v0.11.3

🛠️ Internal updates

• follow jax typing practices with Array and ArrayLike (#693, @alexpejovic)

🐛 Bug fixes

• fix for networks that mix point neurons and morphologically detailed neurons (#702,
  @michaeldeistler)
• carry over groups from constituents of a module (e.g., jx.Cell groups get carried
  over to jx.Network) (#703, @michaeldeistler)

v0.11.2

🐛 Bug fixes

• Bugfix for Networks on GPU: since v0.9.0, networks had been very slow on GPU
  because the voltage equations of cells had been processed in sequence, not in parallel.
  This is now solved, giving a large speed-up for networks consisting of many cells (#691,
  @michaeldeistler, thanks to @VENOM314 for reporting)

📚 Documentation

• Remove all content from the old mkdocs documentation website (#689, @michaeldeistler)

v0.11.1

🐛 Bug fixes

• bugfix for set_ncomp() when the cell consists of a single branch (#686,
  @michaeldeistler)

🛠️ Internal updates

• fix all typos in the codebase by using the typos project (#682, @alexpejovic)

v0.11.0

🧩 New features

• simple conductance synapse added (#659, @kyralianaka)

📚 Documentation

• add a how-to guide on converting NMODL files to Jaxley, see
  here
  (#669, @michaeldeistler, special thanks to @r-makarov for building the tool)

🛠️ Internal updates

• changes to how the membrane area from SWC files is computed when the radius within a
  compartment is not constant. This fix can have an impact on simulation results. The
  updated computation of membrane area matches that of the NEURON simulator (#662,
  @michaeldeistler, thanks to @VENOM314 for reporting).
• remove the custom SWC reader (which had been deprecated in v0.9.0, #662,
  @michaeldeistler).
• fix bug in set_ncomp (# 676, @manuelgloeckler)

v0.10.0

🧩 New features

• functionality to compute the pathwise distance between compartments (#648,
  @michaeldeistler):

from jaxley.morphology import distance_pathwise
path_dists = distance_pathwise(cell.soma.branch(0).comp(0), cell)
cell.nodes["path_dist_from_soma"] = path_dists

🐛 Bug fixes

• fixed synapse recording indices to be within type (#643, @kyralianaka)
• Fix inheriting from a Module #590 (#642, @jnsbck)

🛠️ Internal updates

• module.distance() is now deprecated in favor of jx.morphology.distance_direct()
  (#648, @michaeldeistler)

v0.9.0

✨ Highlights

• This PR implements a new solver, which is now used by default (#625,
  @michaeldeistler). The new solver has the following advantages:
  • Much lower runtime. Across several morphologies, we get a 20% runtime speedup on
    CPU and a 50% runtime speedup on GPU.
  • Almost zero compile time. We get a 50x compile time speedup on CPU and a 3x compile
    time speedup on GPU.
• Utility to delete parts of a morphology (#612, @michaeldeistler):

from jaxley.morphology import morph_delete
cell = morph_delete(cell.branch([1, 2]))

• Utility to connect two cells into a single cell (#612, @michaeldeistler):

from jaxley.morphology import morph_connect
cell = morph_connect(cell1.branch(1).loc(0.0), cell2.branch(2).loc(1.0))

🧩 New features

• the default SWC reader has changed. To use the previous SWC reader, run
  jx.read_swc(..., backend="custom"). However, note that we will remove this reader
  in the future. If the new SWC reader is causing issues for you, please open an issue
  (#612, @michaeldeistler)
• radiuses are now integrated across SWC coordinates, not interpolated
  (#612, @michaeldeistler)
• remove pin of JAX version. New JAX versions (JAX>=0.6.0) resolve slow CPU
  runtime, see here (#623, @michaeldeistler)
• running the d_lambda rule is now much faster, see
  the how-to guide
  (#625, @michaeldeistler)

📚 Documentation

• Introduce the how-to guide on the website (#612, @michaeldeistler)
• reorganize the advanced tutorials into subgroups (#612, @michaeldeistler)
• split the morphology handling tutorials into two notebooks (#612, @michaeldeistler)

🛠️ Internal updates

• improvements to graph-backend for more flexibility in modifying morphologies (#613,
  @michaeldeistler)
• remove root compartment for SWC files (#613, @michaeldeistler)
• enable traversing compartmentalized graph for optimizing solve order (#613,
  @michaeldeistler)
• ._comp_edges are being tracked in the View (#621, @michaeldeistler)
• introduce ._branchpoints_ attribute and track in the View (#612, @michaeldeistler)
• pre_global_comp_index and post_global_comp_index are no longer part of .edges
  by default. To get them, do net.copy_node_property_to_edges("global_comp_index")
  (#625, @michaeldeistler)

🐛 Bug fixes

• ChainTransform forward now working as mirror to inverse (#628, @kyralianaka)
• allow data_set with vectors of values (#606, @chaseking)

🎉 New Contributors

• @chaseking made their first contribution in #606

v0.8.2

• enable intersections of groups, e.g. net.exc.soma (#608, @michaeldeistler)
• allow ion diffusion to be jitted (#609, @michaeldeistler)

v0.8.1

• fixups to tutorial notebooks (#604, @michaeldeistler)
• remove delete_channel() (#604, @michaeldeistler)

v0.8.0

New features

• add leaky integrate-and-fire neurons (#564, @jnsbck), Izhikevich neurons, and rate-based neurons (#601, @michaeldeistler)

Minor updates

• make delta and v_th in IonotropicSynapse trainable parameters (#599, @jnsbck)
• make random postsnaptic compartment selection optional in connectivity functions (#489, @kyralianaka)

Bug fixes

• Fix bug for groups when .set_ncomp was run (#587, @michaeldeistler)
• allow .distance to be jitted (#603, @michaeldeistler)

v0.7.0

New Features

• Allow ion diffusion with cell.diffuse() and add tutorials (#438, @michaeldeistler):

from jaxley.channels import CaNernstReversal
from jaxley.pumps import CaFaradayConcentrationChange

cell.insert(CaFaradayConcentrationChange())
cell.insert(CaNernstReversal())
cell.diffuse("CaCon_i")
cell.set("axial_diffusion_CaCon_i", 1.0)

• Introduce ion pumps (#438, @michaeldeistler)

Bug fixes

• Fix for simulation of morphologies with inhomogenous numbers of compartments (#438, @michaeldeistler)
• Bugfix for types assigned by SWC reader when soma is traced by a single point (#582, @Kartik-Sama, @michaeldeistler).

Code health

• add new release workflow (#588, @jnsbck)
• update FAQ and tutorials (#593, @michaeldeistler)