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Releases: neuronsimulator/nrn

Release 8.1a

16 Mar 22:06
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Release 8.1a Pre-release
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8.1a

Release 8.0.2

02 Feb 18:29
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8.0.2

Release Date : 02-02-2022

Bug Fixes

Python 3.10 bugfixes for RXD and Windows, more details in GitHub PR #1614

Release 8.0.1

28 Jan 22:57
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8.0.1

Release Date : 28-01-2022

What's New

  • Python 3.10 support & wheels

Bug Fixes

For the complete list of bug fixes, see the list in GitHub PR #1603

Improvements / Other Changes

  • Introduce a Sphinx HOC domain for NEURON documentation

Release 8.0.0

30 Apr 15:24
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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

Release 8.0a

24 Jan 15:59
d9b44b1
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8.0a

Release 7.8.2

18 Dec 12:59
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NEURON patch release 7.8.2

This patch release includes several fixes and small improvements. Here is summary:

  • Pointer can be dereferenced only if non-NULL. (#676) 799d783
  • Avoid system directories into rpath (#681) … 438e5e1
  • Build error fix for Random123 on IBM Power9 system with PGI compiler (#684) e24f099
  • ion style error (#685) … 391c77d
  • Bug fix for library name extensions (#687) … 709f267
  • Avoid using xcrun on non-osx platforms (#710) … b4c3c18
  • Avoid rare duplication of RangeVarPlot points due to recursion. (#720) b2cfb1b
  • Set Python_ADDITIONAL_VERSIONS cmake property (#737) … 676c6da
  • sysconfig provenance requires major.minor in libpython name. (#744) bac383e
  • Some PROP_PY_INDEX dependent fragments need #if USE_PYTHON wrapper. (#860)… d5a65c6
  • MPI_Abort if hoc_execerror from python and nhost > 1. (#796) b6852c9
  • Use early numpy wheel for each neuron wheel. (#801) … 39c27cd
  • nrniv -python windows gui event loop not started (#817) … a3a80ae
  • Windows anaconda3 2020 without path. Figure out the python path. (#824) … 59e5538
  • nrnivmodl under cmake no longer uses symbolic links. (#850) … 33c8857
  • Adamjhn gridswarning (#675) … 590d5d3
  • bugfix: Stop rxd keeping section alive and fix CVode/nseg change pro(#693)… … 42e246b
  • _semi_compile raises Exception if bad state (#715) … 993a734
  • bugfix: Distribute mulitcompartment reaction fluxes in MPI. (#728) … bfdcdab
  • Remove hasattr check for _voltage_dependent in rates and reaction(#813)… … d94d858
  • NRN_ENABLE_BINARY_SPECIAL changes from(#682)... 9782fcc

7.8.1

15 Aug 13:52
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  • Easier installation on macOS and Linux; just use: pip3 install neuron
  • More reaction-diffusion integration: PlotShape.plot support, h.distance, node in sec
  • Increased support for Python graphics packages
    • PlotShape.plot and RangeVarPlot.plot both gained support for plotly; RangeVarPlot.plot also gained support for plotnine
  • New, optional mechanism syntax and introspection; mechanism descriptions now displayed in ModelView
    • h.hh.insert(h.allsec()) and soma.insert(h.hh)
    • h.hh.code, h.hh.file, help(h.hh)
    • If the nmodl module is installed: h.hh.ontology_ids, h.hh.ast, h.hh.ions
  • Cleaner mod-file pointer setting syntax
  • Gui redirect support for routing legacy graphics to an interviews alternative
  • Support for cmake compilation in addition to autotools
  • Compilation flag for using 2019 SI unit values (off by default)
  • Miscellaneous bug fixes and optimizations

Possibly breaking change (but very rare in practice):

  • SectionList iteration does not change the currently accessed section; use section methods or sec= instead

NEURON -- VERSION 7.7.1 7.7 (30786951) 2019-06-08

08 Jun 21:47
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NEURON -- VERSION 7.6.7 (603da174) 2019-04-19

04 Jun 20:56
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Request for specfic bug fix

14 Nov 14:39
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Tag to allow pointing a travis build. Specfic request to include the changeset 9fc7197