store first stim value; update docs overview

cleo/base.py

@@ -235,11 +235,16 @@ class Stimulator(InterfaceDevice, NeoExportable):
 
     def __attrs_post_init__(self):
         self.value = self.default_value
+        self._init_saved_vars()
 
     def _init_saved_vars(self):
         if self.save_history:
-            self.t_ms = []
-            self.values = []
+            if self.sim:
+                t0 = self.sim.network.t / ms
+            else:
+                t0 = 0
+            self.t_ms = [t0]
+            self.values = [self.value]
 
     def update(self, ctrl_signal) -> None:
         """Set the stimulator value.

docs/conf.py

@@ -60,8 +60,8 @@
 
 autosectionlabel_prefix_document = True
 
-jupyter_execute_notebooks = "off"
-execution_excludepatterns = ["*ldsctrlest*"]
+jupyter_execute_notebooks = "cache"
+execution_excludepatterns = ["tutorials/*"]
 
 # napoleon_custom_sections = "Visualization Keyword Arguments"
 napoleon_custom_sections = [("Visualization kwargs", "params_style")]

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cleosim"
-version = "0.10.0"
+version = "0.11.0"
 description = "Cleo: the Closed-Loop, Electrophysiology, and Optogenetics experiment simulation testbed"
 authors = [
     "Kyle Johnsen <[email protected]>",
@@ -46,6 +46,7 @@ furo = "^2022.6.21"
 nbdev = "^2.3.12"
 elephant = "^0.13.0"
 seaborn = "^0.13.0"
+jupytext = "^1.15.2"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

tests/ioproc/test_processing.py

@@ -62,11 +62,11 @@ def process(self, state_dict: dict, sample_time_ms: float) -> Tuple[dict, float]
 
 
 def _test_LatencyIOProcessor(myLIOP, t, sampling, inputs, outputs):
+    expected_out = [None if out is None else {"out": out} for out in outputs]
     for i in range(len(t)):
         assert myLIOP.is_sampling_now(t[i]) == sampling[i]
         if myLIOP.is_sampling_now(t[i]):
             myLIOP.put_state({"in": inputs[i]}, t[i])
-        expected_out = [out if out is None else {"out": out} for out in outputs]
         assert myLIOP.get_ctrl_signal(t[i]) == expected_out[i]
 
 

tests/test_base.py

@@ -52,14 +52,14 @@ def test_stimulator(sim, neurons):
     assert my_stim.value == 42
     my_stim.update(43)
     assert my_stim.value == 43
-    assert len(my_stim.values) == len(my_stim.t_ms) == 1  # from update
+    assert len(my_stim.values) == len(my_stim.t_ms) == 2  # from update
 
     sim.update_stimulators({"my_stim": 42})
     assert my_stim.value == 42
-    assert len(my_stim.values) == len(my_stim.t_ms) == 2  # from 2 updates
+    assert len(my_stim.values) == len(my_stim.t_ms) == 3  # from 2 updates
 
     my_stim.reset()
-    assert len(my_stim.values) == len(my_stim.t_ms) == 0  # init
+    assert len(my_stim.values) == len(my_stim.t_ms) == 1  # init
 
     neurons2 = NeuronGroup(1, "v = -70*mV : volt")
     with pytest.raises(Exception):  # neuron2 not in network