From 9fed4a91a3f4673a6db8f73594c5758b67f16cfc Mon Sep 17 00:00:00 2001
From: Brent Huisman <brenthuisman@users.noreply.github.com>
Date: Fri, 2 Jul 2021 09:21:20 +0200
Subject: [PATCH] Update and rename python example (#1602)
- Minor fixes to python examples.
- Fix `mpi.py` to use new label API.
- Rename `mpi.py`.
---
doc/python/decor.rst | 2 +-
python/example/network_ring.py | 9 +++++----
python/example/{mpi.py => network_ring_mpi.py} | 11 ++++++-----
.../example/{mpi_plot.py => network_ring_mpi_plot.py} | 0
4 files changed, 12 insertions(+), 10 deletions(-)
rename python/example/{mpi.py => network_ring_mpi.py} (93%)
rename python/example/{mpi_plot.py => network_ring_mpi_plot.py} (100%)
diff --git a/doc/python/decor.rst b/doc/python/decor.rst
index 8c0104a3..c9412966 100644
--- a/doc/python/decor.rst
+++ b/doc/python/decor.rst
@@ -1,4 +1,4 @@
-.. pycablecell-decor:
+.. _pycablecell-decor:
Cable cell decoration
=====================
diff --git a/python/example/network_ring.py b/python/example/network_ring.py
index 1754ab38..09b3a75c 100755
--- a/python/example/network_ring.py
+++ b/python/example/network_ring.py
@@ -48,10 +48,10 @@ def make_cable_cell(gid):
decor.paint('"dend"', 'pas')
# (4) Attach a single synapse.
- decor.place('"synapse_site"', 'expsyn', "syn")
+ decor.place('"synapse_site"', 'expsyn', 'syn')
# Attach a spike detector with threshold of -10 mV.
- decor.place('"root"', arbor.spike_detector(-10), "detector")
+ decor.place('"root"', arbor.spike_detector(-10), 'detector')
cell = arbor.cable_cell(tree, labels, decor)
@@ -88,13 +88,14 @@ class ring_recipe (arbor.recipe):
src = (gid-1)%self.ncells
w = 0.01
d = 5
- return [arbor.connection((src,"detector"), "syn", w, d)]
+ return [arbor.connection((src,'detector'), 'syn', w, d)]
# (9) Attach a generator to the first cell in the ring.
def event_generators(self, gid):
if gid==0:
sched = arbor.explicit_schedule([1])
- return [arbor.event_generator("syn", 0.1, sched)]
+ weight = 0.1
+ return [arbor.event_generator('syn', weight, sched)]
return []
# (10) Place a probe at the root of each cell.
diff --git a/python/example/mpi.py b/python/example/network_ring_mpi.py
similarity index 93%
rename from python/example/mpi.py
rename to python/example/network_ring_mpi.py
index a7096ede..98a53f69 100644
--- a/python/example/mpi.py
+++ b/python/example/network_ring_mpi.py
@@ -50,10 +50,10 @@ def make_cable_cell(gid):
decor.paint('"dend"', 'pas')
# (4) Attach a single synapse.
- decor.place('"synapse_site"', 'expsyn')
+ decor.place('"synapse_site"', 'expsyn', 'syn')
# Attach a spike detector with threshold of -10 mV.
- decor.place('"root"', arbor.spike_detector(-10))
+ decor.place('"root"', arbor.spike_detector(-10), 'detector')
cell = arbor.cable_cell(tree, labels, decor)
@@ -90,13 +90,14 @@ class ring_recipe (arbor.recipe):
src = (gid-1)%self.ncells
w = 0.01
d = 5
- return [arbor.connection((src,0), (gid,0), w, d)]
+ return [arbor.connection((src,'detector'), 'syn', w, d)]
# (9) Attach a generator to the first cell in the ring.
def event_generators(self, gid):
if gid==0:
sched = arbor.explicit_schedule([1])
- return [arbor.event_generator((0,0), 0.1, sched)]
+ weight = 0.1
+ return [arbor.event_generator('syn', weight, sched)]
return []
# (10) Place a probe at the root of each cell.
@@ -133,7 +134,7 @@ sim.run(ncells*5)
print('Simulation finished')
# (17) Plot the recorded voltages over time.
-print("Storing results ...")
+print('Storing results ...')
df_list = []
for gid in range(ncells):
if len(sim.samples(handles[gid])):
diff --git a/python/example/mpi_plot.py b/python/example/network_ring_mpi_plot.py
similarity index 100%
rename from python/example/mpi_plot.py
rename to python/example/network_ring_mpi_plot.py
--
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