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NEURON Developer’s Meeting

March 18th 2022

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Agenda

  • Introduction from "new" members
  • NEURON News / Announcements
  • NEURON Docs Updates
  • NEURON 8.1 Alpha
  • NEURON Frontiers paper
  • CircleCI for Aarch64 wheels
  • NEURON Hackathon: Digital Event
  • ModelDB CI
  • Ongoing NEURON work
  • Next Meeting

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Introduction From New Members

  • Luc Grosheintz-Laval

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NEURON News / Announcements

  • Number of known papers reporting using NEURON: 2636.
    • This is an increase of 154 since this time last year.
    • Probably misses some indirect usage via e.g. BioNet, Sim4Life, NetPyNE
  • …

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NEURON 8.1 Alpha

  • Arm64/Aarch64 support
  • GPU support: neuron-gpu
  • Universal2 MacOS PKG
  • Python2/3.6 removal
  • Bug fixes & improvements, improvements…

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  • Next steps
    • Try it out!
    • 8.1 release (within days)

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NEURON Frontiers paper

  • Thanks for contributing!

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  • See it on BioRxiv

In Review

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Other changes

TODOs

  • Reaction-diffusion (RxD) programmer’s reference expanded and rewritten; HOC and Python versions now language-specific
  • RxD tutorial index now editable, structured
  • MOD file needed for an RxD tutorial moved into the tutorial to remove dependency on NEURON server
  • CoreNEURON docs expanded
  • Nbsphinx used for jupyter notebooks

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  • Reorganize Python Programmer’s Reference
    • Commonly used is just a list of NEURON classes available in HOC, so doesn’t include e.g. h.Section and many are not commonly needed for Python
  • Friendlier landing page
  • Move the rest of the GUI tutorials over
    • Including the Third Cell Builder tutorial

New to readthedocs since last meeting

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CircleCI for Aarch64 wheels

  • Until now: Python wheels were available for Linux and MacOS (Intel, AMD)�
  • ARM systems are not that common but used in the computing environment including cloud�
  • Contribution from @odidev to add CircleCI support to build Aarch64 wheels�
  • Maintaining multiple CI systems is a bit of pain but
    • Github/Azure doesn’t have ARM servers
    • Cross compilation is significantly slower

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NEURON Hackathon: Digital Event, Spring Edition

  • Frontiers paper helped to present significant improvements and software engineering efforts done over last two years�
  • Delayed: August & Sept 2021 discussions about fundamental improvements in the codebase (e.g. data structures, legacy code, C++ migration)�
  • Resuming this work now and it would be great to sync once again via hackathon
    • Roadmap, strategy and technical planning
    • Prototyping new ideas and tackle interesting issues�
  • Via zoom: find 4-5 hours of overlap in CEST and EDT time zones
    • 2 or 3 days?
    • Doodle next week for the month of April (and May?)

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ModelDB CI

  • Run your NEURON for all ModelDB models - at your fingertips !
  • Create interactive HTML reports
  • Create V1-vs-V2 interactive HTML reports
  • Compare two different graphical runs of the same model
  • Launch it from GitHub Actions
    • Run daily: last-release vs last-nightly ; Manual workflow (specify versions, models)
    • Enhancement: caching of ModelDB models (simple caching for now), Azure artifacts
  • Next steps
    • More improvements
    • Publish nrn-modeldb-ci on Pypiz
  • LIVE WALKTHROUGH

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Ongoing NEURON work

  • Current Kanban Board

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  • Clang-format (a major problem is merging master into old branches)

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Google Groups - NEURON Dev Meeting

  • NEURON Dev Meeting

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  • Shared Google Drive for NEURON Dev Meeting presentations, recordings ...
    • NEURON dev shared folder

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Next meeting

April 15th 2022, 16:00 CEST; 10:00 EDT

�Please suggest agenda items on the wiki:

https://github.com/neuronsimulator/nrn/wiki