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Release 8.0.0
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@github-actions github-actions released this 30 Apr 15:24
· 541 commits to 49c473ef338942736174dc13fcf54e7586505e36 since this release
8.0.0
429d11e

What's New

  • Dynamic selection of legacy vs modern units using HOC/Python API (default : modern)
  • Faster reaction-diffusion support
  • Initial GPU support using integration of CoreNEURON
  • Binary installer for new Apple M1 platform
  • Binary wheel distribution for Python 3.9 and Python 2.7
  • Release of NMODL version 0.3 (available as python wheel)
  • Versioned documentation available via nrn.readthedocs.io
  • CMake as a primary build system for NEURON and Interviews

Breaking Changes

  • h.Section now interprets positional arguments as name, cell. Previously positional arguments were interpreted in the other order. (Calling it with keyword arguments is unchanged.)
  • For 3d reaction-diffusion simulations, the voxelization and segment mapping algorithms have been adjusted, especially around the soma. Voxel indices and sometimes counts will change from previous versions.

Deprecations

  • Five functions in the neuron module: neuron.init, neuron.run, neuron.psection, neuron.xopen, and neuron.quit.
  • Autotools build is deprecated and will be removed in the next release. Use CMake instead.
  • Python 2 and Python 3.5 support is deprecated and will be removed in the next release. Use Python >= 3.6

Bug Fixes

For the complete list of bug fixes, see the list on the GitHub here.

Improvements / Other Changes

  • Allow for two point (single section) SWC somas
  • GitHub Actions and Azure as primary CI systems. Travis CI removed.
  • GitHub Releases provides full source tarballs, binary installers and python wheels.
  • Improved testing and CI infrastructure including GPUs
  • nrn-build-ci repository test nightly builds for Ubuntu 18.04, Ubuntu 20.04, Fedora 32, Fedora 33, CentOS7, CentOS8, Debian Buster (10) and macOS 10.15 platforms.
  • Improved integration of CoreNEURON
  • Support for recent numpy version
  • Various build improvements on Linux, MacOS and HPC platforms
  • Documentation from various repositories is consolidated under nrn repository
  • New releases via Spack and Easybuild package managers
  • Fix deadlock when compiling NEURON with AVX-512
  • Add backward-cpp for better backtraces
  • NEURON_MODULE_OPTIONS environment variable to pass in nrniv options before neuron import

Upgrade Steps

Existing models should work without any changes. In order to upgrade NEURON version you can:

  • Use python wheels provided for Linux or Mac OS platform
  • Use binary installer provided for windows
  • Install from source, preferably using CMake build system
  • For new version, it's always a good idea to start over from scratch with nrnivmodl (deleting existing directory like x86_64)

See Installation section under nrn.readthedocs.io/. In the very rare case that numerical differences exist, check selection of legacy vs modern units.

Contributors

See the list of contributors on respective GitHub projects:

Feedback / Help

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