diff --git a/.mailmap b/.mailmap index edbaf67867c..8534b2b1171 100644 --- a/.mailmap +++ b/.mailmap @@ -108,6 +108,7 @@ Frederik D. Weber Frederik-D-Weber < Fu-Te Wong foucault Fu-Te Wong zuxfoucault Gansheng Tan <49130176+GanshengT@users.noreply.github.com> Gansheng TAN <49130176+GanshengT@users.noreply.github.com> +Gennadiy Belonosov <7503709+Genuster@users.noreply.github.com> Gennadiy <7503709+Genuster@users.noreply.github.com> Giorgio Marinato neurogima <76406896+neurogima@users.noreply.github.com> Guillaume Dumas deep-introspection Guillaume Dumas Guillaume Dumas @@ -155,6 +156,7 @@ José C. García Alanis José C. G. Alanis <12409129+Jo José C. García Alanis José C. García Alanis <12409129+JoseAlanis@users.noreply.github.com> Joshua J Bear Joshua Teves Joshua Teves +Joshua Calder-Travis <38797399+jCalderTravis@users.noreply.github.com> jCalderTravis <38797399+jCalderTravis@users.noreply.github.com> Julius Welzel <52565341+JuliusWelzel@users.noreply.github.com> jwelzel <52565341+JuliusWelzel@users.noreply.github.com> Kaisu Lankinen <41806798+klankinen@users.noreply.github.com> klankinen <41806798+klankinen@users.noreply.github.com> Kambiz Tabavi Kambiz Tavabi @@ -248,6 +250,7 @@ Pierre-Antoine Bannier Pierre-Antoine Bannier Pierre-Antoine Bannier Pierre-Antoine Bannier Praveen Sripad prav Praveen Sripad prav +Proloy Das pdas6 Ram Pari Ram Ramonapariciog Apariciogarcia ramonapariciog Reza Nasri Reza @@ -301,4 +304,5 @@ Yousra Bekhti Yoursa BEKHTI Yoursa BEKHTI Yousra Bekhti Yousra BEKHTI Yousra Bekhti yousrabk +Yiping Zuo Frostime Zhi Zhang <850734033@qq.com> ZHANG Zhi <850734033@qq.com> diff --git a/CITATION.cff b/CITATION.cff index 2b8381675dc..edda3668c4c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,9 +1,9 @@ cff-version: 1.2.0 title: "MNE-Python" message: "If you use this software, please cite both the software itself, and the paper listed in the preferred-citation field." -version: 1.4.0 -date-released: "2023-05-10" -commit: 425e3b34439bfcff68f4f926b886aaba9a02478c +version: 1.5.0 +date-released: "2023-08-15" +commit: 5645d375f52727eb563bd46a45422fc1a55e9f1a doi: 10.5281/zenodo.592483 keywords: - MEG @@ -55,10 +55,10 @@ authors: given-names: Mark - family-names: Holdgraf given-names: Chris - - family-names: Massich - given-names: Joan - family-names: Rockhill given-names: Alex + - family-names: Massich + given-names: Joan - family-names: Bekhti given-names: Yousra - family-names: Appelhoff @@ -67,6 +67,8 @@ authors: given-names: Alan - family-names: Dykstra given-names: Andrew + - family-names: Scheltienne + given-names: Mathieu - family-names: Luke given-names: Rob - family-names: Trachel @@ -77,8 +79,6 @@ authors: given-names: Asish - family-names: Magnuski given-names: Mikołaj - - family-names: Scheltienne - given-names: Mathieu - family-names: Westner given-names: Britta - family-names: Billinger @@ -133,6 +133,8 @@ authors: given-names: Christoph - family-names: Dumas given-names: Guillaume + - family-names: Huberty + given-names: Scott - family-names: Hartmann given-names: Thomas - family-names: Orfanos @@ -204,8 +206,8 @@ authors: given-names: Michiru - family-names: Klein given-names: Natalie - - family-names: Huberty - given-names: Scott + - family-names: Kern + given-names: Simon - family-names: Rantala given-names: Antti - family-names: Maess @@ -228,8 +230,8 @@ authors: given-names: Pierre-Antoine - family-names: Choudhary given-names: Saket - - family-names: Kern - given-names: Simon + - family-names: Gramfort + given-names: Alexandre - family-names: Forster given-names: Carina - family-names: Kim @@ -256,7 +258,6 @@ authors: given-names: Nathalie - family-names: Ward given-names: Nick - - name: dependabot[bot] - family-names: Quinn given-names: Andrew - family-names: Gauthier @@ -283,6 +284,8 @@ authors: given-names: Jan - family-names: Stout given-names: Jeff + - family-names: Calder-Travis + given-names: Joshua - family-names: Eisenman given-names: Larry - family-names: Esch @@ -313,8 +316,6 @@ authors: given-names: Alessandro - family-names: Kovrig given-names: Alexander - - family-names: Gramfort - given-names: Alexandre - family-names: Pascarella given-names: Annalisa - family-names: Karekal @@ -325,6 +326,8 @@ authors: given-names: Chetan - family-names: Zhao given-names: Christina + - family-names: Altukhov + given-names: Dmitrii - family-names: Krzemiński given-names: Dominik - family-names: Welke @@ -333,6 +336,12 @@ authors: given-names: Dominique - family-names: Mikulan given-names: Ezequiel + - family-names: Belonosov + given-names: Gennadiy + - family-names: O'Neill + given-names: George + - family-names: Woessner + given-names: Jacob - family-names: Schiratti given-names: Jean-Baptiste - family-names: Evans @@ -406,6 +415,8 @@ authors: given-names: Tziona - name: akshay0724 - name: sviter + - family-names: Earle-Richardson + given-names: Aaron - family-names: Hindle given-names: Abram - family-names: Koutsou @@ -450,6 +461,8 @@ authors: given-names: Daniel Carlström - family-names: Hasegan given-names: Daniel + - family-names: Tse + given-names: Daniel - family-names: Sleiter given-names: Darin Erat - family-names: Haslacher @@ -462,8 +475,8 @@ authors: given-names: Desislava - family-names: Issagaliyeva given-names: Dinara - - family-names: Altukhov - given-names: Dmitrii + - family-names: Das + given-names: Diptyajit - family-names: Wetzel given-names: Dominik - family-names: Eich @@ -496,11 +509,11 @@ authors: given-names: Geoff - family-names: O'Neill given-names: George - - family-names: O'Neill - given-names: George - name: Giulio - family-names: Maymandi given-names: Hamid + - family-names: Abdelhedi + given-names: Hamza - family-names: Sonntag given-names: Hermann - family-names: Ye @@ -511,8 +524,6 @@ authors: given-names: Hüseyin Orkun - family-names: Machairas given-names: Ilias - - family-names: Woessner - given-names: Jacob - family-names: Kaczmarzyk given-names: Jakub - family-names: Zerfowski @@ -610,6 +621,8 @@ authors: given-names: Pedro - family-names: Molfese given-names: Peter J + - family-names: Das + given-names: Proloy - family-names: Li given-names: Quanliang - family-names: Barthélemy @@ -638,6 +651,8 @@ authors: given-names: Sagun - family-names: Perry given-names: Sam + - family-names: Louviot + given-names: Samuel - family-names: Ruuskanen given-names: Santeri - family-names: Saha @@ -676,6 +691,8 @@ authors: given-names: T - family-names: Donoghue given-names: Thomas + - family-names: Moreau + given-names: Thomas - family-names: Radman given-names: Thomas - family-names: Gates @@ -690,6 +707,8 @@ authors: given-names: Toomas Erik - family-names: Xia given-names: Xiaokai + - family-names: Zuo + given-names: Yiping - family-names: Zhang given-names: Zhi - name: buildqa diff --git a/SECURITY.md b/SECURITY.md index 95069805d69..c61f3bfae87 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -10,9 +10,9 @@ without a proper 6-month deprecation cycle. | Version | Supported | | ------- | ------------------------ | -| 1.5.x | :heavy_check_mark: (dev) | -| 1.4.x | :heavy_check_mark: | -| < 1.4 | :x: | +| 1.6.x | :heavy_check_mark: (dev) | +| 1.5.x | :heavy_check_mark: | +| < 1.5 | :x: | ## Reporting a Vulnerability diff --git a/codemeta.json b/codemeta.json index 84c6797474f..7e8b2cca70a 100644 --- a/codemeta.json +++ b/codemeta.json @@ -5,11 +5,11 @@ "codeRepository": "git+https://github.com/mne-tools/mne-python.git", "dateCreated": "2010-12-26", "datePublished": "2014-08-04", - "dateModified": "2023-05-10", - "downloadUrl": "https://github.com/mne-tools/mne-python/archive/v1.4.0.zip", + "dateModified": "2023-08-15", + "downloadUrl": "https://github.com/mne-tools/mne-python/archive/v1.5.0.zip", "issueTracker": "https://github.com/mne-tools/mne-python/issues", "name": "MNE-Python", - "version": "1.4.0", + "version": "1.5.0", "description": "MNE-Python is an open-source Python package for exploring, visualizing, and analyzing human neurophysiological data. It provides methods for data input/output, preprocessing, visualization, source estimation, time-frequency analysis, connectivity analysis, machine learning, and statistics.", "applicationCategory": "Neuroscience", "developmentStatus": "active", @@ -150,18 +150,18 @@ "givenName":"Chris", "familyName": "Holdgraf" }, - { - "@type":"Person", - "email":"mailsik@gmail.com", - "givenName":"Joan", - "familyName": "Massich" - }, { "@type":"Person", "email":"aprockhill206@gmail.com", "givenName":"Alex", "familyName": "Rockhill" }, + { + "@type":"Person", + "email":"mailsik@gmail.com", + "givenName":"Joan", + "familyName": "Massich" + }, { "@type":"Person", "email":"yousra.bekhti@gmail.com", @@ -186,6 +186,12 @@ "givenName":"Andrew", "familyName": "Dykstra" }, + { + "@type":"Person", + "email":"mathieu.scheltienne@gmail.com", + "givenName":"Mathieu", + "familyName": "Scheltienne" + }, { "@type":"Person", "email":"code@robertluke.net", @@ -216,12 +222,6 @@ "givenName":"Mikołaj", "familyName": "Magnuski" }, - { - "@type":"Person", - "email":"mathieu.scheltienne@gmail.com", - "givenName":"Mathieu", - "familyName": "Scheltienne" - }, { "@type":"Person", "email":"britta.wstnr@gmail.com", @@ -384,6 +384,12 @@ "givenName":"Guillaume", "familyName": "Dumas" }, + { + "@type":"Person", + "email":"", + "givenName":"Scott", + "familyName": "Huberty" + }, { "@type":"Person", "email":"thomas.hartmann@th-ht.de", @@ -602,9 +608,9 @@ }, { "@type":"Person", - "email":"", - "givenName":"Scott", - "familyName": "Huberty" + "email":"simon.kern@online.de", + "givenName":"Simon", + "familyName": "Kern" }, { "@type":"Person", @@ -674,9 +680,9 @@ }, { "@type":"Person", - "email":"simon.kern@online.de", - "givenName":"Simon", - "familyName": "Kern" + "email":"agramfort@fb.com", + "givenName":"Alexandre", + "familyName": "Gramfort" }, { "@type":"Person", @@ -756,12 +762,6 @@ "givenName":"Nick", "familyName": "Ward" }, - { - "@type":"Person", - "email":"", - "givenName":"", - "familyName": "dependabot[bot]" - }, { "@type":"Person", "email":"", @@ -840,6 +840,12 @@ "givenName":"Jeff", "familyName": "Stout" }, + { + "@type":"Person", + "email":"", + "givenName":"Joshua", + "familyName": "Calder-Travis" + }, { "@type":"Person", "email":"leisenman@wustl.edu", @@ -930,12 +936,6 @@ "givenName":"Alexander", "familyName": "Kovrig" }, - { - "@type":"Person", - "email":"agramfort@fb.com", - "givenName":"Alexandre", - "familyName": "Gramfort" - }, { "@type":"Person", "email":"a.pascarella@iac.cnr.it", @@ -966,6 +966,12 @@ "givenName":"Christina", "familyName": "Zhao" }, + { + "@type":"Person", + "email":"dm.altukhov@ya.ru", + "givenName":"Dmitrii", + "familyName": "Altukhov" + }, { "@type":"Person", "email":"raymon92@gmail.com", @@ -990,6 +996,24 @@ "givenName":"Ezequiel", "familyName": "Mikulan" }, + { + "@type":"Person", + "email":"", + "givenName":"Gennadiy", + "familyName": "Belonosov" + }, + { + "@type":"Person", + "email":"g.o'neill@ucl.ac.uk", + "givenName":"George", + "familyName": "O'Neill" + }, + { + "@type":"Person", + "email":"Woessner.jacob@gmail.com", + "givenName":"Jacob", + "familyName": "Woessner" + }, { "@type":"Person", "email":"jean.baptiste.schiratti@gmail.com", @@ -1218,6 +1242,12 @@ "givenName":"", "familyName": "sviter" }, + { + "@type":"Person", + "email":"Jakdaxter31@gmail.com", + "givenName":"Aaron", + "familyName": "Earle-Richardson" + }, { "@type":"Person", "email":"abram.hindle@softwareprocess.es", @@ -1350,6 +1380,12 @@ "givenName":"Daniel", "familyName": "Hasegan" }, + { + "@type":"Person", + "email":"xiezhibin.0.0.superman@gmail.com", + "givenName":"Daniel", + "familyName": "Tse" + }, { "@type":"Person", "email":"darin.sleiter@gmail.com", @@ -1388,9 +1424,9 @@ }, { "@type":"Person", - "email":"dm.altukhov@ya.ru", - "givenName":"Dmitrii", - "familyName": "Altukhov" + "email":"", + "givenName":"Diptyajit", + "familyName": "Das" }, { "@type":"Person", @@ -1482,12 +1518,6 @@ "givenName":"Geoff", "familyName": "Brookshire" }, - { - "@type":"Person", - "email":"g.o'neill@ucl.ac.uk", - "givenName":"George", - "familyName": "O'Neill" - }, { "@type":"Person", "email":"george.oneill.90@gmail.com", @@ -1506,6 +1536,12 @@ "givenName":"Hamid", "familyName": "Maymandi" }, + { + "@type":"Person", + "email":"hamza.abdelhedii@gmail.com", + "givenName":"Hamza", + "familyName": "Abdelhedi" + }, { "@type":"Person", "email":"hermann.sonntag@gmail.com", @@ -1536,12 +1572,6 @@ "givenName":"Ilias", "familyName": "Machairas" }, - { - "@type":"Person", - "email":"Woessner.jacob@gmail.com", - "givenName":"Jacob", - "familyName": "Woessner" - }, { "@type":"Person", "email":"", @@ -1836,6 +1866,12 @@ "givenName":"Peter J", "familyName": "Molfese" }, + { + "@type":"Person", + "email":"proloy@umd.edu", + "givenName":"Proloy", + "familyName": "Das" + }, { "@type":"Person", "email":"glia@dtu.dk", @@ -1920,6 +1956,12 @@ "givenName":"Sam", "familyName": "Perry" }, + { + "@type":"Person", + "email":"", + "givenName":"Samuel", + "familyName": "Louviot" + }, { "@type":"Person", "email":"", @@ -2034,6 +2076,12 @@ "givenName":"Thomas", "familyName": "Donoghue" }, + { + "@type":"Person", + "email":"thomas.moreau.2010@gmail.com", + "givenName":"Thomas", + "familyName": "Moreau" + }, { "@type":"Person", "email":"radman.thomas@gmail.com", @@ -2076,6 +2124,12 @@ "givenName":"Xiaokai", "familyName": "Xia" }, + { + "@type":"Person", + "email":"frostime@foxmail.com", + "givenName":"Yiping", + "familyName": "Zuo" + }, { "@type":"Person", "email":"850734033@qq.com", diff --git a/doc/Makefile b/doc/Makefile index f32527537d5..ee6b0348a37 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -23,7 +23,7 @@ help: @echo " html-noplot to make standalone HTML files without plotting" @echo " clean to clean HTML files" @echo " linkcheck to check all external links for integrity" - @echo " linkcheck-grep to grep the linkcheck resut" + @echo " linkcheck-grep to grep the linkcheck result" @echo " doctest to run all doctests embedded in the documentation (if enabled)" @echo " view to view the built HTML" diff --git a/doc/_static/versions.json b/doc/_static/versions.json index 7abcfa58291..249df8f1c41 100644 --- a/doc/_static/versions.json +++ b/doc/_static/versions.json @@ -1,14 +1,19 @@ [ { - "name": "1.5 (devel)", + "name": "1.6 (devel)", "version": "dev", "url": "https://mne.tools/dev/" }, { - "name": "1.4 (stable)", + "name": "1.5 (stable)", "version": "stable", "url": "https://mne.tools/stable/" }, + { + "name": "1.4", + "version": "1.4", + "url": "https://mne.tools/1.4/" + }, { "name": "1.3", "version": "1.3", diff --git a/doc/changes/0.17.inc b/doc/changes/0.17.inc index fa5a49a5287..82db1975a9f 100644 --- a/doc/changes/0.17.inc +++ b/doc/changes/0.17.inc @@ -24,7 +24,7 @@ Changelog - Add optically pumped magnetometer dataset and example by `Rasmus Zetter`_ and `Eric Larson`_ -- Add ``orgin`` parameter to :meth:`mne.io.Raw.time_as_index` to allow ``times`` to be relative to this ``origin`` by `Joan Massich`_ +- Add ``origin`` parameter to :meth:`mne.io.Raw.time_as_index` to allow ``times`` to be relative to this ``origin`` by `Joan Massich`_ - Add ``title`` argument to :meth:`mne.SourceEstimate.plot` by `Eric Larson`_ diff --git a/doc/changes/0.8.inc b/doc/changes/0.8.inc index 62d3b17d404..c1de1638fdf 100644 --- a/doc/changes/0.8.inc +++ b/doc/changes/0.8.inc @@ -90,7 +90,7 @@ Changelog - Add automated ECG detection using cross-trial phase statistics by `Denis Engemann`_ and `Juergen Dammers`_ -- Add Forward class to succintly display gain matrix info by `Andrew Dykstra`_ +- Add Forward class to succinctly display gain matrix info by `Andrew Dykstra`_ - Add reading and writing of split raw files by `Martin Luessi`_ diff --git a/doc/changes/latest.inc b/doc/changes/1.5.inc similarity index 94% rename from doc/changes/latest.inc rename to doc/changes/1.5.inc index 402be21f154..a272e6c6fdc 100644 --- a/doc/changes/latest.inc +++ b/doc/changes/1.5.inc @@ -16,10 +16,10 @@ Also add a corresponding entry for yourself in doc/changes/names.inc -.. _current: +.. _changes_1_5_0: -Current (1.5.dev0) ------------------- +Version 1.5.0 (2023-08-14) +-------------------------- Enhancements ~~~~~~~~~~~~ @@ -78,3 +78,30 @@ API changes - The ``baseline`` argument can now be array-like (e.g. ``list``, ``tuple``, ``np.ndarray``, ...) instead of only a ``tuple`` (:gh:`11713` by `Clemens Brunner`_) - The ``events`` and ``event_id`` parameters of `:meth:`Epochs.plot() ` now accept boolean values; see docstring for details (:gh:`11445` by `Daniel McCloy`_ and `Clemens Brunner`_) - Deprecated ``gap_description`` keyword argument of :func:`mne.io.read_raw_eyelink`, which will be removed in mne version 1.6, in favor of using :meth:`mne.Annotations.rename` (:gh:`11719` by `Scott Huberty`_) + +Authors +~~~~~~~ +* Aaron Earle-Richardson+ +* Alex Rockhill +* Alexandre Gramfort +* Britta Westner +* Clemens Brunner +* Daniel McCloy +* Daniel Tse+ +* Diptyajit Das+ +* Eric Larson +* Gennadiy Belonosov+ +* George O'Neill +* Hamza Abdelhedi+ +* Jacob Woessner +* Joshua Calder-Travis+ +* Mathieu Scheltienne +* Proloy Das +* Richard Höchenberger +* Rob Luke +* Samuel Louviot+ +* Scott Huberty +* Simon Kern +* Stefan Appelhoff +* Thomas Moreau +* Yiping Zuo+ diff --git a/doc/cited.rst b/doc/cited.rst index 4a239498eb0..7654cf3fd40 100644 --- a/doc/cited.rst +++ b/doc/cited.rst @@ -3,7 +3,7 @@ Papers citing MNE-Python ======================== -Estimates provided by Google Scholar as of 10 May 2023: +Estimates provided by Google Scholar as of 14 August 2023: -- `MNE (1460) `_ -- `MNE-Python (1860) `_ +- `MNE (1540) `_ +- `MNE-Python (2040) `_ diff --git a/doc/whats_new.rst b/doc/whats_new.rst index 1cd64070616..44ec2480100 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -7,7 +7,7 @@ What's new .. currentmodule:: mne -.. include:: changes/latest.inc +.. include:: changes/1.5.inc .. include:: changes/1.4.inc .. include:: changes/1.3.inc .. include:: changes/1.2.inc diff --git a/ignore_words.txt b/ignore_words.txt index a1855634a34..2d542566498 100644 --- a/ignore_words.txt +++ b/ignore_words.txt @@ -36,3 +36,4 @@ nam shs pres aas +vor diff --git a/mne/channels/tests/test_interpolation.py b/mne/channels/tests/test_interpolation.py index c9a0c41ff97..2d24eb16b91 100644 --- a/mne/channels/tests/test_interpolation.py +++ b/mne/channels/tests/test_interpolation.py @@ -162,7 +162,7 @@ def test_interpolation_eeg(offset, avg_proj, ctol, atol, method): # check that interpolation fails when preload is False epochs_eeg.preload = False - with pytest.raises(RuntimeError, match="requires epochs data to be loade"): + with pytest.raises(RuntimeError, match="requires epochs data to be load"): epochs_eeg.interpolate_bads(**kw) epochs_eeg.preload = True diff --git a/mne/label.py b/mne/label.py index cf8bf751f5f..74c865fc0e8 100644 --- a/mne/label.py +++ b/mne/label.py @@ -1644,7 +1644,7 @@ def stc_to_label( def _verts_within_dist(graph, sources, max_dist): - """Find all vertices wihin a maximum geodesic distance from source. + """Find all vertices within a maximum geodesic distance from source. Parameters ---------- diff --git a/mne/report/report.py b/mne/report/report.py index a354769dee9..874d965f721 100644 --- a/mne/report/report.py +++ b/mne/report/report.py @@ -3136,7 +3136,7 @@ def _add_raw_butterfly_segments( try: raw.set_annotations(None) - # Create the figure once and re-use it for performance reasons + # Create the figure once and reuse it for performance reasons with use_browser_backend("matplotlib"): fig = raw.plot( butterfly=True, diff --git a/mne/transforms.py b/mne/transforms.py index cdf81ae6fb3..07005f740c1 100644 --- a/mne/transforms.py +++ b/mne/transforms.py @@ -801,7 +801,7 @@ def _cart_to_sph(cart): def _sph_to_cart(sph_pts): - """Convert spherical coordinates to Cartesion coordinates. + """Convert spherical coordinates to Cartesian coordinates. Parameters ---------- @@ -1208,7 +1208,7 @@ def fit( src_rad_az_pol[0] = np.abs(np.dot(match_sph, src_coeffs)) dest_rad_az_pol = match_rad_az_pol.copy() dest_rad_az_pol[0] = np.abs(np.dot(match_sph, dest_coeffs)) - # 5. Convert matched points to Cartesion coordinates and put back + # 5. Convert matched points to Cartesian coordinates and put back source = _sph_to_cart(src_rad_az_pol.T) source += src_center destination = _sph_to_cart(dest_rad_az_pol.T)