[med-svn] [python-mne] branch master updated (413eda3 -> 148fcb5)
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 18 22:17:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
yoh pushed a change to branch master
in repository python-mne.
from 413eda3 upcoming release drops compat with python 2.6
new 8b4f854 New upstream version 0.13+dfsg
new dd5e628 Merge tag 'upstream/0.13+dfsg'
new 4ee6de7 changelog and patches update
new 4f6e338 Need to export ETS_TOOLKIT=qt4 to avoid cannot set toolkit to qt4 because it has already been set to wx
new 1a32c0c added patch changeset_b9958973c5e331aa488df1c514c8476d7f4c2830.diff to "cherry-pick" b9958973c5e331aa488df1c514c8476d7f4c2830 (ENH+BF+RF: skip two tests requiring mayavi, and include into SkipTest msg caught exception)
new 62dfc4c debian/rules + changelog: - fake http_proxy settings to forbid network access - HOME=build/ to avoid trying to deal with / as HOME
new 0d54c51 New upstream version 0.13+git5-g028f2ee
new b8d73d0 Merge tag 'upstream/0.13+git5-g028f2ee'
new f1c8e76 adjusted version -- needed fresh snapshot of maintenance 0.13 branch
new 668dc1c debian/rules --exclude=test_add_slider_to_section for nose
new 674801b New upstream version 0.13+git8-gcb8707f
new 084ae9f manually filtering out .min.js since were not filtered out automagically
new 46bf566 Merge tag 'upstream/0.13+git8-gcb8707f+dfsg'
new 1f8d284 changelog entry + removing --exclude=test_add_slider_to_section
new 148fcb5 debian/copyright - MIT -> Expat, consistent -Clause for BSD, https url
The 15 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.coveragerc | 1 +
.mailmap | 9 +
.travis.yml | 39 +-
Makefile | 5 +-
README.rst | 112 +-
appveyor.yml | 30 +-
circle.yml | 92 +-
codecov.yml | 14 +
debian/changelog | 32 +
debian/control | 2 +-
debian/copyright | 32 +-
...t_154d7e5da710f08341eba50867da90525f52059c.diff | 25 -
...t_9c7ef6d10f1f767b742525ea31e42a65a0469327.diff | 59 -
...t_b9958973c5e331aa488df1c514c8476d7f4c2830.diff | 61 +
debian/patches/deb_paths | 2 +-
debian/patches/series | 3 +-
debian/rules | 8 +
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 +-
examples/datasets/plot_megsim_data_single_trial.py | 4 +-
examples/datasets/plot_spm_faces_dataset.py | 9 +-
.../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 +-
.../plot_compute_mne_inverse_raw_in_label.py | 1 +
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 | 3 +-
examples/realtime/plot_compute_rt_average.py | 2 +-
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 | 31 +-
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/__init__.py | 1305 +--------------
mne/externals/tempita/{__init__.py => _tempita.py} | 369 ++---
mne/externals/tempita/compat3.py | 20 +-
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 +-
.../{test_highpass.vhdr => test_highpass_hz.vhdr} | 41 +-
.../{test_highpass.vhdr => test_lowpass_s.vhdr} | 105 +-
...test_highpass.vhdr => test_mixed_highpass.vhdr} | 41 +-
...t_highpass.vhdr => test_mixed_highpass_hz.vhdr} | 43 +-
...{test_highpass.vhdr => test_mixed_lowpass.vhdr} | 41 +-
...est_highpass.vhdr => test_mixed_lowpass_s.vhdr} | 105 +-
.../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 | 584 ++++++-
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 | 3 +-
setup.py | 2 +-
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 +-
358 files changed, 22003 insertions(+), 13138 deletions(-)
create mode 100644 codecov.yml
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copy mne/datasets/brainstorm/{bst_resting.py => bst_phantom_elekta.py} (71%)
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copy mne/datasets/{somato/somato.py => multimodal/multimodal.py} (59%)
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copy mne/io/brainvision/tests/data/{test.vhdr => test_partially_disabled_hw_filter.vhdr} (74%)
create mode 100644 mne/io/kit/tests/data/test.elp
create mode 100644 mne/io/kit/tests/data/test.hsp
create mode 100644 mne/io/kit/tests/data/test_umd-raw.sqd
create mode 100644 mne/preprocessing/_fine_cal.py
create mode 100644 mne/preprocessing/tests/test_fine_cal.py
create mode 100644 tutorials/plot_background_filtering.py
create mode 100644 tutorials/plot_brainstorm_phantom_ctf.py
create mode 100644 tutorials/plot_brainstorm_phantom_elekta.py
create mode 100644 tutorials/plot_point_spread.py
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