renamed it.

[skip ci]

cmake.

Conflicts:
	moose-core/python/setup.cmake.py

bda9742 Merge pull request #236 from upibhalla/master
86751f2 Added more accurate error messages to ZombieEnz for reporting missing messages during solver setup
5d93f75 Merge pull request #233 from upibhalla/master
cc47a2d Merge branch 'master' into master
a7ac8f4 Merge pull request #234 from BhallaLab/fix_travis_nov_30
5a08c96 pip is renamed to pip2. This commit passes on local machine.
bf8585d Possible fixes to travis build failure on osx.
f61a591 Added hack for channel not scaling when compartment size is scaled. Checks for child object called scaleFormula.
dff5731 Merge branch 'master' of https://github.com/BhallaLab/moose-core
7f0eb4b Merge pull request #231 from BhallaLab/prefix_python3
1d99906 Fix for spine ordering. Added capability to do unordered_map which may help with some of the performance issues during setup.
296c030 moose-core does not handle debian layout anymore. This should be handled in BhallaLab/moose.
0433574 commenting out changes introduced by 985af4e. Reopened BhallaLab/moose#224.

git-subtree-dir: moose-core
git-subtree-split: bda97426c899b2f366d08bdf30cf0f69876c9567

found.

33d4803ee Merge pull request #228 from upibhalla/master
c9e9fa6fd Update test_muparser.py
419661b6e Update test_muparser.py
7c8ca61a6 Merge branch 'master' of https://github.com/upibhalla/moose-core
b13fc98cc Fix for muparser tests
7eefdca47 Merge branch 'master' into master
1ad271b07 Merge pull request #229 from dilawar/master
30fe94cda Optimizations for rdesigneur in _parseComptField function
d862de4e9 Merge branch 'master' of https://github.com/BhallaLab/moose-core
3eef327f1 Added instructions on what to do post-build.
985af4e11 Fixes BhallaLab/moose#224 and BhallaLab/moose-core#230 .
917d68db0 Merge branch 'master' of github.com:BhallaLab/moose-core
586d48a62 Merge pull request #222 from hrani/master
3c7ce10fa New line added
e7c8d0e81 Merge branch 'master' of http://github.com/hrani/moose-core
7ce91a0f2 import rdesigneur.rmoogli as rmoogli is added at init file, otherwise script that uses rmoogli gives and error "NameError: global name \'rmoogli\' is not defined"
fd5f360d6 Merge branch 'master' of https://github.com/BhallaLab/moose-core
eb76ab120 Fix to Neuron.cpp handling of messages between Ca channels and Ca_conc objects.
f9f188513 Merge branch 'master' into master
67c9b0a85 Disabled seg-fault causing test on python3. Runs with python2.
cd40023f2 disable seg-fault causing function on python3.
761172460 Merge branch 'master' into master
946cb77e7 call plotDEGF only once.
47f6803df iteritems( ) is no longer supported by python3; replacing it with items().
f447f0d35 Passes with python3.4 .
1d26f38c2 import matplotlib in rdesigneur.display only when display is called.
4b56d7a66 dependencies are handled by cmake now. Removing scripts.
20c131a3f Added field Table::plotDump to substitute for the Table::xplot function which has problems with Moose interface to Python.
2c7b9efc9 Merge branch 'master' into master
8005f2f04 loading SBML was commented, now uncommenting while mergering

git-subtree-dir: moose-core
git-subtree-split: 33d4803eed211af61fd8b6f45d71e8675f77f951

e5ba823ba Merge pull request #227 from dilawar/master
9742b9e87 auto_ptr -> unique_ptr .
6f6015e46 scaled down chemDt and diffDt.
68c7001fc Added test.
c57990604 Fixed import issues in rdesigneur.

git-subtree-dir: moose-core
git-subtree-split: e5ba823ba8abd740f2d3323a5dd0c29f727309d0

5d7f7633f Too many python3 incompatibility issues. For now on, gui is only compatible with python2.
599dbd6d3 Testing with python3 as well. If python3 support is not intented, we can fallback this commit.
83be02e60 changes made after addition of groups, some of action are implemented
24cba7d6f  some more clean
cdf16259d at file load dialog, a clean round trip is done
08fc6cd0b at loading time, kkit model is checked for the atleast for 1 compartment and atleast 2 species
373efaa6d check if moose object already exist, if yes use element, else create a object
e37368553 in mousePressEvent further check made for group object along with compartment and other moose object
ae6265ed8 travis is failing, while installing python-libsbml trying to fix providing -H
c70f30098 some clean up with co-ordinates while saving into XML files
dd177002c wrong comparsion with path and moose object was done corrected
24ecdccac some clean up with groups
84be91147 changes made ...

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

268a28862 Merge pull request #224 from upibhalla/master
3ab452e97 Fixed test_nsdf.py. It had relied on the old (and incorrect) function of the spike message to the Table. I have now updated the test_nsdf.py to work with the fixed version of the Table.
616f33a60 Fixed spike timing functionality in Table class. Incorporated into rdesigneur so that tables can record spike times for saving, and users can plot spike times as a dot raster.
7f372b6aa Merge pull request #223 from upibhalla/master
186e91d68 Merge branch 'master' into master
d91a681bf Fix on diffusion scaling in spines, and added Pool::volume field for plotting in rdesigneur.
41c71b147 Merge pull request #221 from upibhalla/master
e27ef8a45 Merge branch 'master' of https://github.com/BhallaLab/moose-core
b07046e15 New Neuron::getSpineIdsFromCompartmentIds function, needed for rdesineur to connect adaptors for spine size and other spine properties.
69d985877 Merge pull request #220 from bhanu151/master
4f67f3338 retracting seqActivation normalization by dt to restore time-step invariance
ca1f36ca6 Merge pull request #219 from hrani/master
be6dc0a28 Hopefully last cleanup
e03c69ddd Hopefully last cleanup
7332ff66b spell correction
d17d383dc absolute import with mtypes just for python3
fb28e1009 Hopefully last one, tested for filepath,moose path and moose object
b782b9552 In merge.py, clean way of cheking the type of path provided, filepath,moose obj, moose path are taken,if source is empty then nothing to copy, if destination was empty list is update with new object
dc0c83027 clean up with in mergeChemModel file
13152346b cleanup in setup file
1f9100b7f cleanup in init file
50cd8feee removed unwanted lines and clean up
e9b88cee7 folder "merge" renamed to "chemMerge", moose.py: func added so that chemMerge can be imported directly,cleanup in test_import.py with the changes made to this commit,merge.py file Neutral object is copied into des path instead of creating and now user have to genesis/SBML format
072913a9c Merge pull request #218 from BhallaLab/missing_merge
fab362fa7 Couple of lines added to moose import test.
064fbea56 Fixed moose.merge import. Added a test which tests moose module import (incomplete).
4211da0e8 Merge pull request #216 from hrani/master
a45e9f0a1 Merge branch 'master' of http://github.com/hrani/moose-core
dacd64039 some more checks made for empty model, empty compartment and for display atleast one reaction should exist for displaying into widget
e0566d476 Merge branch 'master' of https://github.com/BhallaLab/moose-core
2db1b4dac Merge branch 'master' into master
a62961a27 Merge pull request #217 from upibhalla/master
15ee2cc7f Merge branch 'master' of https://github.com/BhallaLab/moose-core
aca164612 Two important fixes for numerics of stochastic solver with diffusion. Affects models using sumtotals and functions.
f5302b08f validator was switched off, which is not correct, so switching ON
87e66a18d if in reaction stoichiometry is not defined then assume 1 and if no unit base unit defined then assume 1 which is mole
38879fd5b Merge pull request #215 from hrani/master
2384657e0 readSBML: explicitly ratio is set to 4, so that e2,e1 is balanced, If units are defined in the rate law for the reaction then checks are made and if not in milli mole the base unit then recalculate, spell correction. writeSBML: instead of printing error msg, saving into string for later use writekkit : instead of printing error msg, saving into string for later use
798c0b6a7 Merge pull request #213 from hrani/master
c1c26f698 Merge branch 'master' into master
aa1cb43e2 Merge pull request #214 from bhanu151/master
b60b73b3a SeqSynHnadler fixes - normalized seqActivation by dt
3d36e7bd1 unwanted print statement is removed
67e026ab8 function definition are read from SBML files, rules which are not read to moose a errorFlag is set out, rateLaw without unit definition, are taken from the substance units and recalculated for all higher reaction, validator checks if model is valid and send out errormsg if not valid, if model doesn't have atleast one compartment, then errormsg is send out
91180c067 Merge pull request #210 from dilawar/master
1f37c10f0 Python3/Python2 import thread has been fixed.
012b5f3ca Preserve the order of plots. Use OrderedDict. Since OrderedDict is not available in python2.6; added implementation.
78f244b0c Utility function to plot tables matching a regular expression.
03dc5a8fc Fixed import error.
2b9e30565 try/except import in moose.py file.
574a12503 Added a test script.
f5202b0cd Merge branch 'master' of github.com:BhallaLab/moose-core
b792838ee Merge pull request #207 from hrani/master
e39c76df2 resolved conflicts
75e289296 all conflict a removed
1e7ebbe3c unwanted statements
98d625b62 Merge branch 'master' into master
cdbe6add9 Fixed clock dt assignment bug in rdesigneur, came up when turnOffElec flag is true (#208)
0da306f5a Fixed clock dt assignment bug in rdesigneur, came up when turnOffElec flag is true
e9526f7c3 Fixes to import plot_util library.
abd664d1e unwanted print statement removed
fd794de74 in print stm space clean up,added findcompartment function to one common place, some space char are allowed in name field, in kkit writer, moose obj which doesn't have compartment are not written, which then appended to error msg for user
5015b14cd Merge branch 'master' of github.com:BhallaLab/moose-core
b32a0bbe9 Fixes to issue204 (#205)
9f88d7c5f Merge pull request #203 from hrani/master
6dbf8bef2 Merge branch 'master' of http://github.com/hrani/moose-core
3c6d41ce4 Restoring contents after bad commit and bad merge
1d34b9b2c Restored some old commit, after the bad commit and after revert fail
f2d3e94ad Restored some old commit, after the bad commit and after revert fail
daa657802 Restoring contents after bad commit and bad merge
30b1c36b2 Merge pull request #202 from upibhalla/master
24c079561 Restoring updates to ksolve including isBuffered flag
d71f6eb53 Merge branch 'master' of https://github.com/BhallaLab/moose-core
eb43e5524 Fixed Rdesigneur verbose flag
5e42df95c Merge branch 'master' of github.com:BhallaLab/moose-core
3c46150a1 Merge branch 'master' of github.com:dilawar/moose-core
b04156b03 Fixes to issue #200. (#201)
1e3bbe04f Merge branch 'master' of github.com:BhallaLab/moose-core
f11ef0a3f Added test script but has not been enabled. This tests the SparseMsg::connectionLists.

git-subtree-dir: moose-core
git-subtree-split: 268a2886219290af163c9c95b755901fa68cfa5d

2657e3345e Merge pull request #199 from dilawar/master
973dd380ba Deleted Makefile.
545b4241c8 Restore synapse folder back to 933b259 . synapseOrder is now working.
90711a865c execute_process is now used to get the extension of python module. See http://bugs.python.org/issue16754 in case build fails on some unix because of 'SO'.
5b0a529c4e We do not reply on VERSION file to create version. TODO: Use config.h.in file to populate VERSION information.
2749918927 Accessing an existing object (#198)
220128f284 Do not run DOQCS with moose-core. Test DOQCS with released package only. Do so in moose-examples repo.
ad2c63da12 Use QUIET_MODE=ON on travis.

git-subtree-dir: moose-core
git-subtree-split: 2657e3345e8b783cf22634680c7561f8dbd9f127

2657e3345e Merge pull request #199 from dilawar/master
973dd380ba Deleted Makefile.
545b4241c8 Restore synapse folder back to 933b259 . synapseOrder is now working.
90711a865c execute_process is now used to get the extension of python module. See http://bugs.python.org/issue16754 in case build fails on some unix because of 'SO'.
5b0a529c4e We do not reply on VERSION file to create version. TODO: Use config.h.in file to populate VERSION information.
2749918927 Accessing an existing object (#198)
220128f284 Do not run DOQCS with moose-core. Test DOQCS with released package only. Do so in moose-examples repo.
ad2c63da12 Use QUIET_MODE=ON on travis.

git-subtree-dir: moose-core
git-subtree-split: 2657e3345e8b783cf22634680c7561f8dbd9f127

Conflicts:
	moose-core/python/moose/moose_test.py

Conflicts:
	CMakeLists.txt

d4417dcffd Fixes to missing function declaration, post cherry-pick.

git-subtree-dir: moose-core
git-subtree-split: d4417dcffdd939de91bebf447ad776945c2fcc65

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

891f2f8 Removed trailing spaces from code by pre-commit hook utility.
0ed2535 Cherry-pick "Added connectionList field to SparseMsg to allow direct control over connection matrix. Some sanity checks in SparseMatrix to go with this"
d62d10d The bug on travis is still not bypassed. If this does not work, disable DOQCS tests on OSX.
618b4d6 Install moose on osx as well. Prerequisite to test DOQCS.
f717f82 Merge branch 'master' of github.com:BhallaLab/moose-core
908820e Lets see if this is a good workaround travis issue travis-ci/travis-ci#6522.
e251f53 Lets see if is a workaround fixes the OSX bug.
4ff7cff Hopefully this will fix issue on travis-osx build failure. Related to travis-ci/travis-ci#6522.
590c09e Don't use timeout in script. So that we can run on macosx as well. Removed timeout command from script. Now it can run on OSX as well.
e2f8afd Only test doqcs on LinuxOS, not on MacOSX.
dc7b55a Fix to travis-ci/travis-ci#6307.
54b8471 Merge branch 'master' of github.com:BhallaLab/moose-core
18c8759 Test docqs agains gsl version/python2 moose-core.
d6ca9cc Fixes by pre-commit hooks. - Removed trailing whitespaces automatically. - insert * coding - utf8 * line on top of each python script automatically.
d4a6939 Using version v0.8 now.
f944afe Added pre-commit pip install pre-commit --user to activate it.
030bfe0 Merge pull request #195 from dilawar/master
d00a5d1 All tests are passing and new code is protected by appropriate macros.
1959771 Merge branch 'async' of github.com:dilawar/moose-core
0f6aba0 Merge branch 'master' of github.com:BhallaLab/moose-core
ac0a4cd Added note on what to do.
b3bf54e Slower version but results are same.
6bc71c9 Async version is slower (80sec vs 70 sec).
d838267 asyncing clock is not producing great results.
eeaafbf Implemented first parallel version.
166f84e Equivalent serial code which can easily be called from std::async now.
e09a0c1 Merge pull request #194 from dilawar/master
d2d1097 Added MACRO to integrate serial and parallel version.
e68acd6 This is good but do parallelism at Clock.cpp
4cebbca Rdesigneur has python3 default import : absolute_import.
f431cca Merge branch 'master' of github.com:BhallaLab/moose-core
85afa6d Some changes to Ksolve. Still seg-faults.
47e023e Time to test the Gsolve performance when threads are enabled.
2bbfd4f Commented out code appropriately.
91c2da6 moose.test( ) is added not cmake but not enabled. Enable them once all scripts are fixed in moose-examples.
a1699fc Optimized GSolve with default 2 threads.
00a9d9e Removed the debug message. Lets check it now. By default it should be not slower than the default version.
7700c07 Fast Ksolve with 2 default threads.
d154eb3 Parallel ksolve.

git-subtree-dir: moose-core
git-subtree-split: 891f2f8bf7359d61f186c3792c6f12b61d8c0afb