v0.5.0

API changes

• Synapse views no longer exist (#447, #453, @jnsbck). Previous code such as

net.IonotropicSynapse.set("IonotropicSynapse_s", 0.2)

must be updated to:

net.set("IonotropicSynapse_s", 0.2)

For a more detailed tutorial on how to index synapses, see
this new tutorial.

• Throughout the codebase, we renamed any occurance of seg (for segment) to comp
  (for compartment). The most notable user-facing changes are:
  • branch = jx.Branch(comp, ncomp=4)
  • cell = jx.read_swc(fname, ncomp=4)
• New defaults for the SWC reader with jx.read_swc(). By default, we now have
  assign_groups=True (previously False) and max_branch_len=None (previously
  300.0).
• We renamed .view to .nodes, e.g., cell.branch(0).nodes (#447, #453, @jnsbck).
• We renamed _update_nodes_with_xyz() to compute_compartment_centers() (#520,
  @jnsbck)
• We updated the way in which transformations are built (#455, @manuelgloeckler).
  Previous code such as

tf = jx.ParamTransform(
    lower={"radius": 0.1, "length": 2.0},
    lower={"radius": 3.0, "length": 20.0},
)

must be updated to:

from jaxley.optimize.transforms import ParamTransform, SigmoidTransform
transforms = [
    {"radius": SigmoidTransform(lower=0.1, upper=3.0)},
    {"length": SigmoidTransform(lower=2.0, upper=20.0)},
]
tf = jt.ParamTransform(transforms)

New features

• Added a new delete_channel() method (#521, @jnsbck)
• Allow to write trainables to the module (#470, @michaeldeistler):

net.make_trainable("radius")
params = net.get_parameters()
net.write_trainables(params)

• Expose the step function to allow for fine-grained simulation (#466, @manuelgloeckler)
• More flexible and throrough viewing (#447, #453, @jnsbck)
• Boolean indexing for cells, branches, and comps (@494, @jnsbck):

r_greater_1 = net.nodes.groupby("global_cell_index")["radius"].mean() > 1
net[r_greater_1].nodes.vis()

• check if recordings are empty (#460, @deezer257)
• enable clamp to be jitted and vmapped with data_clamp() (#374, @kyralianaka)

Bug fixes

• allow for cells that were read from swc to be pickled (#525, @jnsbck)
• fix units of compute_current() in channels (#461, @michaeldeistler)
• fix issues with plotting when the morphology has a different number of compartments
  (#513, @jnsbck)

Documentation

• new tutorial on synapse indexing (#464, @michaeldeistler, @zinaStef)
• new tutorial on parameter sharing (#464, @michaeldeistler, @zinaStef)
• new tutorial on modules and views (#493, @jnsbck)
• improved tutorial on building channel models (#473, @simoneeb)
• get rid of tensorflow dependency by defining our simple dataloader in the tutorial
  (#484, @jnsbck)
• new FAQ about rate-based networks (#531, @michaeldeistler)

Code health

• refactor tests with fixtures (@479, #499, @fabioseel, @jnsbck)
• make several attributes private (#495, @ntolley)
• move read_swc.py to new io folder (#524, @jnsbck)
• faster testing for SWC and plotting (#479, @fabioseel)
• automated tests to check if tutorials can be run (#480, @jnsbck)
• add helpers to deprecate functions and kwargs (#516, @jnsbck)