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0.6.0

New Features

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

  • 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).

  • 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)

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

0.5.0

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)

0.4.0

New features

  • Changing the number of compartments: cell.branch(0).set_ncomp(4) (#436, #440, #445, @michaeldeistler, @jnsbck)
  • New options for plotting: cell.vis(type='comp') and cell.vis(type='morph') (#432, #437, @jnsbck)
  • Speed optimization for jx.integrate(..., voltage_solver="jaxley.stone") (#442, @michaeldeistler)

Documentation

v0.3.0

New features

  • New solver: jx.integrate(..., voltage_solver="jax.sparse") which has very low compile time (#418, @michaeldeistler)
  • Support for different number of compartments per branch at initilization (modifying the number of compartments after initialization is not yet supported, #418, #426, @michaeldeistler)

Bugfixes

  • Bugfix for capacitances and their interplay with axial conductances (Thanks @Tunenip, #426, @michaeldeistler)
  • Bugfixes for tutorials on website

v0.2.1

  • Bugfix for using states in init_state of the channel (#421, @michaeldeistler)
  • Bugfix for tutorial on building custom channels (#421, @michaeldeistler)
  • Add jaxley-mech as dev dependency to use it in testsing (#421, @michaeldeistler)

v0.2.0

New features

  • Cranck-Nicolson solver (#413, @michaeldeistler)
  • Forward Euler solver for compartments and branches (#413, @michaeldeistler)
  • Add option to access states in channel.init_state (#416, @michaeldeistler)

Bugfixes

  • Bugfix for interpolation of x, y, z values (#411, @jnsbck)

v0.1.2

  • Minor fixups for README, website, and PyPI landing page

v0.1.1

  • Minor fixups for README, website, and PyPI landing page

v0.1.0

  • First public version