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_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
• Refactor SLI test for default delays and weights for a connection to Python
• SLI-2-Py : test_amat2_psc_exp
• Register custom markers and add utilities folder
• Make test_mat2_psc_exp more robust
• Added simulation fixture and applied it to several iaf_psc_alpha tests
• Replace sli-test delay after resolution change by pytest
• Refactor SLI test for inhomogeneous poisson generator to Python
• Port test_hh_cond_beta_gap_traub
• [SLI2PY] Remove duplicate test
• Port test_hh_cond_exp_traub
• Port test_mip_corrdet to py
• Transform SLI-test test_gap_junction to pytest
• Refactor SLI test for neurons handling multiplicity to Python
• Port test-hh-psc-alpha-gap
• Add python version of sli test for connection counting
• Fix function name in test_connect_with_threads
• Fix class-level constants in ticket_754 test
• Remove installation of PyNEST egg-info and dependencies from setup.py
• Refactor aeif_cond_alpha_multisynapse test from SLI to Python
• Port test_multimeter_support from SLI-2-Py
• Port test_multimeter_freeze_thaw from SLI-2-Py
• Port mask tests
• Port test-hpc-synapse
• Port test_poisson_generator_ps to py
• Port test_multimeter_stepping from SLI-2-Py
• Refactor SLI test for noise generator to Python
• Port test_multithreading
• Port test-set-vm
• Port test_poisson_ps_intervals to py
• Port test_poisson_ps_min_interval to py
• Port test_multimeter_offset from SLI-2-Py
• Port test_set_delay_extrema
• Remove debug statements from CI helper script
• Add documentation about deadlock in mpi processes
• Transpile test-set-ticks.sli
• Get Sphinx build working in CI
• Remove get_type func from RecordingDevice
• Remove the debian/ folder
• Add new dockerhub repository to the docker documentation
• Fix tutorials in documentation
• Fix typos in spatial docs to render code
• Update documentation organisation and landing page
• Fix various typos in the documentation
• Clean up and fix clickable images in installation instructions
• Update vale version and fix CI package index
• Improve the look of link to EBRAINS Jupyter Hub in documentation
• Add pandas requirement to docs
• Set correct virtual model name in NEST-SONATA documentation
• Improve test coverage by unconditionally installing mpi4py
• Fix formatting of glif_psc and glif_cond documentation
• Fix incorrect name in model docs
• Fix unit typo
• Fix various issues in docs that cause Sphinx warnings
• Remove misplaced code block on documentation landing page