[Mne_analysis] [ANN] MNE-Python 1.0

Alexandre Gramfort alexandre.gramfort at inria.fr
Tue Mar 22 05:48:32 EDT 2022
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[Cross-posting with:
https://secure-web.cisco.com/1M5gJqD9mM400gbjJRrOZWf3YItB4URYB33GNR3Ytby9S5jn0qAsCKQ58fqiOHaiLS1Z67ZMZiiwfwA7rMAwDBwZYUtktEju-zwygqkLCNjIUib-2QDc8yUGv7AWRW5CY4bzjS5252-4Y0qHjeeUK2LP2UjbYeo9F732-UqomhfO3QU9F5F_GIIxyG9jGpner2KU4TkvsVrlfRiwgsNSJU6l8VeItREHRf3QxWc1pg1wBdnxzfffmi5jt1rJNoZlHVzmGDzTjKD_0ZyXrVmHnFfH4j1wcfq-fgp4Uc_zjDe-eqKDzUxlVeT2HmSrcS4uDjmj0XHB4r9IvdA9RjA_gqBPfj48snjinZfHOydNTBb0/https%3A%2F%2Fmne.discourse.group%2Ft%2Fmne-python-is-turning-1-0%2F4595]

🎂 MNE-Python is turning 1.0...

In December 2010, freshly arrived in Boston to work as a postdoc at the
Martinos Center with Matti Hamalainen, I started the MNE-Python project
with NIH funding. Inspired by my early open-source development efforts on
scikit-learn, I wanted to “replicate the scikit-learn model” for the field
of MEG/EEG data analysis. I wanted to create a Python project developed in
the open – on GitHub, with the support of a distributed community of
contributors willing to give a bit of their time to share what works for
them (and what doesn’t!). Very importantly, what I wanted was to encourage
people outside of the Martinos Center at MGH to contribute to the
MNE-Python code while getting public credit for their work. Before
attracting users I needed to find contributors... and for this I needed to
convince them that MNE-Python was not simply my own personal pet project,
but rather something that belongs to its contributors.

It has now been more than 11 years since MNE-Python was started, and as of
now 285 contributors distributed all over the world have made MNE-Python a
mature and successful project. This long effort has also been made possible
by the sustained funding from NIH in the USA, as well as the ERC and ANR
funding agencies in Europe and France. Now, we believe it’s finally time
for MNE-Python to grow up and turn 1.0! 🎂

I am particularly grateful first to Matti Hamalainen for teaching me so
much about MEG and providing the groundwork with the MNE-C code he made
public in 2006. MNE-C had already started the worldwide MNE project before
MNE-Python was conceived.

I am looking forward to seeing how MNE-Python will evolve in the future –
and let’s see if we’ll wait 11 more years for version 2.0… 😇

Alex


--- Release notes ---

A few highlights

============


   -

   📦 New standalone installers for macOS, Windows, and Linux should make
   onboarding of new users much easier and allow for offline installations!
   Download from https://secure-web.cisco.com/1E7Z96nCGF7CJeFWEnvTSEVjxMsMWJUIrXqyAVT2tS-5TxNJlzq1_W65FD0AI4fIYz4YjQg2flkAN57ueXWGpOP4BzejMkF7ObyWnRV7uiDhbQkajthBS4-n2kudwzXQVT60M36rbAAfYy507OE6qdmMDnH3ExaRKP2RV6rFSGgJcnkG_gwExG_WPpTQW2XTrOiU1RSBC8KycJTw0fRgtdbotdpHZcBLYyWmuPrfL16mqPRvoW0QqGq0uNq9y4s87cL9PmvBDdQMWiBEHKnE-DqjpRd0CQzcHkvTMN0pI2k1L9Skqf4hv2VUYDGBEyUZcQ-NKi5xIixCPe-kBDCn2OINt-_86pztSr35e-Ga69m8/https%3A%2F%2Fmne.tools%2Fstable%2Finstall%2Finstallers.html
   -

   📈 A new viewer for Raw, Epoched, Evoked, and ICA data makes interactive
   data exploration much easier and smoother. See
   https://secure-web.cisco.com/10K-ewxr0IseF96ie4CRsdL7ObNUqDH-H7hnOHeLGQFYFPuSTZGsYl6A9RZe2_YeQwZzwmn2zOqahY8mDVm5g1mDB5HPd0RRFkDlYSNQDXAeZc3BLu8hlWqHzzT5pl5X1xovDIdZJnUjCof94w9Ps7IySWA10EeWYT0-ndcuseuqMU6M7SZqi4vKRoI79aIv840dWsBvb7CimMXm-u3U8TkpeV0sge5RjGlPusRV8GKuSlncdttNeajoQdKAuxraqWaZAy9y1yHuHtzK5DXF24Unf-9RT6Zz0RE7GfO-eF2L3NNSPvxNlK64jWj-U4OXzub44EBM0pCe4aUe1y36GywNgqqMuvhGfKyy497-Xsxc/https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-qt-browser
   -

   🧠 We redesigned and decluttered large parts of the coregistration GUI
   to make it easier for you to find the functionality you’re looking for!
   -

   📒 We also added numerous improvements to Reports, including a drastic
   speedup of Raw data plots.
   -

   📍 Lastly, the iEEG contact localization GUI has seen a number of
   improvements, too.



Notable API changes

================

We have changed a few things that will require you to adjust your code.


   -

   The verbose attribute of classes (e.g., mne.io.Raw, mne.Epochs, etc.)
   has been deprecated. Explicitly pass verbose to methods as necessary
   instead.
   -

   In mne.viz.set_browser_backend(), the mne-qt-browser-based backend is
   now called 'qt' rather than 'pyqtgraph' for simplicity.
   -

   mne.Info.pick_channels has been deprecated. Use inst.pick_channels to
   pick channels from Raw, Epochs, and Evoked.
   -

   All data_path functions now return modern pathlib.Path objects rather
   than strings.
   -

   The argument name event_list has been deprecated in favor of events in
   mne.write_events()
   -

   The max_ori_out parameter of mne.beamformer.apply_lcmv() and related
   functions is being removed as only signed estimates are supported.


Full list of API changes:

https://secure-web.cisco.com/1MUT1Jqesc5705duMB0rGSJZpV3U84eFtpQtokNyB3rrt6cbTvu82cWCkrAXc84YmC70HpoFHr3HcCJ9mz6BydIMzF_J96Q6Bx5DiPR18TCeVK1onbH9eMhnlmpZZMoKUzWiYnkuRdcJm56H1G4QbXCkjUBTAF2o-9S4ALSL_PegSB24grE9hXYw7jlCWyKcueDlNxHIaI4csLvniuQotWo72WF2Ginm6bKxJSY2u2quqArUY93xL2z4jkgwHISIwZQGOi4ZXL1v2YHPrmAvk7MQYK-TPC3wP9nC_fdof7sZ3fZ_7BdwUkwgCaEr3MFftqh4x-Z-WFn6vKAs5OK6bHtHMfs5SfbScJJBYqj8Tmaw/https%3A%2F%2Fmne.tools%2Fstable%2Fwhats_new.html%23api-changes


Full changelog

===========

For a full list of improvements and API changes, see:

https://secure-web.cisco.com/1193bu5nqTMokgRi-x4yb-LMpagCsYJktPF66_dX0iNwkGp1ouUOAYRJ-sweSSkKxI4sPL_Oo6NetCYq3x-JKtf2xoDOVvUgN2glkaXPu_Qlr2lgyZ-Zc4_ZcYTdq1RyZBng6GRCJhYTjdnoZTqFeMFLHw0uHtJwfeVE8JGhjkIylLO9_q3DEcNy-Ie7QBzilrbdbYgSKSaTpoCviODGiXd1BjmzrrcZtQPnZ66S9roZZMULTBNvm5K4KpYy4HzOSHMkyB_sCJRUqZr4ebvqbXb8R8mpPs1XfLiW-J78ehhJInG2XOC-PE8c0nh-Qajdxne3UPd1bDOFc2nXyZpwu0nlOGAU1IYWhOASCiNSa1CM/https%3A%2F%2Fmne.tools%2Fstable%2Fwhats_new.html%23version-1-0

Find the full documentation at https://secure-web.cisco.com/1Lco-jSz27nHqwRfP_iz_Pc-MU4WX75-KrksX47QalfSZ_I3dKrMLoeqK9_xCZxpbaQrnYsc1HBl4eRkgiRcoif3AzeydxtUYitAuvduGQEc1DfdQhQ_RkjwnhbSnXngcM8hjXSVW5MUyh6X2FVoEmcYTZ_vt8NqY951kClZM12gJXZC67xwTKlG3RiwLpM7Ubg5YP6SDuD2hECFp9_jhoZG19QVzqP4m8BI39woMAJL_Wa15VJMsOMb3v5ZsULwc_-FjeQ8p1lHMrWtOr9UzRLcTyM4gJaok0WmQD_SSVjr_wsn0GLV_xL0ih5p6wuw1-VrTa1v98NjMaUxTVKosyRWhWnt6PVFTChNCRhxIu_Y/https%3A%2F%2Fmne.tools%2F
<https://secure-web.cisco.com/1TTbDXAx8OxAJNJ-laau04n_sUhMquQuimHSThIVAWRZoCiwT-8Cd6hC1CwbYbXcwBx8oGZWhKkfvuO-lNFMLzpwxUnbVbv6o69rF4ikUae9Y4t-4V4g5UTRNg0XZhSHB_qeCbAKbQLWcT72Dph4tiB2EyZvagAGoHodvvlZfCGwEdsbE0twozUhMbPNl8JCtCVwGr6U0NgNLPH-yMLL4Wtzr-VOSNEAVswWvdvC8z7PwsEKi-Bu_9IpRTdwV38Vtjg3_YirP9Cd_f5e3hM99xu8KTga3-olIk5lx_btJbxF1BrEWy_m_Y4wDFRlA4lBttcxpdIEND_OMR_83azyEW1ppN6PaUdrwIXEbCymOT0k/https%3A%2F%2Fmne.tools%2Fstable%2Findex.html>

Installing the new release

===================

Since quite a few things – including dependencies – have changed, we
recommend creating a new environment with a “fresh” installation.

Or if you fancy, download one of our fresh and shiny new installers!

Visit https://secure-web.cisco.com/18uG4pj1c6z8GiLVgg8mAbO7WWKqUmc6a9wvv5TVhiK688YE3cW-Z9pdBjroPUHm7TXz-FqaLhRpyM3z_wBGoOMdCRHg5uqzozU8TH26CF4Q6Cdmh_C--RTozuvZmNRvlV51-p4C_fFDZNIydaCj54NAsTPcw18ixf1hSxQfUq7TLortnG0ICIhf_PVFX4e3aT4AWPxyny8hREJOUtQqhGHWZ-I2Yb4HxgsMyuH1rS8_zVIhZPEaPXj6E6poMphQxun9j7ZM0Vu3UZ13Ocm0zVm6PhG0Hw86e1OVMRwsFABvxBrnUgXgWzFXN4vC9uUN7yYnpMZEGhEtUKPXICeGLKZJsAwwFQmS7-dit_g1AhY8/https%3A%2F%2Fmne.tools%2Fstable%2Finstall
<https://secure-web.cisco.com/1fguula0v3GOhpyC-u4Zt-DP4fOrwck7G2tVuxIJA5x_5d_ydXh2ocZn1iLx6IZaGdIAJV96xTZgzYHEnv_EwQ5NC0BpmvlQVTJDBhKqtumFzS8lSI_rBRcg_dEysnnDxGtId7-mZhYekZN9EaU6LJT6BLpdAqt-hIqHoSuYg0jfp6O-ss2T0Epc14AaLn4Fe9tNZwhBnF3UFE2sVbF4cXAyd10oDs0ackmCaiYmgKlABqSKbufRxcTpE3Ze9eKJ25pDXLfAj4yXbaaqDKU-d0x3-YlHTbWHsSr8e67LkWaVJ78mb0CYwqNh_E5tCPkz45cUXbehyYb4sD0jgAGXvV5ptJUcC7DpDRHriJsfo-JI/https%3A%2F%2Fmne.tools%2Fstable%2Finstall%2Findex.html> for instructions and download
links.

Feedback

========

If you have any questions or discovered a problem, please feel free to
reach out to us on the MNE Forum: https://secure-web.cisco.com/13b_FZBVqB18s06pqBtFBSemFg2rqISs6Uw7hRKM2WwAEnq-HhW73MMnrlNMDbEBOJODa9a19DrmFy7ThrQHJ0Q9wZ9j-c9ILP4PVT12D6dK4m00F4ojjjGhK7Jg0MNEJG0kcB8MhbckQ8sURWgOs7c7zBmt7YONIzqvfpUHhtfJgFFw7XTfG1rEIdJwZuAnY0T1jBnBa9RbsDb3Wy8RsGO5Lbm7WI0Gf0fWuY-jb0NquQDbMRugU9Plo2WLJuM72JzKvoojKkGNGBRJ0ApGd5Si0FqzohsY1JPMbnFs-bloB-MANDLokGu5kDpnD8pUWOPZUXsCY0TkehfICrS0-T-gUU3QfolUV0gMVSydaQjI/https%3A%2F%2Fmne.discourse.group

As usual, we welcome your bug reports, feature requests, critiques, and, of
course, new contributions. 😁 Development takes place on GitHub. If you
would like to contribute, star ⭐ the project, or just take a peek at the
code, visit https://secure-web.cisco.com/1NqhNUKUKv3k9VOe1lp-HuInsZ5CSvotDLfQ3Gxg8oYoZPs1fUU0Ui76M4MDmgaVZ3Mxduw0xlzg2oaw48fNlsbe2OxrIVE8GqFd9lhOQAuLQAO4imYKkoPfVknvpUlxdITEqXzuravCsdtIEV77kk-tV_wSq0buORGZEbdHfvaSFN3tyReQw61NEVgtDXvoRX_nj1sBr3JmBo23NfvPEdqQc5zD7JAl-eMoF4vqEhv0W54aiDGGeRCbs_J_r1LXv4CdJXcCG7nAyZyHa9sGxogHF2AgbOrgVsbOpf6vQKnN9yyGlwKjqSR7wyIwdUQTe2rDjdvzZbERo3NkAk1-nkQQShy9_Ra8d89-5KFU3N1A/https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-python

You may follow us on Twitter, too: https://secure-web.cisco.com/1jFoG7l8aNbCjGK8qTtW7n0WOI3U5-0gQ8rCpk2up753FztKJHRA8mKYFpJ5i2mkhnRhVXjJQ15lGzY6IDkTgmqyndIo-C07_s3DFIja-tUJ2GWKAkiNGjZhGnjGE33GlysmkY6O2v_poxEFuRAJxYwMlYroWiXXsO4KalqeUBA_v5yUiKCetItdycjL0cvr9aapNZ7C0VU45AY2ruf2fzx-VLqOwT-gvzSMpb5sseh9aAS-Q7mpitGnW8KzXBSUWfriZkamtAEP773_CT6O6EmI2yzUb_tRqGkY7NxWjAgRaLjypQVECnoFokUPurikwg-tuBGZO4xVyKj0K3cSbPGcySaWGEFenVoO6vOo3Z0U/https%3A%2F%2Ftwitter.com%2Fmne_news

We hope you will enjoy the new features and many, many small improvements
we have added, and are looking forward to receiving your feedback.

Stay safe and take care!

The MNE-Python developers


Contributors

==========

MNE-Python is a community-driven project. We are always very happy to
welcome new contributors of code and documentation! 33 people contributed
to this release – and 10 were first-timers! Thank you all so very much for
your time and effort, we truly appreciate it!

First-time contributors:


   -

   Adina Wagner
   -

   Etienne de Montalivet
   -

   Federico Zamberlan
   -

   Jan Zerfowski
   -

   John Veillette
   -

   Matthias Eberlein
   -

   Michiru Kaneda
   -

   Nikolai Chapochnikov
   -

   Scott Huberty
   -

   Senwen Deng


Recurring contributors:


   -

   Adam Li
   -

   Alex Rockhill
   -

   Alexandre Gramfort
   -

   Britta Westner
   -

   Clemens Brunner
   -

   Daniel McCloy
   -

   Eduard Ort
   -

   Eric Larson
   -

   Guillaume Favelier
   -

   Jan Sosulski
   -

   Jeff Stout
   -

   Joshua Teves
   -

   Julia Guiomar Niso Galán
   -

   Luke Bloy
   -

   Marijn van Vliet
   -

   Martin Schulz
   -

   Mathieu Scheltienne
   -

   Mikołaj Magnuski
   -

   Richard Höchenberger
   -

   Robert Luke
   -

   Stefan Appelhoff
   -

   Steve Matindi
   -

   Thomas Hartmann
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