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
• Port issue-1100.sli to Pytest
• Port issue-1140.sli to Pytest
• Port issue-1212.sli to Pytest
• Port issue-1242.sli to Pytest
• Port test_spike_poisson_ps from SLI-2-Py
• Port issue-1305.sli to Pytest
• Port issue-1366.sli to Pytest
• Port issue-1610.sli to Pytest
• Port issue-1640.sli to Pytest
• Port issue-2282.sli to Pytest
• Port test_multisynapse_models from SLI-2-Py
• Port test_sinusoidal_poisson_generator from SLI-2-Py
• Port test_pulsepacket_generator from SLI-2-Py
• Port issue-351.sli to Pytest
• Port issue-368.sli to Pytest
• Delete SLI tests that have been ported to Pytest
• Add sli2py_ignore subdirectories to testsuite
• Port issue-410.sli to Pytest
• Port ticket-80-175-179.sli to py
• Remove redundant SLI tests
• Test iaf ps psp accuracy (sli2py)
• Test iaf ps psp poisson accuracy (sli2py)
• Move deprecated tests to sli2py_ignore directory
• Port test_spike_recorder from SLI-2-Py
• Port test_threaded_spike_recorder from SLI-2-Py
• Port test_spike_rec_reset from SLI-2-Py
• Remove test_spike_transmission_ps.sli and test_spike_transmission_ps_iaf.sli
• Port test_spin_detector from SLI-2-Py
• Port test_step_current_generator from SLI-2-Py
• Port test_ntree_split from SLI-2-Py
• Improve robustness of test_ticket_80_175_179.py
• Port test_oversize_mask from SLI-2-Py
• Port test_rate_connections from SLI-2-Py
• Port ticket-459.sli to Pytest and fix name for ticket_754.py
• Port issue-521.sli to Pytest

122 pull-requests merged.