NEST 3.8

NEST 3.8 is the result of 533 commits by 16 developers since NEST 3.7 which was released on 2024-04-12.

This release adds models with exact and simplified NMDA dynamics, as well as improvements and corrections of model documentation. The model directory was reworked to now feature interactive filtering and new concept overview pages. For the first time, the release contains also documentation of the expected performance for established neuronal network models of different sizes.
On the technical side, an important bug in slicing node collections has been fixed, and various issues caused by version updates of other tools such as NumPy and Python on MacOS have been addressed.

Check out more details in the docs: "What's new in NEST 3.8"

Enhancements

• Add benchmark results to docs
• Add models with exact and simplified NMDA dynamics according to Brunel and Wang (2001)
• Update documentation for iaf_psc_exp
• Add "How NEST Works" diagram and text to NEST docs index page
• Modify model directory documentation UI and related pages
• Add note on parameter corrections for the AMAT2 model (Heiberg et al 2018)

Bug Fixes

• Correct errors in slicing of node collections
• Fix MUSIC support in NEST
• Make test log parsing more robust
• Fix corner case for node collections
• Change numpy datatype to adapt to NumPy 2.0
• Fix Boost dependency for iaf_bw_2001 model
• Fix uploading of CI artifacts
• Hike Python version for macOS tests to 3.12

Maintenance

• Add warning concerning order of parameter creation and change in number of threads
• Add What's New section for 3.8 in docs
• Update benchmark result docs
• Apply security best practices – Update pre-commit configuration
• Clarify documentation related to recorders and recording backends
• Improve speed of dump_connections() in layer_impl.h
• Add microcircuit rate verification comments
• Improve glossary references in documentation
• Fix Izhikevich model equation in the documentation
• Replace aliases that have been removed with NumPy 2.0
• Update VM Badge to v3.7
• Fix minor Sphinx warnings related to broken links
• Fix conductance based neuron model header files
• Fix broken attribution link in docs
• Add deprecation notice to iaf_cond_alpha_mc model documentation
• Update models with adaptation mechanisms and change tag 'adaptive threshold' to 'adaptation'
• Add OpenSSF Scorecard badge to README
• Add whats new link for 3.8
• Fix minor typo in documentation

NEST 3.8-rc2

NEST 3.8 is the result of 441 commits by 16 developers since NEST 3.7 which was released on 2024-04-12.

This release adds models with exact and simplified NMDA dynamics, as well as improvements and corrections of model documentation. For the first time, the release contains documentation of the expected performance for established neuronal network models of different sizes. On the technical side, an important bug in slicing node collections has been fixed, and various issues caused by version updates of other tools such as NumPy and Python on MacOS have been addressed.

Enhancements

• Add benchmark results to docs
• Add models with exact and simplified NMDA dynamics according to Brunel and Wang (2001)
• Update documentation for iaf_psc_exp
• Add "How NEST Works" diagram and text to NEST docs index page
• Add note on parameter corrections for the AMAT2 model (Heiberg et al 2018)

Bug Fixes

• Correct errors in slicing of node collections
• Fix MUSIC support in NEST
• Make test log parsing more robust
• Fix corner case for node collections
• Change numpy datatype to adapt to NumPy 2.0
• Fix Boost dependency for iaf_bw_2001 model
• Fix uploading of CI artifacts
• Hike Python version for macOS tests to 3.12

Maintenance

• Add warning concerning order of parameter creation and change in number of threads
• Add What's New section for 3.8 in docs
• Update benchmark result docs
• Apply security best practices – Update pre-commit configuration
• Clarify documentation related to recorders and recording backends
• Improve speed of dump_connections() in layer_impl.h
• Add microcircuit rate verification comments
• Improve glossary references in documentation
• Fix Izhikevich model equation in the documentation
• Replace aliases that have been removed with NumPy 2.0
• Update VM Badge to v3.7
• Fix minor Sphinx warnings related to broken links
• Fix conductance based neuron model header files
• Fix broken attribution link in docs

NEST 3.8-rc1

NEST 3.8 is the result of 408 commits by 15 developers since NEST 3.7 which was released on 2024-04-12.

This release adds models with exact and simplified NMDA dynamics, as well as improvements and corrections of model documentation. On the technical side, an important bug in slicing node collections has been fixed, and various issues caused by version updates of other tools such as NumPy and Python on MacOS have been addressed.

Enhancements

• Add models with exact and simplified NMDA dynamics according to Brunel and Wang (2001)
• Update documentation for iaf_psc_exp
• Add "How NEST Works" diagram and text to NEST docs index page
• Add note on parameter corrections for the AMAT2 model (Heiberg et al 2018)

Bug Fixes

• Correct errors in slicing of node collections
• Change numpy datatype to adapt to NumPy 2.0
• Hike Python version for macOS tests to 3.12
• Fix MUSIC support in NEST
• Make test log parsing more robust
• Fix corner case for node collections
• Add warning concerning order of parameter creation and change in number of threads
• Fix uploading of CI artifacts

Maintenance

• Apply security best practices – Update pre-commit configuration
• Clarify documentation related to recorders and recording backends
• Improve speed of dump_connections() in layer_impl.h
• Add microcircuit rate verification comments
• Improve glossary references in documentation
• Fix Izhikevich model equation in the documentation
• Replace aliases that have been removed with NumPy 2.0
• Update VM Badge to v3.7
• Fix minor Sphinx warnings related to broken links
• Fix conductance based neuron model header files
• Fix broken attribution link in docs

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"](https://gith...

NEST 3.7-rc1

NEST 3.7 is the result of 1282 commits by 30 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
• 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
• 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
• Correctly handle random parameters appearing in the denominator
• bug fix iaf_psc_exp_multisynapse / sli2py test_iaf_psc_exp_multisynapse
• Add localhost ipv4 to default origins for NEST Server

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
• 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
• 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
• Fix broken formatting in documentation
• Stop IPython from time consuming deep inspection of NodeCollection objects
• Fix padding around links in docs

Additionally ...

NEST 3.6

NEST 3.6 is the result of 1397 commits by 30 developers since NEST 3.5 which was released on 2023-06-22.

NEST 3.6 provides significant performance improvements for highly parallel building and simulating of networks and introduces initial support for astrocytes and neuron-astrocyte interaction.

Many smaller changes prepare the test suite for future internal changes in the SLI/Python interfaces.

Check out more details in the docs: "What's new in NEST 3.6"

Enhancements

• Sort and format Python imports and enable isort check in CI
• Add astrocyte_lr_1994 to NEST for the modeling of astrocytes and neuron-astrocyte interactions
• Improve NEST performance by revised connection exchange and spike delivery
• Cleanup NEST Server environment variable handling
• Improve message about OMP_THREAD_NUM on startup
• Add rectified Gabor distribution for nest.spatial
• Add flags for autapses and multapses in structural_plasticity_synapses
• Separate PyNEST API modules into separate pages in documentation
• Remove NodeCollection pointer from Node class
• Add sphinx-mermaid extension and update userdoc workflow
• Make calcium concentration available for setting
• Enhance module imports in NEST Server
• Enable patching of binary files within the online documentation
• Replace hand-written modelsmodule by a code generation framework
• Add a custom 404 page for Read the docs
• Allow setting volume_transmitter via NodeCollection, instead of naked ID
• Improve error checking in MPI IO backends
• Add support to set mpi address via device status
• Add custom Sphinx extension that lists examples based on model name
• Added package attrs to environment.yml
• Allow NodeCollection slicing with list of NumPy integers
• Add NEST favicon to documentation webpage
• Add support for more addition operations for NodeCollection
• Add warning if local_num_threads set by user disagrees with OMP_NUM_THREADS
• Add glif_psc_double_alpha model
• Add clang-format pre-commit hook

Bug fixes

• Fix type check to use isinstance()
• Correct limit for test on target fields and remove duplicate assertions
• Fix bug in reconstruction of connection data structures after disconnect and fix small problems with examples
• Fix STDP k-value error for edge case
• NEST-SONATA: Enclose pandas import in try block
• Fail gracefully when node_id 0 is used to access non-existent node
• Hike minimum required CMake version to 3.19
• Filter connections also by target when dumping layer connections
• Fix indentation in example in docs
• Add cherry-picked changes from #2843, #2838, and #2830
• Cherry-picked hot-fixes from #2948, #2950, #2952, and #2958

Maintenance

• Fix test_calcium.py formatting to comply with Black
• Add 'what's new' docs for 3.5
• Harden GitHub Actions – GITHUB_TOKEN permissions
• Clean up doxygen comments in nestkernel directory
• Modernize the codebase - convert C-style casts to static_casts
• Serialize all responses used in the NEST Server
• Set sender node id info with correct target lcid
• Update documentation organisation and landing page
• Fix various typos in the documentation
• Update microcircuit docs regarding virtual process constraint and fix images
• Set correct virtual model name in NEST-SONATA documentation
• Fix formatting of glif_psc and glif_cond documentation
• Fix formatting of developer guidelines - naming conventions
• Set copybutton to only copy input lines in docs
• Fix unit typo
• Fix various issues in docs that cause Sphinx warnings
• Remove misplaced code block on documentation landing page
• Fix typo on docs landing page
• Update NEST version post 3.5 release
• Remove duplicate notebook and all references to it.
• Completely revised iaf_psc_alpha user documentation
• Changed total_num_virtual_procs to local_num_threads in hpc benchmark
• Mention parameter t_ref in documentation
• Fix malformed table in models documentation
• Re-add Jupyter notebook download to examples and move script to _ext folder
• Update DOI to NEST 3.5 in README
• Bump restrictedpython from 6.0 to 6.2 in /doc
• Remove test that is no longer relevant
• Add note on using Mamba instead of conda
• Fix 'potential' misspelling
• Rename microcircuit images
• Add details on Hodgkin Huxley models, based on asynchronicity discussion
• Add documentation builds to cmake options
• Fix up typos and missing references to resolve Sphinx warnings
• Update iaf_cond_alpha.cpp
• Fix up HTML output to clean up browser warnings
• Fix indentation in PyNEST API
• Remove mentions of vera++ in docs
• Add text for what's new 3.6

Refactoring of the test suite

• Port test_multiple_multimeter from SLI-2-Py
• Refactor SLI test for spike generator to Python
• Port test_GetConnections from SLI-2-Py
• Port test_multiple_random_source_stepping from SLI-2-Py
• Port test_ginzburg_and_mcculloch from SLI-2-Py
• Port test_distance from SLI-2-Py
• Port issue-77.sli from SLI-2-Py
• Port issue-545.sli to py
• [Port issue-105.sli to Pytest](https://github.com/nest/nest-simu...

NEST 3.6-rc1

NEST 3.6 is the result of 1388 commits by 30 developers since NEST 3.5 which was released on 2023-06-22.

NEST 3.6 provides significant performance improvements for highly parallel building and simulating of networks and introduces initial support for astrocytes and neuron-astrocyte interaction.

Many smaller changes prepare the test suite for future internal changes in the SLI/Python interfaces.

Check out more details in the docs: "What's new in NEST 3.6"

Enhancements

• Sort and format Python imports and enable isort check in CI
• Add astrocyte_lr_1994 to NEST for the modeling of astrocytes and neuron-astrocyte interactions
• Improve NEST performance by revised connection exchange and spike delivery
• Cleanup NEST Server environment variable handling
• Improve message about OMP_THREAD_NUM on startup
• Add rectified Gabor distribution for nest.spatial
• Add flags for autapses and multapses in structural_plasticity_synapses
• Separate PyNEST API modules into separate pages in documentation
• Remove NodeCollection pointer from Node class
• Add sphinx-mermaid extension and update userdoc workflow
• Make calcium concentration available for setting
• Enhance module imports in NEST Server
• Enable patching of binary files within the online documentation
• Replace hand-written modelsmodule by a code generation framework
• Add a custom 404 page for Read the docs
• Allow setting volume_transmitter via NodeCollection, instead of naked ID
• Improve error checking in MPI IO backends
• Add support to set mpi address via device status
• Add custom Sphinx extension that lists examples based on model name
• Added package attrs to environment.yml
• Allow NodeCollection slicing with list of NumPy integers
• Add NEST favicon to documentation webpage
• Add support for more addition operations for NodeCollection
• Add warning if local_num_threads set by user disagrees with OMP_NUM_THREADS
• Add glif_psc_double_alpha model
• Add clang-format pre-commit hook

Bug fixes

• Fix type check to use isinstance()
• Correct limit for test on target fields and remove duplicate assertions
• Fix bug in reconstruction of connection data structures after disconnect and fix small problems with examples
• Fix STDP k-value error for edge case
• NEST-SONATA: Enclose pandas import in try block
• Fail gracefully when node_id 0 is used to access non-existent node
• Hike minimum required CMake version to 3.19
• Filter connections also by target when dumping layer connections
• Fix indentation in example in docs
• Add cherry-picked changes from #2843, #2838, and #2830

Maintenance

• Fix test_calcium.py formatting to comply with Black
• Add 'what's new' docs for 3.5
• Harden GitHub Actions – GITHUB_TOKEN permissions
• Clean up doxygen comments in nestkernel directory
• Modernize the codebase - convert C-style casts to static_casts
• Serialize all responses used in the NEST Server
• Set sender node id info with correct target lcid
• Update documentation organisation and landing page
• Fix various typos in the documentation
• Update microcircuit docs regarding virtual process constraint and fix images
• Set correct virtual model name in NEST-SONATA documentation
• Fix formatting of glif_psc and glif_cond documentation
• Fix formatting of developer guidelines - naming conventions
• Set copybutton to only copy input lines in docs
• Fix unit typo
• Fix various issues in docs that cause Sphinx warnings
• Remove misplaced code block on documentation landing page
• Fix typo on docs landing page
• Update NEST version post 3.5 release
• Remove duplicate notebook and all references to it.
• Completely revised iaf_psc_alpha user documentation
• Changed total_num_virtual_procs to local_num_threads in hpc benchmark
• Mention parameter t_ref in documentation
• Fix malformed table in models documentation
• Re-add Jupyter notebook download to examples and move script to _ext folder
• Update DOI to NEST 3.5 in README
• Bump restrictedpython from 6.0 to 6.2 in /doc
• Remove test that is no longer relevant
• Add note on using Mamba instead of conda
• Fix 'potential' misspelling
• Rename microcircuit images
• Add details on Hodgkin Huxley models, based on asynchronicity discussion
• Add documentation builds to cmake options
• Fix up typos and missing references to resolve Sphinx warnings
• Update iaf_cond_alpha.cpp
• Fix up HTML output to clean up browser warnings
• Fix indentation in PyNEST API
• Remove mentions of vera++ in docs
• Add text for what's new 3.6

Refactoring of the test suite

• Port test_multiple_multimeter from SLI-2-Py
• Refactor SLI test for spike generator to Python
• Port test_GetConnections from SLI-2-Py
• Port test_multiple_random_source_stepping from SLI-2-Py
• Port test_ginzburg_and_mcculloch from SLI-2-Py
• Port test_distance from SLI-2-Py
• Port issue-77.sli from SLI-2-Py
• Port issue-545.sli to py
• Port issue-105.sli to Pytest
• Port issue-264.sli to Pytest
• Port issue-211.sli to Pytest
• [Port issue-1085.sli to Pytest](https://github.com/nest/nest-simulator/pu...

NEST 3.5

NEST 3.5 is the result of 1390 commits by 25 developers since NEST 3.4 which was released on 2023-02-16.

The main focus of this release is a restructured user documentation improving usability and enhancing explanations of use-cases and features.

New features include native support for networks represented in SONATA format, and new and enhanced models such as the spike_train_injector and access to calcium concentration parameters.

Under the hood, a lot of changes have been made to the test suite to improve development workflows. Continuous integration checks now run separately and in parallel. The whole test suite was ported from SLI to a PyTest-based setup.

Enhancements

• Improve parameter test and implementation
• Reformat the codebase and enable black check in CI
• Build NEST with Python, OpenMP, MPI, Boost and GSL for macOS on CI
• Add documentation regarding HPC systems
• Make sphinx build self-sufficient and in-tree-safe
• Add native support for networks represented in SONATA format
• Include a link in PyNEST examples to run them as notebooks
• Streamline and update release notes for 3.4 release
• Add spike_train_injector model
• Make calcium concentration available for setting
• Further improvement of parameter operator test implementation
• Add comment on min delay
• Improve documentation on delays
• Transition version handling to proper semantic versioning when building from Git and release tarballs
• Make multapses and autapses flags more visible in documentation
• Add copy button for code blocks in documentation
• Enable patching of binary files within the online documentation

Bug fixes

• Fix build of extension modules after change to static helper libraries
• Fix uninitialized variable in iaf_psc_exp
• Require Cython >= 0.29.14 to avoid tp_print problem on Read the Docs
• Fix STDP k-value error for edge case
• Correctly build connection infrastructure in GetConnections also when secondary events in use
• Revise some spatial tests to pytest style; avoids numercial issues due to float comparisons
• Catch all exceptions in SimulationManager::update_()
• Fix setting min and max delay after resolution change
• Ensure VP number, RNG type and RNG seed can be set in any order
• Add -lnest to the list of libraries to link extension modules
• Fix conftest fixtures
• Fix skip if-threads
• Fix ResetKernel in SimulationManager
• Microcircuit model quick fix for issue #2741
• Return valid version information also when git is unavailable
• Update the package index files on all CI runners
• NEST-SONATA: Reset parameters after iteration over populations
• Fix indentation in example in docs
• Update doc directory readme
• Add cherry-picked changes from #2843, #2838, and #2830

Maintenance updates

• Fix test_calcium.py formatting to comply with Black
• Fix OpenMP issues on CI under macOS and re-activate testing with threads for macOS
• Port test_poisson_generator_campbell_alpha to py
• Pin the documentation requirements to prevent incompatible dependencies
• Update readthedocs.yml to resolve build error from incompatible urllib3 version
• Add 'what's new' docs for 3.5
• Separated checks
• Fixing bad coding pattern in loops in connection creation
• Fix badges of the different NEST packages
• Removing well-proven and therefore outdated asserts
• Replace NEST typedefs with plain C++ datatypes
• Make kernel attributes ms_per_tic and tics_per_step read-only
• Remove get_thread() function from proxynode class
• Move retrieval of common properties out of send_to_all loop
• Clean up the registration of recording and stimulation backends
• Invert delay-related documentation tagging logic for rate connections
• Make exception-name Python compatible
• Further improve style of parameter test implementation
• Convert multimeter test from SLI to Python implementation
• Make helper libraries static and don't install the archive files
• Remove NEST Server Client from nest-simulator repository
• Make it an error to set multiple threads if NEST was built without thread support
• Refactor rm -rf from testsuite script
• Add conftest.py with skip marker support
• Refactor SLI tests to Python
• Translate SLI test test_delay_check to Python
• Refactor SLI for ac generator and step-current generator to Python
• Fix pycodestyle and move test to new directory
• Refactor Bernoulli synapse SLI test to Python test
• Fix typo in existing CopyModel Pytest and remove obsolete SLI test
• Refactor binary neuron SLI test to Python test
• Port test_compare_delta.sli to py
• Port issue-463.sli to py
• Port Tsodyks tests from SLI to Python
• Convert test_connect_with_threads
• Refactor cond_exp model test from SLI to Python
• Convert mat2_psc_exp SLI test to Python
• Refactor gif_*_exp tests from SLI to pytest
• Port ticket-959.sli to py
• Port ticket-949.sli to py
• Refactor test for cont_delay_synapse from SLI to Python
• Convert test_connect_after_simulate to pytest
• Port ticket-926.sli to py
• Port ticket-941.sli to py
• Convert SLI based tests to Pytest and add common infrastructure for Pytest
• Port test_correlospinmatrix_detector to py
• Port test_corr_det
• Port ticket-921.sli to py
• [Port test_ma...

NEST 3.5-rc1

NEST 3.5 is the result of 1377 commits by 25 developers since NEST 3.4 which was released on 2023-02-16.

New features include native support for networks represented in SONATA format, and new and enhanced models such as the spike_train_injector and access to calcium concentration parameters. In the user documentation, you can now run the PyNEST examples as Jupyter Notebooks. We've also added new docs for using HPC systems with NEST. Under the hood, a lot of changes have been made to the test suite to improve development workflows. Tests now run separately and in parallel. The whole test suite was ported from SLI to a PyTest-based setup.

Enhancement

• Improve parameter test and implementation
• Reformat the codebase and enable black check in CI
• Build NEST with Python, OpenMP, MPI, Boost and GSL for macOS on CI
• Add documentation regarding HPC systems
• Make sphinx build self-sufficient and in-tree-safe
• Add native support for networks represented in SONATA format
• Include a link in PyNEST examples to run them as notebooks
• Streamline and update release notes for 3.4 release
• Add spike_train_injector model
• Make calcium concentration available for setting
• Further improvement of parameter operator test implementation
• Add comment on min delay
• Improve documentation on delays
• Transition version handling to proper semantic versioning when building from Git and release tarballs
• Make multapses and autapses flags more visible in documentation
• Add copy button for code blocks in documentation

Bug

• Fix build of extension modules after change to static helper libraries
• Fix uninitialized variable in iaf_psc_exp
• Require Cython >= 0.29.14 to avoid tp_print problem on Read the Docs
• Fix STDP k-value error for edge case
• Correctly build connection infrastructure in GetConnections also when secondary events in use
• Revise some spatial tests to pytest style; avoids numercial issues due to float comparisons
• Catch all exceptions in SimulationManager::update_()
• Fix setting min and max delay after resolution change
• Ensure VP number, RNG type and RNG seed can be set in any order
• Add -lnest to the list of libraries to link extension modules
• Fix conftest fixtures
• Fix skip if-threads
• Fix ResetKernel in SimulationManager
• Microcircuit model quick fix for issue #2741
• Return valid version information also when git is unavailable
• Update the package index files on all CI runners
• NEST-SONATA: Reset parameters after iteration over populations
• Fix indentation in example in docs
• Update doc directory readme

Maintenance

• Fix test_calcium.py formatting to comply with Black
• Fix OpenMP issues on CI under macOS and re-activate testing with threads for macOS
• Port test_poisson_generator_campbell_alpha to py
• Pin the documentation requirements to prevent incompatible dependencies
• Update readthedocs.yml to resolve build error from incompatible urllib3 version
• Separated checks
• Fixing bad coding pattern in loops in connection creation
• Fix badges of the different NEST packages
• Removing well-proven and therefore outdated asserts
• Replace NEST typedefs with plain C++ datatypes
• Make kernel attributes ms_per_tic and tics_per_step read-only
• Remove get_thread() function from proxynode class
• Move retrieval of common properties out of send_to_all loop
• Clean up the registration of recording and stimulation backends
• Invert delay-related documentation tagging logic for rate connections
• Make exception-name Python compatible
• Further improve style of parameter test implementation
• Convert multimeter test from SLI to Python implementation
• Make helper libraries static and don't install the archive files
• Remove NEST Server Client from nest-simulator repository
• Make it an error to set multiple threads if NEST was built without thread support
• Refactor rm -rf from testsuite script
• Add conftest.py with skip marker support
• Refactor SLI tests to Python
• Translate SLI test test_delay_check to Python
• Refactor SLI for ac generator and step-current generator to Python
• Fix pycodestyle and move test to new directory
• Refactor Bernoulli synapse SLI test to Python test
• Fix typo in existing CopyModel Pytest and remove obsolete SLI test
• Refactor binary neuron SLI test to Python test
• Port test_compare_delta.sli to py
• Port issue-463.sli to py
• Port Tsodyks tests from SLI to Python
• Convert test_connect_with_threads
• Refactor cond_exp model test from SLI to Python
• Convert mat2_psc_exp SLI test to Python
• Refactor gif_*_exp tests from SLI to pytest
• Port ticket-959.sli to py
• Port ticket-949.sli to py
• Refactor test for cont_delay_synapse from SLI to Python
• Convert test_connect_after_simulate to pytest
• Port ticket-926.sli to py
• Port ticket-941.sli to py
• Convert SLI based tests to Pytest and add common infrastructure for Pytest
• Port test_correlospinmatrix_detector to py
• Port test_corr_det
• Port ticket-921.sli to py
• Port test_max_delay and test_min_delay to py
• Port ticket-903.sli to py
• Refactor SLI test to check consistency between dc_generator and variable I_e to Python
• [Port test_corr_matrix_det](https://github.co...

NEST 2.14.2

NEST 2.14.2 is the result of 4 commits by 4 developers since NEST 2.14.1 which was released on 2021-09-08.

This release properly initializes the second initial value of postsynaptic currents in the iaf_psc_exp model to zero. Without the initilization the behavior of the model is undefined, which may go unnoticed and produces wrong results. A typical symptom of the bug are the occurence of correct spike rates in some runs and too high spike rates in others.

Bug fixes

• Fix uninitialized variable in iaf_psc_exp