NEST 2.12.0

@jougs jougs released this Mar 1, 2017 · 1278 commits to master since this release

DOI License

NEST 2.12.0 contains 1763 repository commits from 169 pull requests by 40 developers since v2.10.0.

New models, tests and examples

  • Symmetric STDP model vogels_sprekeler_synapse (Vogels et al., 2011; #218)
  • Support for inhibitory STDP (#284)
  • New neuron model aeif_cond_beta_multisynapse using GSL ODE solver (#439)
  • Generalized integrate-and-fire (GIF) neuron models gif_psc_exp, gif_psc_exp_multisynapse, gif_cond_exp, gif_cond_exp_multisynapse (#261, #516, #579)
  • weight_recorder for recording weights of plastic synapses (#497)
  • Added current based adaptive exponential I&F neurons aeif_psc_alpha, aeif_psc_exp (#513)
  • Implement the full NMDA model for ht_neuron (#491)
  • Added cubic milimeter microcircuit model for PyNEST (#451)
  • New PyNEST example sensitivity_to_perturbation.py (#198)
  • New test and improvements for handling the multiplicity property of Events (#255)
  • Added sigmoid growth curve for structural plasticity (#476)

General improvements

  • Support for two-dimensional parameter arrays in Connect (#465)
  • Added a vim syntax highlighing file (#253)
  • PyNEST raster plot example now uses pandas if available (#422)
  • New environment variables SLI_PATH for adding to the SLI search path and NEST_MODULES for loading modules on startup (#479)
  • New flag supports_precise_spikes for models supporting off-grid events (#475)
  • Connect now supports a new keyword symmetric to also add a reverse connection in a single run, synapses which require this now have the requires_symmetric flag set (#315, #524)
  • Better support for Python 3 and improved build system support for Python-less builds (#313, #342, #452, #620, #631, #634)
  • Cleaned up and more informative logging during Simulate (#269)
  • do_tests.sh prints out the error message in case a test fails (#515)

Documentation and example changes

  • Extended documentation of SLI regexec function (#251)
  • Improve documentation of current filtering in iaf_psc_exp (#276)
  • Fix and clean up hpc_benchmark.sli example (#289)
  • Re-format all PyNEST code to be PEP8 compliant and use NumPy style docstrings (#263, #337)
  • Add documentation on heterogenenous MPI environments (#335)
  • Add information on how to contribute (#320)
  • Added link to NEST Contributor Agreement to documentation index (#235)
  • Added documentation for synaptic elements and growth curves (#219)
  • Added more information about spike generation and precision (#364)
  • Documentation of exact integration method used in current based models (#383)
  • The toplevel README.md now contains all general information about NEST (#423)
  • Added documentation on using gcc on BlueGene/Q (#447)
  • Documentation improvement to ht_neuron and minor code prettification (#387)
  • Updates to Eclipse instructions (#444)
  • Extended README.mds for testsuite and PyNEST (#503)
  • Added info on static linking against non-standard allocators on BG/Q (#489)
  • Add information on filing bugs to contribution guidelines and development documentation (#548, #549)
  • Added full user documentation in markdown (#292, #371)
  • Move gap junction examples to more appropriate directory (#594)
  • More information on conventions for naming models (#611)
  • Extended gap junction documentation in markdown and SLI docstrings (#608, #623)
  • Added information on spike exchange to documentation (#612)
  • Updated installation documentation (#615)
  • Converted NEST by example book chapter to Jupyter notebook and updated for 2.12.0 (#602)
  • Replaced iaf_neuron in docstrings and examples by iaf_psc_alpha (#626)

Performance

  • Improve GetConnections performance up to 118 times (#490)
  • Improved performance of threaded connection generation for large networks up to 80 times (#485)
  • Improved connection parameter skipping with connection rule all_to_all (#568)

Build system and continuous integration

  • Rewrite build system to use CMake instead of autotools (#213, #234, #318, #326, #350)
  • Add CMake option for colored gcc output (#378)
  • TravisCI now checks for PEP8 and counts compiler warnings (#296, #298)
  • Reduce the number of build jobs from a whole matrix to only dependent jobs (#409, #640)
  • Improved logging and more robust parsing of TravisCI log (#395, #413)
  • Add automatic testing for MUSIC (#471)
  • Better handling of precise spike times in spike_detector (#446)

Bug fixes

  • Fixed shadowing of connect() function in SPBuilder (#216)
  • Fix the hard coded decay of synaptic elements in the structural plasticity framework (#215)
  • Fix for importing readline with Anaconda Python (#209)
  • Bug fix for icpc compiler (#232)
  • Syntax fixes for relative imports in Python 3 (#233)
  • Fix uninitialized variables in multisynapse models (#283)
  • Fix compilation on K computer (#288)
  • Fix and document the usage of nosetests for the PyNEST testsuite (#321)
  • Topology now skips non-local potential targets correctly (#282)
  • Properly handle precise times in spike_generator (#327)
  • Fix copyright header test to exclude backup files (#340)
  • Remove PyNEST's link dependency on libreadline (#323)
  • Fix MyModule example build and install problems (#328)
  • Fixed order of setting parameters for synapse models (#333)
  • Fix C++11 compilation error due to stream conversion (#389)
  • Fix handling of params dictionary in Connect (#441)
  • Improve numerical stability of some tests (#466)
  • Record correct quantity for post-synaptic current in iaf_psc_alpha (#500)
  • Use correct unit (ms) for printing MUSIC acceptable latency (#535)
  • Fixing encoding issues in PyNEST (#536)
  • Fix conversion from heterogeneous to homogeneous connector when deleting last synapse of a type (#566)
  • Fix refractoriness handling for adaptive exponential I&F neuron models and hh_cond_exp_traub (#575, #590)
  • Replace operator<< with regular function to avoid issues with K compiler (#587)
  • Fix bug in sp_disconnect() that could lead to heterogeneous connectors not being used any more during spike delivery (#597)
  • Fixed desynchronization of MPI processes due to waveform relaxation (#607)
  • Fixed get_targets() for structural plasticity (#604)
  • Exception when structural plasticity and multiple threads are used (#629)
  • Added check on threading in two PyNEST tests which require it (#642)
  • V-bounded implementation for adaptive exponential I&F neuron and fix for Delta_T=0 (#474)
  • Fix for usage of gap junctions without waveform relaxation (#655)
  • ConnectLayers now connects thread siblings of devices properly (#666)

Under the hood

  • Split and refactor NEST Scheduler and Network classes into separate *Manager classes according to their responsibility (#205)
  • Replaced internal C++ variable U0_ by E_L (#236)
  • Improvements of the framework for iterative solutions (#273)
  • Re-format all code files to have a maximal line width of 80 characters (#297)
  • Move inline functions from *.cpp to *_impl.h (#397)
  • Additional timers and local spike counter for profiling and performance measurements (#434)
  • Removed *_t aliases for built-in C++ data types (#454)
  • Rename Parameter class in Topology to TopologyParameter (#408)
  • Add vera++ config file to repository (#562)
  • Removed plural forms of certain parameter names (#551)
  • New help generator re-written in PyNEST replaces the old SLI generator (#464)
  • Better handling of exceptions during update (#542)

Changed behavior and removed functionality

  • Raise exceptions on incommensurate times (#265)
  • Unified synaptic recordable names for current based models (#502)
  • Added protection against probabilistic wiring to spike_detector (#560)

The long deprecated functions ConvergentConnect, DivergentConnect, RandomConvergentConnect, RandomDivergentConnect and FindConnections were removed in favor of the new unified Connect framework. See the documentation on connection management for details on how to convert your code.

Deprecated functions and models

The following models will be removed in the next major release:

  • iaf_neuron, please use iaf_psc_alpha instead
  • subnet, siblingcontainer and proxynode will be removed without replacement
  • aeif_cond_alpha_RK5, please use plain aeif_cond_alpha instead

Due to the upcoming removal of the subnet model and the concept of a hierarchical network storage, the following functions are also marked as deprecated and will be removed together with the subnet model in the next major release:

  • LayoutNetwork, GetNetwork
  • BeginSubnet, EndSubnet, ChangeSubnet, CurrentSubnet
  • GetNodes, GetLeaves, GetChildren
  • GetLID

The remaining functionality of DataConnect over normal Connect will be integrated into the normal Connect function. Thus DataConnect is marked as deprecated and will be removed once Connect has the same feature set.

For all deprecated models and functions, a corresponding message will be printed upon usage (#580).

Contributors since v2.10.0

  • Alcazar, Jesus Garrido
  • Bachmann, Claudia
  • Blundell, Inga
  • Bos, Hannah
  • Breitwieser, Oliver
  • Deepu, Rajalekshmi
  • Diaz, Sandra
  • Djurfeldt, Mikael
  • Eppler, Jochen Martin
  • Fardet, Tanguy
  • Golosio, Bruno
  • Graber, Steffen
  • Hagen, Espen
  • Hahne, Jan
  • Ippen, Tammo
  • Jordan, Jakob
  • Kunkel, Susanne
  • Lepperød, Mikkel Elle
  • Mahmoudian, Sepehr
  • Morrison, Abigail
  • Muller, Eilif Benjamin
  • Mørk, Håkon
  • Peyser, Alexander
  • Plesser, Hans Ekkehard
  • Plotnikov, Dimitri
  • Rao, Arjun
  • Rothe, Hendrik
  • Schenck, Wolfram
  • Schmidt, Maximilian
  • Schuecker, Jannis
  • Schumann, Till
  • Seeholzer, Alex
  • Setareh, Hesam
  • Shusharin, Alexey
  • Sinha, Ankur
  • Terhorst, Dennis
  • Trensch, Guido
  • Vennemo, Stine Brekke
  • Vieites, Juan Hernando
  • Weidel, Philipp

Citation

If you use this version of NEST, please cite it as Kunkel, Susanne et al. (2017). NEST 2.12.0. Zenodo. 10.5281/zenodo.259534. The full citation is available in different formats on Zenodo.