Update to 0.9.0

v0.9.0

** 2023 08 09 **

After much more delay than anticipated, we are very happy to present a new Arbor release. Nearly 8 months of work is in it, much of which focussed on speed, optimisation, fixes and build system changes. This release includes Python 3.12 wheels as probably one of the first packages on PyPI 😄.

Major new features

• External Connectivity: Arbor can now interface with other simulators or processes through MPI. Contexts now accept a second MPI communicator and Recipes can implement a external_connections_on method to specify how simulations might be interacting. See documentation for more.
• Arbor now supports checkpointing and resume from a previously stored checkpoint. Useful when a certain point in time needs to be explored in multiple directions, when you want to rewind to a previous state, etc. See documentation for more.
• More painted parameters are now scalable through iexpr: temperature, capacitance, resistivity, membrane potential and the following ionic parameters: internal and external concentration, diffusivity, and reversal potential. See documentation.
• A set of ANN activation functions for NMODL have been added: sigmoid(x), relu(x) and tanh(x). Control volume area is exposed through NMODL.
• A revamped backend for ARM CPU's that support Scalable Vector Extension (SVE). Arbor and modcc are now fully compatible, so users who have access to A64FX-based HPC can take full advantage of that hardware.

Breaking changes since v0.8.1

• It is no longer possible to set binning and sampling policies, due to Arbor now having a fixed timestep. Removing exact delivery increases the speed of the simulation due to elimination of small steps, makes the numerics independent of presence of sampling, and also leads to a number of code simplifications.
• Contexts are now constructed kwargs-only. So, arbor.context(12, None) is now arb.context(threads=12, gpu=None). In the case no arguments are supplied, the context initialized to default_allocation, which means it will use the total number of threads and first GPU that are locally available. arbor.simulation constructed without an explicit arbor.context also initializes a default_allocation.
• Version bumps:
• CUDA 11 or higher is required for GPU builds.

Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.8.1...v0.9.0

v0.8.1

** 2022 12 22 **

A 🎄 holiday release! Not much has changed in a month, but we'd like to share it all the same. Notably, the Arbor GUI is co-released as of Arbor v0.8, and v0.8.1 will be no different.

Major new features

• Voltage Processes: add the VOLTAGE_PROCESS mechanism kind to modcc, allowing for direct writing to the membrane voltage (#2033)
• Spack gpu option: added conditional variant for cuda builds to enable GPU-based random number generation (#2043)
• SDE Tutorial (#2044)

Breaking changes since v0.8

• None 💃!

Bug fixed

• Fix ornstein_uhlenbeck example on gpu (#2039)
• Setting ARB_MODCC was broken and nunfunctional. Fixed. (#2029)
• The --cxx flag in arbor-build-catalogue is now properly used; falls back to c++. (#2051)

v0.8

** 2022 11 15 **

Welcome to another installment of the Arbor simulator!

In this release we add a CHANGELOG, where major new features and breaking changes will be mentioned specifically.

Major new features

• 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). https://github.com/arbor-sim/arbor/pull/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. https://github.com/arbor-sim/arbor/pull/1919
• Allow editing morphologies. Supported operations: join_at, split_at, equivalence, equality, apply isometry. https://github.com/arbor-sim/arbor/pull/1957
• Arbor cable cell exporter and backend support in BluePyOpt. https://github.com/arbor-sim/arbor/pull/1959
• Make LIF cells probeable. https://github.com/arbor-sim/arbor/pull/2021

Breaking changes since v0.7:

• 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. https://github.com/arbor-sim/arbor/pull/1978
• Remove the generate-catalogue script. modcc accepts now a list of NMODL files and is able to spit out a catalogue.cpp file. https://github.com/arbor-sim/arbor/pull/1975
• Mechanism ABI version is bumped to 0.3.1. https://github.com/arbor-sim/arbor/pull/1884
• Rename spike detector -> threshold detector. https://github.com/arbor-sim/arbor/pull/1976
• Remove access to time t in NMODL. https://github.com/arbor-sim/arbor/pull/1967
• Major dependency version bumps:
• GCC: 9 and up
• CUDA: 11 and up
• Clang: 10 and up

Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.7...v0.8-rc