Merge commit 'd07f7ea6'

moose-examples/.travis.yml

@@ -2,6 +2,10 @@ dist : trusty
 sudo : required 
 group : edge
 
+language: ruby
+rvm:
+    - 2.2
+
 notifications:
     email:
         recipients:
@@ -19,15 +23,18 @@ install:
     - sudo apt-get -y --force-yes install python-qt4 python-pip graphviz
     - sudo apt-get -y --force-yes install python-h5py python-scipy python-pygraphviz
     - sudo apt-get -y --force-yes install moose 
-    - sudo pip install python-libsbml python-networkx
+    - sudo pip install python-libsbml networkx
+    - gem install travis
 
 script:
+    - nvm use stable
     - # Making sure no python3 incompatible file.
     - python3 -m compileall -q .
     - python2 -m compileall -q .
     - /usr/bin/python -c 'import moose'
     - /usr/bin/python -c 'import moogli'
     - cd _travis && ./find_scripts_to_run.sh && ./run_scripts.sh 
+    - cd _travis && ./download_and_run_doqcs.sh
 
 exclude : [vendor]
 
@@ -35,7 +42,6 @@ deploy:
     provider : pages
     skip_cleanup : true
     github_token : $GHI_TOKEN
-    local_dir : _travis/_site
     on:
         branch : master
 

moose-examples/_travis/BROKEN

@@ -8,3 +8,18 @@
 ./../hopfield/hopfield.py
 ./../hopfield/hopfield1.py
 ./../neuroml/LIF/LIFxml_firing_hsolve.py
+./../hopfield/hopfield.py
+./../hopfield/hopfield1.py
+./../neuroml/LIF/LIFxml_firing_hsolve.py
+./../snippets/Izhikevich_with_synapse.py
+./../snippets/testSigNeur.py
+./../hopfield/hopfield.py
+./../hopfield/hopfield1.py
+./../neuroml/LIF/LIFxml_firing_hsolve.py
+./../snippets/Izhikevich_with_synapse.py
+./../snippets/testSigNeur.py
+./../hopfield/hopfield.py
+./../hopfield/hopfield1.py
+./../neuroml/LIF/LIFxml_firing_hsolve.py
+./../snippets/Izhikevich_with_synapse.py
+./../snippets/testSigNeur.py

moose-examples/_travis/FAILED

-- [ ] ./../snippets/reacDiffConcGradient.py
-
-```
-  timeout: the monitored command dumped core
-```
-- [ ] ./../snippets/loadSbmlmodel.py
-
-```
-  [FATAL] Module python-libsbml is not found.
-  This module can be installed by following command in terminal:
-  	 easy_install python-libsbml
-  Traceback (most recent call last):
-    File "loadSbmlmodel.py", line 122, in <module>
-      modelPath, modelpathexist,msg = main()
-    File "loadSbmlmodel.py", line 84, in main
-      elif sbmlId.path != '/':
-  AttributeError: 'NoneType' object has no attribute 'path'
-```
-- [ ] ./../snippets/crossComptSimpleReac.py
-
-```
-    [FATAL] Module python-libsbml is not found.
-    This module can be installed by following command in terminal:
-    	 easy_install python-libsbml
-    Traceback (most recent call last):
-      File "loadSbmlmodel.py", line 122, in <module>
-        modelPath, modelpathexist,msg = main()
-      File "loadSbmlmodel.py", line 84, in main
-        elif sbmlId.path != '/':
-    AttributeError: 'NoneType' object has no attribute 'path'
-```
-- [ ] ./../snippets/crossComptSimpleReacGSSA.py
-
-```
-  timeout: the monitored command dumped core
-```
-- [ ] ./../traub_2005/py/display_morphology.py
-
-```
-  Traceback (most recent call last):
-    File "display_morphology.py", line 52, in <module>
-      import networkx as nx
-  ImportError: No module named networkx
-```

moose-examples/_travis/GUISCRIPTS

-./../snippets/testWigglySpines.py
-./../snippets/insertSpinesWithoutRdesigneur.py
-./../snippets/loadMorphology.py
-./../snippets/insertSpines.py
-./../snippets/testRdesigneur.py
-./../traub_2005/py/gui.py
-./../hopfield/hopfield_ui.py
 ./../hopfield/guiHopfield.py
+./../hopfield/hopfield_ui.py
+./../izhikevich/demogui_qt.py
+./../moogli/color_update.py
+./../moogli/purkinje_simulation.py
+./../moogli/purkinje_simulation_with_rm.py
+./../moogli/purkinje_simulation_with_rm_and_graph.py
+./../moogli/simple_viewing.py
+./../paper-2015/Fig2_elecModels/Fig2C.py
+./../paper-2015/Fig2_elecModels/Fig2D.py
+./../paper-2015/Fig2_elecModels/Fig2E.py
 ./../paper-2015/Fig4_ReacDiff/Fig4B.py
-./../paper-2015/Fig4_ReacDiff/rxdSpineSize.py
-./../paper-2015/Fig4_ReacDiff/Fig4GHIJ.py
 ./../paper-2015/Fig4_ReacDiff/Fig4CDEF.py
+./../paper-2015/Fig4_ReacDiff/Fig4GHIJ.py
+./../paper-2015/Fig4_ReacDiff/rxdSpineSize.py
 ./../paper-2015/Fig5_CellMultiscale/Fig5A.py
 ./../paper-2015/Fig5_CellMultiscale/Fig5BCD.py
-./../paper-2015/Fig2_elecModels/Fig2E.py
-./../paper-2015/Fig2_elecModels/Fig2C.py
-./../paper-2015/Fig2_elecModels/Fig2D.py
 ./../paper-2015/Fig6_NetMultiscale/Fig6A.py
-./../izhikevich/demogui_qt.py
-./../moogli/simple_viewing.py
-./../moogli/color_update.py
-./../moogli/purkinje_simulation_with_rm.py
-./../moogli/purkinje_simulation.py
-./../moogli/purkinje_simulation_with_rm_and_graph.py
-./../util/moogli_viewer.py
-./../squid/squid_demo.py
 ./../squid/channeleditor.py
+./../squid/squid_demo.py
+./../traub_2005/py/gui.py
+./../util/moogli_viewer.py
+./../snippets/insertSpines.py
+./../snippets/insertSpinesWithoutRdesigneur.py
+./../snippets/loadMorphology.py
+./../snippets/testRdesigneur.py
+./../snippets/testWigglySpines.py

moose-examples/_travis/INTERACTIVE

-./../snippets/transportBranchingNeuron.py
+./../izhikevich/Izhikevich.py
+./../paper-2015/Fig6_NetMultiscale/Fig6BCDE.py
+./../paper-2015/Fig6_NetMultiscale/ReducedModel.py
+./../snippets/IntegrateFireZoo.py
 ./../snippets/crossComptNeuroMesh.py
-./../snippets/gssaRDspiny.py
 ./../snippets/cylinderDiffusion.py
-./../snippets/reacDiffBranchingNeuron.py
 ./../snippets/diffSpinyNeuron.py
-./../snippets/IntegrateFireZoo.py
+./../snippets/gssaRDspiny.py
+./../snippets/reacDiffBranchingNeuron.py
 ./../snippets/reacDiffSpinyNeuron.py
-./../paper-2015/Fig6_NetMultiscale/Fig6BCDE.py
-./../paper-2015/Fig6_NetMultiscale/ReducedModel.py
-./../izhikevich/Izhikevich.py
-./../tutorials/ChemicalBistables/scaleVolumes.py
+./../snippets/transportBranchingNeuron.py
 ./../tutorials/ChemicalBistables/propagationBis.py
+./../tutorials/ChemicalBistables/scaleVolumes.py
 ./../tutorials/ChemicalOscillators/TuringOneDim.py

moose-examples/_travis/SUCCEEDED

-- [x] ./../snippets/wildcard.py
-- [x] ./../snippets/nsdf.py
-- [x] ./../snippets/scriptGssaSolver.py
-- [x] ./../snippets/rxdFuncDiffusionStoch.py
-- [x] ./../snippets/vectors.py
-- [x] ./../snippets/cylinderMotor.py
-- [x] ./../snippets/funcRateHarmonicOsc.py
-- [x] ./../snippets/STDP.py
-- [x] ./../snippets/interpol2d.py
-- [x] ./../snippets/loadCspaceModel.py
-- [x] ./../snippets/cubeMeshSigNeur.py
-- [x] ./../snippets/multicomp_lif.py
-- [x] ./../snippets/pyrun1.py
-- [x] ./../snippets/neuronFromDotp.py
-- [x] ./../snippets/rxdFuncDiffusion.py
-- [x] ./../snippets/synapse.py
-- [x] ./../snippets/lifcomp.py
-- [x] ./../snippets/synapse_tutorial.py
-- [x] ./../snippets/bidirectionalPlasticity.py
-- [x] ./../snippets/hdfdemo.py
-- [x] ./../snippets/threading_demo.py
-- [x] ./../snippets/crossComptOscillator.py
-- [x] ./../snippets/pyrun.py
-- [x] ./../snippets/changeFuncExpression.py
-- [x] ./../snippets/compartment_net.py
-- [x] ./../snippets/tweakingParameters.py
-- [x] ./../snippets/multiComptSigNeur.py
-- [x] ./../snippets/showclocks.py
-- [x] ./../snippets/startstop.py
-- [x] ./../snippets/convert_Genesis2Sbml.py
-- [x] ./../snippets/funcReacLotkaVolterra.py
-- [x] ./../snippets/intfire.py
-- [x] ./../snippets/analogStimTable.py
-- [x] ./../snippets/lif.py
-- [x] ./../snippets/chemDoseResponse.py
-- [x] ./../snippets/tabledemo.py
-- [x] ./../snippets/symcompartment.py
-- [x] ./../snippets/loadKineticModel.py
-- [x] ./../snippets/showmsg.py
-- [x] ./../snippets/onetoonemsg.py
-- [x] ./../snippets/ionchannel.py
-- [x] ./../snippets/scriptKineticSolver.py
-- [x] ./../snippets/vclamp.py
-- [x] ./../snippets/mgblock.py
-- [x] ./../snippets/scriptKineticModel.py
-- [x] ./../snippets/gapjunction.py
-- [x] ./../snippets/diffusion_using_Gillespie.py
-- [x] ./../snippets/singlemsgcross.py
-- [x] ./../snippets/diffEqSolution.py
-- [x] ./../snippets/HsolveInstability.py
-- [x] ./../snippets/interpol.py
-- [x] ./../snippets/randomspike.py
-- [x] ./../snippets/func.py
-- [x] ./../snippets/cspaceSteadyState.py
-- [x] ./../snippets/timetable.py
-- [x] ./../snippets/funcInputToPools.py
-- [x] ./../snippets/savemodel.py
-- [x] ./../snippets/compartment_net_no_array.py
-- [x] ./../snippets/stochasticLotkaVolterra.py
-- [x] ./../snippets/pulsegen.py
-- [x] ./../snippets/RandSpikeStats.py
-- [x] ./../snippets/rxdReacDiffusion.py
-- [x] ./../MemoryNetworks/bidirectional_plastic_switch.py
-- [x] ./../snippets/helloMoose.py
-- [x] ./../traub_2005/py/test_cachans.py
-- [x] ./../traub_2005/py/test_kchans.py
-- [x] ./../traub_2005/py/test_archan.py
-- [x] ./../traub_2005/py/test_nachans.py
-- [x] ./../traub_2005/py/test_singlecomp.py
-- [x] ./../traub_2005/py/test_capool.py
-- [x] ./../parallelSolver/abstrModelEqns2.py
 - [x] ./../cuda/testScript.py
-- [x] ./../passive/passive_soma.py
-- [x] ./../neuroml/lobster_pyloric/channels/ChannelTest.py
-- [x] ./../neuroml/CA1PyramidalCell/CA1_hsolve.py
 - [x] ./../neuroml/CA1PyramidalCell/CA1.py
 - [x] ./../neuroml/LIF/LIFxml_firing.py
+- [x] ./../neuroml/CA1PyramidalCell/CA1_hsolve.py
 - [x] ./../neuroml/GranuleCell/Granule98_hsolve.py
-- [x] ./../rall_1964/rall64.py
+- [x] ./../neuroml/GranuleCell/Granule98.py
 - [x] ./../neuroml/LIF/twoLIFxml_firing.py
-- [x] ./../tutorials/ChemicalBistables/strongBis.py
-- [x] ./../tutorials/ExcInhNetCaPlasticity/ExcInhNet_HigginsGraupnerBrunel2014.py
-- [x] ./../tutorials/ChemicalBistables/simpleBis.py
-- [x] ./../tutorials/ChemicalBistables/findSteadyState.py
-- [x] ./../tutorials/ChemicalOscillators/repressillator.py
-- [x] ./../tutorials/ChemicalOscillators/slowFbOsc.py
-- [x] ./../tutorials/ChemicalOscillators/relaxationOsc.py
+- [x] ./../neuroml/lobster_pyloric/channels/ChannelTest.py
+- [x] ./../parallelSolver/abstrModelEqns2.py
+- [x] ./../passive/passive_soma.py
+- [x] ./../rall_1964/rall64.py
 - [x] ./../squid/squid.py
 - [x] ./../squid/squid_setup.py
-- [x] ./../symcomp/symcomp_readcell.py
 - [x] ./../symcomp/symcomp.py
+- [x] ./../symcomp/symcomp_readcell.py
+- [x] ./../traub_2005/py/test_capool.py
+- [x] ./../traub_2005/py/test_archan.py
+- [x] ./../traub_2005/py/test_cachans.py
+- [x] ./../traub_2005/py/test_nachans.py
+- [x] ./../traub_2005/py/test_kchans.py
+- [x] ./../traub_2005/py/test_singlecomp.py

moose-examples/_travis/TORUN

-./../snippets/scriptGssaSolver.py
-./../snippets/nsdf.py
-./../snippets/wildcard.py
-./../snippets/rxdFuncDiffusionStoch.py
-./../snippets/cylinderMotor.py
+./../cuda/testHsolve.py
+./../cuda/testScript.py
+./../kinetics/test_ksolve.py
+./../neuroml/CA1PyramidalCell/CA1.py
+./../neuroml/CA1PyramidalCell/CA1_hsolve.py
+./../neuroml/GranuleCell/Granule98.py
+./../neuroml/GranuleCell/Granule98_hsolve.py
+./../neuroml/LIF/LIFxml_firing.py
+./../neuroml/LIF/twoLIFxml_firing.py
+./../neuroml/allChannelsCell/allChannelsCell.py
+./../neuroml/lobster_pyloric/STG_net.py
+./../neuroml/lobster_pyloric/channels/ChannelTest.py
+./../parallelSolver/Fig2_v4.py
+./../parallelSolver/abstrModelEqns2.py
+./../passive/passive_soma.py
+./../rall_1964/rall64.py
+./../squid/squid.py
+./../squid/squid_setup.py
+./../symcomp/symcomp.py
+./../symcomp/symcomp_readcell.py
+./../traub_2005/py/display_morphology.py
+./../traub_2005/py/dump_f_i_curves.py
+./../traub_2005/py/fig_a2_fs.py
+./../traub_2005/py/fig_a3.py
+./../traub_2005/py/fig_a4c.py
+./../traub_2005/py/test_archan.py
+./../traub_2005/py/test_cachans.py
+./../traub_2005/py/test_capool.py
+./../traub_2005/py/test_deepaxoaxonic.py
+./../traub_2005/py/test_deepbasket.py
+./../traub_2005/py/test_deeplts.py
+./../traub_2005/py/test_hsolve_tcr.py
+./../traub_2005/py/test_kchans.py
+./../traub_2005/py/test_nachans.py
+./../traub_2005/py/test_nontuftedrs.py
+./../traub_2005/py/test_nrt.py
+./../traub_2005/py/test_singlecomp.py
+./../traub_2005/py/test_spinystellate.py
+./../traub_2005/py/test_supaxoaxonic.py
+./../traub_2005/py/test_supbasket.py
+./../traub_2005/py/test_suplts.py
+./../traub_2005/py/test_suppyrfrb.py
+./../traub_2005/py/test_suppyrrs.py
+./../traub_2005/py/test_tcr.py
+./../traub_2005/py/test_tuftedib.py
+./../traub_2005/py/test_tuftedrs.py
+./../traub_2005/py/vclamptest.py
+./../unsorted/ksolve_with_heavy_load.py
+./../MemoryNetworks/bidirectional_plastic_switch.py
+./../snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py
+./../snippets/HigginsGraupnerBrunel2014_LifetimeCaPlasticity.py
+./../snippets/HsolveInstability.py
+./../snippets/RandSpikeStats.py
 ./../snippets/STDP.py
-./../snippets/vectors.py
-./../snippets/funcRateHarmonicOsc.py
-./../snippets/loadCspaceModel.py
-./../snippets/cubeMeshSigNeur.py
-./../snippets/multicomp_lif.py
-./../snippets/interpol2d.py
-./../snippets/pyrun1.py
-./../snippets/reacDiffConcGradient.py
-./../snippets/rxdFuncDiffusion.py
-./../snippets/neuronFromDotp.py
-./../snippets/synapse.py
-./../snippets/lifcomp.py
+./../snippets/analogStimTable.py
 ./../snippets/bidirectionalPlasticity.py
-./../snippets/synapse_tutorial.py
-./../snippets/recurrentIntFire.py
-./../snippets/crossComptOscillator.py
-./../snippets/hdfdemo.py
-./../snippets/threading_demo.py
-./../snippets/switchKineticSolvers.py
-./../snippets/twocells.py
-./../snippets/pyrun.py
 ./../snippets/changeFuncExpression.py
-./../snippets/multiComptSigNeur.py
+./../snippets/chemDoseResponse.py
 ./../snippets/compartment_net.py
-./../snippets/stimtable.py
-./../snippets/tweakingParameters.py
-./../snippets/showclocks.py
-./../snippets/startstop.py
-./../snippets/function.py
-./../snippets/pulsegen2.py
+./../snippets/compartment_net_no_array.py
 ./../snippets/convert_Genesis2Sbml.py
+./../snippets/crossComptOscillator.py
 ./../snippets/crossComptSimpleReac.py
+./../snippets/crossComptSimpleReacGSSA.py
+./../snippets/cspaceSteadyState.py
+./../snippets/cubeMeshSigNeur.py
+./../snippets/cylinderMotor.py
+./../snippets/diffEqSolution.py
+./../snippets/diffusion_using_Gillespie.py
+./../snippets/findChemSteadyState.py
+./../snippets/func.py
+./../snippets/funcInputToPools.py
+./../snippets/funcRateHarmonicOsc.py
 ./../snippets/funcReacLotkaVolterra.py
-./../snippets/loadSbmlmodel.py
-./../snippets/analogStimTable.py
-./../snippets/chemDoseResponse.py
+./../snippets/function.py
+./../snippets/gapjunction.py
+./../snippets/gssaCylinderDiffusion.py
+./../snippets/hdfdemo.py
+./../snippets/helloMoose.py
+./../snippets/hhcomp.py
+./../snippets/interpol.py
+./../snippets/interpol2d.py
 ./../snippets/intfire.py
+./../snippets/ionchannel.py
 ./../snippets/lif.py
-./../snippets/tabledemo.py
-./../snippets/symcompartment.py
-./../snippets/gssaCylinderDiffusion.py
+./../snippets/lifcomp.py
+./../snippets/loadCspaceModel.py
 ./../snippets/loadKineticModel.py
-./../snippets/findChemSteadyState.py
-./../snippets/showmsg.py
-./../snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py
-./../snippets/onetoonemsg.py
-./../snippets/ionchannel.py
-./../snippets/traub_naf.py
-./../snippets/scriptKineticSolver.py
-./../snippets/hhcomp.py
-./../snippets/vclamp.py
-./../snippets/gapjunction.py
+./../snippets/loadSbmlmodel.py
 ./../snippets/mgblock.py
-./../snippets/scriptKineticModel.py
-./../snippets/singlemsgcross.py
-./../snippets/HsolveInstability.py
-./../snippets/diffEqSolution.py
-./../snippets/diffusion_using_Gillespie.py
+./../snippets/multiComptSigNeur.py
+./../snippets/multicomp_lif.py
+./../snippets/multiscaleOneCompt.py
+./../snippets/neuronFromDotp.py
+./../snippets/nsdf.py
+./../snippets/onetoonemsg.py
+./../snippets/pulsegen.py
+./../snippets/pulsegen2.py
+./../snippets/pyrun.py
+./../snippets/pyrun1.py
 ./../snippets/randomspike.py
-./../snippets/interpol.py
-./../snippets/cspaceSteadyState.py
-./../snippets/func.py
+./../snippets/reacDiffConcGradient.py
+./../snippets/recurrentIntFire.py
 ./../snippets/recurrentLIF.py
-./../snippets/timetable.py
-./../snippets/HigginsGraupnerBrunel2014_LifetimeCaPlasticity.py
-./../snippets/funcInputToPools.py
-./../snippets/stochasticLotkaVolterra.py
-./../snippets/compartment_net_no_array.py
-./../snippets/multiscaleOneCompt.py
-./../snippets/savemodel.py
-./../snippets/RandSpikeStats.py
+./../snippets/rxdFuncDiffusion.py
+./../snippets/rxdFuncDiffusionStoch.py
 ./../snippets/rxdReacDiffusion.py
-./../snippets/pulsegen.py
-./../snippets/crossComptSimpleReacGSSA.py
-./../snippets/helloMoose.py
-./../unsorted/ksolve_with_heavy_load.py
-./../MemoryNetworks/bidirectional_plastic_switch.py
-./../traub_2005/py/test_tuftedrs.py
-./../traub_2005/py/test_supbasket.py
-./../traub_2005/py/test_deepbasket.py
-./../traub_2005/py/display_morphology.py
-./../traub_2005/py/fig_a3.py
-./../traub_2005/py/fig_a2_fs.py
-./../traub_2005/py/test_suppyrrs.py
-./../traub_2005/py/test_suppyrfrb.py
-./../traub_2005/py/test_tuftedib.py
-./../traub_2005/py/test_cachans.py
-./../traub_2005/py/test_tcr.py
-./../traub_2005/py/test_kchans.py
-./../traub_2005/py/test_hsolve_tcr.py
-./../traub_2005/py/dump_f_i_curves.py
-./../traub_2005/py/test_archan.py
-./../traub_2005/py/test_nachans.py
-./../traub_2005/py/fig_a4c.py
-./../traub_2005/py/test_supaxoaxonic.py
-./../traub_2005/py/test_spinystellate.py
-./../traub_2005/py/test_singlecomp.py
-./../traub_2005/py/test_nontuftedrs.py
-./../traub_2005/py/test_capool.py
-./../traub_2005/py/test_suplts.py
-./../traub_2005/py/vclamptest.py
-./../traub_2005/py/test_deepaxoaxonic.py
-./../traub_2005/py/test_deeplts.py
-./../traub_2005/py/test_nrt.py
-./../parallelSolver/Fig2_v4.py
-./../parallelSolver/abstrModelEqns2.py
-./../kinetics/test_ksolve.py
-./../cuda/testScript.py
-./../cuda/testHsolve.py
-./../passive/passive_soma.py
-./../neuroml/CA1PyramidalCell/CA1_hsolve.py
-./../neuroml/CA1PyramidalCell/CA1.py
-./../neuroml/lobster_pyloric/STG_net.py
-./../neuroml/lobster_pyloric/channels/ChannelTest.py
-./../neuroml/allChannelsCell/allChannelsCell.py
-./../neuroml/GranuleCell/Granule98.py
-./../neuroml/GranuleCell/Granule98_hsolve.py
-./../neuroml/LIF/LIFxml_firing.py
-./../neuroml/LIF/twoLIFxml_firing.py
-./../rall_1964/rall64.py
-./../tutorials/ChemicalBistables/strongBis.py
+./../snippets/savemodel.py
+./../snippets/scriptGssaSolver.py
+./../snippets/scriptKineticModel.py
+./../snippets/scriptKineticSolver.py
+./../snippets/showclocks.py
+./../snippets/showmsg.py
+./../snippets/singlemsgcross.py
+./../snippets/startstop.py
+./../snippets/stimtable.py
+./../snippets/stochasticLotkaVolterra.py
+./../snippets/switchKineticSolvers.py
+./../snippets/symcompartment.py
+./../snippets/synapse.py
+./../snippets/synapse_tutorial.py
+./../snippets/tabledemo.py
+./../snippets/threading_demo.py
+./../snippets/timetable.py
+./../snippets/traub_naf.py
+./../snippets/tweakingParameters.py
+./../snippets/twocells.py
+./../snippets/vclamp.py
+./../snippets/vectors.py
+./../snippets/wildcard.py
 ./../tutorials/ChemicalBistables/doseResponse.py
-./../tutorials/ChemicalBistables/simpleBis.py
-./../tutorials/ChemicalBistables/mapkFB.py
 ./../tutorials/ChemicalBistables/findSteadyState.py
-./../tutorials/ExcInhNetCaPlasticity/ExcInhNet_HigginsGraupnerBrunel2014.py
-./../tutorials/ExcInhNet/ExcInhNet_Ostojic2014_Brunel2000.py
-./../tutorials/ChemicalOscillators/slowFbOsc.py
-./../tutorials/ChemicalOscillators/repressillator.py
+./../tutorials/ChemicalBistables/mapkFB.py
+./../tutorials/ChemicalBistables/simpleBis.py
+./../tutorials/ChemicalBistables/strongBis.py
 ./../tutorials/ChemicalOscillators/relaxationOsc.py
-./../symcomp/symcomp.py
-./../symcomp/symcomp_readcell.py
-./../squid/squid.py
-./../squid/squid_setup.py
+./../tutorials/ChemicalOscillators/repressillator.py
+./../tutorials/ChemicalOscillators/slowFbOsc.py
+./../tutorials/ExcInhNet/ExcInhNet_Ostojic2014_Brunel2000.py
+./../tutorials/ExcInhNetCaPlasticity/ExcInhNet_HigginsGraupnerBrunel2014.py

moose-examples/_travis/__temp__

-(0.942477796076938, 0.2827433388230814)
-('CuReadCell: 3 compartments, 0 channels, 0 others
-, dataIndex=2, path=/Msgs[0]/singleMsg[2]>)
-Vm saved to Vm.dat
-K conductance saved to gK.dat
-Na conductance saved to gNa.dat
+        .
\ No newline at end of file

moose-examples/_travis/deploy_gh_pages.py

@@ -31,7 +31,11 @@ def write_to_file( filename, lines ):
         f.write( '\n'.join( lines ) )
 
 def create_static_site( ):
-    subprocess.call( [ 'jekyll', 'b' ], shell = False )
+    try:
+        subprocess.call( [ 'timeout', '240', 'jekyll', 'b' ], shell = False )
+    except Exception as e:
+        print( 'Failed to generate static pages' )
+        print( '\tError was %s' % e )
 
 def main( ):
     global failedTxt_
@@ -39,6 +43,5 @@ def main( ):
     create_static_site( )
 
 
-
 if __name__ == '__main__':
     main()

moose-examples/_travis/download_and_run_doqcs.sh

+#!/usr/bin/env bash
+
+# Definitions of colors in bash
+RESTORE='\033[0m'
+
+RED='\033[00;31m'
+GREEN='\033[00;32m'
+YELLOW='\033[00;33m'
+BLUE='\033[00;34m'
+PURPLE='\033[00;35m'
+CYAN='\033[00;36m'
+LIGHTGRAY='\033[00;37m'
+
+LRED='\033[01;31m'
+LGREEN='\033[01;32m'
+LYELLOW='\033[01;33m'
+LBLUE='\033[01;34m'
+LPURPLE='\033[01;35m'
+LCYAN='\033[01;36m'
+WHITE='\033[01;37m'
+
+function coloredPrint
+{
+    case $1 in 
+        "WARN")
+            echo -e "[WARN] ${LRED} $2 ${RESTORE} $3"
+            ;;
+        "INFO")
+            echo -e "[INFO] ${LGREEN} $2 ${RESTORE} $3"
+            ;;
+        "ERROR")
+            echo -e "[ERROR] ${RED} $2 ${RESTORE} $3"
+            ;;
+        "DEBUG")
+            echo -e "[DEBUG] ${YELLOW} $2 ${RESTORE} $3"
+            ;;
+        "STEP")
+            echo -e "[STEP] ${BLUE} $2 ${RESTORE} $3"
+            ;;
+        "TODO")
+            echo -e "[TODO] ${CYAN} $2 ${RESTORE} $3"
+            ;;
+        *)
+            echo -e "[$1] $2 $3"
+            ;;
+    esac
+}
+
+coloredPrint "INFO" "Downloading DOQCS database silently"
+# Download all models.
+wget -q -A"*.g" -r https://doqcs.ncbs.res.in/database/simfile/
+coloredPrint "INFO" "Done downloading"
+
+echo '' > __UNCLEAN__DOQCS__
+MODELS=`find . -type f -name "*.g"`
+for _model in ${MODELS}; do
+    echo "===================================================================="
+    coloredPrint "INFO" "Running $_model for 1 sec"
+    T1=$(date +%s.%N)
+    OUT=$(timeout 10 python -c "
+import moose
+moose.loadModel( '${_model}', '/model', 'gsl' )
+moose.reinit( )
+moose.start( 1 )
+")
+    T2=$(date +%s.%N)
+    DT=$(echo "$T2-$T1" | bc)
+    OUTTRIMMED=`echo $OUT | xargs`
+    coloredPrint "INFO" "TOOK $DT seconds to run 1 sec."
+    if [[ ! -z $OUTTRIMMED ]]; then 
+        coloredPrint "WARN" "$_model did not load/run cleanly"
+        echo "[] ${_model} \n" >> __UNCLEAN__DOQCS__
+        echo "\`\`\`" >> __UNCLEAN__DOQCS__ 
+        echo "$OUTTRIMMED" >> __UNCLEAN__DOQCS__ 
+        echo "\n\`\`\`" >> __UNCLEAN__DOQCS__ 
+        echo $OUTTRIMMED
+    else
+        coloredPrint "INFO" "$_model loaded just fine. We did NOT check output results"
+    fi
+done
+
+coloredPrint "INFO" "Following scripts did not run cleanly"
+cat __UNCLEAN__DOQCS__

moose-examples/_travis/index.md

@@ -321,3 +321,4 @@ The final element.
       import networkx as nx
   ImportError: No module named networkx
 ```
+# Following scripts failed 

moose-examples/_travis/run_scripts.sh

@@ -26,7 +26,7 @@ if [ ! -f $MATPLOTRC ]; then
     exit
 fi
 
-TIMEOUT=10
+TIMEOUT=${1:-60}     # default timeout is 60 secs.
 NTHREADS=4
 for f in `cat ./TORUN`; do
     d=`dirname $f`
@@ -50,7 +50,7 @@ for f in `cat ./TORUN`; do
             echo "|| Timed-out status: $status" 
             echo "- [ ] $f" >> $BLACKLISTED
             sed -i 's/^/\ \ /' $TEMP
-            printf "\n\`i\`\`\n" >> $BLACKLISTED 
+            printf "\n\`\`\`\n" >> $BLACKLISTED 
             cat $TEMP >> $BLACKLISTED 
             printf "\`\`\`\n" >> $BLACKLISTED 
         else                                    # Failed
@@ -65,12 +65,10 @@ for f in `cat ./TORUN`; do
         fi
     ) & 
 done
-wait
 
 # Auto deploy to README.md file
-python ./deploy_gh_pages.py || echo "failed to generated site"
+python ./deploy_gh_pages.py 
 
-wait
 echo "Following scripts were successful"
 cat $SUCCEEDED
 
@@ -87,5 +85,3 @@ if [ -f $FAILED ]; then
     cat $FAILED
     exit 1
 fi
-
-