Version 0.10.0.dev54+g3e4eed7e2 (development) (2026-11-05)

Dependencies

• Update minimum MNE version to 1.8, by Thomas Binns. (#475)

• Update minimum Python version to 3.11, by Thomas Binns. (#475)

• Updated minimum for:

  • Core dependency numpy >= 2.1

  • Core dependency pandas >= 2.2

  • Core dependency scikit-learn >= 1.5

  • Core dependency scipy >= 1.14

  • Optional dependency nibabel >= 5.2

  • Optional dependency nilearn >= 0.10

  • Optional dependency matplotlib >= 3.9

  • Optional dependency mne-qt-browser >= 0.6

  • Optional dependency pyvista >= 0.44

  • Optional dependency pyvistaqt >= 0.11

  Changes made automatically by mne[bot]. (#482)

• Move matplotlib from an optional to a core dependency, by Thomas Binns. (#500)

• Move developer dependencies from end-user extras groups to developer-facing groups, by Thomas Binns. (#500)

• Remove gui extras group and consolidate optional dependencies into a new full extras group (uses PySide6; the equivalent full-pyqt6 group using PyQt6 is also available), by Thomas Binns. (#500)

• Updated minimum for:

  • Optional dependency nibabel >= 5.3

  Changes made automatically by mne[bot]. (#502)

• Updated minimum for:

  • Core dependency netCDF4 >= 1.7.2

  • Core dependency tqdm >= 4.66

  • Core dependency xarray >= 2024.10

  • Optional dependency h5netcdf >= 1.4

  • Optional dependency joblib >= 0.8

  By Thomas Binns. (#516)

• Added optional dependency h5py >= 3.12, by Thomas Binns. (#516)

Bugfixes

• Fix channel selection to respect selection parameter as "seeds" or "targets" when picks is not None in plot_connectivity(), plot_spectral_connectivity(), plot_temporal_connectivity(), and plot_spectrotemporal_connectivity(), by Thomas Binns. (#467)

• Fix bug in spectral_connectivity_time() where faverage=True with frequency bands included frequencies beyond the requested fmax, by Marieke De Vylder. (#479)

• Ensure output of CaCoh, MIC, and Granger causality methods in spectral_connectivity_epochs() and spectral_connectivity_time(), output of CaCoh and MIC methods in CoherencyDecomposition, and output of symmetric_orth(), is deterministic, by Thomas Binns. (#498)

• Fix metadata being discarded when appending connectivity objects, by Don Yin. (#521)

• Fix erroneous Nyquist checks when passing decimated TFR data to spectral_connectivity_time(), by Don Yin. (#529)

API changes by deprecation

• Return lower-triangular connectivity data by default from spectral_connectivity_epochs(), spectral_connectivity_time(), envelope_correlation(), phase_slope_index(), phase_slope_index_time(), and wsmi(), by Thomas Binns. (#461)

• Replace indices=None with indices='all' as an alias for all-to-all connectivity in connectivity containers and all connectivity-computing functions with an indices parameter, by Thomas Binns. (#461)

• Remove 'symmetric' as an option for indices in connectivity containers, by Thomas Binns. (#461)

• Require indices to be specified as tuples of array-likes for all multivariate methods in spectral_connectivity_epochs() and spectral_connectivity_time(), by Thomas Binns. (#461)

• Require indices to be specified as tuples of array-likes in connectivity container when n_components is provided, by Thomas Binns. (#461)

• Remove deprecated n_times parameter from make_signals_in_freq_bands(), by Thomas Binns. (#469)

• Remove deprecated make_surrogate_data function, by Thomas Binns. (#470)

• Make check_indices validation helper function private, by Thomas Binns. (#491)

• Make envelope_correlation() return an EpochConnectivity object instead of a EpochTemporalConnectivity object, by Thomas Binns. (#497)

• Rename combine method of connectivity containers to combine_epochs(), by Thomas Binns. (#505)

• Remove append and combine methods, n_epochs property, and events and event_id attributes from non-epoched connectivity containers, by Thomas Binns. (#506)

• Isolate n_epochs_used property to non-epoched connectivity containers, by Thomas Binns. (#506)

• Rename the node_in -> node_out coordinate in Connectivity containers to connections, and replace the n_estimated_nodes attribute with n_connections, by Thomas Binns. (#509)

• No longer allow times=None when creating Connectivity objects with a time dimension, by Thomas Binns. (#512)

• Pass the random_state parameter of the simulate() method of connectivity containers to numpy.random.default_rng() instead of numpy.random.RandomState, by Thomas Binns. (#530)

New features

• Add learn_graph() for estimating sparse functional connectivity graphs directly from signal smoothness, by Payam S. Shabestari. (#439)

• Add plot_connectivity(), plot_spectral_connectivity(), plot_temporal_connectivity(), and plot_spectrotemporal_connectivity() for visualising connectivity results, by Thomas Binns. (#460)

• Add missing parameter to control the filling of missing values in dense connectivity matrices in the get_data() method of connectivity containers, for connectivity methods where these values cannot be determined from the lower-/upper-triangular elements, by Thomas Binns. (#461)

• Add 'lower', 'upper', and 'all' as options for indices in connectivity containers and all connectivity-computing functions with an indices parameter, by Thomas Binns. (#461)

• Add automatic filling of missing values in dense connectivity matrices from existing lower-/upper-triangular elements in the get_data() method of connectivity containers, for eligible connectivity methods, by Thomas Binns. (#461)

• Plot multivariate components as separate figures in plot_connectivity(), by Thomas Binns. (#467)

• Speed up spectral_connectivity_epochs() for Morlet wavelet (cwt_morlet) spectra by conjugating each signal once rather than for every connection, by Eric Larson. (#487)

• Add combine_freqs() and combine_times() methods to connectivity containers for combining over frequencies and times, by Thomas Binns. (#505)

Other changes

• Deprecate method names in favour of the following:

  • phase-slope-index → psi

  • envelope correlation → env_corr and env_corr_orth (depending on orthogonalization)

  • SMI → smi

  • wSMI → wsmi

  • VAR(1) and VAR(p) → var

  • Time-varying VAR(1) and Time-varying VAR(p) → var_dynamic

  by Thomas Binns. (#494)

• Clarify supported random number generator seeds in dataset helpers and connectivity simulation by Okan Tiktas. (#520)