From c84a84164d6d354a4fc475efb72c514f6fd68d6a Mon Sep 17 00:00:00 2001
From: Brent Huisman <brenthuisman@users.noreply.github.com>
Date: Wed, 7 Oct 2020 14:50:06 +0200
Subject: [PATCH] Add missing quotes in the Python example and docs. (#1174)
---
doc/gs_single_cell.rst | 14 ++++----------
python/example/single_cell_model.py | 8 ++++----
2 files changed, 8 insertions(+), 14 deletions(-)
diff --git a/doc/gs_single_cell.rst b/doc/gs_single_cell.rst
index 8749e384..08d34b05 100644
--- a/doc/gs_single_cell.rst
+++ b/doc/gs_single_cell.rst
@@ -48,13 +48,9 @@ create the ``cable_cell`` that represents it are as follows:
# (3) Create cell and set properties
cell = arbor.cable_cell(tree, labels)
cell.set_properties(Vm=-40)
- cell.paint('soma', 'hh')
- cell.place('center', arbor.iclamp( 10, 2, 0.8))
- cell.place('center', arbor.spike_detector(-10))
-
- # Discretization: the default discretization in Arbor is 1 compartment per branch.
- # Let's be a bit more precise and make that every 2 μm:
- cell.compartments_length(2)
+ cell.paint('"soma"', 'hh')
+ cell.place('"center"', arbor.iclamp( 10, 2, 0.8))
+ cell.place('"center"', arbor.spike_detector(-10))
Let's unpack that.
@@ -93,8 +89,6 @@ with the named regions and locations.
an :class:`arbor.iclamp<arbor._arbor.iclamp>` with a duration of 2 ms and a current of
0.8 nA, starting at 10 ms. Then, add an :class:`arbor.spike_detector<arbor._arbor.spike_detector>`
with a threshold of -10 mV to the location we've labelled 'center'.
-* Finally, we adjust the :ref:`discretisation <cable-discretisation>` of the simulation
- by setting the compartment length to 2 μm. By default there is one compartment per branch.
Single cell network
----------------------------------------------------
@@ -112,7 +106,7 @@ and provides an interface for recording potentials and running the simulation.
m = arbor.single_cell_model(cell)
# (5) Attach voltage probe sampling at 10 kHz (every 0.1 ms).
- m.probe('voltage', 'center', frequency=10000)
+ m.probe('voltage', '"center"', frequency=10000)
# (6) Run simulation for 100 ms of simulated activity.
m.run(tfinal=100)
diff --git a/python/example/single_cell_model.py b/python/example/single_cell_model.py
index a7ee1ff2..f2159bad 100644
--- a/python/example/single_cell_model.py
+++ b/python/example/single_cell_model.py
@@ -11,15 +11,15 @@ labels = arbor.label_dict({'soma': '(tag 1)',
# (3) Create cell and set properties
cell = arbor.cable_cell(tree, labels)
cell.set_properties(Vm=-40)
-cell.paint('soma', 'hh')
-cell.place('center', arbor.iclamp( 10, 2, 0.8))
-cell.place('center', arbor.spike_detector(-10))
+cell.paint('"soma"', 'hh')
+cell.place('"center"', arbor.iclamp( 10, 2, 0.8))
+cell.place('"center"', arbor.spike_detector(-10))
# (4) Make single cell model.
m = arbor.single_cell_model(cell)
# (5) Attach voltage probe sampling at 10 kHz (every 0.1 ms).
-m.probe('voltage', 'center', frequency=10000)
+m.probe('voltage', '"center"', frequency=10000)
# (6) Run simulation for 100 ms of simulated activity.
m.run(tfinal=100)
--
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