Nest Simulator Versions Save

NEST 3.1 is the result of 460 commits by 17 developers since NEST 3.0 which was released on 2021-06-10.

This release contains many bug fixes and improvements, especially in the Python setup where support for Python environments was improved.

The PyNEST API was extended to support a more intuitive way of setting and retrieving kernel parameters. Where you previously had nest.SetKernelStatus({"resolution": 0.2}) in your simulation script, you can now just write nest.resolution = 0.2. Kernel attributes now come with their own docstrings and even tab-completion works for them! Additionally, PyNEST functions are now directly linked to the API reference throughout the documentation.

The testsuite now handles MPI tests more consistently and uses pytest for all Python tests.

Enhancements

Normal

• Add support for different virtual environment types for Python
• Link PyNEST functions in documentaton
• Automatic conversion of integers to doubles when setting parameters
• Add Arbor backend to GitHub Actions testing matrix
• Modify and improve colors in style sheet for user documentation
• Add intersphinx to NEST documentation with links to related projects
• Check validity of parameters given to SetKernelStatus
• Implement time limit for duration of update cycles
• Add kernel attributes and get/set functions to PyNEST module
• Automatically flag issues and pull-requests as stale
• Link to Zenodo citation page in docs

Bug fixes

Critical

• Run Python tests using Pytest, reorganize MPI-based Python tests and improve error reporting

High

• Set have_connections_changed correctly when we have fewer connections than MPI ranks
• Correct documentation of local_spike_counter
• Fix setting of PYEXECDIR
• Fix use of thread-specific distributions in random parameters
• Restrict calls to set_connections_have_changed() to thread 0
• Fix examples to make them run
• Undo link to PyNEST API in SLI documentation
• Detect pytest executable more robustly
• Fix import nest in NEST Server
• Check that timeout package is installed before running pytests
• Fix out of bound access on pp_pop_psc_delta and pulsepacket_generator
• Fix access of first element of an empty vector in pynestkernel

Normal

• Support apt-installed uwsgi in nest-server
• Fix build log parser failed test list
• Align pkg_resources query with setup.py name
• Fix mismatched parenthesis in setup.py.in

Maintenance

Critical

• Activate additional static code analysis in GitHub Actions

High

• Replace PEP8 by pycodestyle
• Clean up NEST Server and fix deadlock
• Remove Arbor recording backend
• Add pp_pop_psc_delta to deprecation list

Normal

• Add functions to access information about simulation time
• Refactor the Parameter classes
• Add user-level documentation for built-in timers
• Remove outdated CMake options
• Remove 'nest-' from setup.py version
• Update citation information
• Remove machine-specifc code for K computer
• Warn users they are using latest on ReadtheDocs
• Minor improvement to microcircuit example
• Remove undocumented weighted_spikes_{ex,in} from iaf_psc_{alpha,exp} recordables
• Add license to jupyter notebooks
• Fix figure in spatially structured networks tutorial
• Replace pass-by-value with pass-by-const-reference in Vose constructor
• Turn docstring with math into raw string
• Add default values to SetKernelStatus parameters
• Update security support for new release
• Relocate and refactor PyNEST testsuite
• Undo Markdown-to-reStructuredText conversion in doxygen comment
• Pave the way for per-version transition guides
• Remove outdated comment on Python dynamic library flags
• Update Python version check in __init__.py
• Add warning about synaptic plasticity mechanisms and precise spike timing
• Replace the Vose class with std::discrete_distribution
• Copy syn_spec to prevent it being modified
• Update Random123 library to v1.14.0
• Warn about the removal of nest.hl_api
• Update security support for 3.1 release

NEST 2.20.2 is the result of 15 commits by 7 developers since NEST 2.20.1 which was released on 2020-12-02.

This release contains mainly bug fixes and backports. Most notably it brings support for detailed timers (#2086, which allows more consistent comparisons between benchmark results obtained with this and later versions.

In particular it contains

• Add standard and detailed timers for benchmarking purposes for NEST 2.20.2
• Backport documentation for built-in and detailed timers
• Update NEST 2.20.x CMake configuration to support OpenMP fully on OSX
• Revise NEST 2.20.x guide on random numbers to be ajour with NEST 2.12 and later

NEST 2.14.1 is the result of 14 commits by 6 developers since NEST 2.14.0 which was released on 2017-10-20.

This patch release contains an optimization for the Potjans & Diesmann (2014) model and adds builtin detailed timers and corresponding documentation, which allows more consistent comparisons between benchmark results obtained with this and later versions.

NEST 3.0 is the result of 5043 commits by 47 developers since NEST 2.20.0 which was released on 2020-01-28.

With the release of NEST 3.0, we introduce a ton of new features to improve how you create and manage simulations.

NEST 3.0 introduces a more direct approach to accessing neuron and device properties and to interacting with synapses. You can now read and write properties of nodes and connections with the functions get() and set() or by direct member access (e.g., neuron.V_m = -55.0). Parameter objects make mathematical and probabilistic functions available to pick neuron properties, create spatial positions, define connection probabilities, and much more. In addition, it is now way easier to perform operations such as slicing, iterating, and tests for equality on collections of neurons and synapses.

NEST 3.0 replaces the old random number generator library with a new one based on the C++ Standard Library. The new library also provides generators from the Random 123 library, including crypotgraphic generators. Most notably, you can now much more easily seed all generators and change the type of random number generator you are using.

We have improved how recordings from simulations are handled, making the infrastructure more modular and extensible. In addition to the previously supported recording methods, a new backend for SIONlib is now available. The interface for stimulation devices can now handle data from external sources, such as other simulators.

The Topology Module is no longer a separate module; it is integrated within PyNEST, and now referred to as support for spatially-structured networks.

NEST Server is a novel backend to NEST that allows to run simulations via a RESTful API. Instead of directly importing nest into your Python session, the code that controls the simulation is sent over HTTP to NEST Server in this use-case.

Enhancements

Critical

• Introducing NEST 3.0!

High

• Add Urbanczik-Senn synapse and supported neuron model
• Integrate web service for RESTful API to NEST Simulator
• Add option to generate connections from NumPy arrays
• Refactor PyNEST Microcircuit example Potjans_2014
• Add infrastructure for generic input backends to feed devices
• Improve visibility of NEST 3.0 conversion guides
• Update model docs to reStructuredText format II
• Update PyNEST examples to use NEST 3 features
• Enhance Connect to work seamlessly with arrays and lists
• Move to Ubuntu Bionic on Travis
• Modernize random number generator setup
• Add information on NEST and multiprocessing
• Create connections with lists of synapse dictionaries
• Update globals to support execution of hpc_benchmark.py example
• Add PyNEST function to obtain local VPs
• Switch to Github actions for CI testing
• Replace conda environment files with one file covering all needs
• Add MPI-enabled version of NEST Server and NEST Server documentation
• Revise quantal STP example

Normal

• Add support for rate data in MUSIC proxies
• Communication via compressed spikes
• Update issue templates (bugs/features)
• User documentation extractor
• Correct documentation of the stdp_dopamine_synapse model
• Create documentation workflow page
• Create template for documentation issues
• Improve documentation of rate-based models
• Add array indexing to NodeCollections
• Change definition of realtime factor in print_time
• Fix error in serializable
• Allow direct conversion from NodeCollection to numpy
• Avoid naming conflicts by installing shared objects to lib/nest instead of lib
• Add information about nest_vars.sh and update Linux installation instructions
• Copy the current Microcuircit documentation for use with Readthedocs
• Set and get structural plasticity status parameters through set and getKernelStatus
• Add min_rate to specify a non-zero rectfying rate for rate neuron models with input noise (rate_neuron_ipn)
• Systematize error messages for Connect failures
• Get distances between sources and targets in SynapseCollection
• Fix Izhikevich model initial conditions
• Refer to Vim syntax highlighting
• Add special cases for empty NodeCollections
• Add documentation how to install NEST via homebrew
• Add Jonke synapse
• Add getters/setters for excitatory/inhibitory synaptic conductance state
• Add guide about weight normalization
• Clarify conda installation with MPI
• Add badges with versions and statistics to README
• Add functionality for getting/setting synaptic currents in iaf_psc_exp_ps model
• Add tips for installing NEST with conda to documentation
• Efficient initialization of membrane potentials with original and optimized conditions in Potjans_2014
• Update PyNEST README to reStructuredText and fix broken link in documentation
• Make configuration options more visible in documentation
• Use ring buffer that allows for multiple values per slot
• Timers for Benchmarking (related to issue #1471 "Basic Instrumentation")
• Add PyNEST version dunder
• Add description for SIONlib file format to backend documentation
• Add description for "Two neuron example"
• Add documentation about our CI pipeline
• Fast and safe Siegert implementation
• Add synapse_label and receptor_type support to spatial connections
• Add checker for forbidden types
• Revised documentation on synapse specification slightly
• Add a Python script reporting Python imports from the NEST code base.
• Add example for how to store and restore a network.
• Restructure NEST 3.0 guides
• Make activation term exponent for I_NaP and I_T configurable in ht_neuron
• Add instructions for how to work with Eclipse when developing NEST
• Add link to set_verbosity documentation
• Add support for different virtual environment types for Python
• Add instructions for how to work with VS Code when developing NEST
• Add a NEST documentation style guide
• Add documentation on parameter comparators

Bug fixes

Critical

• Use vector of integer for per-thread bool indicators
• Count local devices for each thread
• Correctly initialize result vector in music_rate_in_proxy::get_status()
• Improve BlockVector to fix issues when sorting with recent versions of Boost
• Fix Python compatibility issue on Readthedocs
• Fix GetConnections to not include erroneous connections when using multiple threads
• Fix setting synapse parameters when running connect_arrays multi-threaded
• Clean up t_ref parameter in aeif models
• Fix for failing Read the Docs build
• Remove brackets around NodeCollections in tests
• Fix issue with building Sphinx documentation with recent Jinja version
• Fix catching build warnings in GitHub Actions

High

• Fix misuse of outdated variable that led to an impossible condition
• Use proper delete[] and atomic read in CompletedChecker
• Only check for contains list if params is not empty
• Initialize indicator for changes to connectivity to false
• Enables display of commands with default settings in the .nestrc
• Switch from bisection method to regula falsi method in precise models
• Correct filename quoting
• Move dependencies and fix broken image links
• Only include audio backend header in MyModule if library support is detected
• Fix broken "Network models" link
• Fix NodeCollection fingerprint
• Fix synaptic time constants in model documentation
• Fix NodeCollection creation to correctly raise error when using non-unique or unsorted node IDs
• Handling of out-of-range slicing and indexes for NodeCollections
• Add CMake switch for enabling/disabling the recording backend for Arbor
• Replace Python 3.6 f-strings to achieve Python 3.5 compatibility
• Make multimeter record at correct time when offset is specified
• Add missing initialiser in copy constructor for stdp_nn_pre-centered_connection
• Improve parsing of PyNEST test results and list of failed tests
• Update doc/model_details notebooks to work with NEST 3.0
• Update syn_spec when a synapse parameter is list and we use fixed_total_number
• Slice spatial metadata when slicing a NodeCollection with spatial metadata
• Autodetect Python include path and library file instead of hardcoding them
• Fix GetConnections to correctly get connections with devices as sources when specifying only target
• Fix NodeCollection equality comparison to ensure that the other NodeCollection is of the right type
• Fix wrong connection in STDP NN unit test
• Fix for first spike passing through "tsodyks2" synapse
• Fix hpc_benchmark.py to work when more than 30 ranks are used
• Fix linking problems on OSX in presence of MPI4Py
• Fix test_connect_all_patterns.py on TravisCI
• Fix segfault when mpi4py is imported before NEST
• Fix printing of sliced composite NodeCollection
• Fix incrementation of weight and delay in connect_arrays
• Skip setting of parameter if test is skipped
• Fix measurement of presimulation time in PyNEST Potjans_2014
• Fix int/float data type check
• Fix broken colors in documentation
• Fix doc buildsystem (again)
• Reduce amount of data exchanged in test to ensure stable operation.
• Fix encode error of help text.
• Parse build output of GitHub Actions
• Fix failing assert when connecting spatial populations
• Make sure init_state_ is called for models that need it, and remove redundant ones
• Fix missing state variable initialisation in iaf_chxk_2008
• Fix Python MPI tests
• Fix failing build on ReadtheDocs due to key error
• Correct documentation of local_spike_counter.

Normal

• Identify changed files for static code analysis using git diff for PRs
• Use theme options to show logo on readthedocs
• Clean up handling of path-related environment variables
• Fix broken dependency in old Python on readthedocs
• Fixed minimal typo in user documentation.
• Correct path
• Check if parameter is in model dictionary before setting it
• Revise PyNEST documentation for GetStatus and get()
• Support slicing of NodeCollections in NEST Server
• Return all values when using get() on a SynapseCollection with more than one synapse
• Fix typo in IMapFunction::backtrace
• Fix for printing empty SynapseCollection
• Correctly draw rectangular masks with azimuth_angle != 0
• Fix nest-server not starting with apt-installed uwsgi
• Add missing include file to CMakeLists
• Propagate the cython --version error

Maintenance

Critical

• Remove NEST 3.0 preview warnings
• Bump Python version for macOS build
• Update to latest Python on MacOS Travis CI build
• Fix location for 'spatial' headers
• Parse C++ warnings more specifically
• Rename Stimulating{Backend,Device} to Stimulation{Backend,Device}

High

• Update the conda environment to create the documentation locally
• Build NEST with Boost as default
• Sunset Python 2
• Fixed the Travis Python library path for version 3.6.10
• Remove MyModule example and pertaining documentation
• Restructure build stages to use names instead of individual flags
• Consistently use python3 command instead of python
• Remove stray files in models directory
• Fix math rendering error in documentation
• Fix Part 4 tutorial link
• Add documentation for CollocatedSynapses
• Update NumPy installation on Mac OS X Travis build
• Fix performance issues for weak scale benchmarks caused by creation of DictionaryDatums
• Change Travis macOS build to MINIMAL to avoid timeouts (temporary).
• Restructure recorder documentation to contain all properties.
• Revise Mac installation instructions
• Fix PyNest help and helpdesk commands
• Hike and enforce Python version requirement to 3.8
• Move CI documentation file to new userdoc directory
• Only static code analysis in Travis Build Matrix
• Adapt warning parser to output format on GitHub Actions
• Make quantal_stp_synapse support setting n and a when connecting
• Add a brief description of features of NEST 3.0 to its index

Normal

• Update copyright file in debian directory
• Document kernel status dictionary entries
• Add missing using directives
• Implement communication via Alltoallv for secondary events
• Remove pylab for plotting
• Change EnableStructuralPlasticity documentation to address issue #571
• Improve documentation and location of iaf_chxk_2008 model
• Document purpose of multiplicity-unrolling code in spike delivery
• Refactor beta normalization factor calculation into function
• Update Debian installation instructions
• Add links to the new NEST virtual machine
• Refactor SendBufferPosition, fail on query with rank outside of range
• Refactor/collocate target data
• Fix python 3.8.0 attribute error: module 'cgi' has no attribute 'escape'
• Rename suggest_vp_for_node_id to node_id_to_vp
• Rename has_source_subsequent_targets -> source_has_more_targets
• Improve table of contents
• Update Mac manual link
• Remove pylab and delay pyplot import
• Move "Editor support" from README into documentation
• Move topology documentation into doc folder
• Remove SubnetExpected exception and other references to subnet.
• Update readthedocs style sheet to improve text contrast
• Fix sphinx-build warnings
• Fix default parameters of siegert_neuron
• Remove comments from CMake cache internal
• Update MUSIC tutorial
• Mention mutual exclusivity of MUSIC and Arbor in documentation
• Remove redundant setting of environment variables
• Update documentation on adding spatial masks in user-defined modules
• Reorganize the travis build stages
• Silence startup
• Move JunitXML and run_test functions to their own files
• Update iaf_psc_alpha.h
• Convert exact-integration.ipynb to rst file
• Add documentation on converting from PSC to PSP
• Fix subscripts in ginzburg_neuron model documentation
• Remove "Documentation" label from documentation issue template
• Systematize multiline strings for message text in hl_api
• Fix technical typos and spelling
• Update description for parameter U in Tsodyks synapses
• Remove scrollbars from parameters and other tables on RTD
• Mention NESTML/NEST Desktop in the section "Related projects" on the documentation main page
• Update model documentation output directory
• Add "Acknowledgements" section to welcome page
• Update docstring, add comments, and minor refactoring of Create()
• Remove unused CMake options
• Fix rendering of kernel parameter documentation in PyNEST
• Convert conngen documentation to a proper guide
• Remove orphaned and unmaintained bibliography file
• Make testsuite harness independent of variable replacement
• Minor update to conngen documentation
• Fix issues when showing plots in examples
• Rename spike_detector to spike_recorder
• Merge precisemodule into modelsmodule
• Copy documentation from gh-pages to doc/contribute
• Rename and refactor test_spatial_kernels.py
• Add tests for GetConnections with synapse_model and synapse_label as arguments
• Fix stdout in nest server and add option to disable restriction
• Make NEST installation prefix references consistent
• Update hpc_benchmark.py to avoid error when running with multiple processes
• Simple typos/documentation fixes
• Changes to volume transmitter documentation
• Shrink MPI buffers for spike communication
• Delete iaf_psc_exp_multisynapse.cpp.orig
• Dissolve Topology module and move files to nestkernel/spatial
• Fix duplicate "models" entry and remove dead "topology" entry from documentation TOC
• Remove SLI neuron
• Rename "topology" to "spatial"
• Add test of connecting arrays using MPI
• Update edgecolor to default value in examples and code that use scatterplot
• Remove obsolete volume mask
• Enable MUSIC tests and correct NEST testsuite results summary
• Remove Python 2 compatibility code
• Remove erroneous example in NEST Tutorial
• Minor cleanup of linux_install.rst
• Enhance PyNEST error messages from kernel
• Replace all occurrences of "to old" with "too old"
• Update documentation of glif models
• Update documentation of gif models
• Update GIF toolbox link
• Fix SetKernelStatus examples in documentation
• Fix compiler warnings
• Remove long outdated documentation
• Add tests for receptor_type with CollocatedSynapses
• Revise user-level documentation workflow
• Fix typo in stdp_connection.h
• Create StructuralPlasticityNode separate from Archiving_Node
• Update PyNEST template code to reference current nest 3 code.
• Refactor conngen module to be a ConnBuilder
• Update connection management documentation
• Improve printing of SynapseCollections
• Add documentation on array indexing
• Rename PyNEST microcircuit example titles
• Fix doc buildsystem
• Fix NEST3 transition guide formatting
• Unify spelling of 'postsynaptic'
• Update documentation on parameter dictionaries with lists
• Update NeuroFedora URL in documentation
• Remove stray occurrences of double_t
• Remove unused lines from the part 1 tutorial document.
• Remove contact invitation from HPC systems tab
• Fix typo in test_sp/test_mpitests.py
• Add -Woverloaded-virtual to CI compiler flags
• Avoid misleading warning when connecting
• Improve NodeCollection iterator dereferencing performance when using composite NodeCollections with metadata
• Remove unnecessary notebooks
• Remove colorize.rst from docs
• Explain neuron models in documentation
• Remove "Edit on GitHub" button on Read the Docs
• Update NEST 2.20.x CMake configuration to support OpenMP fully on OSX
• Revise NEST 2.20.x guide on random numbers to be ajour with NEST 2.12 and later
• Remove all mentions of spike multiplicity from user documentation
• Remove broken link in poisson generator documentation
• Clarify the post-pre convention used in plot-weight-matrices example documentation
• Remove SLI examples in model documentation
• Hike Boost minimum version to 1.69
• Remove neuronview example
• Include ACKNOWLEDGMENTS.md directly into main page of ReadtheDocs
• Fix citation for NEST 2.20.1 and add citation for NEST 2.20.2
• Provide links to model_details in relevant model documentation
• Remove unnecessary and properly order remaining includes in gif_cond models
• Add Visual Studio Code settings directory to .gitignore
• Extended gitignore with specific excludes for various IDE config files, macOS-specific files and _build.
• Fixed a number of missing initialisations detected by Eclipse.
• Make file, C++ class and model names consistent for synapses
• Fix broken images in documentation
• Remove hill_tononi_Vp example
• Improve documentation of Run() and RunManager()
• Minor update parallel computing guide
• Update user-level documentation workflow
• Fix wrong code in the getting started documentation
• Move developer space content into docs on master branch
• Remove unused function communicate_Allreduce_max_in_place()
• Add documentation on multicompartment models
• Move connect_arrays() from nest.cpp to connection_manager
• Remove unused event_prototypes_ member
• Invalid node collection error message
• Add functions to access information about simulation time
• C++ implementations of spatial distribution functions
• Add renamed 'time' to 'biological_time' kernel status variable
• Update NEST2-to-NEST3 reference guide
• Add user-level documentation for built-in timers
• Removed outdated CMake options
• Remove 'nest-' from setup.py version

The list contains 322 PRs.

NEST 2.20.1 is the result of 105 commits by 12 developers since NEST 2.20.0 which was released on 2020-01-28.

This release contains mainly bug fixes and backports. Most notably it fixes issue #1394, which lead to incorrect simulation results under certain circumstances.

Fixed bugs

• Use vector of integer for per-thread bool indicators (backport)
• Switch from bisection method to regula falsi method in precise models (backport)
• Improve BlockVector to fix issues when sorting with recent versions of Boost (backport)
• Fix GetConnections to not include erroneous connections when using multiple threads (backport)
• Fix misuse of outdated variable that led to an impossible condition (backport)
• Use proper delete[] and atomic read in CompletedChecker (backport)
• Updated CMakeLists and iterator_pair for MyModule compatibility in 2.20.1
• Add missing initialiser in copy constructor for stdp_nn_pre-centered_connection (backport)

Maintenance

• Final updates in documentation and the debian package for v2.20.1
• Add "Acknowledgements" section to v2.20.1 welcome page
• Refactor SendBufferPosition, fail on query with rank outside of range (backport)
• Autodetect Python include path and library file instead of hardcoding them and bump Python version (backport)
• Deprecate CGConnect in SLI and PyNEST and CG interface functions in PyNEST

---

WARNING: This version of NEST is affected by issue #1394, which can lead to incorrect simulation results under certain circumstances. Please double-check all simulation results obtained with this version and if in doubt, re-run using a different split between MPI processes and threads. The description of the issue contains more details and will be updated when new information becomes available.

---

NEST 2.20.0 is the result of 454 commits in 77 pull requests by 25 developers since NEST 2.18.0 which was released on June 7, 2019.

This release wraps up the 2.x series of NEST and contains many improvements and bug fixes. Highlights are the addition of the generalized leaky integrate-and-fire neuron models by the Allen Institute, STDP synapses with nearest-neighbor spike pairing schemes and improved documentation, available on Read The Docs. Following is a list of all merged pull requests:

Enhancements

Models

• Add STDP synapses with nearest-neighbor spike pairing schemes
• Add generalized leaky integrate-and-fire (GLIF) neuron models by Allen Institute
• Add iaf_psc_alpha_ps neuron model

Installation

• Add conda-forge installation documentation for Linux and MacOSX
• Add Fugaku platform CMake file
• Clean the build process for the NEST Debian packages
• More informative compiler information in CMake summary

Documentation

• Added initial membrane potential options to microcircuit example
• Add initial membrane potential options to microcircuit example
• Add new options for installation and improve instructions for NEST
• Updated/extended macOS install instructions
• Update DOI and release buttons in README; add Zenodo reference to NEST 2.18.0
• Add link on website to new PyNEST templates and update citations
• Provide guidelines to writing to mailing list in documentation

Kernel

• Introduce time-driven spiking connections
• Add support for sending secondary events to and from devices
• Add warning about invalid connection descriptors when new connections are created
• Use an unsigned data type for thread in spike data

Infrastructure

• Fast static check in Travis CI

PyNEST

• New templates for pynest examples and api
• Allow specifying arrays of values in the synapse specification when connecting with fixed_total_number

Bug fixes

Models

• Fix uninitialized variable in iaf_psc_exp
• Fix handling of rate change in poisson_generator_ps

Documentation

• Remove spurious brackets from code example in tutorial
• Fix MUSIC example

Kernel

• Fix multiple definition of rho build complain observed on AArch64 with FCC
• Fix GetConnections to correctly get connections where the target is a global receiving device
• Fix logical error in elseif-statements in connect functions
• Check variables of GSL binomial random generator where they are set
• Ensure number of connections for fixed total number is properly set
• Fix MyModule by incorporating modelsmodule refactoring from #1069
• Avoid segfault when using a weight recorder with a probabilistic synapse

Infrastructure

• Fix cppcheck in Travis CI testsuite

Maintenance

Models

• Fix namespaces in Hodgkin-Huxley neuron models
• Make multimeter and voltmeter class names lower case

Installation

• Fix nest_vars in case of undefined PYTHONPATH
• Cleanup for the K computer specific CMake file for v2.18
• Fix up dependencies in Ubuntu install instructions
• Files needed to build Debian packages (.deb)
• Fix extraction of version number if sources are inside another Git repository
• Let uninstall of NEST Debian package also delete script in profile.d

Documentation

• Convert topology user manual to ReStructuredText
• Update links to model directory in docs
• Fix PyNEST installation instructions
• Update download page for 2.18 and conda-forge
• Correct typo in random number documentation
• Fix PyNEST API generation for documentation using mock
• Add updated NEST examples to Read The Docs
• Replace iaf_neuron by iaf_psc_alpha in MUSIC tutorial
• Autogenerate PyNEST examples from source with sphinx_gallery
• Update syntax formatting for terms in documentation
• Fix broken CSS style
• Update mailing list email address
• Small typographical updates to user documentation

Kernel

• Refactor registration of models in modelsmodule
• Increase maximum line length in source code formatting style from 80 to 120
• Unify coeffarray_as_d and coeffarray_as_uint via union
• Add missing include of sys/time.h
• Fix threading issue when connecting
• Remove spurious thread_local_connectors update
• Fix rounding issue when setting small resolution
• Improve information given by error messages typically triggered by Connect

Infrastructure

• Add tests for libnestutil/streamers.h
• Make version information consistent
• Update FindLibNeurosim to take Python version into account
• Remove the remaining markdown config in docs
• Skip deployment in Travis CI testsuite when not running a build
• Deploy build artifacts only when the build flag is set in the reply section
• Change the deployment branch to master
• Fix cppcheck usage in Travis CI testsuite
• Switch to GCC8 as default in continuous integration tests on Travis
• Fix formatting in test_stdp_nn_synapses.py
• Add security guidelines
• Moving to Python3.x on OsX
• Replace Python version by newest available on Travis

PyNEST

• Fix warnings when Cythonizing pynestkernel.pyx
• Allow installation with Python 3.8

---

WARNING: This version of NEST is affected by issue #1394, which can lead to incorrect simulation results under certain circumstances. Please double-check all simulation results obtained with this version and if in doubt, re-run using a different split between MPI processes and threads. The description of the issue contains more details and will be updated when new information becomes available.

---

NEST 2.18.0 is the result of 116 pull-requests (1128 commits) by 31 developers since NEST 2.16.0 which was released on 2018-08-21.

This release provides a number of new neuron and plasticity models and additional functionality. It improves memory allocation and performance during network construction. It includes a number of bug fixes and is the first release that can be installed via aptitude and in an Conda environment directly from conda-forge.

Enhancements

Model

• Add iaf_cond_alpha_multisynapse model
• Add conductance based I&F model with beta shaped PSCs
• Implemented step_rate_generator for piecewise constant rate input
• Add Clopath STDP synapse and two supported neuron models
• Add new neuron model hh_cond_beta_gap_traub
• Added test_multiarea_model_siegert_rates
• Add optional escape noise in iaf_psc_exp
• Add iaf_psc_alpha_ps neuron model

Installation

• Add conda-forge installation documentation for Linux and MacOSX

Documentation

• Add documentation in Topology User Manual
• hpc_benchmark.sli is now invariant under different MPI-process/thread splits with fixed VP number
• Implement breathe extension and improve generation/format of model documentation for website
• Add documentation on how to create C++-level unit tests

Kernel

• Code compatibility with C++17
• New container for connections
• Allow compile-time configuration of bit-field sizes in Target class
• Add ostream operator template for std::vectors
• Connection sorting using Boost's sorting function

Infrastructure

• Docker image for the NEST simulator
• Build on Travis using clang and gcc compilers
• Conditional travis builds using build stages
• Travis build on OSX

Pynest

• Make detailed exceptions from lower levels available in PyNEST
• Show periodic boundary conditions for masks and kernel
• Serialize output of GetStatus and GetDefaults for JSON
• Add PyNEST function to synchronize MPI processes
• Change to dynamic import in PyNEST API
• Simplify dynamic import of PyNEST submodules

Bug-Fixes

Model

• Fix header installation and multiplicity handling in MyModule
• Fix stability of iaf_psc_exp_ps for equal membrane and synaptic time constants
• Fix creation of inhomogeneous poisson generator with parameters
• Fix normalization factor for iaf_cond_beta
• Fix uninitialized variable in iaf_psc_exp

Installation

• Fix bug in JURON CMake file
• MyModule example missing Event methods
• Fix static linking of modules
• Fix header installation and multiplicity handling in MyModule
• Change target directory for doxygen from source to build

Interpreter

• Fix interpretation of verbosity and debug command line arguments as input script filename
• Prevent execution of --debug and --verbosity options as files

Documentation

• Correct documentation on libneurosim requirements
• Fix broken internal links in doc/guides

Kernel

• Handle number_of_connections<1 in topology
• Make GetConnection filter by synapse label when only target attribute is given
• Take multiplicity into account in local_spike_counter
• Throw error if creating too many connections on one thread
• Enable the use of connections without delay in Topology
• Bugfix: Reliably create masked layer when using topology's convergent connect
• Fix MPI synchronization problem in presence of very small layers
• Fix multiple definition of rho build complain observed on AArch64 with FCC

Infrastructure

• Make test_refractory.py run with make installcheck
• Make testsuite run when nosetests is unavailable
• Fix bug in test_stdp_multiplicity.py
• Use configured instead of standard Python executable
• Make python mpitest run during installcheck
• Fix postsynaptic trace edge case
• Use relative path to logo in documentation
• Fix incorrect flag in ProcessOptions.cmake

Pynest

• Fix issue when running hh_phaseplane.py with Python 2
• nest.Disconnect parameters are consistent with documentation
• Fix broken PyNEST, remove traces of ResumeSimulation
• Check recorder type_id instead of model name in plotting modules

Maintenance

Model

• Make stdp_facetshw synapse consistent with the temporal fix for STDP numerical imprecision
• Update description of rate model neurons and change parameter names
• Fix issues in siegert_neuron
• Add deprecation warnings and changed format of the warnings
• Remove unused functions in hh_psc_alpha models

Installation

• JURON support: Add platform specific CMake files
• Follow-up patch on the CMake with-warning variable and add -Xg flag to CMAKE_CXX_FLAGS
• Add CMake flag to enable/disable hpc synapses
• 32-bit compatibility (64-bit gid on 32-bit architecture)
• CMake option and documentation for using the Intel compiler
• Fix nest_vars in case of undefined PYTHONPATH
• Cleanup for the K computer specific CMake file for v2.18
• Fix up dependencies in Ubuntu install instructions

Interpreter

• Add skip_if_without_music to nest dictionary

Documentation

• New User Documentation for NEST
• Fix the documentation (semantics) for get_synaptic_elements_vacant()
• Refactor source code comment blocks
• Change HTML to CGI module import to eliminate extra Python2 dependency
• Source code comment blocks refactored
• Remove outdated README and empty directory from PyNEST examples
• Upgrade pyyaml in doc requirements due to vulnerability
• Minor updates to pynest tutorial part 2
• Fix documentation in sinusoidal_gamma_generator example
• Correcting documentation on current input in precise neurons (fixes #226).
• Remove outdated plot scripts from examples
• Add advice against using NEST in threaded processes; addresses #361.
• Fix links to NEST resources throughout the source code
• Improve documentation of get_verbosity and set_verbosity in PyNEST
• Convert topology user manual to ReStructuredText
• Update parallel computing docs regarding configuration
• Update links to model directory in docs
• Documentation update for #1177 ("Increase maximum line length in source code formatting style from 80 to 120")

Kernel

• Make lid to gid conversion (and vice versa) in the VPManager more consistent
• Move ConnectionManager methods from impl to h
• Use reverse iterator in get_history
• Rename {get,set}_delay to {get,set}_delay_steps
• Remove unused variables
• Remove old references to resume()
• Refactor GetConnections to improve performance
• Improve connection performance over threads
• Fix code formatting issue introduced by merging #1060
• Add documentation on splitting and repeating simulations, and deprecation warning for ResetNetwork
• Increase maximum line length in source code formatting style from 80 to 120

Infrastructure

• Move Travis-CI build script to extras directory
• Remove outdated release-making script
• Remove emacs support for SLI
• Make the check for copyright headers and unused Names part of the CI run
• Explicit indices
• Add MPI test for correct number of spikes when multiplicity > 1
• Automatic discovery of sli examples in example runner
• Replace bash by sh to eliminate extra dependency
• Add tests for libnestutil/streamers.h
• Make version information consistent

Pynest

• Restore PyNEST functions to top level modules

---

WARNING: This version of NEST is affected by issue #1394, which can lead to incorrect simulation results under certain circumstances. Please double-check all simulation results obtained with this version and if in doubt, re-run using a different split between MPI processes and threads. The description of the issue contains more details and will be updated when new information becomes available.

---

NEST 2.16.0 is the result of 89 merged pull requests by 39 developers since NEST 2.14.0 which was released on 20^th of October 2017.

This release contains many bug fixes and improvements. Most notably it brings a new infrastructure for the storage of connections, which reduces the memory consumption and network build times (Jordan et al., 2018). and extends the rate model framework for novel use-cases (Senden et al., 2018).

Enhancements

Models

• #492: Erfc neuron model
• #671: Adding inhomogeneous poisson generator model
• #845: Allow rectangular and box masks to be rotated
• #849: Aeif psc delta 2 continued
• #858: Extended rate-model framework
• #895: New neuronal population model gif_pop_psc_exp
• #901: Add iaf_psc_exp_ps_lossless model by Krishnan et al
• #966: Fix #825: Improve sign check
• #980: Added parameter to get/set function in tanh_rate model

Installation

• #789: Major change in the installation and testing of packages using multiple python versions
• #890: Add 'install-nodoc' target for make
• #1008: Do not use the -Wall option on K computer

Documentation

• #881: Add balanced random network example using evolution strategies

Kernel

• #812: Record conductance from aeif_cond_beta_multisynapse model
• #823: Add gamma kernel in topology
• #836: Allow negative exponential distributions (fixes #835)
• #920: NEST 5g simulation kernel

Infrastructure

• #844: Install header files

PyNEST

• #867: Add pynest version of hpc benchmark

Fixed Bugs

Models

• #846: Fixes for the gif multisynapse and quantal_stp model
• #860: Fix for #859: Added setting of wfr parameter
• #886: Fix copy/paste bug in copy constructor of Archiving_Node
• #944: Better documentation of hh_cond_exp_traub and Brette-2007-compatible refractory time
• #978: keep conductance positive in gif_cond_exp model

Installation

• #870: Bug fixed on cmake with user modules
• #871: Fixing issue on linking user module libraries with recent GCC versions
• #897: Update NEST Homebrew installation instructions to changes in Homebrew…
• #915: Fix issue 830 - Make fails with UnicodeDecodeError
• #953: Update help generation for MyModule and fix Py27-unicode

Documentation

• #970: Fixes #967: Correct parameter in documentation

Kernel

• #840: Fix handling of PyNEST and SLI commandline arguments
• #887: Fix incorrect error message when connecting with bad delay
• #903: Support linking against topology when building extension modules
• #924: Numerical imprecision stdp
• #963: Fixed a bug in the SecondaryEvent delivery
• #1003: Resize Connector vectors when adding connection models

Infrastructure

• #857: Improve handling of output vars from FindXXX.cmake
• #905: Bump version requirement for CMake to support all features, we actually use
• #917: cmake -Dwith-ltdl= fix
• #983: fixed function invocation in hpc_benchmark.py script
• #984: run nosetests with the Python interpreter (2 vs. 3) that was requeste…

PyNEST

• #840: Fix handling of PyNEST and SLI commandline arguments
• #864: Fix test_disconnect by converting filter object to list for len
• #900: Fix Python3 print problem in some tests.
• #947: Remove assertion that argv[0] is a non-empty string in slistartup

Maintenance

Models

• #995: fixed minor issue in WeightRecorderEvent
• #998: Shuts off the warnings from LLVM/Clang 4.0.0
• #1007: Clean up modification of dynamic recordables map in models

Installation

• #906: Remove check target
• #932: Update document on build of application on K computer frontend

Interpreter

• #948: Obtain help pager information via SLI and handle failures better
• #976: Fix SLI sleep function (fixes #973)

Documentation

• #852: Adapt tarball name in documentation to GitHub convention
• #855: Correct a few typos in documentation comments
• #878: Remove outdated information and redirect to NESTML
• #885: Reinstating code snippets in the Topology User Manual
• #891: Updating import instructions for scipy, sklearn - issue #848
• #912: Fixed doc in GetDefaults
• #913: Return help text
• #927: Documentation of inhomogeneous_poisson_generator
• #930: Updated Topology User Manual for NEST 2.16.
• #943: Added warning against bad use of Rank()
• #950: Fix typo for Hodgkin-Huxley model
• #964: Nest developer space: Description for conversion to 5g
• #965: Fix #949: NEST help files (hlp, html) should end with newline
• #987: README: minor typographic
• #1004: Fix compatibility issues with Python 2

Kernel

• #850: Make Connector properties and growth factor configurable
• #856: Improved structure of secondary event types
• #888: Issue error message when attempting to set an invalid resolution
• #898: Make sure that Run and Cleanup are called after Prepare
• #935: Fix typo in SimulationManager status output
• #956: Fix #954: Avoid the use of unrelated typenames to distinguish template classes
• #962: Improve documentation on setting extent and center (addresses #961)
• #993: Fix 990 / Compilation issues with C++11 and libc++
• #999: Adjust send_recv_count_target_data_
• #1000: Removing pointless comparison with uint

Infrastructure

• #807: Run tests in test_connect_all_patterns.py with mpirun
• #829: Correction in the test of synapse disconnection with mpi
• #884: Updated to VERA++ 1.3.0 in Travis and changed files to comply with style checks
• #909: Reformat and clean up Name definitions
• #914: Fix issue #911
• #928: Fixed issue in help
• #929: Added test for spatial kernels in topology (depends on #823).
• #951: Update platform specific CMake file so it can be used with CMake 3.11.1
• #985: Repo cleanup
• #997: Fix version display during startup
• #1005: Mark more skipped SLI tests as skipped, not success

PyNEST

• #872: Remove strong dependency on matplotlib
• #902: Made path construction os-independent.

Contributors since NEST 2.14.0

• Alberto Antonietti
• Rajalekshmi Deepu
• Moritz Deger
• Sandra Diaz
• Jochen Martin Eppler
• Jesús Garrido
• Steffen Graber
• Espen Hagen
• Jan Hahne
• Tammo Ippen
• Jakob Jordan
• Chrisitan Keup
• Itaru Kitayama
• Jeyashree Krishnan
• Tobias Kühn
• Susanne Kunkel
• Mikkel Elle Lepperød
• Charl Linssen
• Jessica Mitchell
• Håkon Mørk
• Abigail Morrison
• Yannick Nodem
• Luciano Paz
• Alexander Peyser
• Hans Ekkehard Plesser
• Jari Pronold
• Luis Riquelme
• Dimitri Rodarie
• Maximilian Schmidt
• Jannis Schuecker
• Mario Senden
• Alex Serenko
• Alexey Shusharin
• Ankur Sinha
• Sebastian Spreizer
• Dennis Terhorst
• Stine Brekke Vennemo
• Philipp Weidel
• Barna Zajzon

Citation

If you use this version of NEST, please cite it as Linssen, Charl et al. (2018). NEST 2.16.0. Zenodo. 10.5281/zenodo.1400175. The full citation is available in different formats on Zenodo.

NEST v2.14.0 contains 705 repository commits by 33 developers since v2.12.0.

This release is mainly a bug fix release, but also contains some new features, most notably a framework for the simulation of rate neurons (Hahne et al., 2017).

New features

• Multimeter now supports offset for recording (#669, #670)
• Topology now supports elliptical masks and a function to obtain GIDs inside masked areas (#664)
• Currents generated by stimulating devices can now be recorded (#658, #663, #720, #730, #733)
• Split Simulate into Prepare, Run and Cleanup (#650, #692, #778, #803)
• New static synapse benoulli_synapse with probabilistic transmission (#747)
• The global id can now be removed from the filename of recording devices (#760)

Documentation, tests and web resources

• Better download page for NEST website (#689)
• Make help and helpdesk more robust when used from Python and Jupyter notebooks (#688)
• Revised content in the [Introduction to PyNEST}(http://nest-simulator.org/introduction-to-pynest/) (#661)
• Installation documentation now points out that install path should be absolute (#561, #701)
• Topology tests are now automatically run (#302, #705)
• Small fixes for spelling errors (#729)
• Added example script for structural plasticity (#753)
• Updated testsuite readme file (#752)
• Properly set the environment variables for do_tests.sh (#819)

Bug fixes

• Throw exception when connecting fails (#693)
• Fix NumPy test for quantal_stp_synapse (#680, #681)
• Fix crash with wrong data types in SetDefaults for connections (#545, #704)
• music_event_out_proxy now also works correctly in multi-threaded simulations (#696, #710)
• Fixed bug in CopyModel related to the delivery of secondary events (#708, #711)
• GetConnections work correctly now also for _hpc synapses (#714, #521)
• ResetKernel now properly ensures that off_grid_spiking is reset (#716)
• Name insertion is now done in thread-serial contexts only and all plain strings for property handling are replaced with Name objects (#719, #722, #724)
• Fix OSX clang compilation problems and warnings (#74, #732, #729)
• Fix possible deadlock in neuron update loop in multi-threaded code (#718, #734)
• Moved check_synapse_params to specific synapse classes and add tests for synapse parameter check (#735, #736, #739)
• Files starting with .# are now excluded from help generation (#802)
• Time in step_current_generator is now internally represented in steps (#740, #815)
• iaf_psc_exp_ps now handle simultaneous spikes independently (#368, #810)
• Module installation is now prohibited after CopyModel (#746, #804)
• Fix execution of MPI-enabled tests for structural plasticity (#791, #799)
• Compile-time variable CMAKE_NEST_PREFIX now uses absolute path (#749, #783, #796)
• Fix bad_alloc exception (#644, #787)
• Prohibit DataConnect in multi-threaded mode as correct connectivity cannot be guaranteed here (#776)
• Skip test_crash_or_die.sli if NDEBUG is set as this does not work (#272, #770)
• Fix usage of precision in spin_detector and documentation (#767)
• Fix PyNEST helper functions to make them work again (#688, #766)
• Allow compilation with FCC by removing const qualifier (#755)
• Environment variables are now properly set for do_tests.sh (#816, #819)
• Fixed various typos in PyNEST documentation (#816)
• Ensure number of vacant synaptic elements is always >= 0 (#818)

Under the hood

• Changed all files to comply to code style checks. Especially all single line conditionals and loops are now enclosed in curly brackets (#691)
• Remove duplicate constructors for long & double from Time units (#699)
• Support for custom connector models (#683, #686)
• Avoid divisions/calulcation of steps in the Time class (#685, #706)
• Secondary events now contain a time stamp (#707, #709)
• CPPCHECK is activated in the continuous integration by ignored for now (#668)
• Removes binary_neuron_impl.h in favor of code in binary_neuron.h (#813)
• Change in GetStructrualPlasticityStatus format (#775)
• Remove patching of Python's warning function (#662, #769)
• Moved sanity check for structural plasticity vacant elements to decay function (#827)
• Fixes for using a relative install prefix (#828)
• Properly reduce primary_end_ marker for heterogeneous connections (#832, #834)
• Fix problem with iaf_psc_delta_canon in connection with test_dcgen_vs_I_e.sli (#822)
• Refactor ConnectionGenerator Interface and improve documentation (#206, #309, #483)

Build system and continuous integration

• Skipped SLI tests are now marked as skipped, not success (#713)
• Skip help generation without Python or Python versions prior to 2.7.8 (#678, #715, #748, #751)
• Circumvent negative max_width in Travis log parser (#731)
• Ensure correct options for sed are used on BSD-based systems (#713, #744)
• Fix typo in check_code_style.sh, which lead to aborting the continuous integration run in some cases (#814)
• PyNEST test result parsing is now not confused anymore by NEST output (#762, #788)
• Use the minimal image trusty in TravisCI with recommended group option (#757, #785)

Contributors since 2.12.0

• Shailesh Appukuttan
• Milena M. Carvalho
• David Dahmen
• Rajalekshmi Deepu
• Sandra Diaz
• Jochen Martin Eppler
• Tanguy Fardet
• Steffen Graber
• Jan Hahne
• Michael Hoff
• Tammo Ippen
• Jakob Jordan
• David Kappel
• Itaru Kitayama
• Susanne Kunkel
• Sepehr Mahmoudian
• Jessica Mitchell
• Håkon Mørk
• Abigail Morrison
• Eric Müller
• Alexander Peyser
• Hans Ekkehard Plesser
• Maximilian Schmidt
• Jannis Schuecker
• Martin Schulze
• Till Schumann
• Ankur Sinha
• Dennis Terhorst
• Guido Trensch
• Hünkar Can Tunç
• Stine Brekke Vennemo
• Philipp Weidel
• Barna Zajzon

Citation

If you use this version of NEST, please cite it as Peyser, Alexander et al. (2017). NEST 2.14.0. Zenodo. 10.5281/zenodo.882971. The full citation is available in different formats on Zenodo.

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.