v0.8 released!

Version v0.8 has been released! This is the third version released in our 3 month release cadence, again with a bit of delay.

Major new features are:

• Stochastic Differential Equations. Introduces sources of white noise to arbor (and nmodl). Both point and density mechanisms may now use white noise as part of the state updates, turning the ODEs effectively into SDEs. The noise sources are provided per connection end point (point mech.) or control volume (density mech.) and are uncorrelated (spatially, temporally and across different mechanism instantiations). #1884
• Mutable connection table. Add functionality, docs, and examples on editing the connection table. This is a first, small PR on the topic, further functionality will come as requested. #1919
• Allow editing morphologies. Supported operations: join_at, split_at, equivalence, equality, apply isometry. #1957
• Arbor cable cell exporter and backend support in BluePyOpt. #1959
• LIF cells can now be probed. #2021

Breaking changes since the previous release:

• A change in decor API: arbor.cable_cell has the labels and decor arguments swapped. I.e.: (tree, labels, decor) -> (tree, decor, label). Labels are now optional. #1978
• Remove the generate-catalogue script. modcc accepts now a list of NMODL files and is able to spit out a catalogue.cpp file. #1975
• Mechanism ABI version is bumped to 0.3.1. #1884
• Rename spike detector -> threshold detector. #1976
• Remove access to time t in NMODL. #1967
• Major dependency version bumps:
  • GCC: 9 and up
  • CUDA: 11 and up
  • Clang: 10 and up

A full changelog is available in CHANGELOG.md.

The release is out on PyPI (and Spack as well), so give it a go:

python -m venv env && source env/bin/activate
pip install arbor
python -c 'import arbor; print(arbor.__config__)'

Should you encounter any problems, don’t hesitate to let us know.