NEST 3.9

NEST 3.9 is the result of 1217 commits by 24 developers since NEST 3.8 which was released on 2024-08-02.

This release notably adds features for several models, specifically, biologically-inspired features for the e-prop plasticity and the tripartite connectivity, used for astrocytes, which now supports multiple primary connection rules. New additions were made to the documentation including improved neuron model descriptions. Changes include many bug fixes and improvements.

Check out more details in the docs: "What's new in NEST 3.9"

Enhancements

• Enhance e-prop plasticity with biologically inspired features
• Re-organise tripartite connectivity generation to support multiple primary connection rules
• Add Windows docker instructions for installation
• Update built-in timer documentation
• Add detailed neuron documentation
• Enhance gunicorn options in NEST Server
• Add optional support for per-thread timers and timing MPI synchronization
• Add logger for nest-server-mpi

Bug fixes

• Provide a non-invasive fix for the stopwatch issue
• Fix command of nest-server
• Ensure testsuite runs all tests again, run MUSIC tests correctly and set lower bounds for number of tests expected
• Fix data race in NodeManager
• Fix data race in mechanism preventing excessive update times
• Use unique_ptr< SecondaryEvent > to avoid memory leaks
• Properly delete proxy node objects on kernel finalization
• Update the data serialization in hl_api_server.py
• Fix return data in nest-server
• Fix corner cases uncovered by Clang sanitizer
• Fix incorrect initialization in move constructor
• Fix incorrect conversion of string inf to double seen on MinGW
• Fix error with GetConnections when using multiple threads in combination with detailed timers
• Correctly detect that substring was not found
• Fix issue with first spike passing through adaptive synapse
• Fix nest-server-mpi
• Fix parentheses in connection_helpers
• Allow passing OpenMP root directory to -Dwith-openmp
• Check if dot binary exists
• Fix memory safety issue in slistartup.cc

Maintenance

• Fix issue with latest Cython release
• Change version of isort CI OS image from Ubuntu 20.04 to Ubuntu 22.04
• Fix Numpy types
• Improved wrappers and OpenMPI handling in Python MPI tests
• Simplify handling of OTHER labels in new-style mpitests
• Move critical section so it can be avoided by limiting verbosity
• Update instances of conda with mamba in docs
• Hike version number after release of 3.8
• Add what's new for 3.9
• Fix some warnings about mismatching integer types (replaces #3026)
• Remove Potjans and Diesmann microcircuit example from this repo and redirect to new one
• Update Izhikevich model documentation
• Add note about failure modes when using sphinx-build
• Port regression test 707 to Pytests
• Port regression test 708 to Pytests
• Port regression test 888 to Pytests
• Port regression test 737 to Pytests
• Port regression test 735 to Pytests
• Port regression test 157 to Pytests
• Port regression test 293 to Pytests
• Port regression test 156 to Pytests
• Port regression test 382 to Pytests
• Port regression test 349 to Pytests
• Port regression test 310 to Pytests
• Change Ubuntu-20.04 version to 22.04 in CI pipelines
• Fix example for EI clustered network
• Port unittest/test_voltmeter_reset to Pytests
• Port regression test 327 to Pytests
• Port regression test 659 to Pytests
• Handle CalledProcessError better
• Port test_gap_junctions_mpi from SLI to Py
• Port mpitests/issue_600.sli to Pytests
• Port mpitests/issue-281.sli to Python
• Port mpitests/issue_2119.sli to python
• Derive astrocyte_lr_1994 directly from Node
• Add NEAT to related projects in docs
• Improve discoverablility of network models in NEST docs
• Fix sphinx warnings in docs
• Whitespace changes for black-25
• Remove deprecated environment variable from SLI init script
• Port test_count_connections from SLI to Py
• Change doc folder name for nest server and other services
• Update HPC docs with pldd usage
• Add packages for nest-server-mpi
• Update MAM benchmark on website
• Add line number to error message
• Updates to formatting for bumping psf/black version #3330
• Loosen pylint threshold
• Update version of mermaid in documentation
• Fix typo in exact-integration documentation
• Fix typo in multimeter documentation
• Update unit from seconds to Siemens
• Updating documentation for iaf_psc_exp and iaf_cond_exp
• Remove code for dry_run mode
• Optimize computation in iaf_psc_alpha_ps model
• Optimize computation in GrowthCurveGaussian
• Add note to aeif models about refractory period and peculiarities
• Fix Read the Docs warning about JavaScript search functionality
• Fix typo in multimeter docs
• Update boost detection and issue warning message
• Configure Sphinx gallery to copy files from pynest/examples
• Update documentation for mailing list guidelines
• Update documentation on Gap Junctions
• Update README on GitHub
• Fix minor issues in docs
• Fix links in documentation
• Add more minimal CI test
• Remove pointless initialisation of integration step size
• Update C++ docstrings for extended histentry
• Fix spike rate physical units from Hz to spks/s
• Port tests iaf_psc_exp_ps[_lossless] to Pytest
• Fix warnings regarding int-type variables
• Add shellcheck and pre-commit to CI jobs
• Port aeif_cond_beta_multisynapse_test from SLI-2-Py and add test for ..._alpha_...
• Update benchmark docs for 3.9