fix: correct Synapse base class, stale docstrings, and minor type issues

CHANGELOG.md

@@ -13,6 +13,7 @@ Implements Brette et al. (2005), 'Adaptive exponential integrate-and-fire model
 - Fix issue where `build_dynamic_state_utils` `remove_observables` performed in-place deletions on full state dict (#775, @chaseking)
 - Allow data_clamp to clamp multiple different states without silently only clamping the last state (#773, @kyralianaka) and fixed checkpointing for this case (#786, @kyralianaka)
 - Fix issue causing some `View`s to take too long to create (#791, @alexpejovic)
+- Fix missing `self` in `Synapse` base class, stale `uA/cm2` docstrings, invalid `np.ndarray[bool]` annotation, and duplicate import (#792, @haoyu-haoyu)
 
 # 0.13.0
 

jaxley/channels/channel.py

@@ -16,7 +16,7 @@ class Channel:
 
     As in NEURON, a `Channel` is considered a distributed process, which means that its
     conductances are to be specified in `S/cm2` and its currents are to be specified in
-    `uA/cm2`."""
+    `mA/cm2`."""
 
     _name = None
     channel_params = None
@@ -96,7 +96,7 @@ def compute_current(
             params: Parameters of the channel (conductances in `S/cm2`).
 
         Returns:
-            Current in `uA/cm2`.
+            Current in `mA/cm2`.
         """
         raise NotImplementedError
 

jaxley/connect.py

@@ -260,7 +260,7 @@ def connectivity_matrix_connect(
     pre_cell_view: "View",
     post_cell_view: "View",
     synapse_type: "Synapse",
-    connectivity_matrix: np.ndarray[bool],
+    connectivity_matrix: np.ndarray,
     random_post_comp: bool = False,
 ):
     """Connect cells of a network with synapses via a boolean connectivity matrix.

jaxley/integrate.py

@@ -2,7 +2,7 @@
 # licensed under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
 from collections.abc import Callable
 from math import prod
-from typing import Callable, Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import jax
 import jax.numpy as jnp

jaxley/synapses/synapse.py

@@ -58,6 +58,7 @@ def change_name(self, new_name: str):
         return self
 
     def update_states(
+        self,
         states: dict[str, Array],
         delta_t: float,
         pre_voltage: ArrayLike,
@@ -78,6 +79,7 @@ def update_states(
         raise NotImplementedError
 
     def compute_current(
+        self,
         states: dict[str, Array],
         pre_voltage: ArrayLike,
         post_voltage: ArrayLike,