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commit dd5e6282462430006e4dcb27a4549bf0e8133ad9 Merge: 413eda3 8b4f854 Author: Yaroslav Halchenko <[email protected]> Date: Wed Sep 28 20:36:58 2016 -0400 Merge tag 'upstream/0.13+dfsg' Upstream version 0.13+dfsg * tag 'upstream/0.13+dfsg': New upstream version 0.13+dfsg .coveragerc | 1 + .mailmap | 9 + .travis.yml | 39 +- Makefile | 5 +- README.rst | 112 +- appveyor.yml | 30 +- circle.yml | 88 +- codecov.yml | 14 + doc/Makefile | 7 +- doc/_static/style.css | 3 + doc/_templates/class.rst | 2 +- doc/cite.rst | 2 +- doc/conf.py | 17 +- doc/contributing.rst | 370 +++-- doc/faq.rst | 3 +- doc/getting_started.rst | 2 +- doc/index.rst | 15 +- doc/manual/appendix/bem_model.rst | 10 +- doc/manual/cookbook.rst | 2 - doc/manual/decoding.rst | 4 + doc/manual/io.rst | 24 +- doc/manual/pitfalls.rst | 13 - doc/manual/source_localization/inverse.rst | 2 +- doc/python_reference.rst | 34 +- doc/sphinxext/gen_commands.py | 13 +- doc/sphinxext/numpy_ext/__init__.py | 0 doc/sphinxext/numpy_ext/docscrape.py | 512 ------ doc/sphinxext/numpy_ext/docscrape_sphinx.py | 240 --- doc/sphinxext/numpy_ext/numpydoc.py | 192 --- doc/tutorials.rst | 18 +- doc/whats_new.rst | 271 +++- .../plot_mne_inverse_coherence_epochs.py | 6 +- .../plot_decoding_spatio_temporal_source.py | 5 +- ...plot_decoding_time_generalization_conditions.py | 8 +- .../plot_decoding_unsupervised_spatial_filter.py | 67 + examples/decoding/plot_decoding_xdawn_eeg.py | 4 +- examples/decoding/plot_ems_filtering.py | 104 +- examples/inverse/plot_dics_beamformer.py | 14 +- examples/inverse/plot_dics_source_power.py | 12 +- examples/inverse/plot_lcmv_beamformer.py | 4 +- examples/inverse/plot_morph_data.py | 1 - examples/inverse/plot_tf_dics.py | 10 +- .../plot_time_frequency_mixed_norm_inverse.py | 7 +- examples/io/plot_elekta_epochs.py | 68 + examples/preprocessing/plot_run_ica.py | 20 +- examples/preprocessing/plot_xdawn_denoising.py | 5 +- examples/realtime/ftclient_rt_average.py | 1 + examples/realtime/plot_compute_rt_decoder.py | 4 +- examples/realtime/rt_feedback_server.py | 6 +- examples/time_frequency/README.txt | 3 +- .../plot_compute_raw_data_spectrum.py | 2 +- .../plot_source_label_time_frequency.py | 10 +- make/install_python.ps1 | 93 -- mne/__init__.py | 11 +- mne/annotations.py | 55 +- mne/baseline.py | 38 +- mne/beamformer/_dics.py | 16 +- mne/beamformer/_lcmv.py | 2 +- mne/beamformer/tests/test_dics.py | 48 +- mne/beamformer/tests/test_lcmv.py | 18 +- mne/bem.py | 146 +- mne/channels/channels.py | 257 ++- mne/channels/data/layouts/KIT-UMD-3.lout | 158 ++ mne/channels/data/neighbors/KIT-UMD-1_neighb.mat | Bin 0 -> 4750 bytes mne/channels/data/neighbors/KIT-UMD-2_neighb.mat | Bin 0 -> 4832 bytes mne/channels/data/neighbors/KIT-UMD-3_neighb.mat | Bin 0 -> 4794 bytes mne/channels/data/neighbors/__init__.py | 3 + mne/channels/interpolation.py | 7 +- mne/channels/layout.py | 78 +- mne/channels/montage.py | 188 ++- mne/channels/tests/test_channels.py | 34 +- mne/channels/tests/test_interpolation.py | 10 +- mne/channels/tests/test_layout.py | 81 +- mne/channels/tests/test_montage.py | 103 +- mne/chpi.py | 149 +- mne/commands/mne_browse_raw.py | 10 + mne/commands/mne_coreg.py | 20 +- mne/commands/mne_flash_bem.py | 6 +- mne/commands/mne_kit2fiff.py | 6 +- mne/commands/mne_make_scalp_surfaces.py | 20 +- mne/commands/mne_show_fiff.py | 6 + mne/commands/tests/test_commands.py | 44 +- mne/connectivity/spectral.py | 13 +- mne/connectivity/tests/test_spectral.py | 51 +- mne/coreg.py | 168 +- mne/cov.py | 221 ++- mne/cuda.py | 9 +- mne/data/coil_def.dat | 17 +- mne/data/mne_analyze.sel | 8 +- mne/datasets/__init__.py | 1 + mne/datasets/brainstorm/__init__.py | 3 +- mne/datasets/brainstorm/bst_auditory.py | 3 +- .../{bst_resting.py => bst_phantom_ctf.py} | 19 +- .../{bst_resting.py => bst_phantom_elekta.py} | 20 +- mne/datasets/brainstorm/bst_raw.py | 3 +- mne/datasets/brainstorm/bst_resting.py | 3 +- mne/datasets/megsim/urls.py | 2 +- mne/datasets/multimodal/__init__.py | 4 + .../{somato/somato.py => multimodal/multimodal.py} | 15 +- mne/datasets/sample/sample.py | 3 +- mne/datasets/somato/somato.py | 3 +- mne/datasets/spm_face/spm_data.py | 3 +- mne/datasets/testing/_testing.py | 3 +- mne/datasets/tests/test_datasets.py | 10 + mne/datasets/utils.py | 96 +- mne/decoding/__init__.py | 6 +- mne/decoding/base.py | 114 +- mne/decoding/csp.py | 385 +++-- mne/decoding/ems.py | 149 +- mne/decoding/search_light.py | 629 ++++++++ mne/decoding/tests/test_csp.py | 134 +- mne/decoding/tests/test_ems.py | 46 +- mne/decoding/tests/test_search_light.py | 170 ++ mne/decoding/tests/test_time_frequency.py | 41 + mne/decoding/tests/test_time_gen.py | 25 +- mne/decoding/tests/test_transformer.py | 141 +- mne/decoding/time_frequency.py | 152 ++ mne/decoding/time_gen.py | 97 +- mne/decoding/transformer.py | 363 ++++- mne/defaults.py | 29 +- mne/dipole.py | 220 ++- mne/epochs.py | 1010 +++++------- mne/event.py | 562 ++++++- mne/evoked.py | 677 +++----- mne/externals/h5io/_h5io.py | 186 ++- mne/externals/tempita/_looper.py | 4 +- mne/filter.py | 1664 ++++++++++++++------ mne/fixes.py | 1107 ++++--------- mne/forward/__init__.py | 2 +- mne/forward/_compute_forward.py | 2 +- mne/forward/_field_interpolation.py | 5 +- mne/forward/_make_forward.py | 3 +- mne/forward/forward.py | 116 +- mne/forward/tests/test_field_interpolation.py | 14 +- mne/forward/tests/test_forward.py | 5 +- mne/forward/tests/test_make_forward.py | 5 +- mne/gui/__init__.py | 2 +- mne/gui/_coreg_gui.py | 214 ++- mne/gui/_fiducials_gui.py | 53 +- mne/gui/_file_traits.py | 97 +- mne/gui/_kit2fiff_gui.py | 277 +++- mne/gui/help/kit2fiff.json | 5 +- mne/gui/tests/test_coreg_gui.py | 73 +- mne/gui/tests/test_fiducials_gui.py | 2 +- mne/gui/tests/test_file_traits.py | 6 +- mne/gui/tests/test_kit2fiff_gui.py | 18 +- mne/inverse_sparse/mxne_inverse.py | 2 +- mne/io/__init__.py | 3 +- mne/io/array/array.py | 2 +- mne/io/array/tests/test_array.py | 42 +- mne/io/base.py | 784 +++++---- mne/io/brainvision/brainvision.py | 315 +++- mne/io/brainvision/tests/data/test.vhdr | 24 +- .../brainvision/tests/data/test_highpass_hz.vhdr | 103 ++ mne/io/brainvision/tests/data/test_lowpass_s.vhdr | 103 ++ .../data/{test.vhdr => test_mixed_highpass.vhdr} | 103 +- .../tests/data/test_mixed_highpass_hz.vhdr | 103 ++ .../data/{test.vhdr => test_mixed_lowpass.vhdr} | 103 +- .../tests/data/test_mixed_lowpass_s.vhdr | 103 ++ .../test_old_layout_latin1_software_filter.eeg | Bin 0 -> 29116 bytes .../test_old_layout_latin1_software_filter.vhdr | 156 ++ .../test_old_layout_latin1_software_filter.vmrk | 14 + ...vhdr => test_partially_disabled_hw_filter.vhdr} | 63 +- mne/io/brainvision/tests/test_brainvision.py | 198 ++- mne/io/bti/bti.py | 11 +- mne/io/bti/tests/test_bti.py | 98 +- mne/io/cnt/cnt.py | 88 +- mne/io/cnt/tests/test_cnt.py | 7 +- mne/io/compensator.py | 37 +- mne/io/constants.py | 109 +- mne/io/ctf/info.py | 20 + mne/io/ctf/tests/test_ctf.py | 1 + mne/io/edf/edf.py | 17 +- mne/io/edf/tests/test_edf.py | 48 +- mne/io/eeglab/eeglab.py | 96 +- mne/io/eeglab/tests/test_eeglab.py | 45 +- mne/io/fiff/raw.py | 162 +- mne/io/fiff/tests/test_raw_fiff.py | 625 +++++--- mne/io/kit/constants.py | 61 +- mne/io/kit/coreg.py | 7 +- mne/io/kit/kit.py | 65 +- mne/io/kit/tests/data/test.elp | 37 + mne/io/kit/tests/data/test.hsp | 514 ++++++ mne/io/kit/tests/data/test_umd-raw.sqd | Bin 0 -> 99692 bytes mne/io/kit/tests/test_coreg.py | 15 + mne/io/kit/tests/test_kit.py | 83 +- mne/io/meas_info.py | 131 +- mne/io/nicolet/nicolet.py | 2 +- mne/io/open.py | 20 +- mne/io/pick.py | 45 +- mne/io/proj.py | 23 +- mne/io/reference.py | 53 +- mne/io/tag.py | 2 +- mne/io/tests/data/test-ave-2.log | 6 +- mne/io/tests/data/test-ave.log | 3 +- mne/io/tests/test_compensator.py | 56 +- mne/io/tests/test_meas_info.py | 83 +- mne/io/tests/test_pick.py | 29 +- mne/io/tests/test_proc_history.py | 15 +- mne/io/tests/test_raw.py | 12 +- mne/io/tests/test_reference.py | 112 +- mne/io/write.py | 13 +- mne/label.py | 79 +- mne/minimum_norm/tests/test_inverse.py | 34 +- mne/minimum_norm/tests/test_time_frequency.py | 23 +- mne/minimum_norm/time_frequency.py | 8 +- mne/preprocessing/__init__.py | 2 +- mne/preprocessing/_fine_cal.py | 84 + mne/preprocessing/ecg.py | 60 +- mne/preprocessing/eog.py | 15 +- mne/preprocessing/ica.py | 423 +++-- mne/preprocessing/infomax_.py | 127 +- mne/preprocessing/maxfilter.py | 4 +- mne/preprocessing/maxwell.py | 335 ++-- mne/preprocessing/ssp.py | 7 +- mne/preprocessing/tests/test_ecg.py | 24 +- mne/preprocessing/tests/test_eeglab_infomax.py | 283 ++-- mne/preprocessing/tests/test_eog.py | 6 +- mne/preprocessing/tests/test_fine_cal.py | 40 + mne/preprocessing/tests/test_ica.py | 164 +- mne/preprocessing/tests/test_infomax.py | 40 +- mne/preprocessing/tests/test_maxwell.py | 292 ++-- mne/preprocessing/tests/test_ssp.py | 28 +- mne/preprocessing/tests/test_stim.py | 13 +- mne/preprocessing/tests/test_xdawn.py | 204 ++- mne/preprocessing/xdawn.py | 641 +++++--- mne/proj.py | 4 +- mne/realtime/epochs.py | 15 +- mne/realtime/fieldtrip_client.py | 2 + mne/realtime/stim_server_client.py | 8 +- mne/realtime/tests/test_fieldtrip_client.py | 3 + mne/realtime/tests/test_mockclient.py | 24 +- mne/realtime/tests/test_stim_client_server.py | 4 +- mne/report.py | 38 +- mne/selection.py | 76 +- mne/simulation/evoked.py | 25 +- mne/simulation/raw.py | 8 +- mne/simulation/source.py | 145 +- mne/simulation/tests/test_evoked.py | 28 +- mne/simulation/tests/test_raw.py | 70 +- mne/simulation/tests/test_source.py | 59 +- mne/source_estimate.py | 254 ++- mne/source_space.py | 69 +- mne/stats/cluster_level.py | 17 +- mne/stats/parametric.py | 15 +- mne/stats/regression.py | 3 +- mne/stats/tests/test_cluster_level.py | 8 +- mne/stats/tests/test_regression.py | 15 +- mne/surface.py | 159 +- mne/tests/test_annotations.py | 43 +- mne/tests/test_bem.py | 58 +- mne/tests/test_chpi.py | 109 +- mne/tests/test_cov.py | 114 +- mne/tests/test_dipole.py | 64 +- mne/tests/test_docstring_parameters.py | 26 +- mne/tests/test_epochs.py | 631 ++++---- mne/tests/test_event.py | 149 +- mne/tests/test_evoked.py | 171 +- mne/tests/test_filter.py | 376 +++-- mne/tests/test_fixes.py | 184 +-- mne/tests/test_import_nesting.py | 5 +- mne/tests/test_label.py | 73 +- mne/tests/test_line_endings.py | 8 +- mne/tests/test_proj.py | 41 +- mne/tests/test_report.py | 39 +- mne/tests/test_selection.py | 4 +- mne/tests/test_source_estimate.py | 18 +- mne/tests/test_source_space.py | 15 +- mne/tests/test_surface.py | 39 +- mne/tests/test_transforms.py | 2 +- mne/tests/test_utils.py | 223 ++- mne/time_frequency/__init__.py | 10 +- mne/time_frequency/_stockwell.py | 10 +- mne/time_frequency/csd.py | 292 +++- mne/time_frequency/multitaper.py | 60 +- mne/time_frequency/psd.py | 179 +-- mne/time_frequency/tests/test_ar.py | 8 +- mne/time_frequency/tests/test_csd.py | 301 +++- mne/time_frequency/tests/test_psd.py | 171 +- mne/time_frequency/tests/test_stockwell.py | 51 +- mne/time_frequency/tests/test_tfr.py | 219 ++- mne/time_frequency/tfr.py | 1557 ++++++++++-------- mne/transforms.py | 12 +- mne/utils.py | 479 +++++- mne/viz/_3d.py | 130 +- mne/viz/__init__.py | 6 +- mne/viz/circle.py | 7 +- mne/viz/epochs.py | 102 +- mne/viz/evoked.py | 583 ++++++- mne/viz/ica.py | 367 +++-- mne/viz/misc.py | 116 +- mne/viz/raw.py | 253 ++- mne/viz/tests/test_3d.py | 18 +- mne/viz/tests/test_decoding.py | 8 +- mne/viz/tests/test_epochs.py | 26 +- mne/viz/tests/test_evoked.py | 73 +- mne/viz/tests/test_ica.py | 117 +- mne/viz/tests/test_misc.py | 31 +- mne/viz/tests/test_raw.py | 78 +- mne/viz/tests/test_topo.py | 42 +- mne/viz/tests/test_topomap.py | 63 +- mne/viz/tests/test_utils.py | 35 +- mne/viz/topo.py | 47 +- mne/viz/topomap.py | 300 +++- mne/viz/utils.py | 594 ++++++- setup.cfg | 1 + setup.py | 1 + tutorials/plot_artifacts_correction_filtering.py | 69 +- tutorials/plot_artifacts_correction_ica.py | 136 +- .../plot_artifacts_correction_maxwell_filtering.py | 2 +- tutorials/plot_artifacts_correction_rejection.py | 8 +- tutorials/plot_artifacts_correction_ssp.py | 3 +- tutorials/plot_background_filtering.py | 951 +++++++++++ tutorials/plot_brainstorm_auditory.py | 37 +- tutorials/plot_brainstorm_phantom_ctf.py | 112 ++ tutorials/plot_brainstorm_phantom_elekta.py | 106 ++ tutorials/plot_compute_covariance.py | 7 +- tutorials/plot_dipole_fit.py | 2 +- tutorials/plot_eeg_erp.py | 30 +- tutorials/plot_epoching_and_averaging.py | 7 +- tutorials/plot_epochs_to_data_frame.py | 8 +- tutorials/plot_forward.py | 18 +- tutorials/plot_ica_from_raw.py | 5 +- tutorials/plot_info.py | 2 +- tutorials/plot_introduction.py | 51 +- tutorials/plot_mne_dspm_source_localization.py | 29 +- tutorials/plot_modifying_data_inplace.py | 28 +- tutorials/plot_object_epochs.py | 7 +- tutorials/plot_object_raw.py | 44 +- tutorials/plot_point_spread.py | 171 ++ tutorials/plot_sensors_decoding.py | 20 +- tutorials/plot_sensors_time_frequency.py | 6 +- ...plot_stats_cluster_1samp_test_time_frequency.py | 73 +- tutorials/plot_stats_cluster_methods.py | 3 +- tutorials/plot_stats_cluster_spatio_temporal.py | 6 +- .../plot_stats_cluster_spatio_temporal_2samp.py | 5 +- ...ster_spatio_temporal_repeated_measures_anova.py | 6 +- tutorials/plot_stats_cluster_time_frequency.py | 89 +- ...uster_time_frequency_repeated_measures_anova.py | 86 +- .../plot_stats_spatio_temporal_cluster_sensors.py | 3 +- tutorials/plot_visualize_epochs.py | 14 +- tutorials/plot_visualize_evoked.py | 33 +- tutorials/plot_visualize_raw.py | 54 +- 343 files changed, 22134 insertions(+), 11303 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
