Release 8.0.2

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

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

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:

• NEURON : https://github.com/neuronsimulator/nrn/graphs/contributors
• CoreNEURON : https://github.com/BlueBrain/CoreNeuron/graphs/contributors
• NMODL : https://github.com/BlueBrain/nmodl/graphs/contributors

Feedback / Help

• Software related issues should be reported on the GitHub : https://github.com/neuronsimulator/nrn/issues/new/choose
• For developing models and any scientific questions, see NEURON forum : https://www.neuron.yale.edu/phpBB/
• If you want to participate / contribute to the development of NEURON, you can join monthly developers meeting : https://github.com/neuronsimulator/nrn/wiki

Release 8.0a

8.0a

Release 7.8.2

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

• 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

Version 7.7.1

NEURON -- VERSION 7.6.7 (603da174) 2019-04-19

Version 7.6.7

Request for specfic bug fix

Tag to allow pointing a travis build. Specfic request to include the changeset 9fc7197