NEST 3.7

NEST 3.7 is the result of 1392 commits by 34 developers since NEST 3.6 which was released on 2023-09-28.

This release most notably brings support for spike-based machine learning using eligibility traces, a tripartite and a pairwise-poisson connection rule. Structurally the extension module interface has been redefined and now supports module unloading. Changes contain many bug fixes and improvements.

As of NEST 3.7, NEST requires a C++17 compatible compiler.

Check out more details in the docs: "What's new in NEST 3.7"

Enhancements

• Add a tripartite connection rule for neuron-astrocyte connectivity
• Models no longer wrapped in SLI Module, model registration and thread-setting in managers revised
• Further improve iaf_psc_alpha documentation
• Add detailed timers for gathering and delivering secondary events
• Port MPI tests from SLI to Python, Part I
• Create NEST Extension Interface for NEST compatible with new registration scheme and unloading
• Move registration of ConnBuilders, Backends, growth curves from nestmodule to respective managers, allowing unloading
• Align documentation of connection management with connectivity concepts publication (v2)
• User configurable voltage initialization for the compartmental model
• Implement e-prop plasticity
• New connection rule for Poisson-distributed number of synapses between neuron pairs
• Add iaf_tum_2000: a neuron model with integrated short-term plasticity synapse
• Add plantuml to docs
• Add ignore_and_fire neuron model
• Align documentation of connection management with connectivity concepts publication
• Add EI_clustered_network by Rostami et al to PyNEST examples
• Add CLion IDE developer documentation
• Modify doc index page
• Improve doc install pages
• Improve docs for guides and getting started
• Update model documentation for iaf_psc_delta model
• Add a section in installation docs about running NEST with EBRAINS

Bug fixes

• Properly suppress pylint complaints about unused plt in tests
• Allow isort pre-commit to make in-place changes
• Replace assertDictContainsSubset() which has been removed in Python 3.12
• Ensure Connect() does not allow passing parameters that need to be set at the synapse-model level
• Register only spikes actually sent with weight_recorder
• Properly handle OpenMP linker flags
• Ensure all MPI communication to is handled by master thread
• Ensure assert_valid_syn_id() is always called with correct thread id
• Avoid MPI deadlocks on SynapseCollection.get()/set()
• Fix data race in nestkernel/per_thread_bool_indicator.cpp
• astrocyte_lr_1994: Store result of expression evaluation in proper variable
• Make -Dwith-mpi respect provided path and ensure "default off" options are turned on only by explicit ON
• Correctly handle random parameters appearing in the denominator
• Fix MUSIC support in NEST
• bug fix iaf_psc_exp_multisynapse / sli2py test_iaf_psc_exp_multisynapse
• Add localhost ipv4 to default origins for NEST Server
• Update docstring for pynest ResetKernel() to include module unloading

Maintenance

• Harden GitHub Actions – Harden Runner and pin Actions
• Code re-organization for shorter build times (or taming the 96% troll)
• Update test failing due to removed scipy method
• Fix tests and examples to pass Pylint test R1730
• Port test-set-start-stop-origin.sli from Sli-2-Py
• Organize Python dependencies in separate requirements files
• Apply security best practices – Update Dependabot
• Apply security best practices – Add CodeQL workflow
• Apply security best practices – Dependency review
• Apply security best practices – Create OpenSSF Scorecard workflow
• Sli2py iaf_psc_alpha_multisynapse
• Add GCC compiler problem matcher to CI
• Port test_thread_local_ids.sli to Pytest
• Port test_steppedsim.sli to Pytest
• Port test_wfr_settings.sli to Pytest
• Port issue-311 from SLI-2-Py
• Update extension for API extractor
• Copy documentation to CI artifacts
• Port sinusoidal generator tests (SLI-2-Py)
• Port test_setconnections_threads.sli to Pytest
• Minor cleanup of code and comments
• Update clang-format version to 17.0.4 and activate InsertBraces
• port test_iaf_psc_exp to py
• Fix misplaced assert statement causing a lot of warnings
• Sort results of NEST releases on Zenodo by most recent
• Fix broken links in documentation
• Add note about missing random generators for osx-arm64
• Add missing keyword to glif neuron model documentation
• Move tests that are irrelevant post-sli to sli2py_ignore
• Add missing links to examples in model documentation
• Update the documentaton regarding Windows
• Update documentation of video tutorial to clarify version
• Remove unused doxygen groups in developer documentation
• Remove last mentions of C++11 as default
• Set buffer shrink limit to 20% by default (activates shrinking) and fix documentation
• Fix path to docker compose file in documentation
• Add brief install instructions for the NESTML package in our ppa
• Simplify clearing of spike buffers
• Increase admonition to warning
• Clean doc for NEST Server and related projects
• Modify doc extensions to check for correct files
• Fix various Sphinx warnings
• Fix typo in documentation of iaf_psc_alpha
• Rename the variable "Ca" in astrocyte_lr_1994 to "Ca_astro"
• Add doi to the BibTeX entry
• Sli2py test iaf ps psp poisson generator accuracy
• Fix broken links in documentation
• Add note to expect changes to tripartite syntax and semantics
• Automatically adjust column widths in testsuite report
• Fix minor integer type mismatches
• Add CMAKE option for optimizing performance of benchmarks
• Fix broken formatting in documentation
• Stop IPython from time consuming deep inspection of NodeCollection objects
• Fix padding around links in docs
• Add link to 3.7 whats new page in docs
• Remove duplicate .spatial hint in docs

Plus 38 pull-requests doing version bumps of CI dependencies.