diff --git a/.mailmap b/.mailmap index 10afa14ea85..d71df509cc2 100644 --- a/.mailmap +++ b/.mailmap @@ -114,11 +114,13 @@ Giorgio Marinato neurogima <76406896+neurogima@users Guillaume Dumas deep-introspection Guillaume Dumas Guillaume Dumas Hamid Maymandi <46011104+HamidMandi@users.noreply.github.com> Hamid <46011104+HamidMandi@users.noreply.github.com> +Hasrat Ali Arzoo <56307533+hasrat17@users.noreply.github.com> hasrat17 <56307533+hasrat17@users.noreply.github.com> Hongjiang Ye YE Hongjiang Hubert Banville hubertjb Hüseyin Orkun Elmas Hüseyin Hyonyoung Shin <55095699+mcvain@users.noreply.github.com> mcvain <55095699+mcvain@users.noreply.github.com> Ingoo Lee dlsrnsi +Ivo de Jong ivopascal Jaakko Leppakangas Jaakko Leppakangas Jaakko Leppakangas jaeilepp Jaakko Leppakangas jaeilepp diff --git a/CITATION.cff b/CITATION.cff index c1850a2f55b..936f3f90677 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: 1.6.0 -date-released: "2023-11-20" -commit: 498cf789685ede0b29e712a1e7220c69443e8744 +version: 1.7.0 +date-released: "2024-04-19" +commit: a3743420a8eef774dafd2908f0de89c4d37fcd01 doi: 10.5281/zenodo.592483 keywords: - MEG @@ -35,10 +35,10 @@ authors: given-names: Teon - family-names: Sassenhagen given-names: Jona - - family-names: Luessi - given-names: Martin - family-names: McCloy given-names: Daniel + - family-names: Luessi + given-names: Martin - family-names: King given-names: Jean-Remi - family-names: Höchenberger @@ -53,10 +53,10 @@ authors: given-names: Marijn - family-names: Wronkiewicz given-names: Mark - - family-names: Holdgraf - given-names: Chris - family-names: Rockhill given-names: Alex + - family-names: Holdgraf + given-names: Chris - family-names: Massich given-names: Joan - family-names: Bekhti @@ -117,12 +117,12 @@ authors: given-names: Martin - family-names: Foti given-names: Nick + - family-names: Huberty + given-names: Scott - family-names: Nangini given-names: Cathy - family-names: García Alanis given-names: José C - - family-names: Huberty - given-names: Scott - family-names: Hauk given-names: Olaf - family-names: Maddox @@ -165,6 +165,10 @@ authors: given-names: Christopher - family-names: Raimundo given-names: Félix + - family-names: Woessner + given-names: Jacob + - family-names: Kaneda + given-names: Michiru - family-names: Alday given-names: Phillip - family-names: Pari @@ -189,6 +193,10 @@ authors: given-names: Alexandre - family-names: Gütlin given-names: Dirk + - family-names: Heinila + given-names: Erkka + - family-names: Armeni + given-names: Kristijan - name: kjs - family-names: Weinstein given-names: Alejandro @@ -202,14 +210,10 @@ authors: given-names: Dmitrii - family-names: Peterson given-names: Erica - - family-names: Heinila - given-names: Erkka - family-names: Hanna given-names: Jevri - family-names: Houck given-names: Jon - - family-names: Kaneda - given-names: Michiru - family-names: Klein given-names: Natalie - family-names: Roujansky @@ -220,16 +224,18 @@ authors: given-names: Antti - family-names: Maess given-names: Burkhard + - family-names: Forster + given-names: Carina - family-names: O'Reilly given-names: Christian + - family-names: Welke + given-names: Dominik - family-names: Kolkhorst given-names: Henrich - family-names: Banville given-names: Hubert - family-names: Zhang given-names: Jack - - family-names: Woessner - given-names: Jacob - family-names: Maksymenko given-names: Kostiantyn - family-names: Clarke @@ -242,8 +248,6 @@ authors: given-names: Pierre-Antoine - family-names: Choudhary given-names: Saket - - family-names: Forster - given-names: Carina - family-names: Kim given-names: Cora - family-names: Klotzsche @@ -268,6 +272,8 @@ authors: given-names: Nick - family-names: Ruuskanen given-names: Santeri + - family-names: Herbst + given-names: Sophie - family-names: Radanovic given-names: Ana - family-names: Quinn @@ -278,8 +284,6 @@ authors: given-names: Basile - family-names: Welke given-names: Dominik - - family-names: Welke - given-names: Dominik - family-names: Stephen given-names: Emily - family-names: Hornberger @@ -294,22 +298,30 @@ authors: given-names: Giorgio - family-names: Anevar given-names: Hafeza + - family-names: Abdelhedi + given-names: Hamza - family-names: Sosulski given-names: Jan - family-names: Stout given-names: Jeff - family-names: Calder-Travis given-names: Joshua + - family-names: Zhu + given-names: Judy D - family-names: Eisenman given-names: Larry - family-names: Esch given-names: Lorenz - family-names: Dovgialo given-names: Marian + - family-names: Alibou + given-names: Nabil - family-names: Barascud given-names: Nicolas - family-names: Legrand given-names: Nicolas + - family-names: Kapralov + given-names: Nikolai - family-names: Falach given-names: Rotem - family-names: Deslauriers-Gauthier @@ -320,6 +332,10 @@ authors: given-names: Steve - family-names: Bierer given-names: Steven + - family-names: Binns + given-names: Thomas Samuel + - family-names: Stenner + given-names: Tristan - family-names: Férat given-names: Victor - family-names: Peterson @@ -350,8 +366,6 @@ authors: given-names: Gennadiy - family-names: O'Neill given-names: George - - family-names: Abdelhedi - given-names: Hamza - family-names: Schiratti given-names: Jean-Baptiste - family-names: Evans @@ -362,16 +376,14 @@ authors: given-names: Jordan - family-names: Teves given-names: Joshua - - family-names: Zhu - given-names: Judy D - - family-names: Armeni - given-names: Kristijan - family-names: Mathewson given-names: Kyle - family-names: Gwilliams given-names: Laura - family-names: Varghese given-names: Lenny + - family-names: Hamilton + given-names: Liberty - family-names: Gemein given-names: Lukas - family-names: Hecker @@ -393,6 +405,8 @@ authors: given-names: Niklas - family-names: Kozynets given-names: Oleh + - family-names: Molfese + given-names: Peter J - family-names: Ablin given-names: Pierre - family-names: Bertrand @@ -407,24 +421,20 @@ authors: given-names: Sena - family-names: Khan given-names: Sheraz - - family-names: Herbst - given-names: Sophie - family-names: Datta given-names: Sumalyo - family-names: Papadopoulo given-names: Theodore + - family-names: Donoghue + given-names: Thomas - family-names: Jochmann given-names: Thomas - - family-names: Binns - given-names: Thomas Samuel - family-names: Merk given-names: Timon - family-names: Flak given-names: Tod - family-names: Dupré la Tour given-names: Tom - - family-names: Stenner - given-names: Tristan - family-names: NessAiver given-names: Tziona - name: akshay0724 @@ -441,6 +451,8 @@ authors: given-names: Adina - family-names: Ciok given-names: Alex + - family-names: Kiefer + given-names: Alexander - family-names: Gilbert given-names: Andy - family-names: Pradhan @@ -515,6 +527,8 @@ authors: given-names: Evgeny - family-names: Zamberlan given-names: Federico + - family-names: Hofer + given-names: Florian - family-names: Pop given-names: Florin - family-names: Weber @@ -530,6 +544,8 @@ authors: given-names: Gonzalo - family-names: Maymandi given-names: Hamid + - family-names: Arzoo + given-names: Hasrat Ali - family-names: Sonntag given-names: Hermann - family-names: Ye @@ -540,10 +556,10 @@ authors: given-names: Hüseyin Orkun - family-names: Machairas given-names: Ilias - - family-names: Skelin - given-names: Ivan - family-names: Zubarev given-names: Ivan + - family-names: de Jong + given-names: Ivo - family-names: Kaczmarzyk given-names: Jakub - family-names: Zerfowski @@ -576,8 +592,6 @@ authors: given-names: Lau Møller - family-names: Barbosa given-names: Leonardo S - - family-names: Hamilton - given-names: Liberty - family-names: Alfine given-names: Lorenzo - family-names: Hejtmánek @@ -596,6 +610,8 @@ authors: given-names: Marcin - family-names: Henney given-names: Mark Alexander + - family-names: Oberg + given-names: Martin - family-names: Schulz given-names: Martin - family-names: van Harmelen @@ -639,8 +655,6 @@ authors: given-names: Padma - family-names: Silva given-names: Pedro - - family-names: Molfese - given-names: Peter J - family-names: Das given-names: Proloy - family-names: Chu @@ -661,6 +675,8 @@ authors: given-names: Reza - family-names: Koehler given-names: Richard + - family-names: Scholz + given-names: Richard - family-names: Stargardsky given-names: Riessarius - family-names: Oostenveld @@ -691,6 +707,8 @@ authors: given-names: Senwen - family-names: Antopolskiy given-names: Sergey + - family-names: Shirazi + given-names: Seyed (Yahya) - family-names: Wong given-names: Simeon - family-names: Wong @@ -711,8 +729,6 @@ authors: given-names: Svea Marie - family-names: Wang given-names: T - - family-names: Donoghue - given-names: Thomas - family-names: Moreau given-names: Thomas - family-names: Radman @@ -727,12 +743,17 @@ authors: given-names: Tommy - family-names: Anijärv given-names: Toomas Erik + - family-names: Kumaravel + given-names: Velu Prabhakar + - family-names: Turner + given-names: Will - family-names: Xia given-names: Xiaokai - family-names: Zuo given-names: Yiping - family-names: Zhang given-names: Zhi + - name: btkcodedev - name: buildqa - name: luzpaz preferred-citation: diff --git a/SECURITY.md b/SECURITY.md index e627242d244..82d4c9e45de 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -10,9 +10,9 @@ without a proper 6-month deprecation cycle. | Version | Supported | | ------- | ------------------------ | -| 1.7.x | :heavy_check_mark: (dev) | -| 1.6.x | :heavy_check_mark: | -| < 1.6 | :x: | +| 1.8.x | :heavy_check_mark: (dev) | +| 1.7.x | :heavy_check_mark: | +| < 1.7 | :x: | ## Reporting a Vulnerability diff --git a/codemeta.json b/codemeta.json index b2922b2194d..ebfe798c648 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": "2023-11-20", - "downloadUrl": "https://github.com/mne-tools/mne-python/archive/v1.6.0.zip", + "dateModified": "2024-04-19", + "downloadUrl": "https://github.com/mne-tools/mne-python/archive/v1.7.0.zip", "issueTracker": "https://github.com/mne-tools/mne-python/issues", "name": "MNE-Python", - "version": "1.6.0", + "version": "1.7.0", "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", @@ -37,7 +37,7 @@ "macOS" ], "softwareRequirements": [ - "python>=3.8", + "python>=3.9", "numpy>=1.21.2", "scipy>=1.7.1", "matplotlib>=3.5.0", @@ -46,9 +46,7 @@ "decorator", "packaging", "jinja2", - "importlib_resources>=5.10.2; python_version<'3.9'", - "lazy_loader>=0.3", - "defusedxml" + "lazy_loader>=0.3" ], "author": [ { @@ -99,18 +97,18 @@ "givenName":"Jona", "familyName": "Sassenhagen" }, - { - "@type":"Person", - "email":"mluessi@nmr.mgh.harvard.edu", - "givenName":"Martin", - "familyName": "Luessi" - }, { "@type":"Person", "email":"dan@mccloy.info", "givenName":"Daniel", "familyName": "McCloy" }, + { + "@type":"Person", + "email":"mluessi@nmr.mgh.harvard.edu", + "givenName":"Martin", + "familyName": "Luessi" + }, { "@type":"Person", "email":"jeanremi.king+github@gmail.com", @@ -153,18 +151,18 @@ "givenName":"Mark", "familyName": "Wronkiewicz" }, - { - "@type":"Person", - "email":"choldgraf@gmail.com", - "givenName":"Chris", - "familyName": "Holdgraf" - }, { "@type":"Person", "email":"aprockhill206@gmail.com", "givenName":"Alex", "familyName": "Rockhill" }, + { + "@type":"Person", + "email":"choldgraf@gmail.com", + "givenName":"Chris", + "familyName": "Holdgraf" + }, { "@type":"Person", "email":"mailsik@gmail.com", @@ -345,6 +343,12 @@ "givenName":"Nick", "familyName": "Foti" }, + { + "@type":"Person", + "email":"", + "givenName":"Scott", + "familyName": "Huberty" + }, { "@type":"Person", "email":"cnangini@gmail.com", @@ -357,12 +361,6 @@ "givenName":"José C", "familyName": "García Alanis" }, - { - "@type":"Person", - "email":"", - "givenName":"Scott", - "familyName": "Huberty" - }, { "@type":"Person", "email":"olaf.hauk@mrc-cbu.cam.ac.uk", @@ -489,6 +487,18 @@ "givenName":"Félix", "familyName": "Raimundo" }, + { + "@type":"Person", + "email":"Woessner.jacob@gmail.com", + "givenName":"Jacob", + "familyName": "Woessner" + }, + { + "@type":"Person", + "email":"rcmdnk@gmail.com", + "givenName":"Michiru", + "familyName": "Kaneda" + }, { "@type":"Person", "email":"phillip.alday@mpi.nl", @@ -561,6 +571,18 @@ "givenName":"Dirk", "familyName": "Gütlin" }, + { + "@type":"Person", + "email":"erkkahe@gmail.com", + "givenName":"Erkka", + "familyName": "Heinila" + }, + { + "@type":"Person", + "email":"kristijan.armeni@gmail.com", + "givenName":"Kristijan", + "familyName": "Armeni" + }, { "@type":"Person", "email":"kjs@llama", @@ -603,12 +625,6 @@ "givenName":"Erica", "familyName": "Peterson" }, - { - "@type":"Person", - "email":"erkkahe@gmail.com", - "givenName":"Erkka", - "familyName": "Heinila" - }, { "@type":"Person", "email":"jevri.hanna@gmail.com", @@ -621,12 +637,6 @@ "givenName":"Jon", "familyName": "Houck" }, - { - "@type":"Person", - "email":"rcmdnk@gmail.com", - "givenName":"Michiru", - "familyName": "Kaneda" - }, { "@type":"Person", "email":"neklein@andrew.cmu.edu", @@ -657,12 +667,24 @@ "givenName":"Burkhard", "familyName": "Maess" }, + { + "@type":"Person", + "email":"carinaforster0611@gmail.com", + "givenName":"Carina", + "familyName": "Forster" + }, { "@type":"Person", "email":"christian.oreilly@gmail.com", "givenName":"Christian", "familyName": "O'Reilly" }, + { + "@type":"Person", + "email":"dominik.welke@ae.mpg.de", + "givenName":"Dominik", + "familyName": "Welke" + }, { "@type":"Person", "email":"", @@ -681,12 +703,6 @@ "givenName":"Jack", "familyName": "Zhang" }, - { - "@type":"Person", - "email":"Woessner.jacob@gmail.com", - "givenName":"Jacob", - "familyName": "Woessner" - }, { "@type":"Person", "email":"makkostya@ukr.net", @@ -723,12 +739,6 @@ "givenName":"Saket", "familyName": "Choudhary" }, - { - "@type":"Person", - "email":"carinaforster0611@gmail.com", - "givenName":"Carina", - "familyName": "Forster" - }, { "@type":"Person", "email":"", @@ -801,6 +811,12 @@ "givenName":"Santeri", "familyName": "Ruuskanen" }, + { + "@type":"Person", + "email":"ksherbst@gmail.com", + "givenName":"Sophie", + "familyName": "Herbst" + }, { "@type":"Person", "email":"", @@ -825,12 +841,6 @@ "givenName":"Basile", "familyName": "Pinsard" }, - { - "@type":"Person", - "email":"dominik.welke@ae.mpg.de", - "givenName":"Dominik", - "familyName": "Welke" - }, { "@type":"Person", "email":"dominik.welke@web.de", @@ -879,6 +889,12 @@ "givenName":"Hafeza", "familyName": "Anevar" }, + { + "@type":"Person", + "email":"hamza.abdelhedii@gmail.com", + "givenName":"Hamza", + "familyName": "Abdelhedi" + }, { "@type":"Person", "email":"mail@jan-sosulski.de", @@ -897,6 +913,12 @@ "givenName":"Joshua", "familyName": "Calder-Travis" }, + { + "@type":"Person", + "email":"", + "givenName":"Judy D", + "familyName": "Zhu" + }, { "@type":"Person", "email":"leisenman@wustl.edu", @@ -915,6 +937,12 @@ "givenName":"Marian", "familyName": "Dovgialo" }, + { + "@type":"Person", + "email":"", + "givenName":"Nabil", + "familyName": "Alibou" + }, { "@type":"Person", "email":"", @@ -927,6 +955,12 @@ "givenName":"Nicolas", "familyName": "Legrand" }, + { + "@type":"Person", + "email":"4dvlup@gmail.com", + "givenName":"Nikolai", + "familyName": "Kapralov" + }, { "@type":"Person", "email":"falachrotem@gmail.com", @@ -957,6 +991,18 @@ "givenName":"Steven", "familyName": "Bierer" }, + { + "@type":"Person", + "email":"t.s.binns@outlook.com", + "givenName":"Thomas Samuel", + "familyName": "Binns" + }, + { + "@type":"Person", + "email":"ttstenner@gmail.com", + "givenName":"Tristan", + "familyName": "Stenner" + }, { "@type":"Person", "email":"victor.ferat@live.Fr", @@ -1047,12 +1093,6 @@ "givenName":"George", "familyName": "O'Neill" }, - { - "@type":"Person", - "email":"hamza.abdelhedii@gmail.com", - "givenName":"Hamza", - "familyName": "Abdelhedi" - }, { "@type":"Person", "email":"jean.baptiste.schiratti@gmail.com", @@ -1083,18 +1123,6 @@ "givenName":"Joshua", "familyName": "Teves" }, - { - "@type":"Person", - "email":"", - "givenName":"Judy D", - "familyName": "Zhu" - }, - { - "@type":"Person", - "email":"kristijan.armeni@gmail.com", - "givenName":"Kristijan", - "familyName": "Armeni" - }, { "@type":"Person", "email":"kylemath@gmail.com", @@ -1113,6 +1141,12 @@ "givenName":"Lenny", "familyName": "Varghese" }, + { + "@type":"Person", + "email":"", + "givenName":"Liberty", + "familyName": "Hamilton" + }, { "@type":"Person", "email":"", @@ -1179,6 +1213,12 @@ "givenName":"Oleh", "familyName": "Kozynets" }, + { + "@type":"Person", + "email":"pmolfese@gmail.com", + "givenName":"Peter J", + "familyName": "Molfese" + }, { "@type":"Person", "email":"pierreablin@gmail.com", @@ -1221,12 +1261,6 @@ "givenName":"Sheraz", "familyName": "Khan" }, - { - "@type":"Person", - "email":"ksherbst@gmail.com", - "givenName":"Sophie", - "familyName": "Herbst" - }, { "@type":"Person", "email":"", @@ -1241,15 +1275,15 @@ }, { "@type":"Person", - "email":"", + "email":"tdonoghue.research@gmail.com", "givenName":"Thomas", - "familyName": "Jochmann" + "familyName": "Donoghue" }, { "@type":"Person", - "email":"t.s.binns@outlook.com", - "givenName":"Thomas Samuel", - "familyName": "Binns" + "email":"", + "givenName":"Thomas", + "familyName": "Jochmann" }, { "@type":"Person", @@ -1269,12 +1303,6 @@ "givenName":"Tom", "familyName": "Dupré la Tour" }, - { - "@type":"Person", - "email":"ttstenner@gmail.com", - "givenName":"Tristan", - "familyName": "Stenner" - }, { "@type":"Person", "email":"tzionan@mail.tau.ac.il", @@ -1329,6 +1357,12 @@ "givenName":"Alex", "familyName": "Ciok" }, + { + "@type":"Person", + "email":"", + "givenName":"Alexander", + "familyName": "Kiefer" + }, { "@type":"Person", "email":"7andy121@gmail.com", @@ -1551,6 +1585,12 @@ "givenName":"Federico", "familyName": "Zamberlan" }, + { + "@type":"Person", + "email":"hofaflo@gmail.com", + "givenName":"Florian", + "familyName": "Hofer" + }, { "@type":"Person", "email":"florinpop@me.com", @@ -1599,6 +1639,12 @@ "givenName":"Hamid", "familyName": "Maymandi" }, + { + "@type":"Person", + "email":"", + "givenName":"Hasrat Ali", + "familyName": "Arzoo" + }, { "@type":"Person", "email":"hermann.sonntag@gmail.com", @@ -1631,15 +1677,15 @@ }, { "@type":"Person", - "email":"", + "email":"ivan.zubarev@aalto.fi", "givenName":"Ivan", - "familyName": "Skelin" + "familyName": "Zubarev" }, { "@type":"Person", - "email":"ivan.zubarev@aalto.fi", - "givenName":"Ivan", - "familyName": "Zubarev" + "email":"ivopascal@gmail.com", + "givenName":"Ivo", + "familyName": "de Jong" }, { "@type":"Person", @@ -1737,12 +1783,6 @@ "givenName":"Leonardo S", "familyName": "Barbosa" }, - { - "@type":"Person", - "email":"", - "givenName":"Liberty", - "familyName": "Hamilton" - }, { "@type":"Person", "email":"lorenzo.alfine@gmail.com", @@ -1797,6 +1837,12 @@ "givenName":"Mark Alexander", "familyName": "Henney" }, + { + "@type":"Person", + "email":"", + "givenName":"Martin", + "familyName": "Oberg" + }, { "@type":"Person", "email":"dev@mgschulz.de", @@ -1929,12 +1975,6 @@ "givenName":"Pedro", "familyName": "Silva" }, - { - "@type":"Person", - "email":"pmolfese@gmail.com", - "givenName":"Peter J", - "familyName": "Molfese" - }, { "@type":"Person", "email":"proloy@umd.edu", @@ -1995,6 +2035,12 @@ "givenName":"Richard", "familyName": "Koehler" }, + { + "@type":"Person", + "email":"", + "givenName":"Richard", + "familyName": "Scholz" + }, { "@type":"Person", "email":"rie.acad@gmail.com", @@ -2085,6 +2131,12 @@ "givenName":"Sergey", "familyName": "Antopolskiy" }, + { + "@type":"Person", + "email":"shirazi@ieee.org", + "givenName":"Seyed (Yahya)", + "familyName": "Shirazi" + }, { "@type":"Person", "email":"", @@ -2145,12 +2197,6 @@ "givenName":"T", "familyName": "Wang" }, - { - "@type":"Person", - "email":"tdonoghue.research@gmail.com", - "givenName":"Thomas", - "familyName": "Donoghue" - }, { "@type":"Person", "email":"thomas.moreau.2010@gmail.com", @@ -2193,6 +2239,18 @@ "givenName":"Toomas Erik", "familyName": "Anijärv" }, + { + "@type":"Person", + "email":"", + "givenName":"Velu Prabhakar", + "familyName": "Kumaravel" + }, + { + "@type":"Person", + "email":"williamfrancisturner@gmail.com", + "givenName":"Will", + "familyName": "Turner" + }, { "@type":"Person", "email":"xia@xiaokai.me", @@ -2211,6 +2269,12 @@ "givenName":"Zhi", "familyName": "Zhang" }, + { + "@type":"Person", + "email":"btk.codedev@gmail.com", + "givenName":"", + "familyName": "btkcodedev" + }, { "@type":"Person", "email":"", diff --git a/doc/_static/versions.json b/doc/_static/versions.json index 8141440bd16..48e4006f494 100644 --- a/doc/_static/versions.json +++ b/doc/_static/versions.json @@ -1,14 +1,19 @@ [ { - "name": "1.7 (devel)", + "name": "1.8 (devel)", "version": "dev", "url": "https://mne.tools/dev/" }, { - "name": "1.6 (stable)", + "name": "1.7 (stable)", "version": "stable", "url": "https://mne.tools/stable/" }, + { + "name": "1.6", + "version": "1.6", + "url": "https://mne.tools/1.6/" + }, { "name": "1.5", "version": "1.5", diff --git a/doc/changes/devel.rst b/doc/changes/devel.rst deleted file mode 100644 index 0e80d522b51..00000000000 --- a/doc/changes/devel.rst +++ /dev/null @@ -1,5 +0,0 @@ -.. See doc/development/contributing.rst for description of how to add entries. - -.. _current: - -.. towncrier-draft-entries:: Version |release| (development) diff --git a/doc/changes/devel/11234.newfeature.rst b/doc/changes/devel/11234.newfeature.rst deleted file mode 100644 index 46cc408a3d9..00000000000 --- a/doc/changes/devel/11234.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Detecting Bad EEG/MEG channels using the local outlier factor (LOF) algorithm in :func:`mne.preprocessing.find_bad_channels_lof`, by :newcontrib:`Velu Prabhakar Kumaravel`. \ No newline at end of file diff --git a/doc/changes/devel/11282.apichange.rst b/doc/changes/devel/11282.apichange.rst deleted file mode 100644 index 9112db897cf..00000000000 --- a/doc/changes/devel/11282.apichange.rst +++ /dev/null @@ -1 +0,0 @@ -The default value of the ``zero_mean`` parameter of :func:`mne.time_frequency.tfr_array_morlet` will change from ``False`` to ``True`` in version 1.8, for consistency with related functions. By `Daniel McCloy`_. diff --git a/doc/changes/devel/11282.bugfix.rst b/doc/changes/devel/11282.bugfix.rst deleted file mode 100644 index 72e6e73a42a..00000000000 --- a/doc/changes/devel/11282.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fixes to interactivity in time-frequency objects: the rectangle selector now works on TFR image plots of gradiometer data; and in ``TFR.plot_joint()`` plots, the colormap limits of interactively-generated topomaps match the colormap limits of the main plot. By `Daniel McCloy`_. \ No newline at end of file diff --git a/doc/changes/devel/11282.newfeature.rst b/doc/changes/devel/11282.newfeature.rst deleted file mode 100644 index 5c19d68f351..00000000000 --- a/doc/changes/devel/11282.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -New class :class:`mne.time_frequency.RawTFR` and new methods :meth:`mne.io.Raw.compute_tfr`, :meth:`mne.Epochs.compute_tfr`, and :meth:`mne.Evoked.compute_tfr`. These new methods supersede functions :func:`mne.time_frequency.tfr_morlet`, and :func:`mne.time_frequency.tfr_multitaper`, and :func:`mne.time_frequency.tfr_stockwell`, which are now considered "legacy" functions. By `Daniel McCloy`_. \ No newline at end of file diff --git a/doc/changes/devel/12190.bugfix.rst b/doc/changes/devel/12190.bugfix.rst deleted file mode 100644 index d7ef2e07444..00000000000 --- a/doc/changes/devel/12190.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Allow :func:`mne.viz.plot_compare_evokeds` to plot eyetracking channels, and improve error handling, y `Scott Huberty`_. \ No newline at end of file diff --git a/doc/changes/devel/12195.newfeature.rst b/doc/changes/devel/12195.newfeature.rst deleted file mode 100644 index 0c7e044abce..00000000000 --- a/doc/changes/devel/12195.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add ability reject :class:`mne.Epochs` using callables, by `Jacob Woessner`_. \ No newline at end of file diff --git a/doc/changes/devel/12206.bugfix.rst b/doc/changes/devel/12206.bugfix.rst deleted file mode 100644 index 6cf72e266b9..00000000000 --- a/doc/changes/devel/12206.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug in :meth:`mne.Epochs.apply_function` where data was handed down incorrectly in parallel processing, by `Dominik Welke`_. \ No newline at end of file diff --git a/doc/changes/devel/12206.newfeature.rst b/doc/changes/devel/12206.newfeature.rst deleted file mode 100644 index 9ef966ed208..00000000000 --- a/doc/changes/devel/12206.newfeature.rst +++ /dev/null @@ -1,3 +0,0 @@ -Custom functions applied via :meth:`mne.io.Raw.apply_function`, :meth:`mne.Epochs.apply_function` or :meth:`mne.Evoked.apply_function` can now use ``ch_idx`` or ``ch_name`` to get access to the currently processed channel during channel wise processing. - -:meth:`mne.Evoked.apply_function` can now also work on full data array instead of just channel wise, analogous to :meth:`mne.io.Raw.apply_function` and :meth:`mne.Epochs.apply_function`, by `Dominik Welke`_. \ No newline at end of file diff --git a/doc/changes/devel/12207.newfeature.rst b/doc/changes/devel/12207.newfeature.rst deleted file mode 100644 index 7d741a06bf5..00000000000 --- a/doc/changes/devel/12207.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Allow :class:`mne.time_frequency.EpochsTFR` as input to :func:`mne.epochs.equalize_epoch_counts`, by `Carina Forster`_. \ No newline at end of file diff --git a/doc/changes/devel/12218.newfeature.rst b/doc/changes/devel/12218.newfeature.rst deleted file mode 100644 index 4ea286f0a22..00000000000 --- a/doc/changes/devel/12218.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Speed up export to .edf in :func:`mne.export.export_raw` by using ``edfio`` instead of ``EDFlib-Python``. diff --git a/doc/changes/devel/12236.bugfix.rst b/doc/changes/devel/12236.bugfix.rst deleted file mode 100644 index ad807ea3487..00000000000 --- a/doc/changes/devel/12236.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Remove incorrect type hints in :func:`mne.io.read_raw_neuralynx`, by `Richard Höchenberger`_. diff --git a/doc/changes/devel/12237.newfeature.rst b/doc/changes/devel/12237.newfeature.rst deleted file mode 100644 index e89822f27ed..00000000000 --- a/doc/changes/devel/12237.newfeature.rst +++ /dev/null @@ -1,2 +0,0 @@ -Added a helper function :func:`mne.preprocessing.eyetracking.convert_units` to convert eyegaze data from pixel-on-screen values to radians of visual angle. Also added a helper function :func:`mne.preprocessing.eyetracking.get_screen_visual_angle` to get the visual angle that the participant screen subtends, by `Scott Huberty`_. - diff --git a/doc/changes/devel/12238.newfeature.rst b/doc/changes/devel/12238.newfeature.rst deleted file mode 100644 index 631722bc07a..00000000000 --- a/doc/changes/devel/12238.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Inform the user about channel discrepancy between provided info, forward operator, and/or covariance matrices in :func:`mne.beamformer.make_lcmv`, by :newcontrib:`Nikolai Kapralov`. \ No newline at end of file diff --git a/doc/changes/devel/12248.bugfix.rst b/doc/changes/devel/12248.bugfix.rst deleted file mode 100644 index bc4124a2267..00000000000 --- a/doc/changes/devel/12248.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug with accessing the last data sample using ``raw[:, -1]`` where an empty array was returned, by `Eric Larson`_. diff --git a/doc/changes/devel/12250.newfeature.rst b/doc/changes/devel/12250.newfeature.rst deleted file mode 100644 index 20d67dead77..00000000000 --- a/doc/changes/devel/12250.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -We added type hints for the return values of :func:`mne.read_evokeds` and :func:`mne.io.read_raw`. Development environments like VS Code or PyCharm will now provide more help when using these functions in your code. By `Richard Höchenberger`_ and `Eric Larson`_. (:gh:`12297`) diff --git a/doc/changes/devel/12250.notable.rst b/doc/changes/devel/12250.notable.rst deleted file mode 100644 index 7616894e636..00000000000 --- a/doc/changes/devel/12250.notable.rst +++ /dev/null @@ -1,11 +0,0 @@ -In this version, we started adding type hints (also known as "type annotations") to select parts of the codebase. -This meta information will be used by development environments (IDEs) like VS Code and PyCharm automatically to provide -better assistance such as tab completion or error detection even before running your code. - -So far, we've only added return type hints to :func:`mne.io.read_raw`, :func:`mne.read_epochs`, :func:`mne.read_evokeds` and -all format-specific ``read_raw_*()`` and ``read_epochs_*()`` functions. Now your editors will know: -these functions return evoked and raw data, respectively. We are planning add type hints to more functions after careful -evaluation in the future. - -You don't need to do anything to benefit from these changes – your editor will pick them up automatically and provide the -enhanced experience if it supports it! diff --git a/doc/changes/devel/12264.dependency.rst b/doc/changes/devel/12264.dependency.rst deleted file mode 100644 index c511b3448a8..00000000000 --- a/doc/changes/devel/12264.dependency.rst +++ /dev/null @@ -1 +0,0 @@ -``defusedxml`` is now an optional (rather than required) dependency and needed when reading EGI-MFF data, NEDF data, and BrainVision montages, by `Eric Larson`_. \ No newline at end of file diff --git a/doc/changes/devel/12268.newfeature.rst b/doc/changes/devel/12268.newfeature.rst deleted file mode 100644 index caf46fec03f..00000000000 --- a/doc/changes/devel/12268.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add ``method="polyphase"`` to :meth:`mne.io.Raw.resample` and related functions to allow resampling using :func:`scipy.signal.upfirdn`, by `Eric Larson`_. \ No newline at end of file diff --git a/doc/changes/devel/12269.newfeature.rst b/doc/changes/devel/12269.newfeature.rst deleted file mode 100644 index 321bd02070e..00000000000 --- a/doc/changes/devel/12269.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -The package build backend was switched from ``setuptools`` to ``hatchling``. This will only affect users who build and install MNE-Python from source. By `Richard Höchenberger`_. (:gh:`12281`) \ No newline at end of file diff --git a/doc/changes/devel/12279.bugfix.rst b/doc/changes/devel/12279.bugfix.rst deleted file mode 100644 index 93aee511fec..00000000000 --- a/doc/changes/devel/12279.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Correctly handle temporal gaps in Neuralynx .ncs files via :func:`mne.io.read_raw_neuralynx`, by `Kristijan Armeni`_ and `Eric Larson`_. \ No newline at end of file diff --git a/doc/changes/devel/12282.bugfix.rst b/doc/changes/devel/12282.bugfix.rst deleted file mode 100644 index e743d0b6071..00000000000 --- a/doc/changes/devel/12282.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug where parent directory existence was not checked properly in :meth:`mne.io.Raw.save`, by `Eric Larson`_. diff --git a/doc/changes/devel/12289.newfeature.rst b/doc/changes/devel/12289.newfeature.rst deleted file mode 100644 index 8110e4cf737..00000000000 --- a/doc/changes/devel/12289.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -:meth:`mne.Annotations.to_data_frame` can now output different formats for the ``onset`` column: seconds, milliseconds, datetime objects, and timedelta objects. By `Daniel McCloy`_. diff --git a/doc/changes/devel/12299.other.rst b/doc/changes/devel/12299.other.rst deleted file mode 100644 index 61c4bf56725..00000000000 --- a/doc/changes/devel/12299.other.rst +++ /dev/null @@ -1 +0,0 @@ -Adopted towncrier_ for changelog entries, by `Eric Larson`_. diff --git a/doc/changes/devel/12308.apichange.rst b/doc/changes/devel/12308.apichange.rst deleted file mode 100644 index 4d1b8e13923..00000000000 --- a/doc/changes/devel/12308.apichange.rst +++ /dev/null @@ -1 +0,0 @@ -The parameter for providing data to :func:`mne.time_frequency.tfr_array_morlet` and :func:`mne.time_frequency.tfr_array_multitaper` has been switched from ``epoch_data`` to ``data``. Only use the ``data`` parameter to avoid a warning. Changes by `Thomas Binns`_. \ No newline at end of file diff --git a/doc/changes/devel/12309.newfeature.rst b/doc/changes/devel/12309.newfeature.rst deleted file mode 100644 index 8e732044a8e..00000000000 --- a/doc/changes/devel/12309.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add method :meth:`mne.SourceEstimate.save_as_surface` to allow saving GIFTI files from surface source estimates, by `Peter Molfese`_. diff --git a/doc/changes/devel/12311.newfeature.rst b/doc/changes/devel/12311.newfeature.rst deleted file mode 100644 index c5e074278f9..00000000000 --- a/doc/changes/devel/12311.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -:class:`mne.Epochs` can now be constructed using :class:`mne.Annotations` stored in the ``raw`` object, by specifying ``events=None``. By `Alex Rockhill`_. \ No newline at end of file diff --git a/doc/changes/devel/12318.other.rst b/doc/changes/devel/12318.other.rst deleted file mode 100644 index 94890e1dfc4..00000000000 --- a/doc/changes/devel/12318.other.rst +++ /dev/null @@ -1 +0,0 @@ -Automate adding of PR number to towncrier stubs, by `Eric Larson`_. diff --git a/doc/changes/devel/12319.bugfix.rst b/doc/changes/devel/12319.bugfix.rst deleted file mode 100644 index 16eb1a3350a..00000000000 --- a/doc/changes/devel/12319.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug where section parameter in :meth:`mne.Report.add_html` was not being utilized resulting in improper formatting, by :newcontrib:`Martin Oberg`. diff --git a/doc/changes/devel/12323.newfeature.rst b/doc/changes/devel/12323.newfeature.rst deleted file mode 100644 index f10fdf5cf23..00000000000 --- a/doc/changes/devel/12323.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add :meth:`~mne.SourceEstimate.savgol_filter`, :meth:`~mne.SourceEstimate.filter`, :meth:`~mne.SourceEstimate.apply_hilbert`, and :meth:`~mne.SourceEstimate.apply_function` methods to :class:`mne.SourceEstimate` and related classes, by `Hamza Abdelhedi`_. \ No newline at end of file diff --git a/doc/changes/devel/12324.bugfix.rst b/doc/changes/devel/12324.bugfix.rst deleted file mode 100644 index ec7f2c5849d..00000000000 --- a/doc/changes/devel/12324.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Add ``tol`` parameter to :meth:`mne.events_from_annotations` so that the user can specify the tolerance to ignore rounding errors of event onsets when using ``chunk_duration`` is not None (default is 1e-8), by `Michiru Kaneda`_ diff --git a/doc/changes/devel/12326.other.rst b/doc/changes/devel/12326.other.rst deleted file mode 100644 index f0bd6a377d6..00000000000 --- a/doc/changes/devel/12326.other.rst +++ /dev/null @@ -1 +0,0 @@ -Updated the text in the preprocessing tutorial to use :meth:`mne.io.Raw.pick` instead of the legacy :meth:`mne.io.Raw.pick_types`, by :newcontrib:`btkcodedev`. diff --git a/doc/changes/devel/12332.newfeature.rst b/doc/changes/devel/12332.newfeature.rst deleted file mode 100644 index 0a7a82227ba..00000000000 --- a/doc/changes/devel/12332.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add ability to export STIM channels to EDF in :meth:`mne.io.Raw.export`, by `Clemens Brunner`_. \ No newline at end of file diff --git a/doc/changes/devel/12336.bugfix.rst b/doc/changes/devel/12336.bugfix.rst deleted file mode 100644 index c7ce44b8dab..00000000000 --- a/doc/changes/devel/12336.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Allow :meth:`mne.io.Raw.interpolate_bads` and :meth:`mne.Epochs.interpolate_bads` to work on ``ecog`` and ``seeg`` data; for ``seeg`` data a spline is fit to neighboring electrode contacts on the same shaft, by `Alex Rockhill`_ \ No newline at end of file diff --git a/doc/changes/devel/12343.newfeature.rst b/doc/changes/devel/12343.newfeature.rst deleted file mode 100644 index 9825f924e48..00000000000 --- a/doc/changes/devel/12343.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Speed up raw FIF reading when using small buffer sizes by `Eric Larson`_. \ No newline at end of file diff --git a/doc/changes/devel/12345.bugfix.rst b/doc/changes/devel/12345.bugfix.rst deleted file mode 100644 index fa592c6926c..00000000000 --- a/doc/changes/devel/12345.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix clicking on an axis of :func:`mne.viz.plot_evoked_topo` when multiple vertical lines ``vlines`` are used, by `Mathieu Scheltienne`_. diff --git a/doc/changes/devel/12348.bugfix.rst b/doc/changes/devel/12348.bugfix.rst deleted file mode 100644 index aad91ed9dec..00000000000 --- a/doc/changes/devel/12348.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug in :func:`mne.preprocessing.maxwell_filter` where calibration was incorrectly applied during virtual sensor reconstruction, by `Eric Larson`_ and :newcontrib:`Motofumi Fushimi`. diff --git a/doc/changes/devel/12354.bugfix.rst b/doc/changes/devel/12354.bugfix.rst deleted file mode 100644 index f3c944c9373..00000000000 --- a/doc/changes/devel/12354.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug in :meth:`mne.viz.EvokedField.set_vmax` that prevented setting the color limits of the MEG magnetic field density, by `Marijn van Vliet`_ diff --git a/doc/changes/devel/12357.bugfix.rst b/doc/changes/devel/12357.bugfix.rst deleted file mode 100644 index d38ce54d5f5..00000000000 --- a/doc/changes/devel/12357.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix faulty indexing in :func:`mne.io.read_raw_neuralynx` when picking a single channel, by `Kristijan Armeni`_. \ No newline at end of file diff --git a/doc/changes/devel/12358.other.rst b/doc/changes/devel/12358.other.rst deleted file mode 100644 index 788db1d1a41..00000000000 --- a/doc/changes/devel/12358.other.rst +++ /dev/null @@ -1 +0,0 @@ -Refresh code base to use Python 3.9 syntax using Ruff UP rules (pyupgrade), by `Clemens Brunner`_. \ No newline at end of file diff --git a/doc/changes/devel/12371.newfeature.rst b/doc/changes/devel/12371.newfeature.rst deleted file mode 100644 index 4d28ff1f5ce..00000000000 --- a/doc/changes/devel/12371.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Speed up :func:`mne.io.read_raw_neuralynx` on large datasets with many gaps, by `Kristijan Armeni`_. \ No newline at end of file diff --git a/doc/changes/devel/12376.dependency.rst b/doc/changes/devel/12376.dependency.rst deleted file mode 100644 index 148ce8ac9ec..00000000000 --- a/doc/changes/devel/12376.dependency.rst +++ /dev/null @@ -1 +0,0 @@ -For developers, ``pytest>=8.0`` is now required for running unit tests, by `Eric Larson`_. diff --git a/doc/changes/devel/12380.bugfix.rst b/doc/changes/devel/12380.bugfix.rst deleted file mode 100644 index 8c5ee5a6fca..00000000000 --- a/doc/changes/devel/12380.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug where :func:`mne.preprocessing.compute_proj_ecg` and :func:`mne.preprocessing.compute_proj_eog` could modify the default ``reject`` and ``flat`` arguments on multiple calls based on channel types present, by `Eric Larson`_. diff --git a/doc/changes/devel/12382.apichange.rst b/doc/changes/devel/12382.apichange.rst deleted file mode 100644 index aa38b436cf0..00000000000 --- a/doc/changes/devel/12382.apichange.rst +++ /dev/null @@ -1 +0,0 @@ -Change :func:`mne.stc_near_sensors` ``surface`` default from the ``'pial'`` surface to the surface in ``src`` if ``src`` is not ``None`` in version 1.8, by `Alex Rockhill`_. diff --git a/doc/changes/devel/12382.bugfix.rst b/doc/changes/devel/12382.bugfix.rst deleted file mode 100644 index 8409f016206..00000000000 --- a/doc/changes/devel/12382.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bad channels not handled properly in :func:`mne.stc_near_sensors` by `Alex Rockhill`_. diff --git a/doc/changes/devel/12383.newfeature.rst b/doc/changes/devel/12383.newfeature.rst deleted file mode 100644 index f896572eb93..00000000000 --- a/doc/changes/devel/12383.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add ability to detect minima peaks found in :class:`mne.Evoked` if data is all positive and maxima if data is all negative. \ No newline at end of file diff --git a/doc/changes/devel/12389.bugfix.rst b/doc/changes/devel/12389.bugfix.rst deleted file mode 100644 index 85892df97a8..00000000000 --- a/doc/changes/devel/12389.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug where :func:`mne.preprocessing.regress_artifact` projection check was not specific to the channels being processed, by `Eric Larson`_. diff --git a/doc/changes/devel/12393.bugfix.rst b/doc/changes/devel/12393.bugfix.rst deleted file mode 100644 index 017f81b398b..00000000000 --- a/doc/changes/devel/12393.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Change how samples are read when using ``data_format='auto'`` in :func:`mne.io.read_raw_cnt`, by `Jacob Woessner`_. \ No newline at end of file diff --git a/doc/changes/devel/12394.newfeature.rst b/doc/changes/devel/12394.newfeature.rst deleted file mode 100644 index de456e91461..00000000000 --- a/doc/changes/devel/12394.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add ability to remove bad marker coils in :func:`mne.io.read_raw_kit`, by `Judy D Zhu`_. \ No newline at end of file diff --git a/doc/changes/devel/12399.bugfix.rst b/doc/changes/devel/12399.bugfix.rst deleted file mode 100644 index cf53e91b5c8..00000000000 --- a/doc/changes/devel/12399.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bugs with :class:`mne.Report` CSS where TOC items could disappear at the bottom of the page, by `Eric Larson`_. \ No newline at end of file diff --git a/doc/changes/devel/12410.bugfix.rst b/doc/changes/devel/12410.bugfix.rst deleted file mode 100644 index c5d939845b0..00000000000 --- a/doc/changes/devel/12410.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -In :func:`~mne.viz.plot_compare_evokeds`, actually plot GFP (not RMS amplitude) for EEG channels when global field power is requested by `Daniel McCloy`_. \ No newline at end of file diff --git a/doc/changes/devel/12420.other.rst b/doc/changes/devel/12420.other.rst deleted file mode 100644 index 8b949d25dc7..00000000000 --- a/doc/changes/devel/12420.other.rst +++ /dev/null @@ -1 +0,0 @@ -Clarify in the :ref:`EEG referencing tutorial ` that an average reference projector ready is required for inverse modeling, by :newcontrib:`Nabil Alibou` diff --git a/doc/changes/devel/12430.bugfix.rst b/doc/changes/devel/12430.bugfix.rst deleted file mode 100644 index 688e7066fa8..00000000000 --- a/doc/changes/devel/12430.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Reformats channel and detector lookup in :func:`mne.io.read_raw_snirf` from array based to dictionary based. Removes incorrect assertions that every detector and source must have data associated with every registered optode position, by :newcontrib:`Alex Kiefer`. \ No newline at end of file diff --git a/doc/changes/devel/12436.bugfix.rst b/doc/changes/devel/12436.bugfix.rst deleted file mode 100644 index 7ddbd9f5d21..00000000000 --- a/doc/changes/devel/12436.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix :ref:`tut-working-with-seeg` use of :func:`mne.stc_near_sensors` to use the :class:`mne.VolSourceEstimate` positions and not the pial surface, by `Alex Rockhill`_ diff --git a/doc/changes/devel/12441.bugfix.rst b/doc/changes/devel/12441.bugfix.rst deleted file mode 100644 index 87a2d10a710..00000000000 --- a/doc/changes/devel/12441.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix prefiltering information management for EDF/BDF, by `Michiru Kaneda`_ diff --git a/doc/changes/devel/12443.newfeature.rst b/doc/changes/devel/12443.newfeature.rst deleted file mode 100644 index f704e45b4a5..00000000000 --- a/doc/changes/devel/12443.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add option to pass ``image_kwargs`` to :class:`mne.Report.add_epochs` to allow adjusting e.g. ``vmin`` and ``vmax`` of the epochs image in the report, by `Sophie Herbst`_. \ No newline at end of file diff --git a/doc/changes/devel/12444.bugfix.rst b/doc/changes/devel/12444.bugfix.rst deleted file mode 100644 index c27fb5e8425..00000000000 --- a/doc/changes/devel/12444.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix validation of ``ch_type`` in :func:`mne.preprocessing.annotate_muscle_zscore`, by `Mathieu Scheltienne`_. diff --git a/doc/changes/devel/12445.newfeature.rst b/doc/changes/devel/12445.newfeature.rst deleted file mode 100644 index ccaef2c2c07..00000000000 --- a/doc/changes/devel/12445.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add support for multiple raw instances in :func:`mne.preprocessing.compute_average_dev_head_t` by `Eric Larson`_. diff --git a/doc/changes/devel/12446.newfeature.rst b/doc/changes/devel/12446.newfeature.rst deleted file mode 100644 index 734721ce628..00000000000 --- a/doc/changes/devel/12446.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Support partial pathlength factors for each wavelength in :func:`mne.preprocessing.nirs.beer_lambert_law`, by :newcontrib:`Richard Scholz`. diff --git a/doc/changes/devel/12450.other.rst b/doc/changes/devel/12450.other.rst deleted file mode 100644 index 48265f87416..00000000000 --- a/doc/changes/devel/12450.other.rst +++ /dev/null @@ -1 +0,0 @@ -Move private data preparation functions for BrainVision export from ``pybv`` to ``mne``, by `Clemens Brunner`_. \ No newline at end of file diff --git a/doc/changes/devel/12451.bugfix.rst b/doc/changes/devel/12451.bugfix.rst deleted file mode 100644 index 2aca44529f1..00000000000 --- a/doc/changes/devel/12451.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix errant redundant use of ``BIDSPath.split`` when writing split raw and epochs data, by `Eric Larson`_. diff --git a/doc/changes/devel/12451.dependency.rst b/doc/changes/devel/12451.dependency.rst deleted file mode 100644 index 8227dd779ad..00000000000 --- a/doc/changes/devel/12451.dependency.rst +++ /dev/null @@ -1 +0,0 @@ -``pytest-harvest`` is no longer used as a test dependency, by `Eric Larson`_. diff --git a/doc/changes/devel/12454.newfeature.rst b/doc/changes/devel/12454.newfeature.rst deleted file mode 100644 index 5a4a9cc9cdb..00000000000 --- a/doc/changes/devel/12454.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Completing PR 12453. Add option to pass ``image_kwargs`` per channel type to :class:`mne.Report.add_epochs`. \ No newline at end of file diff --git a/doc/changes/devel/12456.bugfix.rst b/doc/changes/devel/12456.bugfix.rst deleted file mode 100644 index 01e15b3c22e..00000000000 --- a/doc/changes/devel/12456.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Disable config parser interpolation when reading BrainVision files, which allows using the percent sign as a regular character in channel units, by `Clemens Brunner`_. \ No newline at end of file diff --git a/doc/changes/devel/12461.other.rst b/doc/changes/devel/12461.other.rst deleted file mode 100644 index b6fcea48fc7..00000000000 --- a/doc/changes/devel/12461.other.rst +++ /dev/null @@ -1 +0,0 @@ -Fix dead links in ``README.rst`` documentation by :newcontrib:`Will Turner`. \ No newline at end of file diff --git a/doc/changes/devel/12462.newfeature.rst b/doc/changes/devel/12462.newfeature.rst deleted file mode 100644 index 4624579ba26..00000000000 --- a/doc/changes/devel/12462.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -:func:`mne.epochs.make_metadata` now accepts strings as ``tmin`` and ``tmax`` parameter values, simplifying metadata creation based on time-varying events such as responses to a stimulus, by `Richard Höchenberger`_. diff --git a/doc/changes/devel/12463.newfeature.rst b/doc/changes/devel/12463.newfeature.rst deleted file mode 100644 index d041b0c912f..00000000000 --- a/doc/changes/devel/12463.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Include date of acquisition and filter parameters in ``raw.info`` for :func:`mne.io.read_raw_neuralynx` by `Kristijan Armeni`_. \ No newline at end of file diff --git a/doc/changes/devel/12464.other.rst b/doc/changes/devel/12464.other.rst deleted file mode 100644 index 6839c4ebe61..00000000000 --- a/doc/changes/devel/12464.other.rst +++ /dev/null @@ -1,2 +0,0 @@ -Replacing percent format with f-strings format specifiers , by :newcontrib:`Hasrat Ali Arzoo`. - diff --git a/doc/changes/devel/12467.newfeature.rst b/doc/changes/devel/12467.newfeature.rst deleted file mode 100644 index 457a2746d17..00000000000 --- a/doc/changes/devel/12467.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add ``picks`` parameter to :meth:`mne.io.Raw.plot`, allowing users to select which channels to plot. This makes makes the raw data plotting API consistent with :meth:`mne.Epochs.plot` and :meth:`mne.Evoked.plot`, by :newcontrib:`Ivo de Jong`. \ No newline at end of file diff --git a/doc/changes/devel/12470.bugfix.rst b/doc/changes/devel/12470.bugfix.rst deleted file mode 100644 index d8d72843304..00000000000 --- a/doc/changes/devel/12470.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -- Fix the default color of :meth:`mne.viz.Brain.add_text` to properly contrast with the figure background color, by `Marijn van Vliet`_. diff --git a/doc/changes/devel/12474.bugfix.rst b/doc/changes/devel/12474.bugfix.rst deleted file mode 100644 index 875d7574f7b..00000000000 --- a/doc/changes/devel/12474.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -- Changed default ECoG and sEEG electrode sizes in brain plots to better reflect real world sizes, by `Liberty Hamilton`_ diff --git a/doc/changes/devel/12476.bugfix.rst b/doc/changes/devel/12476.bugfix.rst deleted file mode 100644 index 464ef11307c..00000000000 --- a/doc/changes/devel/12476.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fixed bugs with handling of rank in :class:`mne.decoding.CSP`, by `Eric Larson`_. \ No newline at end of file diff --git a/doc/changes/devel/12481.bugfix.rst b/doc/changes/devel/12481.bugfix.rst deleted file mode 100644 index a9108fe4040..00000000000 --- a/doc/changes/devel/12481.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -- Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_. \ No newline at end of file diff --git a/doc/changes/devel/12483.bugfix.rst b/doc/changes/devel/12483.bugfix.rst deleted file mode 100644 index 601bf94838c..00000000000 --- a/doc/changes/devel/12483.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Improve compatibility with other Qt-based GUIs by handling theme icons better, by `Eric Larson`_. diff --git a/doc/changes/devel/12484.bugfix.rst b/doc/changes/devel/12484.bugfix.rst deleted file mode 100644 index 2430f534661..00000000000 --- a/doc/changes/devel/12484.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -- Fix problem caused by onsets with NaN values using :func:`mne.io.read_raw_eeglab` by `Jacob Woessner`_ \ No newline at end of file diff --git a/doc/changes/devel/12489.bugfix.rst b/doc/changes/devel/12489.bugfix.rst deleted file mode 100644 index 9172ec64f7e..00000000000 --- a/doc/changes/devel/12489.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix cleaning of channel names for non vectorview or CTF dataset including whitespaces or dash in their channel names, by `Mathieu Scheltienne`_. diff --git a/doc/changes/devel/12491.dependency.rst b/doc/changes/devel/12491.dependency.rst deleted file mode 100644 index 423082320ca..00000000000 --- a/doc/changes/devel/12491.dependency.rst +++ /dev/null @@ -1 +0,0 @@ -The minimum supported version of Qt bindings is 5.15, by `Eric Larson`_. diff --git a/doc/changes/devel/12498.bugfix.rst b/doc/changes/devel/12498.bugfix.rst deleted file mode 100644 index 2655cf692d1..00000000000 --- a/doc/changes/devel/12498.bugfix.rst +++ /dev/null @@ -1,2 +0,0 @@ -Fix bug with :meth:`mne.preprocessing.ICA.plot_sources` for ``evoked`` data where the -legend contained too many entries, by `Eric Larson`_. diff --git a/doc/changes/devel/12507.bugfix.rst b/doc/changes/devel/12507.bugfix.rst deleted file mode 100644 index c172701bb93..00000000000 --- a/doc/changes/devel/12507.bugfix.rst +++ /dev/null @@ -1,5 +0,0 @@ -Fix bug where using ``phase="minimum"`` in filtering functions like -:meth:`mne.io.Raw.filter` constructed a filter half the desired length with -compromised attenuation. Now ``phase="minimum"`` has the same length and comparable -suppression as ``phase="zero"``, and the old (incorrect) behavior can be achieved -with ``phase="minimum-half"``, by `Eric Larson`_. diff --git a/doc/changes/devel/12509.other.rst b/doc/changes/devel/12509.other.rst deleted file mode 100644 index e3709653025..00000000000 --- a/doc/changes/devel/12509.other.rst +++ /dev/null @@ -1,2 +0,0 @@ -Update the list of sensor types in docstrings, tutorials and the glossary by `Nabil Alibou`_. - diff --git a/doc/changes/devel/12510.newfeature.rst b/doc/changes/devel/12510.newfeature.rst deleted file mode 100644 index 3194e47e6a9..00000000000 --- a/doc/changes/devel/12510.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add ``physical_range="channelwise"`` to :meth:`mne.io.Raw.export` for exporting to EDF, which can improve amplitude resolution if individual channels vary greatly in their offsets, by `Clemens Brunner`_. \ No newline at end of file diff --git a/doc/changes/devel/12513.newfeature.rst b/doc/changes/devel/12513.newfeature.rst deleted file mode 100644 index 7189adaf3c0..00000000000 --- a/doc/changes/devel/12513.newfeature.rst +++ /dev/null @@ -1,2 +0,0 @@ -Added the ability to reorder report contents via :meth:`mne.Report.reorder` (with -helper to get contents with :meth:`mne.Report.get_contents`), by `Eric Larson`_. diff --git a/doc/changes/devel/12518.newfeature.rst b/doc/changes/devel/12518.newfeature.rst deleted file mode 100644 index 306254ee6be..00000000000 --- a/doc/changes/devel/12518.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add ``exclude_after_unique`` option to :meth:`mne.io.read_raw_edf` and :meth:`mne.io.read_raw_edf` to search for exclude channels after making channels names unique, by `Michiru Kaneda`_ diff --git a/doc/changes/devel/12523.bugfix.rst b/doc/changes/devel/12523.bugfix.rst deleted file mode 100644 index 3ce8cea9d11..00000000000 --- a/doc/changes/devel/12523.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Remove FDT file format check for strings in EEGLAB's EEG.data in :func:`mne.io.read_raw_eeglab` and related functions by :newcontrib:`Seyed Yahya Shirazi` diff --git a/doc/changes/devel/12526.bugfix.rst b/doc/changes/devel/12526.bugfix.rst deleted file mode 100644 index b853cdc751a..00000000000 --- a/doc/changes/devel/12526.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Correct reading of ``info["subject_info"]["his_id"]`` in :func:`mne.io.read_raw_snirf`, by `Eric Larson`_. diff --git a/doc/changes/devel/12535.bugfix.rst b/doc/changes/devel/12535.bugfix.rst deleted file mode 100644 index eeeda0bffac..00000000000 --- a/doc/changes/devel/12535.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Calling :meth:`~mne.io.Raw.compute_psd` with ``method="multitaper"`` is now expressly disallowed when ``reject_by_annotation=True`` and ``bad_*`` annotations are present (previously this was nominally allowed but resulted in ``nan`` values in the PSD). By `Daniel McCloy`_. diff --git a/doc/changes/devel/12536.bugfix.rst b/doc/changes/devel/12536.bugfix.rst deleted file mode 100644 index 2b4a709186f..00000000000 --- a/doc/changes/devel/12536.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -:meth:`~mne.io.Raw.compute_psd` and :func:`~mne.time_frequency.psd_array_welch` will now use FFT windows aligned to the onsets of good data spans when ``bad_*`` annotations are present. By `Daniel McCloy`_. diff --git a/doc/changes/devel/12537.bugfix.rst b/doc/changes/devel/12537.bugfix.rst deleted file mode 100644 index 911bdce444e..00000000000 --- a/doc/changes/devel/12537.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug in loading of complex/phase TFRs. By `Daniel McCloy`_. diff --git a/doc/changes/devel/12544.bugfix.rst b/doc/changes/devel/12544.bugfix.rst deleted file mode 100644 index d6e3210ec45..00000000000 --- a/doc/changes/devel/12544.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug with :func:`mne.SourceSpaces.export_volume` where the ``img.affine`` was not set properly, by `Eric Larson`_. \ No newline at end of file diff --git a/doc/changes/v0.24.rst b/doc/changes/v0.24.rst index 1eb4abd2193..5f92e3dbdf6 100644 --- a/doc/changes/v0.24.rst +++ b/doc/changes/v0.24.rst @@ -89,7 +89,7 @@ Enhancements - :func:`mne.concatenate_raws`, :func:`mne.concatenate_epochs`, and :func:`mne.write_evokeds` gained a new parameter ``on_mismatch``, which controls behavior in case not all of the supplied instances share the same device-to-head transformation (:gh:`9438` by `Richard Höchenberger`_) -- Add support for multiple datablocks (acquistions with pauses) in :func:`mne.io.read_raw_nihon` (:gh:`9437` by `Federico Raimondo`_) +- Add support for multiple datablocks (acquisitions with pauses) in :func:`mne.io.read_raw_nihon` (:gh:`9437` by `Federico Raimondo`_) - Add new function :func:`mne.preprocessing.annotate_break` to automatically detect and mark "break" periods without any marked experimental events in the continuous data (:gh:`9445` by `Richard Höchenberger`_) diff --git a/doc/changes/v1.7.rst b/doc/changes/v1.7.rst new file mode 100644 index 00000000000..e8f8e2e8e7b --- /dev/null +++ b/doc/changes/v1.7.rst @@ -0,0 +1,180 @@ +.. _changes_1_7_0: + +1.7.0 (2024-04-19) +================== + +Notable changes +--------------- + +- In this version, we started adding type hints (also known as "type annotations") to select parts of the codebase. + This meta information will be used by development environments (IDEs) like VS Code and PyCharm automatically to provide + better assistance such as tab completion or error detection even before running your code. + + So far, we've only added return type hints to :func:`mne.io.read_raw`, :func:`mne.read_epochs`, :func:`mne.read_evokeds` and + all format-specific ``read_raw_*()`` and ``read_epochs_*()`` functions. Now your editors will know: + these functions return evoked and raw data, respectively. We are planning add type hints to more functions after careful + evaluation in the future. + + You don't need to do anything to benefit from these changes – your editor will pick them up automatically and provide the + enhanced experience if it supports it! (`#12250 `__) + + +Dependencies +------------ + +- ``defusedxml`` is now an optional (rather than required) dependency and needed when reading EGI-MFF data, NEDF data, and BrainVision montages, by `Eric Larson`_. (`#12264 `__) +- For developers, ``pytest>=8.0`` is now required for running unit tests, by `Eric Larson`_. (`#12376 `__) +- ``pytest-harvest`` is no longer used as a test dependency, by `Eric Larson`_. (`#12451 `__) +- The minimum supported version of Qt bindings is 5.15, by `Eric Larson`_. (`#12491 `__) + + +Bugfixes +-------- + +- Fix bug where section parameter in :meth:`mne.Report.add_html` was not being utilized resulting in improper formatting, by :newcontrib:`Martin Oberg`. (`#12319 `__) +- Fix bug in :func:`mne.preprocessing.maxwell_filter` where calibration was incorrectly applied during virtual sensor reconstruction, by `Eric Larson`_ and :newcontrib:`Motofumi Fushimi`. (`#12348 `__) +- Reformats channel and detector lookup in :func:`mne.io.read_raw_snirf` from array based to dictionary based. Removes incorrect assertions that every detector and source must have data associated with every registered optode position, by :newcontrib:`Alex Kiefer`. (`#12430 `__) +- Remove FDT file format check for strings in EEGLAB's EEG.data in :func:`mne.io.read_raw_eeglab` and related functions by :newcontrib:`Seyed Yahya Shirazi` (`#12523 `__) +- Fixes to interactivity in time-frequency objects: the rectangle selector now works on TFR image plots of gradiometer data; and in ``TFR.plot_joint()`` plots, the colormap limits of interactively-generated topomaps match the colormap limits of the main plot. By `Daniel McCloy`_. (`#11282 `__) +- Allow :func:`mne.viz.plot_compare_evokeds` to plot eyetracking channels, and improve error handling, y `Scott Huberty`_. (`#12190 `__) +- Fix bug in :meth:`mne.Epochs.apply_function` where data was handed down incorrectly in parallel processing, by `Dominik Welke`_. (`#12206 `__) +- Remove incorrect type hints in :func:`mne.io.read_raw_neuralynx`, by `Richard Höchenberger`_. (`#12236 `__) +- Fix bug with accessing the last data sample using ``raw[:, -1]`` where an empty array was returned, by `Eric Larson`_. (`#12248 `__) +- Correctly handle temporal gaps in Neuralynx .ncs files via :func:`mne.io.read_raw_neuralynx`, by `Kristijan Armeni`_ and `Eric Larson`_. (`#12279 `__) +- Fix bug where parent directory existence was not checked properly in :meth:`mne.io.Raw.save`, by `Eric Larson`_. (`#12282 `__) +- Add ``tol`` parameter to :meth:`mne.events_from_annotations` so that the user can specify the tolerance to ignore rounding errors of event onsets when using ``chunk_duration`` is not None (default is 1e-8), by `Michiru Kaneda`_ (`#12324 `__) +- Allow :meth:`mne.io.Raw.interpolate_bads` and :meth:`mne.Epochs.interpolate_bads` to work on ``ecog`` and ``seeg`` data; for ``seeg`` data a spline is fit to neighboring electrode contacts on the same shaft, by `Alex Rockhill`_ (`#12336 `__) +- Fix clicking on an axis of :func:`mne.viz.plot_evoked_topo` when multiple vertical lines ``vlines`` are used, by `Mathieu Scheltienne`_. (`#12345 `__) +- Fix bug in :meth:`mne.viz.EvokedField.set_vmax` that prevented setting the color limits of the MEG magnetic field density, by `Marijn van Vliet`_ (`#12354 `__) +- Fix faulty indexing in :func:`mne.io.read_raw_neuralynx` when picking a single channel, by `Kristijan Armeni`_. (`#12357 `__) +- Fix bug where :func:`mne.preprocessing.compute_proj_ecg` and :func:`mne.preprocessing.compute_proj_eog` could modify the default ``reject`` and ``flat`` arguments on multiple calls based on channel types present, by `Eric Larson`_. (`#12380 `__) +- Fix bad channels not handled properly in :func:`mne.stc_near_sensors` by `Alex Rockhill`_. (`#12382 `__) +- Fix bug where :func:`mne.preprocessing.regress_artifact` projection check was not specific to the channels being processed, by `Eric Larson`_. (`#12389 `__) +- Change how samples are read when using ``data_format='auto'`` in :func:`mne.io.read_raw_cnt`, by `Jacob Woessner`_. (`#12393 `__) +- Fix bugs with :class:`mne.Report` CSS where TOC items could disappear at the bottom of the page, by `Eric Larson`_. (`#12399 `__) +- In :func:`~mne.viz.plot_compare_evokeds`, actually plot GFP (not RMS amplitude) for EEG channels when global field power is requested by `Daniel McCloy`_. (`#12410 `__) +- Fix :ref:`tut-working-with-seeg` use of :func:`mne.stc_near_sensors` to use the :class:`mne.VolSourceEstimate` positions and not the pial surface, by `Alex Rockhill`_ (`#12436 `__) +- Fix prefiltering information management for EDF/BDF, by `Michiru Kaneda`_ (`#12441 `__) +- Fix validation of ``ch_type`` in :func:`mne.preprocessing.annotate_muscle_zscore`, by `Mathieu Scheltienne`_. (`#12444 `__) +- Fix errant redundant use of ``BIDSPath.split`` when writing split raw and epochs data, by `Eric Larson`_. (`#12451 `__) +- Disable config parser interpolation when reading BrainVision files, which allows using the percent sign as a regular character in channel units, by `Clemens Brunner`_. (`#12456 `__) +- - Fix the default color of :meth:`mne.viz.Brain.add_text` to properly contrast with the figure background color, by `Marijn van Vliet`_. (`#12470 `__) +- - Changed default ECoG and sEEG electrode sizes in brain plots to better reflect real world sizes, by `Liberty Hamilton`_ (`#12474 `__) +- Fixed bugs with handling of rank in :class:`mne.decoding.CSP`, by `Eric Larson`_. (`#12476 `__) +- - Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_. (`#12481 `__) +- Improve compatibility with other Qt-based GUIs by handling theme icons better, by `Eric Larson`_. (`#12483 `__) +- - Fix problem caused by onsets with NaN values using :func:`mne.io.read_raw_eeglab` by `Jacob Woessner`_ (`#12484 `__) +- Fix cleaning of channel names for non vectorview or CTF dataset including whitespaces or dash in their channel names, by `Mathieu Scheltienne`_. (`#12489 `__) +- Fix bug with :meth:`mne.preprocessing.ICA.plot_sources` for ``evoked`` data where the + legend contained too many entries, by `Eric Larson`_. (`#12498 `__) +- Fix bug where using ``phase="minimum"`` in filtering functions like + :meth:`mne.io.Raw.filter` constructed a filter half the desired length with + compromised attenuation. Now ``phase="minimum"`` has the same length and comparable + suppression as ``phase="zero"``, and the old (incorrect) behavior can be achieved + with ``phase="minimum-half"``, by `Eric Larson`_. (`#12507 `__) +- Correct reading of ``info["subject_info"]["his_id"]`` in :func:`mne.io.read_raw_snirf`, by `Eric Larson`_. (`#12526 `__) +- Calling :meth:`~mne.io.Raw.compute_psd` with ``method="multitaper"`` is now expressly disallowed when ``reject_by_annotation=True`` and ``bad_*`` annotations are present (previously this was nominally allowed but resulted in ``nan`` values in the PSD). By `Daniel McCloy`_. (`#12535 `__) +- :meth:`~mne.io.Raw.compute_psd` and :func:`~mne.time_frequency.psd_array_welch` will now use FFT windows aligned to the onsets of good data spans when ``bad_*`` annotations are present. By `Daniel McCloy`_. (`#12536 `__) +- Fix bug in loading of complex/phase TFRs. By `Daniel McCloy`_. (`#12537 `__) +- Fix bug with :func:`mne.SourceSpaces.export_volume` where the ``img.affine`` was not set properly, by `Eric Larson`_. (`#12544 `__) + + +API changes by deprecation +-------------------------- + +- The default value of the ``zero_mean`` parameter of :func:`mne.time_frequency.tfr_array_morlet` will change from ``False`` to ``True`` in version 1.8, for consistency with related functions. By `Daniel McCloy`_. (`#11282 `__) +- The parameter for providing data to :func:`mne.time_frequency.tfr_array_morlet` and :func:`mne.time_frequency.tfr_array_multitaper` has been switched from ``epoch_data`` to ``data``. Only use the ``data`` parameter to avoid a warning. Changes by `Thomas Binns`_. (`#12308 `__) +- Change :func:`mne.stc_near_sensors` ``surface`` default from the ``'pial'`` surface to the surface in ``src`` if ``src`` is not ``None`` in version 1.8, by `Alex Rockhill`_. (`#12382 `__) + + +New features +------------ + +- Detecting Bad EEG/MEG channels using the local outlier factor (LOF) algorithm in :func:`mne.preprocessing.find_bad_channels_lof`, by :newcontrib:`Velu Prabhakar Kumaravel`. (`#11234 `__) +- Inform the user about channel discrepancy between provided info, forward operator, and/or covariance matrices in :func:`mne.beamformer.make_lcmv`, by :newcontrib:`Nikolai Kapralov`. (`#12238 `__) +- Support partial pathlength factors for each wavelength in :func:`mne.preprocessing.nirs.beer_lambert_law`, by :newcontrib:`Richard Scholz`. (`#12446 `__) +- Add ``picks`` parameter to :meth:`mne.io.Raw.plot`, allowing users to select which channels to plot. This makes makes the raw data plotting API consistent with :meth:`mne.Epochs.plot` and :meth:`mne.Evoked.plot`, by :newcontrib:`Ivo de Jong`. (`#12467 `__) +- New class :class:`mne.time_frequency.RawTFR` and new methods :meth:`mne.io.Raw.compute_tfr`, :meth:`mne.Epochs.compute_tfr`, and :meth:`mne.Evoked.compute_tfr`. These new methods supersede functions :func:`mne.time_frequency.tfr_morlet`, and :func:`mne.time_frequency.tfr_multitaper`, and :func:`mne.time_frequency.tfr_stockwell`, which are now considered "legacy" functions. By `Daniel McCloy`_. (`#11282 `__) +- Add ability reject :class:`mne.Epochs` using callables, by `Jacob Woessner`_. (`#12195 `__) +- Custom functions applied via :meth:`mne.io.Raw.apply_function`, :meth:`mne.Epochs.apply_function` or :meth:`mne.Evoked.apply_function` can now use ``ch_idx`` or ``ch_name`` to get access to the currently processed channel during channel wise processing. +- :meth:`mne.Evoked.apply_function` can now also work on full data array instead of just channel wise, analogous to :meth:`mne.io.Raw.apply_function` and :meth:`mne.Epochs.apply_function`, by `Dominik Welke`_. (`#12206 `__) +- Allow :class:`mne.time_frequency.EpochsTFR` as input to :func:`mne.epochs.equalize_epoch_counts`, by `Carina Forster`_. (`#12207 `__) +- Speed up export to .edf in :func:`mne.export.export_raw` by using ``edfio`` instead of ``EDFlib-Python``. (`#12218 `__) +- Added a helper function :func:`mne.preprocessing.eyetracking.convert_units` to convert eyegaze data from pixel-on-screen values to radians of visual angle. Also added a helper function :func:`mne.preprocessing.eyetracking.get_screen_visual_angle` to get the visual angle that the participant screen subtends, by `Scott Huberty`_. (`#12237 `__) +- We added type hints for the return values of :func:`mne.read_evokeds` and :func:`mne.io.read_raw`. Development environments like VS Code or PyCharm will now provide more help when using these functions in your code. By `Richard Höchenberger`_ and `Eric Larson`_. (:gh:`12297`) (`#12250 `__) +- Add ``method="polyphase"`` to :meth:`mne.io.Raw.resample` and related functions to allow resampling using :func:`scipy.signal.upfirdn`, by `Eric Larson`_. (`#12268 `__) +- The package build backend was switched from ``setuptools`` to ``hatchling``. This will only affect users who build and install MNE-Python from source. By `Richard Höchenberger`_. (:gh:`12281`) (`#12269 `__) +- :meth:`mne.Annotations.to_data_frame` can now output different formats for the ``onset`` column: seconds, milliseconds, datetime objects, and timedelta objects. By `Daniel McCloy`_. (`#12289 `__) +- Add method :meth:`mne.SourceEstimate.save_as_surface` to allow saving GIFTI files from surface source estimates, by `Peter Molfese`_. (`#12309 `__) +- :class:`mne.Epochs` can now be constructed using :class:`mne.Annotations` stored in the ``raw`` object, by specifying ``events=None``. By `Alex Rockhill`_. (`#12311 `__) +- Add :meth:`~mne.SourceEstimate.savgol_filter`, :meth:`~mne.SourceEstimate.filter`, :meth:`~mne.SourceEstimate.apply_hilbert`, and :meth:`~mne.SourceEstimate.apply_function` methods to :class:`mne.SourceEstimate` and related classes, by `Hamza Abdelhedi`_. (`#12323 `__) +- Add ability to export STIM channels to EDF in :meth:`mne.io.Raw.export`, by `Clemens Brunner`_. (`#12332 `__) +- Speed up raw FIF reading when using small buffer sizes by `Eric Larson`_. (`#12343 `__) +- Speed up :func:`mne.io.read_raw_neuralynx` on large datasets with many gaps, by `Kristijan Armeni`_. (`#12371 `__) +- Add ability to detect minima peaks found in :class:`mne.Evoked` if data is all positive and maxima if data is all negative. (`#12383 `__) +- Add ability to remove bad marker coils in :func:`mne.io.read_raw_kit`, by `Judy D Zhu`_. (`#12394 `__) +- Add option to pass ``image_kwargs`` to :class:`mne.Report.add_epochs` to allow adjusting e.g. ``vmin`` and ``vmax`` of the epochs image in the report, by `Sophie Herbst`_. (`#12443 `__) +- Add support for multiple raw instances in :func:`mne.preprocessing.compute_average_dev_head_t` by `Eric Larson`_. (`#12445 `__) +- Completing PR 12453. Add option to pass ``image_kwargs`` per channel type to :class:`mne.Report.add_epochs`. (`#12454 `__) +- :func:`mne.epochs.make_metadata` now accepts strings as ``tmin`` and ``tmax`` parameter values, simplifying metadata creation based on time-varying events such as responses to a stimulus, by `Richard Höchenberger`_. (`#12462 `__) +- Include date of acquisition and filter parameters in ``raw.info`` for :func:`mne.io.read_raw_neuralynx` by `Kristijan Armeni`_. (`#12463 `__) +- Add ``physical_range="channelwise"`` to :meth:`mne.io.Raw.export` for exporting to EDF, which can improve amplitude resolution if individual channels vary greatly in their offsets, by `Clemens Brunner`_. (`#12510 `__) +- Added the ability to reorder report contents via :meth:`mne.Report.reorder` (with + helper to get contents with :meth:`mne.Report.get_contents`), by `Eric Larson`_. (`#12513 `__) +- Add ``exclude_after_unique`` option to :meth:`mne.io.read_raw_edf` and :meth:`mne.io.read_raw_edf` to search for exclude channels after making channels names unique, by `Michiru Kaneda`_ (`#12518 `__) + + +Other changes +------------- + +- Updated the text in the preprocessing tutorial to use :meth:`mne.io.Raw.pick` instead of the legacy :meth:`mne.io.Raw.pick_types`, by :newcontrib:`btkcodedev`. (`#12326 `__) +- Clarify in the :ref:`EEG referencing tutorial ` that an average reference projector ready is required for inverse modeling, by :newcontrib:`Nabil Alibou` (`#12420 `__) +- Fix dead links in ``README.rst`` documentation by :newcontrib:`Will Turner`. (`#12461 `__) +- Replacing percent format with f-strings format specifiers , by :newcontrib:`Hasrat Ali Arzoo`. (`#12464 `__) +- Adopted towncrier_ for changelog entries, by `Eric Larson`_. (`#12299 `__) +- Automate adding of PR number to towncrier stubs, by `Eric Larson`_. (`#12318 `__) +- Refresh code base to use Python 3.9 syntax using Ruff UP rules (pyupgrade), by `Clemens Brunner`_. (`#12358 `__) +- Move private data preparation functions for BrainVision export from ``pybv`` to ``mne``, by `Clemens Brunner`_. (`#12450 `__) +- Update the list of sensor types in docstrings, tutorials and the glossary by `Nabil Alibou`_. (`#12509 `__) + + +Authors +------- +* Alex Rockhill +* Alexander Kiefer+ +* Alexandre Gramfort +* Britta Westner +* Carina Forster +* Clemens Brunner +* Daniel McCloy +* Dominik Welke +* Eric Larson +* Erkka Heinila +* Florian Hofer +* Hamza Abdelhedi +* Hasrat Ali Arzoo+ +* Ivo de Jong+ +* Jacob Woessner +* Judy D Zhu +* Kristijan Armeni +* Liberty Hamilton +* Marijn van Vliet +* Martin Oberg+ +* Mathieu Scheltienne +* Michiru Kaneda +* Motofumi Fushimi+ +* Nabil Alibou+ +* Nikolai Kapralov+ +* Peter J. Molfese +* Richard Höchenberger +* Richard Scholz+ +* Scott Huberty +* Seyed (Yahya) Shirazi+ +* Sophie Herbst +* Stefan Appelhoff +* Thomas Donoghue +* Thomas Samuel Binns +* Tristan Stenner +* Velu Prabhakar Kumaravel+ +* Will Turner+ +* btkcodedev+ diff --git a/doc/development/whats_new.rst b/doc/development/whats_new.rst index 61c14a876f9..920194e7fb2 100644 --- a/doc/development/whats_new.rst +++ b/doc/development/whats_new.rst @@ -8,7 +8,7 @@ Changes for each version of MNE-Python are listed below. .. toctree:: :maxdepth: 1 - ../changes/devel.rst + ../changes/v1.7.rst ../changes/v1.6.rst ../changes/v1.5.rst ../changes/v1.4.rst diff --git a/doc/documentation/cited.rst b/doc/documentation/cited.rst index 7654cf3fd40..31c19589b16 100644 --- a/doc/documentation/cited.rst +++ b/doc/documentation/cited.rst @@ -3,7 +3,7 @@ Papers citing MNE-Python ======================== -Estimates provided by Google Scholar as of 14 August 2023: +Estimates provided by Google Scholar as of 19 April 2024: -- `MNE (1540) `_ -- `MNE-Python (2040) `_ +- `MNE (1730) `_ +- `MNE-Python (2570) `_ diff --git a/examples/decoding/decoding_spoc_CMC.py b/examples/decoding/decoding_spoc_CMC.py index 4d49fb1e350..0a02a61052c 100644 --- a/examples/decoding/decoding_spoc_CMC.py +++ b/examples/decoding/decoding_spoc_CMC.py @@ -64,7 +64,7 @@ # Define a two fold cross-validation cv = KFold(n_splits=2, shuffle=False) -# Run cross validaton +# Run cross validation y_preds = cross_val_predict(clf, X, y, cv=cv) # Plot the True EMG power and the EMG power predicted from MEG data diff --git a/mne/commands/mne_browse_raw.py b/mne/commands/mne_browse_raw.py index 0c3d81a16e9..2e662e1768b 100644 --- a/mne/commands/mne_browse_raw.py +++ b/mne/commands/mne_browse_raw.py @@ -84,7 +84,7 @@ def run(): "-p", "--preload", dest="preload", - help="Preload raw data (for faster navigaton)", + help="Preload raw data (for faster navigation)", default=False, action="store_true", ) diff --git a/mne/datasets/sleep_physionet/tests/test_physionet.py b/mne/datasets/sleep_physionet/tests/test_physionet.py index 7cf57632057..5147be94ab9 100644 --- a/mne/datasets/sleep_physionet/tests/test_physionet.py +++ b/mne/datasets/sleep_physionet/tests/test_physionet.py @@ -30,8 +30,8 @@ def _keep_basename_only(paths): def _get_expected_url(name): base = "https://physionet.org/physiobank/database/sleep-edfx/" - midle = "sleep-cassette/" if name.startswith("SC") else "sleep-telemetry/" - return base + midle + "/" + name + middle = "sleep-cassette/" if name.startswith("SC") else "sleep-telemetry/" + return base + middle + "/" + name def _get_expected_path(base, name): diff --git a/mne/fixes.py b/mne/fixes.py index 98b1ce805cd..f7534377b5a 100644 --- a/mne/fixes.py +++ b/mne/fixes.py @@ -113,7 +113,7 @@ def _csc_matrix_cast(x): def rng_uniform(rng): - """Get the unform/randint from the rng.""" + """Get the uniform/randint from the rng.""" # prefer Generator.integers, fall back to RandomState.randint return getattr(rng, "integers", getattr(rng, "randint", None)) diff --git a/mne/io/fiff/tests/test_raw_fiff.py b/mne/io/fiff/tests/test_raw_fiff.py index 91125de98be..dc3c732979d 100644 --- a/mne/io/fiff/tests/test_raw_fiff.py +++ b/mne/io/fiff/tests/test_raw_fiff.py @@ -1292,7 +1292,7 @@ def test_crop(): assert raw1[:][0].shape == (1, 2001) # degenerate - with pytest.raises(ValueError, match="No samples.*when include_tmax=Fals"): + with pytest.raises(ValueError, match="No samples.*when include_tmax=False"): raw.crop(0, 0, include_tmax=False) # edge cases cropping to exact duration +/- 1 sample diff --git a/mne/io/kit/coreg.py b/mne/io/kit/coreg.py index 0887a4b4022..3e691249790 100644 --- a/mne/io/kit/coreg.py +++ b/mne/io/kit/coreg.py @@ -72,7 +72,7 @@ def read_mrk(fname): elif fname.suffix == ".pickled": warn( "Reading pickled files is unsafe and not future compatible, save " - "to a standard format (text or FIF) instea, e.g. with:\n" + "to a standard format (text or FIF) instead, e.g. with:\n" r"np.savetxt(fid, pts, delimiter=\"\\t\", newline=\"\\n\")", FutureWarning, ) diff --git a/mne/preprocessing/_peak_finder.py b/mne/preprocessing/_peak_finder.py index 99272ae0fda..078e4aadb23 100644 --- a/mne/preprocessing/_peak_finder.py +++ b/mne/preprocessing/_peak_finder.py @@ -85,7 +85,7 @@ def peak_finder(x0, thresh=None, extrema=1, verbose=None): left_min = min_mag # Deal with first point a little differently since tacked it on - # Calculate the sign of the derivative since we taked the first point + # Calculate the sign of the derivative since we took the first point # on it does not necessarily alternate like the rest. signDx = np.sign(np.diff(x[:3])) if signDx[0] <= 0: # The first point is larger or equal to the second diff --git a/tools/generate_codemeta.py b/tools/generate_codemeta.py index 9e697cecc55..a1c1fac77b4 100644 --- a/tools/generate_codemeta.py +++ b/tools/generate_codemeta.py @@ -44,6 +44,7 @@ "De Santis", "Dupré la Tour", "de la Torre", + "de Jong", "de Montalivet", "van den Bosch", "Van den Bossche",