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split off simulation code into separate package #12980

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drammock opened this issue Nov 21, 2024 · 11 comments
Open

split off simulation code into separate package #12980

drammock opened this issue Nov 21, 2024 · 11 comments

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@drammock
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Hi @mne-tools/mne-python-steering-committee

@ctrltz and colleagues have been doing some work on simulating MNE objects (above and beyond what we currently support), in the new https://github.com/ctrltz/meegsim package. They have expressed interest in incorporating their work into MNE-Python, and after a few discussions with @larsoner @agramfort and @britta-wstnr we've settled on a tentative plan to "spin off" our existing simulation code into a new package (mne-simulation or so) similar to what was done for connectivity a few years ago, and then give @ctrltz and colleagues write-access to that repo so they can add their code and also have a much smaller/faster test/CI suite. Existing simulation code would be deprecated in MNE-Python release 1.9 and removed in 1.10.

This issue is your chance to weigh in on whether you think it best to:

  1. follow the above plan
  2. keep existing simulation code in MNE-Python, and add new code into the main repo
  3. keep existing simulation code in MNE-Python, and don't add the new MEEGsim functionality
  4. something else (?)
@drammock
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drammock commented Nov 21, 2024

one possible downside to the "spinoff" approach that I've just thought of, is the risk of losing git history (edit: and hence contributor credit) for the existing code. I think there's probably a way to preserve it, via something like:

  • fresh-clone MNE-Python repo
  • filter + rewrite history to only include the simulation files
  • make a commit that fixes all the imports (e.g., changes from .forward import whatever to from mne.forward import whatever)
  • add in all the other packaging-related scaffolding

@mscheltienne
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+1, glad someone is working on simulation!

@ctrltz
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ctrltz commented Nov 21, 2024

Thank you, @drammock! Tagging @minajamshidi and @astudenova to keep them in the loop.

@sappelhoff
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+1 to spin off under mne-tools/mne-simulation!

@larsoner
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+1 for spin off with some git history magic suggested by @drammock . There is probably a way to do it that preserves committer and date and such but mangles the commit numbers (which is okay)

@hoechenberger
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Go for it 👍

@cbrnr
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cbrnr commented Nov 21, 2024

Also 👍 for spin off!

@britta-wstnr
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+1 from me, too. Really excited about the cool options that @ctrltz, @minajamshidi, and @astudenova support in MEEGsim! 😍

@adam2392
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+1 supporting simulation would help so much research in this space.

@agramfort
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+1 too.

We could even start thinking into adding ML based generative models. There is a bunch of cool works in this space eg

https://www.biorxiv.org/content/10.1101/2023.08.23.554148v1
https://github.com/LiuyinYang1101/EEGDiffWave

@drammock
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OK thanks everyone for weighing in. I'll start working on the deprecation + spin-off this week. I'll leave this open, but convert the title to be normative, so we can close it when the spin-off is complete.

@drammock drammock changed the title RFC: splitting simulation code into separate package split off simulation code into separate package Nov 25, 2024
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