Pin zero_mean in conn_spec's TF decomposition; test CI on Python 3.10…

.github/workflows/flake.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Set up Python 🔧
         uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
+          python-version: '3.11'
 
       - name: Install dependencies 🔧
         run: |

.github/workflows/pr.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout 🛎️

.github/workflows/test_doc.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - name: Checkout 🛎️
@@ -40,7 +40,7 @@ jobs:
       - name: Set up Python 🔧
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.11'
 
       - name: Install dependencies 🔧
         run: |

.gitignore

@@ -122,4 +122,6 @@ docs/source/auto_examples/
 
 node_modules/
 package.json
-yarn.lock
+yarn.lock
+docs/source/sg_execution_times.rst
+

docs/source/conf.py

@@ -89,7 +89,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -276,7 +276,7 @@
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"https://docs.python.org/": None}
+intersphinx_mapping = {"python": ("https://docs.python.org/3", None)}
 
 # -- Options for todo extension ----------------------------------------------
 

docs/source/overview/ovw_whatsnew.rst

@@ -12,6 +12,14 @@ Bug fixes
 * Support mne-python versions newer than 1.5.0, up to the current release (:commit:`9a81a6dc`)
 * Restore a compatibility shim so mne keeps working with NumPy >= 2.4, which removed ``np.in1d`` while mne still relies on it internally (:commit:`ad7cfe65`)
 * Fix type comparison in :func:`frites.dataset.ds_utils.multi_to_uni_conditions` and in :func:`frites.plot.plot_conn_circle` (:commit:`cee7ed4a`)
+* Fix :func:`frites.conn.conn_spec` in multitaper mode : the cross- and auto-spectra are now averaged over tapers (the complex coefficients used to be averaged before, cancelling most of the signal). Coherence and PLV values change for every multitaper user (:pull:`69`)
+* Fix the hanning smoothing kernel of :func:`frites.conn.conn_spec` (``sm_times`` of 2 samples gave a NaN output, 3 samples no smoothing) (:pull:`69`)
+* The cross-spectrum (``metric='sxy'``) of :func:`frites.conn.conn_spec` is now complex (the imaginary part used to be silently dropped) (:pull:`69`)
+* :func:`frites.conn.conn_spec` sets ``zero_mean=False`` explicitly in the time-frequency decomposition : mne changed its default to ``True``, which silently changed the results between mne versions
+
+Dependencies
+++++++++++++
+* Tested against mne 1.5 up to 1.13 (mne >= 1.13 requires Python >= 3.11) and Python 3.10 to 3.12 ; the continuous integration matrix moved from Python 3.8/3.9 to 3.10/3.11/3.12
 
 v0.4.4
 ------
@@ -22,7 +30,7 @@ New Features
 * New function :func:`frites.core.ent_nd_g` to compute entropy on tensors (:commit:`17587a15`)
 * New function :func:`frites.conn.conn_ii` to estimate the interaction information (:commit:`10938b46`)
 * New function :func:`frites.conn.conn_pid` to estimate the partial information decomposition (:commit:`ac9798dd`)
-- New function :func:`frites.conn.conn_fit` to estimate the feature specific information transfer (:PR:`59`) - :author:`aopy`
+- New function :func:`frites.conn.conn_fit` to estimate the feature specific information transfer (:pull:`59`) - :author:`aopy`
 
 Bug fixes
 +++++++++

frites/__init__.py

@@ -70,8 +70,10 @@ def set_mpl_style(style='frites'):
         Style name. Use either "frites" for a white background or "ggfrites"
         for a grey brackground like with ggplot.
     """
-    from pkg_resources import resource_filename
+    # pkg_resources (setuptools) is no longer available by default on
+    # Python >= 3.12 and is deprecated; use the stdlib instead
+    from importlib.resources import files
     import matplotlib.pyplot as plt
     assert style in ["frites", "ggfrites"]
-    path_style = resource_filename('frites', f'data/{style}.mplstyle')
-    plt.style.use(path_style)
+    path_style = files('frites') / 'data' / f'{style}.mplstyle'
+    plt.style.use(str(path_style))

frites/conn/conn_tf.py

@@ -63,6 +63,12 @@ def _tf_decomp(data, sf, freqs, mode='morlet', n_cycles=7.0, mt_bandwidth=None,
         complex coefficients across tapers cancels most of the signal and does
         not give the multitaper estimator.
     """
+    # mne changed the default of `zero_mean` from False (<=1.5) to True. Fix it
+    # explicitly so that the results do not depend on the mne version (a
+    # user-defined value in kw_cwt / kw_mt takes precedence)
+    kw_cwt = {'zero_mean': False, **kw_cwt}
+    kw_mt = {'zero_mean': False, **kw_mt}
+
     if mode == 'morlet':
         out = tfr_array_morlet(
             data, sf, freqs, n_cycles=n_cycles, output='complex', decim=decim,

frites/conn/tests/test_conn_spec.py

@@ -150,7 +150,7 @@ def test_multitaper_reference(self):
         # reference : (trials, chans, tapers, freqs, times)
         w = tfr_array_multitaper(x.data, sfreq, freqs, n_cycles=n_cycles,
                                  time_bandwidth=tw, output='complex',
-                                 verbose=False)
+                                 zero_mean=False, verbose=False)
         s_xy = (w[:, 0] * np.conj(w[:, 1])).mean(1)
         s_xx = (np.abs(w[:, 0]) ** 2).mean(1)
         s_yy = (np.abs(w[:, 1]) ** 2).mean(1)
@@ -183,7 +183,7 @@ def test_sxy_complex(self):
         assert np.abs(sxy.data.imag).max() > 0
         # morlet cross-spectrum is exactly w_x * conj(w_y)
         w = tfr_array_morlet(x.data, sfreq, freqs, n_cycles=n_cycles,
-                             output='complex', verbose=False)
+                             output='complex', zero_mean=False, verbose=False)
         sxy = conn_spec(x, metric='sxy', dtype=np.complex128, **kw)
         np.testing.assert_allclose(sxy.sel(roi='x-y').data,
                                    w[:, 0] * np.conj(w[:, 1]), rtol=1e-6)

setup.py

@@ -30,8 +30,8 @@ def read(fname):
 core_deps = ['matplotlib', 'networkx', 'numba', 'dcor']
 test_deps = ['pytest', 'pytest-sugar', 'pytest-cov', 'codecov']
 doc_deps = [
-    'sphinx==7.0.0 ', 'sphinx-gallery', 'pydata-sphinx-theme>=0.6.3',
-    'sphinxcontrib-bibtex==1.0.0', 'numpydoc', 'xlrd', 'openpyxl', 'seaborn',
+    'sphinx>=7.4', 'sphinx-gallery', 'pydata-sphinx-theme>=0.6.3',
+    'sphinxcontrib-bibtex>=2.6', 'numpydoc', 'xlrd', 'openpyxl', 'seaborn',
     'memory-profiler', 'sphinx-panels', 'sphinx-copybutton'
 ]
 flake_deps = ['flake8', 'pep8-naming']
@@ -67,8 +67,7 @@ def read(fname):
                  'Intended Audience :: Science/Research',
                  'Intended Audience :: Education',
                  'Intended Audience :: Developers',
-                 "Programming Language :: Python :: 3.8",
-                 "Programming Language :: Python :: 3.9",
                  "Programming Language :: Python :: 3.10",
                  "Programming Language :: Python :: 3.11",
+                 "Programming Language :: Python :: 3.12",
                  ])