v0.6.0

Pin of JAX version

Installing Jaxley will no longer install the newest version of JAX. We realized that, on CPU, with version jax==0.4.32 or newer, simulation time in Jaxley is 10x slower and gradient time is 5x slower as compared to older versions of JAX. Newer versions of JAX can be made equally fast as older versions by setting os.environ['XLA_FLAGS'] = '--xla_cpu_use_thunk_runtime=false' at the beginning of your jupyter notebook (#570, @michaeldeistler).

New Features

• Add ability to record synaptic currents (#523, @ntolley). Recordings can be turned on with

net.record("i_IonotropicSynapse")

• refactor plotting (#539, @jnsbck).
  • rm networkx dependency
  • add Network.arrange_in_layers
  • disentangle moving of cells and plotting in Network.vis. To get the same as net.vis(layers=[3,3]), one now has to do:

net.arrange_in_layers([3,3])
net.vis()

• Allow parameter sharing for groups of different sizes, i.e. due to inhomogenous numbers of compartments or for synapses with the same (pre-)synaptic parameters but different numbers of post-synaptic partners. (#514, @jnsbck)

• Add jaxley.io.graph for exporting and importing of jaxley modules to and from networkx graph objects (#355, @jnsbck).

  • Adds a new (and improved) SWC reader, which is more flexible and should also be easier to extend in the future.

  from jaxley.io.graph import swc_to_graph, from_graph
  graph = swc_to_graph(fname)
  # do something to the swc graph, i.e. prune it
  pruned_graph = do_something_to_graph(graph)
  cell = from_graph(pruned_graph, ncomp=4)

  • Adds a new to_graph method for jaxley modules, which exports a module to a networkX graph. This allows to seamlessly work with networkX's graph manipulation or visualization functions.
  • "graph" can now also be selected as a backend in the read_swc.
  • See the improved SWC reader tutorial for more details.

Code Health

• changelog added to CI (#537, #558, @jnsbck)

• Add regression tests and supporting workflows for maintaining baselines (#475, #546, @jnsbck).

  • Regression tests can be triggered by commenting "/test_regression" on a PR.
  • Regression tests can be done locally by running NEW_BASELINE=1 pytest -m regression i.e. on main and then pytest -m regression on feature, which will produce a test report (printed to the console and saved to .txt).

• Allow inspecting the version via import jaxley as jx; print(jx.__version__) (#577, @michaeldeistler).

Bug fixes

• Fixed inconsistency with type assertions arising due to numpy functions returning different dtypes on platforms like Windows (#567, @Kartik-Sama)