2d9849222d Add 3 new demos for rdesigneur (#41)
f25999106c update sbml file to store scenepos
2f78a07958 Fixed testHSolve script.
c537773939 Use python based relpath. The realpath utility is too old on travis.
5dbee3920d Merge pull request #39 from upibhalla/master
5a2af75f90 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
fda496c533 minor fix to scaleVolumes demo
0fe42549ce Added ex8.1 for CICR in a multiscale model. Some updates to ex8.2 and the README
2e1b2035f4 Added rdesigneur tutorial for synaptic-input triggered CICR
59a458b611 Fix to units for permeability for ConcChan, affects ex7.2_CICR.py
2b026c5ab5 Updated some demos, added new ex7.2 which demonstrates CICR, endo-compartments, and the operation of ConcChans.
a6adb6acc1 mooseaddChemSolver changed to mooseAddChemSolver, commented buildXreac and filterXreac
27855bb699 Renamed the file. First argument takes the method name.
12f57e76ba Update test_ksolve_lsode.py
6355deb202 This version is used to compare results for BhallaLab/moose-core#281.
611f68a88b Added script to test lsoda.
2aa25c3ff4 Merge pull request #38 from upibhalla/master
b32b8248fc Added Rdesigneur tutorial to show spine geometry change controlled by chemical signaling, and its electrical and chemical consequences
069138a897 Added new Rdesigneur demo for NeuroMesh, involving a multiscale simulation across PSD, spine head, and dendrite.
c8206c5cb9 Added index.md to keep the status of broken/successful and blacklisted scripts.
0ee1478166 Removed status of scripts from master branch.
8bac923266 Don't append to README at every run. Just rewrite it.
69bfa16e5c Broken scripts are added to README.md file.
a6d062ad68 When file fails. Emit output.
504aed9095 Don't run any script which has 'import moogli' in it.
14eb93c141 Install coreutils for realpath.
2267214e07 modify README.md file.
0304f392bd Don't run if `import moogli` is found.
c4c58a7c86 Fixed failed to cd to repository before any scripts can be run.
913d133aeb print pwd. This is a debug step.
730066df6b README.md links to the gh-pages.
1a83c474fa Fix url of repository.
370d36a30e return error code 1 as soon as error occurs.
3a86cc9a85 Fixed typo.
b5a56a5805 Write to index.md file.
1dcd80c04c Return status 1 when any file failed to be executed.
70b11410a6 Add status to readme file.
967effce16 Now test on travis.
8b597e68fa Ran travis test out of source.
8cb1aefab9 cmake does most of the work to write to temp file. Run it from outside of directory.
8a0ab11f11 Update.
ba3f15e080 Updated run script.
61b70ef299 Fixed some scripts overwritten by mistake.
8891b79972 If second option is not given, compute md5sum.
cd54b2f8f2 Cleanup after updating README.md file.
006e7f3536 new gitignore.
b242bfa3aa Append to README.md file.
f2498cbbe1 Relative to CMakeFile.txt which is at top-level.
01b6c5225d Fixed scripts which were overwritten.
8a546d03de Also add files which were not run [skip ci].
451e470cf6 Print URL in BROKEN scripts as well.
604eb8211c Relative to CMakeFile.txt which is at top-level.
cbe1b6ccbd shell script reads if file exists.
f4f2e21e71 Added more dependencies.
9a297c615f Added successul scripts to  output as well.
65e2b09f73 More details file.
85bee3c897 run test in topmost level of directory.
09023f61ef Cleanup for travis and auto-update for page containing broken scripts. (#37)
fb6a2d066d Better testing of scripts on travis using cmake (#36)
aa68204303 Merge branch 'master' into master
35d531282d Removed non-existent commands.
8f4f282c6e Ignore vendor directory.
3e42018200 Use GHI_TOKEN variable.
bce33fb3d4 Run deploy script as well.
62c3fae7f5 Deploy the results on gh-pages.
9e159c469f Added matplotlib to dependencies. Many script failing.
c3d75d36cd Fixes to master branch Travis's failure  (#35)
b33db0b393 Merge pull request #31 from upibhalla/master
76d4e61f4d Further cleanup of tutorials/Rdesigneur. Added nice multiscale example. Updated its README. Added a couple of neuronal morphology files to play with.
b8630af8c1 Added random and periodic synaptic input stimulus to Rdesigneur. Made an example of each in Rdesigneur tutorial.
6ff0c3d27f Merge branch 'master' of https://github.com/upibhalla/moose-examples
52bff7e45b Added new Rdesigneur tutorial examples to show how to use the new voltage clamp feature. Did some reorganizing of example names.
de331905c1 Show broken or fixed scripts at the end of run. (#34)
00f66c3cfe Merge branch 'master' into master
2fe1a06594 Fixes to travis failure for master branch (#33)
d7ed125b6a Merge branch 'master' of https://github.com/upibhalla/moose-examples
3380e9bc90 Added new Rdesigneur examples to go with new features for cellProto definition
584f4aa34d Update INTERACTIVE
1f98eec417 Update .travis.yml
279362600b indentation clean up
cd75c017a4 Update rxdSpineSize.py
be269052df Update scaleVolumes.py
ac90c0a673 Update rxdSpineSize.py
f116a6697a Updates mostly to Rdesignuer tutorials
a5cf6e2788 Resolved various merge conflicts
10e9ef4407 Added some new tutorials and a README
451c90b85d Fixes to snippets, updates to ChemBistable tutorials
2cb64c2519 Fixed script. raw_input is back. Will break with python3.
22b5f82d39 Merge branch 'master' of github.com:BhallaLab/moose-examples
a5f3c07ec8 Merge branch 'master' of github.com:BhallaLab/moose-examples
9bd3506e15 Added timing information and fix the python3 changes.
8eb005552e Parallel Ksolve.
49f7c06025 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
78b563be6b Updated to match newer rdesigneur

git-subtree-dir: moose-examples
git-subtree-split: 2d9849222d6f4e153745d5c4b077e7ecb81f0ede

3047477 python3/python2 compatible call to raw_input.

git-subtree-dir: moose-examples
git-subtree-split: 3047477ce74705290cb282ac1dca7fcff3f4cf3f

bd41d0688 Wait for user to press button before quiting displaying plots. Use matplotlib.pyplot instead of pylab.

git-subtree-dir: moose-examples
git-subtree-split: bd41d068806ceba8e0ded0c73da536415aaeebd4

6e8a629 Merge branch 'master' of github.com:BhallaLab/moose-examples
d4e4fb0 Increased timeout to 60 sec.
b4ca7ef Merge branch 'master' of github.com:BhallaLab/moose-examples
2628bfb Potential fix to travis-ci/travis-ci#6307.
56c2805 Argument 1 to run_script is optional, by default its value is 60 secs.
24c45c2 Increased timeout to 60 sec.
c4395a4 Using ruby2.2 for jekyll on travis build.
8917843 Removed wait statement after parallel section.
f75bf0c Install travis using gem2.2
1a62999 Merge branch 'master' of github.com:BhallaLab/moose-examples
3f7399f Added colors in script itself. Download and test travis is called from .travis.yml now. At the end of test print summary of models. Fixed typo in bash-function. Passes on local machine.
516885b Fixed typo in bash-function.
ed06ca1 At the end of test print summary of models.
6778aed Download and test travis is called from .travis.yml now.
bf1cae8 Added colors in script itself.
2abbc43 Timeout with 3 minuts.
6316728 Added script to test genesis scripts.
9127f4f Testing deploy again with changes to config file.
416f650 If travis fails to generate static page, do not consider it as build failure. Update to travis script.
4715089 pip install python-networkx to pip install networkx.

git-subtree-dir: moose-examples
git-subtree-split: 6e8a629e31d05bc2c98ce817e7fcde8fd0d5c2cd

7ab9e3c Let static page generation fail.
c26d7c7 Build using travis and deploy onto github pages.
feeaf6b Added theme for static pages.
ae1fecb Merge branch 'dirty' of github.com:BhallaLab/moose-examples
c25e57e Passing locally.
2a2db61 Moved the integration to branch 'dirty'
83a516c Test the dirty branch with jekyll.
9667dee Added jekyll to create static page.
742362a Testing Jekyll and travis integration.
9aa4a3d Prepare index.md  file post test.
e885ea5 Modified shell script so it does not hang.
828464a Code to update README.md file with broken scripts.
9a6b3b1 Deploy keys are added. Testing...
74fb0ae Set theme jekyll-theme-minimal
a4e7ce1 Deploy to github pages. Testing.
e3f9a41 Added code to deploy on moose-examples static page.
ab45904 Default timeout is 30 secs [ skip ci ]
3e30131 Added python-pygraphviz to dependencies.
b825107 Added python-scipy on travis.
73d8bff Merge branch 'master' into traub_2005
60a9f7d Update README.md
4d30457 Updated VClamp commandIn destFinfo name in test_tcr
8846ae5 Fixes for nonexistent NRN data
03735e8 Fixed syntax error
24c349d Multiple workarounds to directory paths and data files from neuron
ccc1039 Fixed typo with data directory creation in traub 2005
a15893b Fixed issue where new ZombieCompartment breaks old code using Compartment
024aa0e Added attempt to automatic data directory creation
96a815c updated ref to old table API
78dcbb1 Merge branch 'traub_2005' of https://github.com/BhallaLab/moose-examples into traub_2005
bc5c37d Added fix for #28 (metaclass portability)
b347fa4 Fixes to load-sbml script.
202bb51 Merge branch 'master' of git://github.com/malav4994/moose-examples into PR-25
a20f451 On this branch, making traub_2005 test with recent release. Added subha on this branch. Removed everyone else.
ac68f92 Ignore the traub_2015 directory on travis BhallaLab/moose-examples#28.
caaa45e Removed a png file [skip ci]
cf27b12 Added python-h5py on travis. The hdf5 related scripts needs this module to run on travis.
afbb591 Merge remote-tracking branch 'origin/traub_2005'
dc92ae8 Include traub_2005 in scripts to be tested on travis.
ee70916 If a script is timedout after 30sec, dont consider it a failure. Fixed the result status of timeout command on 14.04 as indicated in manual http://git.savannah.gnu.org/cgit/coreutils.git/tree/src/timeout.c
9f70d7f Fixes to import in loadSbmlmodel file. Read SBML fails.
bbb3fe0 Increased timeout to 3m and using 4 parallel process.
b5a856e Using backend agg to overcome build failure on travis. This way we will not launch the graphics on travis.
450b3da Removed debug print
d34a833 Fix to issue 28
41f5c8b modified some of the snippets files for documentation

git-subtree-dir: moose-examples
git-subtree-split: 7ab9e3cfd8d74f79a73282572d4df4301b6df976

37bf0cc This might pass with upcoming release 3.1.3.
feef205 Merge branch 'master' of github.com:BhallaLab/moose-examples
c41af29 import fix to another file.
2d30a30 Output comparision of GPU & CPU (#26)
7295a8f numpy.array changed to np.array
664f843 Maximum timeout is 1m for all script.
0458697 Fixes to one more script. Error due to merge conflicts.
27fddec Updated script.
0694972 Run scripts now launches 8 process in parallel.
15d3aa7 Merge branch 'master' of github.com:BhallaLab/moose-examples
62d6c58 Enabled trap in bash script. Kill running test when user presses ctrl+c.
65fb8a8 Added beta cmake based test flow.
987c3fb Moved CMakeLists.txt to _travis folder. Old bash style build system is sufficient.
d4a081f Removed one more duplicate file.
9b13403 Removed duplicate files.
98b5eb0 Fixes to script. Runs fine now.
c42aa93 One more fix.
626221e Removed merge conflict.
f1b0bc4 Fixed one more script to make it work.
09ca09e Merge branch 'master' of github.com:BhallaLab/moose-examples
204d5e4 This is removed b'cos Rdesignuer does the job
8c7c00c can pass command line arguments also
70f83d0 cleanup in return type from None to moose.shell
fe4238b indentation for python3
3e81764 indentation fixes for python3
66f1bb0 Removed <<<<, ===  and >>> from improper merge.
0719a5d Merge commit '349abe7e'
7054325 mooseaddChemSolver is needed in loadSbmlModel file
6116c7e Indentation cleanup
9fd501a conflict cleanups
fe297f6 indentation correction
2b24c64 indentation correction
0e329d5 Merge branch 'master' of http://github.com/BhallaLab/moose-examples
7ce262e corrected indentation
864776c added deleted files
87a6963 temp deleted
0f1e722 Resolved merge conflict
0ff3b05 temp deletion
69062d9 For crossComptSimpleReac a temp fix so that segfault doesn't occur, rest cleanup
729f216 deleted unwanted files and added new files
7318878 cleanups
045aa11 Fixed assert by Upi
2b16c59 Deleted temp files.
3881f8a khali khali
97599aa Fixed docstring on example.

git-subtree-dir: moose-examples
git-subtree-split: 37bf0cc0a733d5b4c61659f9eb6e747f57530273

git-subtree-dir: moose-examples
git-subtree-split: cd2a2b99b4aff3a581bfbfc5786ff9504f0f2cb8