Fix deprecation of shape assignment in numpy 2.5+

min-requirements.txt

@@ -1,8 +1,8 @@
 # Auto-generated by tools/update_requirements.py
 --only-binary numpy,scipy
 --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-matplotlib==3.7
-numpy==1.24
-scipy==1.10
-networkx==3.0
-nibabel==5.0
+matplotlib==3.9
+numpy==2.0
+scipy==1.13
+networkx==3.3
+nibabel==5.3

nitime/algorithms/spectral.py

@@ -20,7 +20,6 @@
 # To support older versions of numpy that don't have tril_indices:
 from nitime.index_utils import tril_indices, triu_indices
 
-
 # Set global variables for the default NFFT to be used in spectral analysis and
 # the overlap:
 default_nfft = 64
@@ -308,7 +307,7 @@ def periodogram_csd(s, Fs=2 * np.pi, Sk=None, NFFT=None, sides='default',
 
     """
     s_shape = s.shape
-    s.shape = (-1, s_shape[-1])
+    s = s.reshape((-1, s_shape[-1]))
     # defining an Sk_loc is a little opaque, but it avoids having to
     # reset the shape of any user-given Sk later on
     if Sk is not None:
@@ -322,7 +321,7 @@ def periodogram_csd(s, Fs=2 * np.pi, Sk=None, NFFT=None, sides='default',
             N = s.shape[-1]
         Sk_loc = fftpack.fft(s, n=N)
     # reset s.shape
-    s.shape = s_shape
+    s = s.reshape(s_shape)
 
     M = Sk_loc.shape[0]
 
@@ -550,7 +549,7 @@ def multi_taper_psd(
     NFFT = spectra.shape[-1]
     K = len(eigvals)
     # collapse spectra's shape back down to 3 dimensions
-    spectra.shape = (M, K, NFFT)
+    spectra = spectra.reshape((M, K, NFFT))
 
     last_freq = NFFT // 2 + 1 if sides == 'onesided' else NFFT
 
@@ -593,12 +592,12 @@ def multi_taper_psd(
         freqs = np.linspace(0, Fs, NFFT, endpoint=False)
 
     out_shape = s.shape[:-1] + (len(freqs),)
-    sdf_est.shape = out_shape
+    sdf_est = sdf_est.reshape(out_shape)
     if jackknife:
-        jk_var.shape = out_shape
+        jk_var = jk_var.reshape(out_shape)
         return freqs, sdf_est, jk_var
     else:
-        nu.shape = out_shape
+        nu = nu.reshape(out_shape)
         return freqs, sdf_est, nu
 
 
@@ -690,7 +689,7 @@ def multi_taper_csd(s, Fs=2 * np.pi, NW=None, BW=None, low_bias=True,
     NFFT = spectra.shape[-1]
     K = len(eigvals)
     # collapse spectra's shape back down to 3 dimensions
-    spectra.shape = (M, K, NFFT)
+    spectra = spectra.reshape((M, K, NFFT))
 
     # compute the cross-spectral density functions
     last_freq = NFFT // 2 + 1 if sides == 'onesided' else NFFT

nitime/algorithms/tests/test_autoregressive.py

@@ -1,9 +1,10 @@
 import numpy as np
 import numpy.testing as npt
 
+from numpy import trapezoid
+
 import nitime.algorithms as tsa
 import nitime.utils as utils
-from nitime._compat import trapezoid
 
 # Set the random seed:
 np.random.seed(1)

nitime/tests/test_algorithms.py

@@ -6,9 +6,10 @@
 from scipy import fftpack, signal
 
 import nitime
+from numpy import trapezoid
+
 from nitime import algorithms as tsa
 from nitime import utils as ut
-from nitime._compat import trapezoid
 
 #Define globally
 test_dir_path = os.path.join(nitime.__path__[0], 'tests')

nitime/tests/test_timeseries.py

@@ -922,7 +922,7 @@ def test_timearray_math_functions(f, tu):
     "Calling TimeArray.min() .max(), mean() should return TimeArrays"
     a = np.arange(2, 11)
     b = ts.TimeArray(a, time_unit=tu)
-    if f == "ptp" and ts._NP_2:
+    if f == "ptp":
         want = np.ptp(a)
     else:
         want = getattr(a, f)()

nitime/timeseries.py

@@ -33,10 +33,6 @@
 # Our own
 from nitime import descriptors as desc
 
-try:
-    _NP_2 = int(np.__version__.split(".")[0]) >= 2
-except Exception:
-    _NP_2 = True
 
 #-----------------------------------------------------------------------------
 # Module globals
@@ -319,11 +315,7 @@ def mean(self, *args, **kwargs):
         return ret
 
     def ptp(self, *args, **kwargs):
-        if _NP_2:
-            ptp = np.ptp
-        else:
-            ptp = np.ndarray.ptp
-        ret = TimeArray(ptp(self, *args, **kwargs),
+        ret = TimeArray(np.ptp(self, *args, **kwargs),
                         time_unit=base_unit)
         ret.convert_unit(self.time_unit)
         return ret

nitime/utils.py

@@ -756,7 +756,7 @@ def tapered_spectra(s, tapers, NFFT=None, low_bias=True):
     # compute the y_{i,k}(f) -- full FFT takes ~1.5x longer, but unpacking
     # results of real-valued FFT eats up memory
     t_spectra = fftpack.fft(tapered, n=NFFT, axis=-1)
-    t_spectra.shape = rest_of_dims + (K, NFFT)
+    t_spectra = t_spectra.reshape(rest_of_dims + (K, NFFT))
     if eigvals is None:
         return t_spectra
     return t_spectra, eigvals
@@ -834,7 +834,7 @@ def detect_lines(s, tapers, p=None, **taper_kws):
     numr[...,0] = 1; # don't care about DC
     # denominator -- strength of residual
     spectra = np.rollaxis(spectra, -2, 0)
-    U0.shape = (K,) + (1,) * (spectra.ndim-1)
+    U0 = U0.reshape((K,) + (1,) * (spectra.ndim-1))
     denomr = spectra - U0*mu
     denomr = np.sum(np.abs(denomr)**2, axis=0) / (2*K-2)
     denomr[...,0] = 1;

pyproject.toml

@@ -31,15 +31,15 @@ classifiers = [
     "Topic :: Scientific/Engineering",
 ]
 dependencies = [
-    "matplotlib>=3.7",
-    "numpy>=1.24",
-    "scipy>=1.10",
+    "matplotlib>=3.9",
+    "numpy>=2.0",
+    "scipy>=1.13",
 ]
 
 [project.optional-dependencies]
 full = [
-    "networkx>=3.0",
-    "nibabel>=5.0",
+    "networkx>=3.3",
+    "nibabel>=5.3",
 ]
 
 [project.urls]

requirements.txt

@@ -1,8 +1,8 @@
 # Auto-generated by tools/update_requirements.py
 --only-binary numpy,scipy
 --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-matplotlib>=3.7
-numpy>=1.24
-scipy>=1.10
-networkx>=3.0
-nibabel>=5.0
+matplotlib>=3.9
+numpy>=2.0
+scipy>=1.13
+networkx>=3.3
+nibabel>=5.3