fix: rm networkx dep, update changelog

jaxleyverse · Dec 3, 2024 · d714a5a · d714a5a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,15 @@ net.record("i_IonotropicSynapse")
   - 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).
   - If a PR introduces new baseline tests or reduces runtimes, then a new baseline can be created by commenting "/update_regression_baselines" on the PR.
 
+- 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:
+```python
+net.arrange_in_layers([3,3])
+net.vis()
+```
+
 # 0.5.0
 
 ### API changes

diff --git a/jaxley/modules/network.py b/jaxley/modules/network.py
@@ -436,7 +436,7 @@ def vis(
 
         Args:
             detail: Either of [point, full]. `point` visualizes every neuron in the
-                network as a dot (and it uses `networkx` to obtain cell positions).
+                network as a dot.
                 `full` plots the full morphology of every neuron. It requires that
                 `compute_xyz()` has been run and allows for indivual neurons to be
                 moved with `.move()`.

diff --git a/pyproject.toml b/pyproject.toml
@@ -28,7 +28,6 @@ keywords = ["neuroscience", "biophysics", "simulator", "jax"]
 dependencies = [
     "jax",
     "matplotlib",
-    "networkx",
     "numpy",
     "pandas>=2.2.0",
     "tridiax",