changelog for 9.0.0 (#3613)

Author: nrnhines

docs/changelog.md

@@ -1,3 +1,138 @@
+# NEURON 9.0
+
+## 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](https://nrn.readthedocs.io/en/latest/guide/porting_mechanisms_to_cpp.html#porting-mechanisms-to-cpp) 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)
+
+
 # NEURON 8.2
 
 ## 8.2.7
@@ -216,7 +351,7 @@ _Release Date_ : 25-03-2022
 
 ### Bug Fixes
 * Can use ParallelContext.mpiabort_on_error(0) to say do not call to MPI_Abort on error (#1567)
-* OpenMPI initialisation crash: argv[argc] should be null. (#1682)
+* OpenMPI initialization crash: argv[argc] should be null. (#1682)
 * Avoid segfault if error during construction of POINT_PROCESS (#1627)
 * Fixes a 1D/3D voxelization problem where frusta are outside the 3D grid. (#1227)
 * Allow for two point (single section) SWC somas (#1144)