For a more detailed tutorial on how to index synapses, see
[this new tutorial](https://jaxley.readthedocs.io/en/latest/tutorials/09_advanced_indexing.html).
- 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
python
tf = jx.ParamTransform(
lower={"radius": 0.1, "length": 2.0},
lower={"radius": 3.0, "length": 20.0},
)
must be updated to:
python
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):
python
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):
python
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)