Bump to numpy2

gdist 2.9.2 supports it

Author: vinaysraghavan

naplib/utils/surfdist.py

@@ -24,7 +24,7 @@ def load_freesurfer_label(annot_input, label_name):
     labels, _, names = read_annot(annot_input)
     names = [i.decode("utf-8") for i in names]
     label_value = names.index(label_name)
-    label_nodes = np.array(np.where(np.in1d(labels, label_value)), dtype=np.int32)
+    label_nodes = np.array(np.where(np.isin(labels, label_value)), dtype=np.int32)
 
     return label_nodes
 
@@ -81,7 +81,7 @@ def triangles_keep_cortex(triangles, cortex):
     # for or each face/triangle keep only those that only contain nodes within the list of cortex nodes
     input_shape = triangles.shape
     triangle_is_in_cortex = np.all(
-        np.reshape(np.in1d(triangles.ravel(), cortex), input_shape), axis=1
+        np.reshape(np.isin(triangles.ravel(), cortex), input_shape), axis=1
     )
 
     cortex_triangles_old = np.array(triangles[triangle_is_in_cortex], dtype=np.int32)
@@ -100,7 +100,7 @@ def translate_src(src, cortex):
     """
     Convert source nodes to new surface (without medial wall).
     """
-    src_new = np.array(np.where(np.in1d(cortex, src))[0], dtype=np.int32)
+    src_new = np.array(np.where(np.isin(cortex, src))[0], dtype=np.int32)
 
     return src_new
 

requirements.txt

@@ -1,20 +1,29 @@
-matplotlib>=3.1.0
-numpy>=1.15.0,<2.0 # numpy>=2.0 is incompatible with gdist, a dependency of surfdist
-scipy>=1.5.0
-pandas>=1.0.0
-statsmodels>=0.13.0
+# Core Scientific Stack (Updated for NumPy 2.0 ABI/API compatibility)
+numpy>=2.0.0
+scipy>=1.13.0
+pandas>=2.2.2
+matplotlib>=3.9.0
+statsmodels>=0.14.2
+scikit-learn>=1.5.0
+
+# Data Storage & IO
+h5py>=3.11.0
 hdf5storage>=0.1.1
-seaborn>=0.12.0
 pyyaml
-TextGrid
-scikit-learn
-joblib
-mne
-h5py
-patsy
+nibabel>=5.2.1
+
+# Visualization
+seaborn>=0.13.0
+plotly>=5.22.0
+
+# Domain Specific & Specialized
+gdist>=2.9.2
+mne>=1.7.1
+scikit-spatial>=7.1.0
 tdt>=0.5.0
-packaging
-plotly>=5.0.0
-nibabel>=5.0.0
-scikit-spatial>=5.0.0
-gdist>=2.0.0
+TextGrid
+
+# Utilities
+joblib>=1.4.2
+patsy>=0.5.6
+packaging>=24.0

tests/preprocessing/test_filter.py

@@ -10,7 +10,7 @@ def bandpower(x, fs, fmin, fmax):
     f, Pxx = scipy.signal.periodogram(x, fs=fs)
     ind_min = np.argmax(f > fmin) - 1
     ind_max = np.argmax(f > fmax) - 1
-    return np.trapz(Pxx[ind_min: ind_max], f[ind_min: ind_max])
+    return np.trapezoid(Pxx[ind_min: ind_max], f[ind_min: ind_max])
 
 @pytest.fixture(scope='module')
 def data():