NEURON 9.0

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