From d5292d09d44580c56460f766459b3d2aa6ad4480 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Fri, 2 Mar 2018 16:17:54 +0530
Subject: [PATCH] Squashed 'moose-examples/' changes from bd41d06..7f3d27f
7f3d27f Merge branch 'master' into chennapoda
3047477 python3/python2 compatible call to raw_input.
d314d4c Documentation update #1 (#225)
cd494a6 Merge commit 'b5ec7b3c82c0e59d0390efcc5dde7d98eacd4cf9'
8032817 Merge commit 'd07f7ea6c3357b98b62e1abe9d133be39a797de8'
17cf9ef Merge commit 'f27ad43950c241570675ceb06273217f03905859'
ad1dcdc Merge commit 'b0021958d104e020f5d0c441e2f4b81bf84508fb'
a6f09fc Merge commit 'b3c864062a4b50ac942a8fdcb0cb6c1df6a456c7' as 'moose-examples'
e699bcd moose-examples keep creating troble. May be I don't know how to handle git subtree.
6c967df Merge commit '0014d8268ef8184db15745884208636c1f05e76a'
0014d82 Squashed 'moose-core/' changes from 2c3fe7516..052318cb4
45411b6 Follow up fixes to calcium-hsolve (#221)
98ae1a9 Merge commit '378bf23c784397b37f2c58212d3a3d16aa0ebee5' as 'moose-examples'
378bf23 Squashed 'moose-examples/' content from commit 3a960983fe
82043db Dirty commit in moose-examples as well.
f2a691b Merge commit '60c5802aead9b0f4cbc639511ad1b9038b0cd178'
60c5802 Squashed 'moose-examples/' changes from 0c5527e77d..3a960983fe
53206f8 Squashed 'moose-core/' changes from fe77059f98..2c3fe7516a
0e36128 Merge commit '53206f84b69d3127a34a915b1580dcd73a593bd8'
d38e324 Merge branch 'master' into asiaszmek
82ee30f Merge commit '37cdf0cc44f9a8b73b536c4a3a91cdcbd59eada0'
37cdf0c Squashed 'moose-gui/' changes from 49779ba730..38da92b048
dfa3249 Squashed 'moose-examples/' changes from 80169bcc5c..0c5527e77d
b960aed Merge commit 'dfa32490a149f41e14a364403f57b08c40bcd3ef'
e6e83b7 Squashed 'moose-core/' content from commit fe77059f98
3404d0b Merge commit 'e6e83b761e93923f3853512e1814a412296927a7' as 'moose-core'
be87aea Deleted moose-core due to dirty history in upstream moose-core.
48fc973 Squashed 'moose-examples/' changes from 2eb5fa888f..80169bcc5c
1051706 Merge commit '48fc9733220a09f3b5899c999226e664ae5188bc'
304173c Merge commit 'd27e942f2f8c0b1a3be34da0058ab374ac843400'
d27e942 Squashed 'moose-core/' changes from 69e0354705..b096503233
0f74138 Calcium hsolve (#218)
fbf9dbd Fixes to bad-merging.
2ea8560 Travis required changes after yesterday upgrade.
849103d Merge commit '320e525a5a34fbd3f1cb572b6de38eca0c0876f0'
320e525 Squashed 'moose-gui/' changes from d282884250..49779ba730
7fe1c2e Squashed 'moose-core/' changes from 2ecab963b2..69e0354705
faf993a Merge commit '7fe1c2e7fe0b0d1cbe153cefb10618f62fe107cb'
edd901d Squashed 'moose-examples/' content from commit 2eb5fa888
be2d4ec Merge commit 'edd901da062503717c40cddad23d69bf51782f08' as 'moose-examples'
git-subtree-dir: moose-examples
git-subtree-split: 7f3d27fa0f2b5c5f2ace0e8cfddae2b5944b9186
---
paper-2015/Fig6_NetMultiscale/ReducedModel.py | 5 ++++-
snippets/IntegrateFireZoo.py | 8 +++++++-
snippets/compartment_net.py | 5 +++++
snippets/cylinderDiffusion.py | 7 ++++---
snippets/diffSpinyNeuron.py | 8 ++++++--
snippets/gssaRDspiny.py | 7 +++++--
snippets/reacDiffBranchingNeuron.py | 16 +++++-----------
snippets/wildcard.py | 6 ++++--
tutorials/ChemicalBistables/propagationBis.py | 5 ++++-
tutorials/ChemicalBistables/scaleVolumes.py | 8 +++++---
tutorials/ChemicalBistables/simpleBis.py | 5 ++++-
tutorials/ChemicalOscillators/TuringOneDim.py | 5 ++++-
12 files changed, 57 insertions(+), 28 deletions(-)
diff --git a/paper-2015/Fig6_NetMultiscale/ReducedModel.py b/paper-2015/Fig6_NetMultiscale/ReducedModel.py
index 3f151cb3..d7314107 100644
--- a/paper-2015/Fig6_NetMultiscale/ReducedModel.py
+++ b/paper-2015/Fig6_NetMultiscale/ReducedModel.py
@@ -885,4 +885,7 @@ if __name__=='__main__':
plt.show()
plt.savefig( fname + '.svg', bbox_inches='tight')
print( "Hit 'enter' to exit" )
- input()
+ try:
+ raw_input()
+ except Exception as e:
+ input( )
diff --git a/snippets/IntegrateFireZoo.py b/snippets/IntegrateFireZoo.py
index 0fe761a0..dc40a584 100644
--- a/snippets/IntegrateFireZoo.py
+++ b/snippets/IntegrateFireZoo.py
@@ -120,7 +120,13 @@ def main():
#choiceKey = 'LIF'
#### No need, am inputting it from the user on the terminal
choiceKeys = list(neuronChoices.keys()) # keys() does not retain the order in dict defn above!
- choiceIndex = eval(str(input('Choose a number corresponding to your desired neuron: '+str([(i,key) for (i,key) in enumerate(choiceKeys)])+' -- ')))
+
+ try:
+ v = raw_input('Choose a number corresponding to your desired neuron: '+str([(i,key) for (i,key) in enumerate(choiceKeys)])+' -- ')
+ except NameError as e:
+ v = input('Choose a number corresponding to your desired neuron: '+str([(i,key) for (i,key) in enumerate(choiceKeys)])+' -- ')
+
+ choiceIndex = eval(v)
choiceKey = choiceKeys[choiceIndex]
neuronChoice = neuronChoices[choiceKey]
diff --git a/snippets/compartment_net.py b/snippets/compartment_net.py
index 55b95f54..b77b25db 100644
--- a/snippets/compartment_net.py
+++ b/snippets/compartment_net.py
@@ -177,5 +177,10 @@ def main():
plt.show()
+
+if __name__ == '__main__':
+ main()
+
+
#
# compartment_net.py ends here
diff --git a/snippets/cylinderDiffusion.py b/snippets/cylinderDiffusion.py
index a2c21570..f7c5095a 100644
--- a/snippets/cylinderDiffusion.py
+++ b/snippets/cylinderDiffusion.py
@@ -184,11 +184,12 @@ def main():
print((atot2/atot, btot2/btot, ctot2/ctot, dtot2/dtot))
print(('Initial to final (b+c)=', (btot2 + ctot2) / (btot + ctot )))
print("\nHit '0' to exit")
- eval(str(input()))
-
+ try:
+ raw_input( )
+ except NameError as e: # python3
+ input( )
quit()
-
# Run the 'main' if this script is executed standalone.
if __name__ == '__main__':
main()
diff --git a/snippets/diffSpinyNeuron.py b/snippets/diffSpinyNeuron.py
index 5749b95e..06ae26d3 100644
--- a/snippets/diffSpinyNeuron.py
+++ b/snippets/diffSpinyNeuron.py
@@ -103,7 +103,7 @@ def makeModel():
stoich2.filterXreacs()
Ca_input_dend = moose.vec( '/model/chem/compt0/Ca_input' )
- print((len( Ca_input_dend )))
+ print(len( Ca_input_dend ))
for i in range( 60 ):
Ca_input_dend[ 3 + i * 3 ].conc = 2.0
@@ -197,8 +197,12 @@ def finalizeDisplay( plotlist, cPlotDt ):
pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
line1, = plotlist[0].plot( pos, x.vector, label=x.name )
plotlist[4].canvas.draw()
+
print( "Hit '0' to exit" )
- raw_input()
+ try:
+ raw_input()
+ except NameError as e: #python3
+ input( )
def makeChemModel( compt, doInput ):
"""
diff --git a/snippets/gssaRDspiny.py b/snippets/gssaRDspiny.py
index 6308e5bc..8b3269ad 100644
--- a/snippets/gssaRDspiny.py
+++ b/snippets/gssaRDspiny.py
@@ -180,8 +180,11 @@ def finalizeDisplay( plotlist, cPlotDt ):
pos = numpy.arange( 0, x.vector.size, 1 ) * cPlotDt
line1, = plotlist[0].plot( pos, x.vector, label=x.name )
plotlist[4].canvas.draw()
- print( "Hit '0' to exit" )
- eval(str(input()))
+ print( "Hit any key to exit" )
+ try:
+ raw_input( )
+ except NameError as e:
+ input( )
def makeChemModel( compt ):
"""
diff --git a/snippets/reacDiffBranchingNeuron.py b/snippets/reacDiffBranchingNeuron.py
index 96ddc145..018717d2 100644
--- a/snippets/reacDiffBranchingNeuron.py
+++ b/snippets/reacDiffBranchingNeuron.py
@@ -112,28 +112,22 @@ def finalizeDisplay( plotlist, cPlotDt ):
line1, = plotlist[0].plot( pos, x.vector, label=x.name )
plt.legend()
plotlist[1].canvas.draw()
- print( "Hit '0' to exit" )
- eval(str(input()))
+ print( "Hit any key to exit" )
+ try:
+ a = raw_input( )
+ except NameError as e:
+ a = input( )
def makeChemModel( compt ):
"""
This function sets up a simple oscillatory chemical system within
the script. The reaction system is::
-<<<<<<< HEAD
s ---a---> a // s goes to a, catalyzed by a.
s ---a---> b // s goes to b, catalyzed by a.
a ---b---> s // a goes to s, catalyzed by b.
b -------> s // b is degraded irreversibly to s.
-=======
-
- s ---a---> a // s goes to a, catalyzed by a.
- s ---a---> b // s goes to b, catalyzed by a.
- a ---b---> s // a goes to s, catalyzed by b.
- b -------> s // b is degraded irreversibly to s.
-
->>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
in sum, **a** has a positive feedback onto itself and also forms **b**.
**b** has a negative feedback onto **a**.
Finally, the diffusion constant for **a** is 1/10 that of **b**.
diff --git a/snippets/wildcard.py b/snippets/wildcard.py
index ee2aee82..ba2712e4 100644
--- a/snippets/wildcard.py
+++ b/snippets/wildcard.py
@@ -91,13 +91,15 @@ def wildcard_test():
for element in moose.wildcardFind(wildcard):
print(('\t', element.path))
- # `#` can be used only once and matches all subsequent characters in name
+
+ # `?` can be used any number of times but substitutes a single character
wildcard = '/alfa/bravo/charl?e'
print(('\nElements Matching:', wildcard))
for element in moose.wildcardFind(wildcard):
print(('\t', element.path))
- # `?` can be used any number of times but substitutes a single character
+
+ # `#` can be used only once and matches all subsequent characters in name
wildcard = '/alfa/bravo/fox#'
print(('\nElements Matching:', wildcard))
for element in moose.wildcardFind(wildcard):
diff --git a/tutorials/ChemicalBistables/propagationBis.py b/tutorials/ChemicalBistables/propagationBis.py
index add79df3..8b982c63 100644
--- a/tutorials/ChemicalBistables/propagationBis.py
+++ b/tutorials/ChemicalBistables/propagationBis.py
@@ -159,7 +159,10 @@ def main():
fig.canvas.draw()
print( "Hit 'enter' to exit" )
- eval(input())
+ try:
+ raw_input( )
+ except NameError as e: # python3
+ input( )
diff --git a/tutorials/ChemicalBistables/scaleVolumes.py b/tutorials/ChemicalBistables/scaleVolumes.py
index 66b869ff..49bf206e 100644
--- a/tutorials/ChemicalBistables/scaleVolumes.py
+++ b/tutorials/ChemicalBistables/scaleVolumes.py
@@ -153,9 +153,11 @@ def main():
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
pylab.show( block=False )
- print(('vol = ', vol, 'hit enter to go to next plot'))
- input()
-
+ print( 'vol = %f . hit enter to go to next plot' % vol )
+ try:
+ raw_input()
+ except NameError as e:
+ input( )
quit()
# Run the 'main' if this script is executed standalone.
diff --git a/tutorials/ChemicalBistables/simpleBis.py b/tutorials/ChemicalBistables/simpleBis.py
index 4c577f55..3bbfc700 100644
--- a/tutorials/ChemicalBistables/simpleBis.py
+++ b/tutorials/ChemicalBistables/simpleBis.py
@@ -134,7 +134,10 @@ def main():
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
- raw_input( 'Press any key to quit' )
+ try:
+ raw_input( 'Press any key to quit' )
+ except NameError as e:
+ input( 'Press any key to quit' )
# Run the 'main' if this script is executed standalone.
diff --git a/tutorials/ChemicalOscillators/TuringOneDim.py b/tutorials/ChemicalOscillators/TuringOneDim.py
index e755d257..bc27761a 100644
--- a/tutorials/ChemicalOscillators/TuringOneDim.py
+++ b/tutorials/ChemicalOscillators/TuringOneDim.py
@@ -160,7 +160,10 @@ def main():
fig.canvas.draw()
print( "Hit 'enter' to exit" )
- raw_input( )
+ try:
+ raw_input( )
+ except NameError as e: # python3
+ input( )
--
GitLab