NEST 3.4

NEST 3.4 is the result of 1214 commits by 24 developers since NEST 3.3 which was released on 2022-03-22.

This release contains bug fixes and improvements. Most notably it reorganizes the documentation to improve findability of different topics, both in the source on GitHub and on Read the docs. Read about more updates in the docs…

Enhancements

• Cherry-picked changes for post-release doc-patching
• Cherry-picked changes to add userdict in PyNEST
• Show colored messages in CMake output
• Restructure the userdoc directory
• Update installation pages for Read the docs
• Create new Read the docs theme with custom index
• Update review guidelines
• Add example demonstrating spike-based Sudoku solver
• Add example demonstrating spike-based simulations of Pong
• Add functions yielding source neurons given target neurons
• Add links in docs to glossary
• Expose prepared flag via kernel status dictionary
• Add introductory text for models in documentation
• Add += operator for compartment model
• Add spike-transmission test to multithreading test
• Allow to disconnect with SynapseCollections as arguments
• Add support for Parameter objects for indegree and outdegree in syn_specs
• Getter for NodeCollection step on C++ level
• Abort NEST if run using mpirun but compiled without support for MPI
• Add compiler version to nest-config
• Allow more than one optimization flag to be set when running CMake
• Allow setting host and port for the MPI enabled NEST Server from environment variables

Bug fixes

• Fix spatial attribute positions of sliced NodeCollection
• Make pynestkernel compatible with NumPy 1.24
• Correctly connect MUSIC output proxies when using multiple MPI processes in NEST
• Generalize double and integer synapse parameters in connect_arrays()
• Fix problems with Conda path substitutions in binaries
• Fix CMake check of Random123 generators
• Fix error handling in test suite
• Deprecate spike_dilutor and prohibit its use with multiple threads
• Prohibit multimeter-recording from noise_generator in multithreaded mode
• Ensure correct model id and model name when models are copied
• Use MAKE variable to pass correct info to child.
• Add conversion from IntegerDatum to ConstantParameter in create_parameter()
• Adjust documentation to the actual behaviour of -Dwith-optimize
• Fix errors in clang-format version handling
• Remove padding of extent if not specified when creating free positions
• Collect all information on changes in "what's new"
• Correct library information provided to extension modules
• Use the PR base as reference SHA when getting changed files
• Update models to accept parameter objects as node parameters
• Temporarily disable OpenMP for MacOS CI runner until libomp problem solved
• Fix memory leak with ResetKernel
• Use Python 3.8 compatible lru_cache
• Move MUSIC status printout up in the summary
• Fix mocker regex to avoid failures when building documentation
• Fix typo in model docstring
• Ensure that test_get_set.py works also in without threading
• Fix output of nest.spatial in Read the Docs

Maintenance updates

• Remove warning for conda-forge install
• Add link to release notes for 3.3
• Add missing PyNEST examples to documentation
• Change assertEqual to assertAlmostEqual in node parametrization tests
• Alter text in documentation for 'release notes'
• Transfer changes from release branch back to master
• Fix Sudoku link in examples
• Add note to What's new in 3.4 about new functions
• Update port in NESTServerClient
• Version shared objects
• Remove deprecated models iaf_psc_alpha_canon and pp_pop_psc_delta
• Use updateValue< long > instead of update_value_int in quantal_stp_synapse
• Fix stdout and status of nest-server
• Rename calibrate method to pre_run_hook
• Enable full MacOS build as part of CI
• Remove pathlib from requirements.txt as this is a Python-builtin now
• Removed CMAKE_INSTALL_PREFIX from default MacOS install instructions
• Add GIF / GLIF acronyms to model title in documentation
• Improve Docker usage documentation
• Ensure that thread-shared variable is initialized by single thread
• Report actual number of synapse created in PyNEST Brunel examples
• Ensure consistent return values in "impossible" situations even if assertions are compiled out
• Remove remaining uses of float datatype from C++ code
• Represent singularity-safe propagators for IAF models as classes
• Fix broken link in documentation
• Fix sign in equation documentation of spatial connection kernels
• Mark MPI as required if explicitly requested during CMake configuration
• Update clang-format requirement and code to version 13
• Change all apostrophe and quote characters to plain ASCII
• Remove the SLI-based NEST configuration file
• Add note about PYNEST_QUIET in docstring
• Include NEST GPU into the documentation
• Add link to NEST Desktop lecture material
• Align CONTRIBUTING.md with contributing section on Read the docs
• Update environment.yml and fix link to API documentation
• Fix some dimensions in developer documentation adex neurons
• Fix image scaling in docs
• Conda packages for Apple's M1 are available now
• Add documentation on discretization of uniformly distributed delays
• Fix and update model_details notebooks
• Install assimulo from conda-forge
• Remove PIL dependency in Sudoku Example
• Make kernel parameter documentation in kernel and PyNEST consistent
• Refactor functions to use MPI_Allreduce
• Update documentation for CreateParameter
• Modernize the code base and make it more compliant to common C++ style guides
• Improve clarity of -Dwith-python error message
• Modernize the codebase - remove unused imports
• Ensure do_tests.sh completes even when tests fail
• Modernize the codebase - overrides, nullptrs and redundant voids
• Pull updates into release branch
• Modernize the codebase - check for nullptr
• Modernize the codebase - and, or, not
• Modernize the codebase - remove leftover NULLs
• Remove superfluous data structure for secondary events
• Correct rounding of synaptic delays in the cortical microcircuit examples
• Change NEST Server default port to 52425
• Replace std::vector in SecondaryEvent with std::set
• Add missing tests of MUSIC models
• Use std::max and std::min
• Refactor collocate_spike_data_buffers
• Remove superfluous css and js bootstrap files
• Correct docstring capitalization of Sudoku and Pong PyNest examples
• Fix missing colon and correct comment
• Add note about resetting behavior of local_spike_counter
• Add documentation about Simulate() in Run() function
• Add node name to PortAlreadyPublished error in music_cont_in_proxy
• Remove leftover reference to nosetests
• Add documentation on order in inputs to nest.math.min and max functions
• Fix position of headings in Read the Docs
• Revising comments on Event class
• Improve documentation on some HH models
• Improved comments on weight positivity for conductance-based multisynapse models
• Fix rendering of references in local build of documentation
• Documentation UX revamp and internal CMake docbuild restructuring
• Remove VERA++ static code checking
• Correct documentation for aeif_psc models
• Capitalize Simulator in NEST Simulator
• Reduce the size of header field in Read the Docs
• Add note that nest.help('model_name') only works if the documentation is built
• Clean up and rename post trace computation notebook
• Fix for building user-level documentation local
• Remove autogenerated file from models directory
• Fix various typos
• Replace while-loop with C++ find_if function
• Correct default port for NEST Server MPI
• Change order of pre_run hook in SimulationManager
• Avoid using Dynamic_cast
• Make get_thread virtual in Node class