Merge pull request #223 from naplab/update_numpy2

Bump to NumPy 2.x

Author: vinaysraghavan

.github/workflows/python-package.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Python package
 
 on:
@@ -11,34 +8,47 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8","3.9","3.10"]
+        # 3.13 is now available and worth testing for NumPy 2.0+
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+        cache: 'pip' # Automatically caches your dependencies
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest pytest-cov
+        
+        # Install requirements first
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install pyyaml TextGrid
-        pip install --user -U mne-bids
+        
+        # Install remaining packages without --user
+        pip install pyyaml TextGrid mne-bids
+        
+        # Final sanity check to ensure NumPy 2.0 didn't get downgraded
+        python -c "import numpy; print(f'Using NumPy {numpy.__version__}')"
+
     - name: Lint with flake8
       run: |
-        # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with pytest and get coverage
       run: |
-        pytest tests/ --cov=./naplib/ --cov-report=xml
+        # Using -v helps identify exactly which test crashes if collection fails
+        pytest -v tests/ --cov=./naplib/ --cov-report=xml
+
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4 # Updated to v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }} # v4 often requires a token

naplib/features/aligner.py

@@ -307,7 +307,7 @@ def align_files(self, audio_dir, text_dir, names=None):
                 if old_fs == 16000:
                     write_wavfile(join(self.tmp_dir, wavfile_), 16000, wavdata)
                 else:
-                    wavdata = scipy_resample(wavdata, int(16000. / old_fs))
+                    wavdata = scipy_resample(wavdata, int(len(wavdata) * 16000. / old_fs))
                     write_wavfile(join(self.tmp_dir, wavfile_), 16000, wavdata)
 
 

naplib/utils/surfdist.py

@@ -4,6 +4,7 @@
 """
 
 import gdist
+import matplotlib as mpl
 import matplotlib.pyplot as plt
 from matplotlib.colors import LightSource
 import numpy as np
@@ -24,7 +25,7 @@ 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 +82,7 @@ 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 +101,7 @@ 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
 
@@ -190,10 +191,7 @@ def surfdist_viz(
 
     # if cmap is given as string, translate to matplotlib cmap
     if isinstance(cmap, str):
-        try:
-            cmap = plt.cm.get_cmap(cmap)
-        except AttributeError:
-            cmap = plt.get_cmap(cmap)
+        cmap = mpl.colormaps[cmap]
 
     if ax is None:
         premade_ax = False

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
-hdf5storage>=0.1.1
-seaborn>=0.12.0
+# 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>=0.2.0
 pyyaml
-TextGrid
-scikit-learn
-joblib
-mne
-h5py
-patsy
+nibabel>=5.2.1
+
+# Visualization
+seaborn>=0.13.0
+plotly>=5.22.0
+
+# Domain Specific & Specialized
+tvb-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():