NEST 3.1

NEST 3.1 is the result of 460 commits by 17 developers since NEST 3.0 which was released on 2021-06-10.

This release contains many bug fixes and improvements, especially in the Python setup where support for Python environments was improved.

The PyNEST API was extended to support a more intuitive way of setting and retrieving kernel parameters. Where you previously had nest.SetKernelStatus({"resolution": 0.2}) in your simulation script, you can now just write nest.resolution = 0.2. Kernel attributes now come with their own docstrings and even tab-completion works for them! Additionally, PyNEST functions are now directly linked to the API reference throughout the documentation.

The testsuite now handles MPI tests more consistently and uses pytest for all Python tests.

Enhancements

Normal

• Add support for different virtual environment types for Python
• Link PyNEST functions in documentaton
• Automatic conversion of integers to doubles when setting parameters
• Add Arbor backend to GitHub Actions testing matrix
• Modify and improve colors in style sheet for user documentation
• Add intersphinx to NEST documentation with links to related projects
• Check validity of parameters given to SetKernelStatus
• Implement time limit for duration of update cycles
• Add kernel attributes and get/set functions to PyNEST module
• Automatically flag issues and pull-requests as stale
• Link to Zenodo citation page in docs

Bug fixes

Critical

• Run Python tests using Pytest, reorganize MPI-based Python tests and improve error reporting

High

• Set have_connections_changed correctly when we have fewer connections than MPI ranks
• Correct documentation of local_spike_counter
• Fix setting of PYEXECDIR
• Fix use of thread-specific distributions in random parameters
• Restrict calls to set_connections_have_changed() to thread 0
• Fix examples to make them run
• Undo link to PyNEST API in SLI documentation
• Detect pytest executable more robustly
• Fix import nest in NEST Server
• Check that timeout package is installed before running pytests
• Fix out of bound access on pp_pop_psc_delta and pulsepacket_generator
• Fix access of first element of an empty vector in pynestkernel

Normal

• Support apt-installed uwsgi in nest-server
• Fix build log parser failed test list
• Align pkg_resources query with setup.py name
• Fix mismatched parenthesis in setup.py.in

Maintenance

Critical

• Activate additional static code analysis in GitHub Actions

High

• Replace PEP8 by pycodestyle
• Clean up NEST Server and fix deadlock
• Remove Arbor recording backend
• Add pp_pop_psc_delta to deprecation list

Normal

• Add functions to access information about simulation time
• Refactor the Parameter classes
• Add user-level documentation for built-in timers
• Remove outdated CMake options
• Remove 'nest-' from setup.py version
• Update citation information
• Remove machine-specifc code for K computer
• Warn users they are using latest on ReadtheDocs
• Minor improvement to microcircuit example
• Remove undocumented weighted_spikes_{ex,in} from iaf_psc_{alpha,exp} recordables
• Add license to jupyter notebooks
• Fix figure in spatially structured networks tutorial
• Replace pass-by-value with pass-by-const-reference in Vose constructor
• Turn docstring with math into raw string
• Add default values to SetKernelStatus parameters
• Update security support for new release
• Relocate and refactor PyNEST testsuite
• Undo Markdown-to-reStructuredText conversion in doxygen comment
• Pave the way for per-version transition guides
• Remove outdated comment on Python dynamic library flags
• Update Python version check in __init__.py
• Add warning about synaptic plasticity mechanisms and precise spike timing
• Replace the Vose class with std::discrete_distribution
• Copy syn_spec to prevent it being modified
• Update Random123 library to v1.14.0
• Warn about the removal of nest.hl_api
• Update security support for 3.1 release