1 + x * y * term2 + y**2 * term3
+
+ # # print(ellip, costhet, sinthet)
+ # # print(r2)
+
+ # d_logamplitude = 0.5 * gamma / (log_ten * r2)
+
+ # d_ellip_transf = 0.5 * gamma * ellip * (1 - ellip) * (q**2 - 1) * (x**2 * costhet**2 - y**2 * sinthet**2) / r2
+
+ # d_theta = 0.5 * gamma * ellip * (1 - ellip) * (x**2 - y**2) * sinthet * costhet / r2
+
+ # d_gamma = 0.5 * np.log10(r2)
+
+ # # print(d_logamplitude)
+ # # print(d_ellip_transf)
+ # # print(d_theta)
+ # # print(d_gamma)
+
+ # return [d_logamplitude, d_ellip_transf, d_theta, d_gamma]
+
+
def interval_transform(x, a, b):
return np.log(x - a) - np.log(b - x)
From cd7e040a5b50f3d146c167e22b9b2b9e2075b77b Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Thu, 5 Oct 2023 15:09:25 -0400
Subject: [PATCH 09/20] Add option to fit unbinned data in 1D
---
turbustat/statistics/base_pspec2.py | 82 +++++++++++++++++++++--------
1 file changed, 61 insertions(+), 21 deletions(-)
diff --git a/turbustat/statistics/base_pspec2.py b/turbustat/statistics/base_pspec2.py
index 2a2d3482..895c0262 100644
--- a/turbustat/statistics/base_pspec2.py
+++ b/turbustat/statistics/base_pspec2.py
@@ -106,7 +106,8 @@ def compute_radial_pspec(self, logspacing=False, max_bin=None, **kwargs):
# Attach units to freqs
self._freqs = self.freqs / u.pix
- def fit_pspec(self, brk=None, log_break=False, low_cut=None,
+ def fit_pspec(self, fit_unbinned=True,
+ brk=None, log_break=False, low_cut=None,
high_cut=None, min_fits_pts=10, weighted_fit=False,
bootstrap=False, bootstrap_kwargs={},
verbose=False):
@@ -118,6 +119,10 @@ def fit_pspec(self, brk=None, log_break=False, low_cut=None,
Parameters
----------
+ fit_unbinned : bool, optional
+ Fits the unbinned 2D power-spectrum to the linear model. Default is True.
+ Use False to fit the binned 1D power-spectrum instead and replicate fitting
+ in earlier TurbuStat versions.
brk : float or None, optional
Guesses for the break points. If given as a list, the length of
the list sets the number of break points to be fit. If a choice is
@@ -150,29 +155,62 @@ def fit_pspec(self, brk=None, log_break=False, low_cut=None,
self._bootstrap_flag = bootstrap
- # Make the data to fit to
- if low_cut is None:
- # Default to the largest frequency, since this is just 1 pixel
- # in the 2D PSpec.
- self.low_cut = 1. / (0.5 * float(max(self.ps2D.shape)) * u.pix)
- else:
- self.low_cut = self._to_pixel_freq(low_cut)
+ if fit_unbinned:
+ yy_freq, xx_freq = make_radial_freq_arrays(self.ps2D.shape)
+
+ freqs_2d = np.sqrt(yy_freq**2 + xx_freq**2) / u.pix
+
+ # Make the data to fit to
+ if low_cut is None:
+ # Default to the largest frequency, since this is just 1 pixel
+ # in the 2D PSpec.
+ self.low_cut = 1. / (0.5 * float(max(self.ps2D.shape)) * u.pix)
+ else:
+ self.low_cut = self._to_pixel_freq(low_cut)
+
+ if high_cut is None:
+ # self.high_cut = self.freqs.max().value / u.pix
+ self.high_cut = freqs_2d.value.max() / u.pix
+ else:
+ self.high_cut = self._to_pixel_freq(high_cut)
+
+
+ clip_mask = clip_func(freqs_2d.value,
+ self.low_cut.value,
+ self.high_cut.value)
+
+
+ x = np.log10(freqs_2d.value[clip_mask])
+ y = np.log10(self.ps2D[clip_mask])
- if high_cut is None:
- self.high_cut = self.freqs.max().value / u.pix
else:
- self.high_cut = self._to_pixel_freq(high_cut)
+ # Make the data to fit to
+ if low_cut is None:
+ # Default to the largest frequency, since this is just 1 pixel
+ # in the 2D PSpec.
+ self.low_cut = 1. / (0.5 * float(max(self.ps2D.shape)) * u.pix)
+ else:
+ self.low_cut = self._to_pixel_freq(low_cut)
+
+ if high_cut is None:
+ self.high_cut = self.freqs.max().value / u.pix
+ else:
+ self.high_cut = self._to_pixel_freq(high_cut)
- x = np.log10(self.freqs[clip_func(self.freqs.value, self.low_cut.value,
- self.high_cut.value)].value)
+ x = np.log10(self.freqs[clip_func(self.freqs.value, self.low_cut.value,
+ self.high_cut.value)].value)
- clipped_ps1D = self.ps1D[clip_func(self.freqs.value,
- self.low_cut.value,
- self.high_cut.value)]
- y = np.log10(clipped_ps1D)
+ clipped_ps1D = self.ps1D[clip_func(self.freqs.value,
+ self.low_cut.value,
+ self.high_cut.value)]
+ y = np.log10(clipped_ps1D)
if weighted_fit:
+ if fit_unbinned:
+ raise NotImplementedError("Error propagation for the unbinned modeling is not "
+ "implemented yet.")
+ # Currently this will run only for the binned fitting.
clipped_stddev = self.ps1D_stddev[clip_func(self.freqs.value,
self.low_cut.value,
self.high_cut.value)]
@@ -246,7 +284,7 @@ def fit_pspec(self, brk=None, log_break=False, low_cut=None,
x = sm.add_constant(x)
if weighted_fit:
- model = sm.WLS(y, x, missing='drop', weights=1 / y_err**2)
+ model = sm.WLS(y, x, missing='drop', weights=weights)
else:
model = sm.OLS(y, x, missing='drop')
@@ -614,8 +652,6 @@ def plot_fit(self, show_2D=False, show_residual=True,
good_interval = clip_func(self.freqs.value, self.low_cut.value,
self.high_cut.value)
- y_fit = self.fit.fittedvalues
-
if show_residual:
if isinstance(self.slope, np.ndarray):
# Broken linear model
@@ -679,7 +715,11 @@ def plot_fit(self, show_2D=False, show_residual=True,
fmt=symbol, markersize=5, alpha=0.5,
capsize=10, elinewidth=3)
- ax_1D.plot(np.log10(xvals[fit_index]), y_fit, linestyle='-',
+ xvals_plot = np.log10(xvals[fit_index]).ravel()
+ # y_fit = self.fit.fittedvalues
+ y_fit = self.fit.predict(sm.add_constant(xvals_plot))
+
+ ax_1D.plot(xvals_plot, y_fit, linestyle='-',
label=label, linewidth=3, color=fit_color)
if show_residual:
From 63a2f531eb94f431e6ba0d93e6d9003cd5439aae Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Thu, 5 Oct 2023 15:58:30 -0400
Subject: [PATCH 10/20] Implemented additional LogEllip2DPowerLaw tests
---
turbustat/tests/test_ellipplaw.py | 88 ++++++++++++++++++++++++++++++-
1 file changed, 87 insertions(+), 1 deletion(-)
diff --git a/turbustat/tests/test_ellipplaw.py b/turbustat/tests/test_ellipplaw.py
index ac16cdb6..ad1b501b 100644
--- a/turbustat/tests/test_ellipplaw.py
+++ b/turbustat/tests/test_ellipplaw.py
@@ -101,7 +101,7 @@ def test_simple_ellipplaw_2D_anisotropic(plaw, ellip, theta):
npt.assert_allclose(theta, fit_theta, atol=0.01)
-@pytest.mark.parametrize('plaw', [2, 3, 4])
+@pytest.mark.parametrize('plaw', [0.5, 1, 1.5, 2, 3, 4, 4.5, 5., 6])
def test_simple_ellipplaw_2D_isotropic(plaw):
# Must have ellip = 1 for this test. Just be sure...
@@ -176,3 +176,89 @@ def test_simple_ellipplaw_2D_isotropic(plaw):
# And theta should not move
assert test_stderr[2] == 0.
+
+
+@pytest.mark.parametrize('plaw', [0.5, 1, 1.5, 2, 3, 4, 4.5, 5., 6])
+def test_direct_ellipplaw_2D_isotropic(plaw):
+
+ from astropy.modeling import Fittable2DModel, Parameter, fitting
+
+ # Must have ellip = 1 for this test. Just be sure...
+ # ellip = 1.
+ ellip = 0.99999
+ # ellip = 0.5
+
+ # Theta doesn't matter, but we'll test for what happens when the
+ # elliptical parameters are left free.
+ theta = np.pi / 2.
+
+ imsize = 256
+
+ # Generate a red noise model
+ psd = make_extended(imsize, powerlaw=plaw, ellip=ellip, theta=theta,
+ return_fft=True)
+
+ psd = np.abs(psd)**2
+
+ # Initial guesses are based on the azimuthally-average spectrum, so it's
+ # valid to give it good initial guesses for the index
+ # Guess it is fairly elliptical. Tends not to be too sensitive to this.
+ ellip_transf = interval_transform(ellip, 0, 1.)
+ # We fit twice w/ thetas offset by pi / 2, so theta also should not be too
+ # sensitive.
+
+ p0 = (3.7,
+ ellip_transf,
+ np.pi / 2.,
+ - (2. + np.random.normal(scale=0.5)))
+
+ yy, xx = np.mgrid[-imsize / 2:imsize / 2, -imsize / 2:imsize / 2]
+
+ # Don't fit the 0, 0 point. It isn't defined by the model.
+ valids = psd != 0.
+
+ assert np.isfinite(psd[valids]).all()
+ assert (psd[valids] > 0.).all()
+
+ model = LogEllipticalPowerLaw2D(*p0)
+
+ # TODO: These are leftover from testing the fit_deriv implementation
+ # there seems to be an instability in how the gradient is calculated.
+ # Return to this in the future.
+
+ # p0_f = list(p0)
+ # p0_f[2] = (p0[2] + np.pi / 2.) % np.pi
+ # model = LogEllipticalPowerLaw2D(*p0_f)
+
+ fitter = fitting.LevMarLSQFitter(calc_uncertainties=True)
+ # fitter = fitting.LevMarLSQFitter(calc_uncertainties=False)
+
+ # fitter = fitting.TRFLSQFitter(calc_uncertainties=True)
+
+ fit_model = fitter(model,
+ xx[valids],
+ yy[valids],
+ np.log10(psd[valids]),
+ weights=None,
+ estimate_jacobian=True)
+ # estimate_jacobian=False)
+
+ # Do the parameters match?
+
+ params = fit_model.parameters
+
+ # print(f"Init params: {p0}")
+ # print(f"Fit params: {params}")
+ # print(fitter.fit_info)
+
+ # Require the index to be within 0.1 of the actual,
+ # the ellipticity to be within 0.02, and the theta to be within ~3 deg
+
+ npt.assert_allclose(-plaw, params[-1], rtol=0.01, atol=1e-2)
+
+ npt.assert_allclose(1.0, inverse_interval_transform(params[1], 0, 1),
+ rtol=0.01, atol=1e-2)
+
+ # Theta should be the original
+ assert theta == np.pi / 2.
+
From 7bb038940dabdde8cebd5c32adddede1f1821705 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Thu, 5 Oct 2023 17:37:06 -0400
Subject: [PATCH 11/20] Fix weights not being defined
---
turbustat/statistics/base_pspec2.py | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/turbustat/statistics/base_pspec2.py b/turbustat/statistics/base_pspec2.py
index 895c0262..325a3b0b 100644
--- a/turbustat/statistics/base_pspec2.py
+++ b/turbustat/statistics/base_pspec2.py
@@ -106,7 +106,7 @@ def compute_radial_pspec(self, logspacing=False, max_bin=None, **kwargs):
# Attach units to freqs
self._freqs = self.freqs / u.pix
- def fit_pspec(self, fit_unbinned=True,
+ def fit_pspec(self, fit_unbinned=False,
brk=None, log_break=False, low_cut=None,
high_cut=None, min_fits_pts=10, weighted_fit=False,
bootstrap=False, bootstrap_kwargs={},
@@ -219,6 +219,10 @@ def fit_pspec(self, fit_unbinned=True,
y_err = 0.434 * clipped_stddev / clipped_ps1D
+ weights = 1 / y_err**2
+ else:
+ weights = None
+
if brk is not None:
# Try the fit with a break in it.
if not log_break:
@@ -230,11 +234,6 @@ def fit_pspec(self, fit_unbinned=True,
assert brk.unit == u.dimensionless_unscaled
brk = brk.value
- if weighted_fit:
- weights = 1 / y_err**2
- else:
- weights = None
-
brk_fit = Lm_Seg(x, y, brk, weights=weights)
brk_fit.fit_model(verbose=verbose, cov_type='HC3')
From b54b88e5eecbdbc8acbce0aae3b676cc22125496 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Thu, 5 Oct 2023 17:38:18 -0400
Subject: [PATCH 12/20] Ignore notebook checkpoints
---
.gitignore | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitignore b/.gitignore
index e41d8cc6..0d8f4d2f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -64,6 +64,7 @@ docs/api
*.pyc
*.DS_Store
+*.ipynb_checkpoints
turbustat/version.py
turbustat/cython_version.py
From 8f37ffa600f58be384a0b71affc68b24b462ac4c Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Thu, 5 Oct 2023 17:43:28 -0400
Subject: [PATCH 13/20] Remove pytest-openfiles (see #246)
---
tox.ini | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/tox.ini b/tox.ini
index 41baae71..3ee9fcbd 100644
--- a/tox.ini
+++ b/tox.ini
@@ -32,8 +32,8 @@ extras =
all: all
commands =
pip freeze
- !cov: pytest --open-files --pyargs turbustat {toxinidir}/docs {posargs}
- cov: pytest --open-files --pyargs turbustat {toxinidir}/docs --cov turbustat --cov-config={toxinidir}/setup.cfg {posargs}
+ !cov: pytest --pyargs turbustat {toxinidir}/docs {posargs}
+ cov: pytest --pyargs turbustat {toxinidir}/docs --cov turbustat --cov-config={toxinidir}/setup.cfg {posargs}
cov: coverage xml -o {toxinidir}/coverage.xml
[testenv:build_docs]
From f0b7aa339ee8a3881350da5f5be6f14227df5024 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Thu, 5 Oct 2023 18:15:09 -0400
Subject: [PATCH 14/20] Add binned vs unbinned check for power spectra fits
---
turbustat/tests/test_pspec.py | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/turbustat/tests/test_pspec.py b/turbustat/tests/test_pspec.py
index f2ed4fdc..c759eea7 100644
--- a/turbustat/tests/test_pspec.py
+++ b/turbustat/tests/test_pspec.py
@@ -187,6 +187,35 @@ def test_pspec_weightfit(plaw):
npt.assert_allclose(-plaw, test.slope, rtol=0.02)
+@pytest.mark.parametrize('plaw', np.arange(0.5, 5, 0.67))
+def test_pspec_unbin_vs_bin(plaw):
+ '''
+ The slopes with azimuthal constraints should be the same. When elliptical,
+ the power will be different along the different directions, but the slope
+ should remain the same.
+ '''
+
+ imsize = 64
+ theta = 0
+
+ # Generate a red noise model
+ img = make_extended(imsize, powerlaw=plaw, ellip=1., theta=theta,
+ return_fft=False)
+
+ test = PowerSpectrum(fits.PrimaryHDU(img))
+ test.run(fit_kwargs={'fit_unbinned': True},
+ fit_2D=False)
+
+ # Ensure slopes are consistent to within 2%
+ npt.assert_allclose(-plaw, test.slope, rtol=0.02)
+
+ test.run(fit_kwargs={'fit_unbinned': False},
+ fit_2D=False)
+
+ # Ensure slopes are consistent to within 2%
+ npt.assert_allclose(-plaw, test.slope, rtol=0.02)
+
+
@pytest.mark.parametrize('theta',
[0., np.pi / 4., np.pi / 2., 7 * np.pi / 8.])
def test_pspec_fit2D(theta):
From 0ef9ba4a8e6d919cfd103abb2e86098d9768201d Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Fri, 6 Oct 2023 16:27:15 -0400
Subject: [PATCH 15/20] Add kwarg in run for enabling unbinned 1D power
spectrum fitting
---
turbustat/statistics/mvc/mvc.py | 13 +++++++++----
turbustat/statistics/pspec_bispec/pspec.py | 20 ++++++++++++++------
turbustat/statistics/vca_vcs/vca.py | 16 ++++++++++++----
turbustat/tests/test_pspec.py | 4 ++--
4 files changed, 37 insertions(+), 16 deletions(-)
diff --git a/turbustat/statistics/mvc/mvc.py b/turbustat/statistics/mvc/mvc.py
index 0f888f12..d284fef6 100644
--- a/turbustat/statistics/mvc/mvc.py
+++ b/turbustat/statistics/mvc/mvc.py
@@ -229,7 +229,8 @@ def run(self, verbose=False, beam_correct=False,
use_pyfftw=False, threads=1, pyfftw_kwargs={},
radial_pspec_kwargs={},
low_cut=None, high_cut=None,
- fit_2D=True, fit_kwargs={}, fit_2D_kwargs={},
+ fit_kwargs={}, fit_unbinned=False,
+ fit_2D=True, fit_2D_kwargs={},
save_name=None, xunit=u.pix**-1, use_wavenumber=False):
'''
Full computation of MVC. For fitting parameters and radial binning
@@ -253,10 +254,12 @@ def run(self, verbose=False, beam_correct=False,
Low frequency cut off in frequencies used in the fitting.
high_cut : `~astropy.units.Quantity`, optional
High frequency cut off in frequencies used in the fitting.
- fit_2D : bool, optional
- Fit an elliptical power-law model to the 2D power spectrum.
fit_kwargs : dict, optional
Passed to `~PowerSpectrum.fit_pspec`.
+ fit_unbinned : bool, optional
+ Passed to `~PowerSpectrum.fit_pspec`. Default is False.
+ fit_2D : bool, optional
+ Fit an elliptical power-law model to the 2D power spectrum.
fit_2D_kwargs : dict, optional
Keyword arguments for `~MVC.fit_2Dpspec`. Use the
`low_cut` and `high_cut` keywords to provide fit limits.
@@ -280,7 +283,9 @@ def run(self, verbose=False, beam_correct=False,
**pyfftw_kwargs)
self.compute_radial_pspec(**radial_pspec_kwargs)
- self.fit_pspec(low_cut=low_cut, high_cut=high_cut, **fit_kwargs)
+ self.fit_pspec(low_cut=low_cut, high_cut=high_cut,
+ fit_unbinned=fit_unbinned,
+ **fit_kwargs)
if fit_2D:
self.fit_2Dpspec(low_cut=low_cut, high_cut=high_cut,
diff --git a/turbustat/statistics/pspec_bispec/pspec.py b/turbustat/statistics/pspec_bispec/pspec.py
index 4cf96a42..bc040aa3 100644
--- a/turbustat/statistics/pspec_bispec/pspec.py
+++ b/turbustat/statistics/pspec_bispec/pspec.py
@@ -122,9 +122,9 @@ def run(self, verbose=False, beam_correct=False,
apodize_kernel=None, alpha=0.2, beta=0.0,
use_pyfftw=False, threads=1,
pyfftw_kwargs={},
- low_cut=None, high_cut=None,
- fit_2D=True, radial_pspec_kwargs={}, fit_kwargs={},
- fit_2D_kwargs={},
+ low_cut=None, high_cut=None, radial_pspec_kwargs={},
+ fit_kwargs={}, fit_unbinned=False,
+ fit_2D=True, fit_2D_kwargs={},
xunit=u.pix**-1, save_name=None,
use_wavenumber=False):
'''
@@ -157,12 +157,14 @@ def run(self, verbose=False, beam_correct=False,
Low frequency cut off in frequencies used in the fitting.
high_cut : `~astropy.units.Quantity`, optional
High frequency cut off in frequencies used in the fitting.
- fit_2D : bool, optional
- Fit an elliptical power-law model to the 2D power spectrum.
radial_pspec_kwargs : dict, optional
Passed to `~PowerSpectrum.compute_radial_pspec`.
fit_kwargs : dict, optional
Passed to `~PowerSpectrum.fit_pspec`.
+ fit_unbinned : bool, optional
+ Passed to `~PowerSpectrum.fit_pspec`. Default is False.
+ fit_2D : bool, optional
+ Fit an elliptical power-law model to the 2D power spectrum.
fit_2D_kwargs : dict, optional
Keyword arguments for `PowerSpectrum.fit_2Dpspec`. Use the
`low_cut` and `high_cut` keywords to provide fit limits.
@@ -178,6 +180,10 @@ def run(self, verbose=False, beam_correct=False,
if pyfftw_kwargs.get('threads') is not None:
pyfftw_kwargs.pop('threads')
+ # Pop fit_unbinned if given as kwarg in dict.
+ if fit_kwargs.get('fit_unbinned') is not None:
+ fit_kwargs.pop('fit_unbinned')
+
self.compute_pspec(apodize_kernel=apodize_kernel,
alpha=alpha, beta=beta,
beam_correct=beam_correct,
@@ -186,7 +192,9 @@ def run(self, verbose=False, beam_correct=False,
self.compute_radial_pspec(**radial_pspec_kwargs)
- self.fit_pspec(low_cut=low_cut, high_cut=high_cut, **fit_kwargs)
+ self.fit_pspec(fit_unbinned=fit_unbinned,
+ low_cut=low_cut, high_cut=high_cut,
+ **fit_kwargs)
if fit_2D:
self.fit_2Dpspec(low_cut=low_cut, high_cut=high_cut,
diff --git a/turbustat/statistics/vca_vcs/vca.py b/turbustat/statistics/vca_vcs/vca.py
index 31b8e429..8baa9d88 100644
--- a/turbustat/statistics/vca_vcs/vca.py
+++ b/turbustat/statistics/vca_vcs/vca.py
@@ -129,7 +129,8 @@ def run(self, verbose=False, beam_correct=False,
pyfftw_kwargs={},
radial_pspec_kwargs={},
low_cut=None, high_cut=None,
- fit_2D=True, fit_kwargs={}, fit_2D_kwargs={},
+ fit_kwargs={}, fit_unbinned=False,
+ fit_2D=True, fit_2D_kwargs={},
save_name=None, xunit=u.pix**-1, use_wavenumber=False):
'''
Full computation of VCA.
@@ -163,10 +164,12 @@ def run(self, verbose=False, beam_correct=False,
Low frequency cut off in frequencies used in the fitting.
high_cut : `~astropy.units.Quantity`, optional
High frequency cut off in frequencies used in the fitting.
- fit_2D : bool, optional
- Fit an elliptical power-law model to the 2D power spectrum.
fit_kwargs : dict, optional
Passed to `~PowerSpectrum.fit_pspec`.
+ fit_unbinned : bool, optional
+ Passed to `~PowerSpectrum.fit_pspec`. Default is False.
+ fit_2D : bool, optional
+ Fit an elliptical power-law model to the 2D power spectrum.
fit_2D_kwargs : dict, optional
Keyword arguments for `~VCA.fit_2Dpspec`. Use the
`low_cut` and `high_cut` keywords to provide fit limits.
@@ -183,6 +186,10 @@ def run(self, verbose=False, beam_correct=False,
if pyfftw_kwargs.get('threads') is not None:
pyfftw_kwargs.pop('threads')
+ # Pop fit_unbinned if given as kwarg in dict.
+ if fit_kwargs.get('fit_unbinned') is not None:
+ fit_kwargs.pop('fit_unbinned')
+
self.compute_pspec(apodize_kernel=apodize_kernel,
alpha=alpha, beta=beta,
beam_correct=beam_correct,
@@ -190,7 +197,8 @@ def run(self, verbose=False, beam_correct=False,
**pyfftw_kwargs)
self.compute_radial_pspec(**radial_pspec_kwargs)
- self.fit_pspec(low_cut=low_cut, high_cut=high_cut, **fit_kwargs)
+ self.fit_pspec(low_cut=low_cut, high_cut=high_cut, fit_unbinned=fit_unbinned,
+ **fit_kwargs)
if fit_2D:
self.fit_2Dpspec(low_cut=low_cut, high_cut=high_cut,
diff --git a/turbustat/tests/test_pspec.py b/turbustat/tests/test_pspec.py
index c759eea7..b801c775 100644
--- a/turbustat/tests/test_pspec.py
+++ b/turbustat/tests/test_pspec.py
@@ -203,13 +203,13 @@ def test_pspec_unbin_vs_bin(plaw):
return_fft=False)
test = PowerSpectrum(fits.PrimaryHDU(img))
- test.run(fit_kwargs={'fit_unbinned': True},
+ test.run(fit_unbinned=True,
fit_2D=False)
# Ensure slopes are consistent to within 2%
npt.assert_allclose(-plaw, test.slope, rtol=0.02)
- test.run(fit_kwargs={'fit_unbinned': False},
+ test.run(fit_unbinned=False,
fit_2D=False)
# Ensure slopes are consistent to within 2%
From 9a71dfbd2b6429f00c40d2f1aa851488f187cbde Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Fri, 6 Oct 2023 16:35:36 -0400
Subject: [PATCH 16/20] Handle type error failure
---
turbustat/statistics/base_pspec2.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/turbustat/statistics/base_pspec2.py b/turbustat/statistics/base_pspec2.py
index 325a3b0b..95eebc6c 100644
--- a/turbustat/statistics/base_pspec2.py
+++ b/turbustat/statistics/base_pspec2.py
@@ -88,7 +88,7 @@ def compute_radial_pspec(self, logspacing=False, max_bin=None, **kwargs):
'''
# Check if azimuthal constraints are given
- if kwargs.get("theta_0"):
+ if "theta_0" in kwargs:
azim_constraint_flag = True
else:
azim_constraint_flag = False
From 8740fdaa66cc3c841dbe0adc1e365b16690e1958 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Fri, 6 Oct 2023 17:07:00 -0400
Subject: [PATCH 17/20] Found one more type error case
---
turbustat/statistics/scf/scf.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/turbustat/statistics/scf/scf.py b/turbustat/statistics/scf/scf.py
index 18ecff47..fdb0cdee 100644
--- a/turbustat/statistics/scf/scf.py
+++ b/turbustat/statistics/scf/scf.py
@@ -258,12 +258,12 @@ def compute_spectrum(self, **kwargs):
if self.scf_surface is None:
self.compute_surface()
- if kwargs.get("logspacing"):
+ if "logspacing" in kwargs:
warn("Disabled log-spaced bins. This does not work well for the"
" SCF.", TurbuStatMetricWarning)
kwargs.pop('logspacing')
- if kwargs.get("theta_0"):
+ if "theta_0" in kwargs:
azim_constraint_flag = True
else:
azim_constraint_flag = False
From e03bd349b0937e0cc892b5e1553fe42b174fab6b Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Fri, 6 Oct 2023 17:22:14 -0400
Subject: [PATCH 18/20] Add minimal py311 testing
---
.github/workflows/main.yml | 5 +++++
tox.ini | 2 +-
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 91da142d..8ec86501 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -14,6 +14,11 @@ jobs:
fail-fast: false
matrix:
include:
+ - os: ubuntu-latest
+ python-version: '3.11'
+ name: Python 3.11 with minimal dependencies
+ toxenv: py311-test
+
- os: ubuntu-latest
python-version: '3.10'
name: Python 3.10 with minimal dependencies
diff --git a/tox.ini b/tox.ini
index 3ee9fcbd..2759c61a 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,6 +1,6 @@
[tox]
envlist =
- py{37,38,39,310}-test{,-all,-dev,-cov}
+ py{37,38,39,310,311}-test{,-all,-dev,-cov}
build_docs
codestyle
requires =
From f69f06138c9dbfa8fb9db42c6f00c005bb6737d4 Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Fri, 6 Oct 2023 19:41:12 -0400
Subject: [PATCH 19/20] Add new versions to packaging action
---
.github/workflows/python-publish.yml | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 377f4c0d..8e1ccb78 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -14,7 +14,7 @@ jobs:
- uses: actions/setup-python@v4
name: Install Python
with:
- python-version: '3.9'
+ python-version: '3.11'
- name: Install cibuildwheel
run: |
python -m pip install --upgrade pip
@@ -22,7 +22,7 @@ jobs:
- name: Build wheels
run: python -m cibuildwheel --output-dir wheelhouse
env:
- CIBW_BUILD: cp37-manylinux_x86_64 cp38-manylinux_x86_64 cp39-manylinux_x86_64 cp310-manylinux_x86_64
+ CIBW_BUILD: cp37-manylinux_x86_64 cp38-manylinux_x86_64 cp39-manylinux_x86_64 cp310-manylinux_x86_64 cp311-manylinux_x86_64
CIBW_TEST_EXTRAS: test
CIBW_TEST_COMMAND: pytest --pyargs turbustat
- uses: actions/upload-artifact@v3
@@ -41,7 +41,7 @@ jobs:
- uses: actions/setup-python@v4
name: Install Python
with:
- python-version: '3.9'
+ python-version: '3.11'
- name: Install cibuildwheel
run: |
python -m pip install --upgrade pip
@@ -49,7 +49,7 @@ jobs:
- name: Build wheels
run: python -m cibuildwheel --output-dir wheelhouse
env:
- CIBW_BUILD: cp37-* cp38-* cp39-* cp310-*
+ CIBW_BUILD: cp37-* cp38-* cp39-* cp310-* cp311-*
CIBW_TEST_EXTRAS: test
CIBW_TEST_COMMAND: pytest --pyargs turbustat
- uses: actions/upload-artifact@v3
@@ -68,7 +68,7 @@ jobs:
- uses: actions/setup-python@v4
name: Install Python
with:
- python-version: '3.9'
+ python-version: '3.11'
- name: Install cibuildwheel
run: |
python -m pip install --upgrade pip
@@ -76,7 +76,7 @@ jobs:
- name: Build wheels
run: python -m cibuildwheel --output-dir wheelhouse
env:
- CIBW_BUILD: cp37-* cp38-* cp39-*
+ CIBW_BUILD: cp39-* cp310-* cp311-*
CIBW_TEST_EXTRAS: test
CIBW_TEST_COMMAND: pytest --pyargs turbustat
- uses: actions/upload-artifact@v3
@@ -91,7 +91,7 @@ jobs:
- uses: actions/setup-python@v4
name: Install Python
with:
- python-version: '3.9'
+ python-version: '3.11'
- name: Install build
run: |
python -m pip install --upgrade pip
@@ -112,7 +112,7 @@ jobs:
with:
name: artifact
path: dist
- - uses: pypa/gh-action-pypi-publish@master
+ - uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.pypi_password }}
From efb85a3953141bfa9ae2d3bb1ec7b3aa02c432fc Mon Sep 17 00:00:00 2001
From: e-koch <koch.eric.w@gmail.com>
Date: Fri, 6 Oct 2023 21:40:06 -0400
Subject: [PATCH 20/20] Update cibuildwheel calls
---
.github/workflows/python-publish.yml | 28 ++++++++--------------------
1 file changed, 8 insertions(+), 20 deletions(-)
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 8e1ccb78..5efff0bb 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -10,17 +10,13 @@ jobs:
matrix:
os: [ubuntu-latest]
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- uses: actions/setup-python@v4
name: Install Python
with:
python-version: '3.11'
- - name: Install cibuildwheel
- run: |
- python -m pip install --upgrade pip
- python -m pip install cibuildwheel
- name: Build wheels
- run: python -m cibuildwheel --output-dir wheelhouse
+ uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_BUILD: cp37-manylinux_x86_64 cp38-manylinux_x86_64 cp39-manylinux_x86_64 cp310-manylinux_x86_64 cp311-manylinux_x86_64
CIBW_TEST_EXTRAS: test
@@ -37,17 +33,13 @@ jobs:
matrix:
os: [macos-latest]
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- uses: actions/setup-python@v4
name: Install Python
with:
python-version: '3.11'
- - name: Install cibuildwheel
- run: |
- python -m pip install --upgrade pip
- python -m pip install cibuildwheel
- name: Build wheels
- run: python -m cibuildwheel --output-dir wheelhouse
+ uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_BUILD: cp37-* cp38-* cp39-* cp310-* cp311-*
CIBW_TEST_EXTRAS: test
@@ -64,19 +56,15 @@ jobs:
matrix:
os: [windows-latest]
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- uses: actions/setup-python@v4
name: Install Python
with:
python-version: '3.11'
- - name: Install cibuildwheel
- run: |
- python -m pip install --upgrade pip
- python -m pip install cibuildwheel
- name: Build wheels
- run: python -m cibuildwheel --output-dir wheelhouse
+ uses: pypa/cibuildwheel@v2.16.2
env:
- CIBW_BUILD: cp39-* cp310-* cp311-*
+ CIBW_BUILD: cp39-*win_amd64 cp310-*win_amd64 cp311-*win_amd64
CIBW_TEST_EXTRAS: test
CIBW_TEST_COMMAND: pytest --pyargs turbustat
- uses: actions/upload-artifact@v3
@@ -87,7 +75,7 @@ jobs:
name: Build source distribution
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- uses: actions/setup-python@v4
name: Install Python
with: