Release 9.0.0

Release Date : 30-09-2025

NEURON 9.0 marks a major milestone with significant under-the-hood
updates. This release features a redesign of internal data structures
using the Structure-Of-Arrays (SoA) memory layout, replacement of
pointers by DataHandles that are automatically updated when internal
memory layout changes, migration of the
codebase and translation of MOD files to C++, and the introduction of
random number generator construct natively in the NMODL (and legacy but still default nocmodl) language.
Additionally, many legacy NMODL constructs have been removed, and legacy
code and libraries have been replaced with modern alternatives like
Eigen, ensuring improved performance and maintainability.

What follows are a selection of the ~1500 pull request squash/merge
commits to the master branch since
the start of the 9.0a tag on 17-07-2023

What's New

• Use of SoA memory layout for internal data structures (#2027, #2381, #2712)
  This is a prerequisite for adopting CoreNEURON GPU functionality natively into NEURON.
• Replace pointers with DataHandles. DataHandles pointing to RANGE variables
  always point to the correct value when memory is permuted or reallocated.
• Support for random number generator language construct (RANDOM) in NMODL (#2627)
• Replace pthread-based threading implementation with std::thread (#1859)
• Introduce meaningful Python types: HOC classes associated with Python types (#1858)
• Formalization of C API for NEURON (first version) (#2357, #3557)
• Introduce nanobind to gradually replace C Python API usage (#2545)
• Requires C++17 compiler and flex >= 2.6 (#1893)
• CoreNEURON repository is merged into NEURON (#2055)
• CoreNEURON report extensions (#3507, #3542)
• Modern implementation of NMODL (eventually to replace the nocmodl MOD file translator) is merged into NEURON (#3333)
• Support for numpy>=2 added (#3040)
• Replace legacy Meschach source copy with Eigen library (#2470)

Breaking Changes

• MOD files are compiled as C++ instead of C (see migration guide for VERBATIM blocks)
• API changes in the functions related to random numbers, see #2618
• Restored usage of TABLE statement in hh.mod, results are now same as 8.0.2 (see #1764)
• NMODL: Disallow use of ion variable in the CONSTANT block (#1955)
• NMODL: Disallow declaring variables and functions with the same name (#1992)
• Usage of Eigen library could introduce floating point differences, but they are very small, validated and can be ignored

Removal / Deprecation

• Removed HOC function parent_node (Issue 3571) (#3576)
• Removed usage of legacy OS X carbon libraries (#1869)
• Removed legacy LINDA code and Java bindings (#1919, #1937)
• Removed unused NMODL methods: adams, heun, clsoda, seidel, simplex, gear (#2032)
• Removed support for Python 3.7 and 3.8 (#2194, #3108)
• Removed support for legacy units and dynamic units selection (#2539)
• Removed unused NEMO simulator compatibility (#3035)
• Removed checkpoint feature (h.checkpoint()), superseded by SaveState (#3092)
• Removed legacy Random.MLCG and Random.ACG random number generators (#3189, #3190)
• Removed support for mod2c transpiler for CoreNEURON (#2247)
• Removed unused NMODL constructs: PUTQ, GETQ, RESET, MATCH, TERMINAL, SECTION,
  IFERROR, MODEL_LEVEL, PLOT, SENS, etc (#1956, #1974, #1975, #2001, #2004, #2005)
• Removed __MWERKS__ (CodeWarrior compiler) related code (#2655)
• Removed obsolete uxnrnbbs code (#2203)
• Removed old tqueue implementations (#2225, #2740)
• Removed unused RxD code_matrix_to_rxd_sparse (#3547)
• Py_NoSiteFlag is deprecated for site_import (#3286)

Bug Fixes

• Fix segfault from unref hoc_obj, see #1857 (#1917)
• Fix bug in rxd reactions involving rxd parameters (#1933)
• Fix CoreNEURON bug when checkpointing VecPlay instances (#2148)
• Fix nocmodl bug with unused STATE + COMPARTMENT variable in KINETIC block (#2210)
• Fix for dynamic ECS diffusion characteristics (#2229)
• Various fixes for compatibility with newer NVHPC compiler releases (#2239, #2591)
• Fix Windows and Mac crash on multiline HOC statements input from terminal (#2258)
• Fix for Vector.max_ind (#2251)
• Fix for detecting ION channel type in LoadBalance (#2310)
• Fix for RangeVarPlot adding extra point at section ends when using plotly (#2410)
• Fixed mod file array variable assignment (seg.mech.array[i] = x) (#2504)
• Various fixes in RxD features (#2593, #2588)
• Fix CoreNEURON bug causing in-memory model copy with file mode (#2767)
• Fix CoreNEURON bug when using array variables in MOD files (#2779)
• Fix lexer for ONTOLOGY parsing (#3091)
• Fix issue while using Anaconda Python on MacOS (#3088)
• Fix ParallelContext bbs memory leaks (#3563)
• Fix RxD indexing bug (#3337)
• Fix handling of hh.mod when using CoreNEURON (#3301)
• On h.quit(), terminal settings are same as when neuron.hoc was imported (#3259)
• int replaced by floor to accept negative coordinates (#3264)
• Fix sanitizer leak involving neuron import h, gui (#3243)
• Fix leaks in get_endian_character (#3257)
• Fix leak in pysec_children and pysec_subtree (#3255)
• Python 3.13.1 broke [s for s in sl] where sl is a SectionList (#3276)

Other Improvements and Changes

• Allow segment.mechanism.func(args) to call a FUNCTION or PROCEDURE (#2475)
• Simplify INDEPENDENT statement as only t variable is accepted (#2013)
• Fix various memory leaks and related improvements (#3255, #3257, #3243, #2456)
• Support for reading reporting related information with in-memory mode (#2555)
• NMODL language documentation update (#2152, #2771, #2885)
• Documentation improvements including transfer from https://neuron.yale.edu to https://nrn.readthedocs.io (#1901, #2922, #2971, #3106, #3187)
• Various test, CI, and build infrastructure improvements (#1991, #2260, #2474)
• Migrate many C code parts to C++ (#2083, #2305)
• Support online LFP calculation in CoreNEURON (via SONATA reports for BBP use cases) (#2118, #2360)
• Adopt CoreNEURON cell permute functionality into NEURON (#2598)
• Allow legacy a.b(i) syntax for 1d arrays (extend to PointProcess.var[i] and ob.dblarray[i]) (#2256)
• Add an ability to run NEURON ModelDB CI using label (#2108)
• Remove unused code parts under various preprocessor variables (#2007)
• Return error/exit codes properly in nrniv -c and nrnivmodl (#1871)
• No limit on number of ion mechanisms that can be used (#3089)
• Added Jupyter support for ModelView (#1907)
• Make notebooks work with bokeh>=3 (#3061)
• Added new method ParallelContext.get_partition() (#2351)
• Unified docs: one file for all languages (#3466)
• Improve rxd memory usage with __slots__ (#3572)
• nrn_function_call now works with non-double returns (#3559)
• Replaced % string formatting with f-strings (#3552)
• SectionList.size() and len(sectionlist) skip deleted sections (#3524)
• Add .size() to the SectionList object, returns the number of sections
  in the list (#3520)
• CVode no_cap uses direct backing store instead of Node* (#3314)
• Documentation updated to use from neuron import n (#3459)
• Default node order is cell contiguous (except for thread rootnodes) (#3300)
• Support multicompartment reactions with source & destination in the ecs (#3296)
• Update rxd.MultipleGeometry to support 3D and hybrid models (#3389)
• Add NMODL warning if a FUNCTION does not have a return statement (#3404)
• Update species on region exception message (#3351)
• Updated rxd reactions to allow pure backward reactions (#3273)
• Vector.apply for Python functions (#3362)
• Allow python callbacks for xstatebutton and xcheckbox (#3355)

Release 9.0.rc1

9.0.rc1

Release 9.0.rc0

9.0.rc0

Release 8.2.7

Release Date : 25-05-2025

This release allows use of Python 3.13. Pins numpy to >=2. Includes backports for several fixes.

Bug Fixes

• On h.quit(), leave terminal settings in same state as when neuron.hoc was imported.

Release 8.2.7.dev

Works with Python 3.13

For pip install, need to choose a *.whl file that is consistent with your OS (linux or macosx) and Python version (e.g. cp313). Download it and pip install <downloaded-file.whl>
or, for example install straight from the full url, e.g.
pip install https://github.com/neuronsimulator/nrn/releases/download/8.2.7.dev/neuron-8.2.7.dev0-cp313-cp313-macosx_10_15_x86_64.whl

Release 8.2.6

Release Date : 24-07-2024

This release pins numpy to <2 and includes backports for several fixes.

Bug Fixes

• Informative error when cannot import hoc module
• ParallelContext: hoc_ac_ encodes global id of submitted process.
• Python 3.12 compatibility with Windows installer (#2963)
• Windows 11 fix for nrniv -python (#2946)
• Fix for dynamic ECS diffusion characteristics.
• python38 is back. For testing can use rx3doptlevel=0 bash bldnrnmacpkgcmake.sh
• Fix cvode.use_fast_imem(1) error with electrode time varying conductance.
• Apple M1 cmake failure in cloning subrepository. See #2326.
• Update iv

Release 8.2.5.dev

8.2.5.dev

Release 8.2.4

Changelog

Bug Fixes

• Python 3.12 compatibility fixes
  • replace distutils with setuptools
  • fix segfault on exit
• updates to CI
  • move from MacOS 11 to MacOS 12
  • add MUSIC
  • bugfix for coverage CI
• small bugfix for edge case in RX3D
• unified setup.py
• misc cmake improvements

Improvements / Other Changes

• Disabled RXD code in notebook to avoid breaking docs build (see GitHub Issue #2710)
• Disabled RXD tests on Windows (see GitHub Issue #2585)

Release 8.2.3

Changelog

• The primary purpose of 8.2.3 is to fix the HOC cursor control problems of the wheel and windows installed versions.
• Many fragments from current master to allow building of installers. with current compiler toolchains and github actions.

Bug Fixes

• Fix MacOS linux wheel HOC backspace.
• Fix Windows HOC cursor issues.
• Fix Windows 11 HOC icon.
• Fix Windows and MacOS segfault on multiline HOC statements input from terminal.
• Fix build issues with current compiler toolchains and github actions.
• Deal with .inputrc if missing on Windows

NOTE: In this release, the release tarball full-src-package-8.2.3.tar.gz and nrn-full-src-package-8.2.3.tar.gz are the same. All future releases will include tarballs with the naming convention of nrn-full-src-package-<version>.tar.gz.

Release 9.0a

9.0 Alpha

Release Date : 17-07-2023

pip

pip install neuron==9.0a

PyPi

https://pypi.org/project/NEURON/9.0a0/#files