build fails.

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

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

git-subtree-dir: moose-examples
git-subtree-split: 3a960983fe23dad8e0b34883e61510d05a2f3b2a

3a960983fe Merge branch 'master' into asiaszmek

git-subtree-dir: moose-examples
git-subtree-split: 3a960983fe23dad8e0b34883e61510d05a2f3b2a

38da92b048 Fixes to bad-merging.
812d2d97f8 Merge commit '320e525a'
6fc726e560 All changes from previous repository. No new file is added here.

git-subtree-dir: moose-gui
git-subtree-split: 38da92b0481f53ffd2cdc75d8f7aec49408dc4ae

git-subtree-dir: moose-core
git-subtree-split: fe77059f98c5a6cab2e106f78b7eb505f4f62850

80169bcc5c Resolved a merge error.
d5caa39361 use moose.element over  moose.HHChannel.
26e9aac794 Merge branch 'master' of github.com:BhallaLab/moose-examples
9b83291de6 Merge branch 'master' of github.com:BhallaLab/moose-examples
2f46ad096d Convert u'ABCD' to 'ABCD' to probably fix the python3 issue on travis. Works fine with python3 on ubuntu 16.04/Debian8.
6232b3a888 Send email to malav if build fails.
4a92db239b Merge branch 'master' of github.com:BhallaLab/moose-examples
4800cd62df Adding python-libsbml to dependencies.
c045972c2e Fixed second script as well.
e927a88875 Merge branch 'master' of github.com:BhallaLab/moose-examples
626afb8242 Added a hack to make this script work with both python3 and python2.
24fdc9e1b7 Indentation for python3
e9e5d92828  Using force-yes with -y
3c60a8263a Upi fix the assert error
ca2d4090e7 Upi cleaned up the file
a9ddced2bc Merge branch 'master' of https://github.com/BhallaLab/moose-examples
b4715d09ba First commit.

git-subtree-dir: moose-examples
git-subtree-split: 80169bcc5c7263fa76f53b4ebd54b0fe20c5cef5

49779ba730 As per Upi suggestion, co-ordinates are reprocessed for genesis file (yaxis is negated) at loading time so that, at the interface level co-ordinate are played around independently and while saving scene co-ordinates are save.
1f32b418d2 Kd is calculated for second order reaction only and value is displayed in object editor,Notes header is added, and unit for Kd is added in default.py
254d1f077a Enzyme can't be connected for second order reaction
3038c31d1a missing import math
355d721e4f added libsbml and moogli is removed
0343ce3e11 Added a Model information, like number of compartment,group,pool,function,reaction etc when model is loaded for the first time

git-subtree-dir: moose-gui
git-subtree-split: 49779ba730bbbb214728c86d3550fc2b27d8ef24

69e0354705 Create CONTRIBUTING.md
b096503233 Added travis related setttings update.
REVERT: 2ecab963b2 Merge commit 'af3c29a4'
REVERT: b3b597f411 Removed legacy Makefile based build flow. CMake is only build-system now. #180.
REVERT: 20dc0a5989 a warning message is sent out \n 1.if function is not connected to output and \n 2.yet to write back StimulusTable is to genesis. \n No more transformation with y axis as it has already taken care in kkit.py file
REVERT: 9373d1bc16 python Counter function removed, just to give backward compatibility for Centos6 for python 2.6
REVERT: e8300d7e92 added to ask User if merged model to be saved
REVERT: 933b259710 Made ReadSwc less verbose. Fixed bug in SeqSynHandler in application of sequencePower.
REVERT: 662eaa2e13 Added sequencePower term to SeqSynHandler to achieve greater specificity for sequences vs all inputs on at once.
REVERT: 7ccc8a2b1e Merge branch 'master' of https://github.com/BhallaLab/moose-core
REVERT: fe5765ca7b More fixes to plot_utils
REVERT: 6a9a618e72 Fixed the error in plot_tables utility.
REVERT: 658af76a47 Fix for Table.vector bug (#179)
REVERT: 423dc9dc69 Merge branch 'master' of https://github.com/BhallaLab/moose-core
REVERT: 200871a9f7 Added in hack for rmoogli to display time
REVERT: 157c501b98 reaction or enzyme name is empty then id is taken as name while reading files from SBML
REVERT: 43a2350406 color and textcolor inchanged for enzyme
REVERT: 02de4c37ee Bugfix for SparseMsg, corrects allocation of synapses when setting connectionList

git-subtree-dir: moose-core
git-subtree-split: 69e0354705cd27d3dad42ba33610f960d270660e

git-subtree-dir: moose-examples
git-subtree-split: 2eb5fa888ff20afdc478366881255201b51a58b8

installing openscenegraph-dev error-prone.

7318878 cleanups
9b83291 Merge branch 'master' of github.com:BhallaLab/moose-examples
2f46ad0 Convert u'ABCD' to 'ABCD' to probably fix the python3 issue on travis. Works fine with python3 on ubuntu 16.04/Debian8.
6232b3a Send email to malav if build fails.
4a92db2 Merge branch 'master' of github.com:BhallaLab/moose-examples
4800cd6 Adding python-libsbml to dependencies.
c045972 Fixed second script as well.
e927a88 Merge branch 'master' of github.com:BhallaLab/moose-examples
626afb8 Added a hack to make this script work with both python3 and python2.
24fdc9e Indentation for python3
e9e5d92  Using force-yes with -y
3c60a82 Upi fix the assert error
ca2d409 Upi cleaned up the file
a9ddced Merge branch 'master' of https://github.com/BhallaLab/moose-examples
b4715d0 First commit.
2c4fa33 This is removed b'cos Rdesignuer does the job
4ca1f6d missing closing braces
d120484 small correction for input eval with is str
18990fd enter key replaced to zero, as function \'input\' with \'enter\' key give SyntaxError: unexpected EOF while parsing
0db144c Ready for put into demo #15.
39aa6e4 Closed docstring.
f2dc6be Merge commit '07ef36e1'

git-subtree-dir: moose-examples
git-subtree-split: 731887849ac227fa304780406ff913c69af425ca

6104940 units added to k1,k2,k3
a3a80bf Using force-yes with -y to avoid problem with gpg keys. Probably breaking due to policy change in apt install.
c994d93 one more attempt -y is removed
b869143 one more attempt expired key
a172670 checking with travis expired key
8ee7c22 checking with travis expired key
a208321 travis has a problem installing moose with -y opition trying this
ff92eb5 print stm with python3 and changes made WRT to pool and bufpool with isBuffered flag
744f262 isbuffered is editable and if value is set/unset
a46cec9 cleanup in demo, filemenu links

git-subtree-dir: moose-gui
git-subtree-split: 61049405f17b22f27c74e7834dc1b2cfbab61699

f3d0477 Merge branch 'master' of https://github.com/BhallaLab/moose-core
176a5f0 solver's short form should also be taken
8624e24 Merge branch 'master' of https://github.com/BhallaLab/moose-core
6c964b1 Added isBuffered field to Pool to let users convert the object class to BufPool, and vice versa.
97db69e moose::Neuron uses global RNG object. Global RNG object behaviour is following. - moose.seed(0) or moose.seed( ) assign a random value to seed. Use   random_device if avaible else time(NULL) is used. - moose.seed( x) set moose.seed to x.
c1dec94 Fixed long argument for mtseed in moosemodule.cpp
54c94f7 Modified travis scripts and reenabled developers to the list.
31dd779 Fixed import error with python3. No module should be imported in python/moose/__init__.py . Added a note for developers. This should fix the travis.

git-subtree-dir: moose-core
git-subtree-split: f3d0477a3ea5045db044aaae94b46a133527dbc7

2ba6bd5 cleanup
d0f5918 replace writeKkit to moosewriteKkit
cb067ac correct from writeKkit to mooseWriteKkit
6b1bff4 Ubuntu16.04 with networkx and pygraphviz has some bug, for now small fix, automatic layout will be done spring_layout format
dbe6875 Update .travis.yml
8a71426 Update README.md
fcbacd5 Added travis file to moose-gui.
ddcfbdc Removed shebangs from python scripts.
d5cf170 Fixed the address of Free Software Foundation Inc.
b88d5cc Merge commit 'aca40347'
e0cea9f Squashed 'moose-gui/' changes from 1ef13c9-1ef13c9

git-subtree-dir: moose-gui
git-subtree-split: 2ba6bd5d8e6b022edf3f3aa1a567462ab7ddf6ed

8038f56 documentation is moved under main function
6ebca4d Corrected kkitwrite function
1726122 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
fbcaef7 added line to show how to set solver to sbml files
07a11d3 Merge pull request #11 from dilawar/master
536b53e Construct absolute path relative to script directory.
f5a7d84 All files must be python2 and python3 compatible [skip ci]
6895e56 All compiles with python2 and python3.
d9cb5b7 This version compiles with python2.
d80ec97 print_statement is the first statement of file.
74c70bc Custom fixes to print end='' statement on python2. Whenever possible import from __future__.
8977107 python-qt4 instead of python-pyqt4 is valid name package.
5e47fd8 Install and do not use moogli.
7b8c680 Fixed all files breaking with python3 compielall module.
e00a845 Fixed two more files.
3f789a1 Fixed one more script.
54f9549 Fixed syntax of this file as well.
63b9c43 Fix some more syntax issues.
5446b0e All scripts are now python3 compatible.
e5e259f This script is broken.
3e420f0 Merge remote-tracking branch 'bhallalab/master'
92ba920 Merge branch 'master' of github.com:dilawar/moose-examples
8a47205 Fixed print( , end='' ) with python2
f756065 Fixed print_function in couple of scripts.
3c6fbe0 Converted files to be campatible with python3 with tool 2to3.
da8c0dc Ran 2to3 on all examples. See which scripts are failing on travis.
469e3f3 These scripts were not chmod to executable. Removed hashbang from header.
3429792 Merge branch 'master' of github.com:BhallaLab/moose-examples
d34c8df Merge branch 'master' of github.com:BhallaLab/moose-examples
d56f575 Changelog:     - No python3 incompatible file should be added to repo.     - moose contains moogli now. No need to install it separately.
31137eb Fixed, python2 incompatible print function use.
a5375cc Merge commit '00a12e20'
15de0ce Since none of the following files was executable, removed shebangs.
4a20952 To run this file libsbml needs to be installed and not compile with moose as its at python level
092eec8 Doxygen_1.8.9 is added which should be used to generate doxygen files,Rdesigneur folder is creater under "user" folder and corrected index.rst file is updated, deleted "html" folder,Rdesigneur markdown file with correct date,"snippet " and "tutorial"folder is created with relevant files to generate html files
bee94a1 Merge commit '3c9138df'
4590e9e Merge branch 'master' of https://github.com/BhallaLab/moose-examples
62e3218 Moved docs to moose. Removed temp directory.
dc5a230 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
c8f96c5 Once simulation is done, store the results in png file.
5c36c87 Used 2to3 tool to make these scripts python3 compatibles. Also saving results to a png file after run is over.

git-subtree-dir: moose-examples
git-subtree-split: 8038f56ec24965353de70fb460ceccff3861f7b1

7c9fe23 Fixes to issue #167. (#168)
3f077c1 Resolved merge conflict with Table.h
9b175c8 Major bugfix for Table and derived class Streamer, to fix error introduced by duplicating the 'name' field which is already defined for Neutral. Minor bugfix for melement.cpp
f0d4c02 Update INSTALL.md
2737220 Fixes to issue165 (#166)
a934676 Update .travis.yml
601d06a Fixes to PYTHON3 build failure on travis.
9d9d925 Tested locally for linux. The scripts seems to be fine on openSUSE-42.2
93bbd4f By default travis pick up /opt/bin/python when `which python` is used. Do not use this construct in script. Moved travis related scripts to a hidden folder .travis.
c0d3871 If python3 exists (installed on travis), then check for the compatibility otherwise don't.
65a85da Almost there. Calling script from top of directory.
0db2016 Make trusty default build environment. python3-matplotlib is not available by default.
d8c1c6a setuid to root for linux script.
4c90f04 Some more fixes in travis script.
429420b Cleanup, osx related travis macros.
e287118 Disable OSX build here on master brach. Created issue #165 to build and test for MacOSX.
87aeb1a Travis build scripts for macosx and linux are in ./scripts folder.
24643bc Some more fixes to travis build failure on OSX.
a05826e Fixing brew taps and build dependencies.
ea0ede1 This commit is just to test the OSX build on travis. Unfortunately there is no way to test it offline.
1b6f42a Fixes to travis scripts.
b0baaab Excluded linux and osx build from config file.
626fd30 Testing with OsX support on travis. xcode-8.1. Most likely to break
ab933ad Fixes to recent travis build failure. make all python files python3 compatible in addition to #164.
72afc02 Enabled macosx build on travis. Though allowing failure for now.
bedb51e Fixes for issue #164. Also hotfix for branch chamcham.
e821a9d Fixes due to API change in SBML support.
bb8c850 Fixes to #164.
806605d Fixed the prog -> position. Hotfix for release.
2cba78a Merge branch '3.1.1' of github.com:BhallaLab/moose-core into 3.1.1
82c3024 Fixes to #163.
598433e Related to BhallaLab/moose#204.
48c5535 formating
0cec9d2 spell correction
6d66bc1 function to add and delete solvers to Chemical solver
eefafa9 filename changed
c9208a9 added mooseWriteKkit, moosedeleteChemSolver,mooseaddChemSolver and cleaned up write/ReadSBML as mooseWriteSBML, mooseReadSBML for consistency in moose.py
d462c7e Removed saveModel which doesn't exists anymore
8c5af82 Fixes to issue 129 (#162)
eee822b Fixes to recent build failure on travis.
bdc1436 Alternative implementation of moose.Streamer  (#161)
94444f9 Notify user if python-libsbml is not found.
db41ad5 Merge pull request #157 from dilawar/master
c11cb03 Added recently added C++ files in synapses folder.
5868a2f Added libsbml test. Runs only when python2 is used.
716305c Fixes to boost build failure on travis.
4355f02 Various fixes to libsbml related part.
acf46ff Fixes to lintian errors [ skip ci ]
75c8f34 Similar fixes to writeSBML file.
54f127e Cleanup and fixed pylint error     power( ) -> pow( )     Instead of try catch, check for libsbml at the begining and warn user.
d24b389 Fixes to test_sbml scripts. The basic functions are working.
0430732 BhallaLab/moose-core#156 .  Created writeSBML and readBSML functions in moose.py
c56b347 BhallaLab/moose-core#156 . Removed deprecated sbml functions.
0e09e0b VERSION is a temp file.
29190b6 Merge branch 'master' of github.com:BhallaLab/moose-core
2c8156a Changed the environement variable which cmake uses to search for GSL.
ee4ae8a Merge branch 'master' of github.com:dilawar/moose-core
da93767 Fixes to recent travis failure. All files are now compile with python2 and python3.
0ec89d2 Added test to make sure each python script compiles with python2 as well.
98d6c31 Merge branch 'master' of github.com:BhallaLab/moose-core
3bc4e6c Update .travis.yml
c1f4c84 Adding pre-commit hooks. BhallaLab/moose#189 .
8847b26 Update .travis.yml
6b2fa39 Disabling libsbml on travis. It does not build with clang.
12a72da python-libsbml doesn't build with clang. Allowing failure for clang compiler on travis (test commit).
be83da8 Fixed import statement in genesis. Related to python3 import.
ac29a99 Enable QUIET_MODE for Release. No information is printed onto console when moosemodule is loaded.
6e871fa Changes : 0. Mixed tabs and spaces are turned into 4 spaces. 1. Python code is python3 compatible. 2. Removed libmumbl from source tree. Not in active development.
5916f7f Fixed a typo in travis.
246bc58 Merge commit '04170cb4'
0390d6a Updated.
993f8f7 Fixed, python2 incompatible print function use.
030aea3 Some updates to fix static hdf5 libraries.
4255ecf This project build pymoose, gui and its examples. TODO: ctest must check each example as well.
c92e761 Builds whole moose project.
d40fbe6 Added some sanity tests for both moose and moogli.
29fd242 Even when format is set, stream!
f96fe68 One test failing on nargis (centos-6). Try it locally.
eb61ab7 ctest script setups its environment. No need to have set environment for each tests.
1b43dc7 This fixes python3 linking problem on openSUSE-Leap. Not sure about travis.
ec15bd2 Linking error with boost-filesystem.
0847eb2 This might or might now work with python3. Taking a shot.
e7a87b8 Some changes in Makefile. Protected some boost related code with USE_BOOST macros.

git-subtree-dir: moose-core
git-subtree-split: 7c9fe237abfcd49b45a3c843567f2c2ddcd67d65

3f8c345 Make sure all python scripts are python3 compatible. BhallaLab/moose#202.
937fdf4 Allow failure with clang compiler. python-libsbml module doest not get build with clang.
b7f1834 Merge commit '1680bac6'
d28a94d Changes to cmake file so that we can find the correct static library.
67c0d52 Fix a development warning in cmake.
9bb0aa9 Removing shebangs from the python scripts. These scripts were never called as standalone executables.
3b2296b A test commit to package hdf5-devel BhallaLab/moose#201.
06adf59 Fixed another typo in FindGSL. Library list was converted to string.
3893081 Fixed a typo in FindGSL file.
b635a2c FindGSL also looks for GSL_VERSION now.
6bcc61d Fixes to travis failure.
88d49cb Updated CMake and FindGSL.
0fb10a5 Fixes to extension bug.
a9b9f2a Some fixes to static library dependencies [skip ci]
6614991 Cleanup in cmake files. Using bash scripts to generate subprojects. This way I can handle environment variables cleanly.
7fc33ef New hdf5 version generates static library with different name. Fix it.
1b55fa5 This should pass on travis.
700bb53 Merge commit 'd0a6060b'
cd0ae83 Merge commit 'b5a7c2e2'
358b59f Merge commit '273124ec'
02fa6cf Merge commit '8bfef2e6'
e7138d9 Merge commit '6c8f2012'
0462858 Merge commit '96580978'
fdadcf4 A test case test_sbml_support.py which inturn calls to write moosewriteSBML which needs networkx which is added as a dependency for travis
c90cae4 Oops moment. Fixed the typo in compiler flag for apple-clang
1878ce8 updated apple-clang flags in compiler. Fix to missing symbols from stl.
f50cfe2 Merge commit '2af833a0'
72de2fa Moved docs to moose. Removed temp directory.

git-subtree-dir: moose-core
git-subtree-split: 3f8c345800c8227e975ae3cf9c714dc6c2c014ee

TODO: ctest must check each example as well.

c2c32b9 Before tagging runing with clang.
1cc19f1 updated runtime to annotation field in moose
3ad9558 runTime and solver type is read from xml file to moose, cleaning in names
5de1f05 function output to pool object set's "setN" as input is "nOut"
ae24a3d Merge branch 'master' of https://github.com/BhallaLab/moose-core
7b43f70 Fixed Function unzombification for increment messages. Added update for time in Zombie Functions.
f4310e6 for now function output connected to pool via setConc message, but there is "increment" which depend on the function input this will be fixed later
f286dca removed writekkit.py duplicate file
6d299eb replace all the obj under /kinetics or /kinetics/group which is required by genesis format
a6dad52 Merge branch 'master' of https://github.com/BhallaLab/moose-core
0ddbd21 Gsolve updates to monitor number of reac events. Stoich updates to avoid crashes when handling edge cases without objects in model.
2ab410d function can be connected to pool,bufpool and reaction
086ef95 using networkX spring_layout rather than grapviz dot layout
0000d51 Ids begining with numbers needed to processed with dash for sbml compartability,No substrate, no product enzymes are not written down, function are now placed under compartment and for backwarcs compartability with genesis they are placed under BufPool
f0f1444 Merge branch 'master' of github.com:BhallaLab/moose-core
e0c6c1a Allow failure with clang. I could not reproduce the error on my local machine.
9e4db61 First skeleton changes to the Gsolver to track the number of reaction firings for each reaction. Also some fixes to the SeqSynHandler.
cff32e4 Fixes to include path of muparsers. This is passing on openSUSE.
2117969 Added missing SeqSynHandler source file to CMake.
58ddb2b Added SeqSynHandler class to deal with single-neuron sequence recognition models
1e42ece Merge branch 'master' of https://github.com/BhallaLab/moose-core
659a908 Fixes for Ksolve accuracy, and some ReadKkit edge cases
7c3e72e small correction
0d7f908 clean up for Annotation, plots, reactions, enz
a2f6a95 Merge branch 'master' of http://github.com/BhallaLab/moose-core
fb70792 empty reaction are not written,units corrections, plot paths are written from compartment level unlike before from model level
a1593e9 Disabled pip install python-sbml with clang.
13acd0f Disabled SBML test for time being till issue #145 and #152 are resolved.
f3b42fd Merge branch 'master' of https://github.com/BhallaLab/moose-core
b16311e Fixed unicode conversion for docstrings Put in sorting of fields in showfields.
793ae62 Added pygraphviz to pip3 install list. pygraphviz is a dependency for SBML.
396e607 Both python2-networkx and python3-networkx can't be installed simultaneously. Fixes that on travis.
ac02cea Added python-networkx to python3 dependency. Test run on travis.
dd4fc4e Removed option WITH_SBML deprecated warning [skip ci]
c6c60e6 Removed c++ sbml support code. Test run on travis.
c73e4cd Removed C++ sbml code.
68ea7c2 Changed SBML script to make them compatible with python3.
8614680 Fixed Leakage class
8b15511 Merge branch 'master' of https://github.com/BhallaLab/moose-core
24a01e8 Added ICa for NMDA channel to known plot variables for rdesigneur
52ae361 Fix to issue #147.
c251c0d reaction rateLaw and enz's km is corrected
a03cb6a initial concentration is set if hasOnlySubstanceUnit=false with correct units
7018230 Fixes for SynChan modulation, added a couple of synaptic channel prototypes
66bfcff Upi fixed the scaling factor
b6532e8 Merge branch 'master' of http://github.com/BhallaLab/moose-core
b7a3ad4 MMEnz is created
37c5312 Deprecating sbml related code on travis. Don't download SBML debian package and install.
791762a plots populated to moose if defined in the sBML file
b05a983 Adding python-networkx as dependency in travis.     python-networkx seems to be required to run SBML related code (needs confirmation?)     python-networkx is a dependency for moose-gui.
76c5381 print statement needed paranthese
d52bd19 fixed a work around for small bug in the draw_grapviz function in networkx-1.11 which no longer import toplevel namespace, readSBML:cleanup
2fd15b6 updated to read SBML file into moose
422bbc0 One of the testcase where model loaded in moose are written to SBML file
dbc5412 Removing sbml build from cmake. SBML test is failing.
8876581 Merge branch 'master' of https://github.com/BhallaLab/moose-core
66f55c2 A check made to see if python-libsbml modules is installed if yes then reading and writing to SBML is done, else a warning message to install module is done
073ef60 Merge pull request #144 from dilawar/master
94b686a Fix to BhallaLab/moose-core#143.
b460557 Removing c++ depenedency of libsbml and its files
fea73c3 Merge pull request #141 from subhacom/master
7644e69 Fixed adding spike generators in ReadCell dotp.
3928fae Merge remote-tracking branch 'upstream/master'
5822181 Merge branch 'master' of https://github.com/subhacom/moose-core
79d5a5c Updated generated neuroml2 module and test file.
5a4197c Merge branch 'master' of https://github.com/BhallaLab/moose-core
06aea5b SBML is removed from the make file
2a5bc46 Merge branch 'master' of https://github.com/BhallaLab/moose-core
1a55310 Fixes for enzyme rate scaling when reading kkit files
8f44029 Merge pull request #140 from dilawar/master
f9e8720 Merge branch 'master' of github.com:BhallaLab/moose-core
1aee89a When WITH_SBML=OFF is given from command line, do not compile its support.
c959613 Merge branch 'master' of https://github.com/BhallaLab/moose-core
00a9171 Fixed access functions for kinetic objects and solvers
d70da97 some more colors to ignore which are light
4d89fd6 color if not defined in genesis then random color from pyqt Qcolor matplotlib files are taken as saved, matplotlib
5ecd2b1 all the co-ordinate are calculated and pass from kkit to this file and only we run in commandline then auto-coordinates are calculated with appropriate zoom factor
27bfae9 using graphviz_layout instead of pygraphviz_layout to get the position for auto-coordinates for layout the moodels
1f93ddb Removing pygraphviz lib dependency and using pygraphviz_layout to get the position of spring_layout
2c421a0 readSBML gets x and y co-ordinates from the file and loads it
eba7d75 cleanup in layout co-ordinates to save the model from moose to genesis
17863ee Layout co-ordinates from GUI is saved into SBML file, 2.Automatic Layout done using pyqgraphviz when model saved from command line to SBML file. InitialConc are saved with mole as default units
395daa7 Fix for muParser for C++ 10
ef2196e Adding quot operator in muparser.
6deb249 Merge branch 'master' of github.com:BhallaLab/moose-core
a6f8bab Updates to rdesigneur
b922890 Fix dependency on hdf5
6f7e46d cleanup
b943072 added networkx's Graph for layout the co-ordinates when model is save to SBML at commandline, if model saved at GUI level then pyqt's scenepos which is used for layout in GUI, those co-ordinates are used
8b1a05d Co-ordinates,group,textcolor and background color are written to SBML file in Annotation field
2718470 auto co-ordinates if one saves model from commandline and also cleanup with co-ordinates for genesis
41b6bfb color index is cleanedup according to genesis requirement and co-ordinates calculation is removed, since I am sending ScenePos
ce6b740 cleanup in writing genesis file with scene co-ordinates and few other clean up
8f2a3e1 Added compiler macros for AppleClang.
076ecf6 libsbml-5.9.0 is not available on brew. Build breaks with sbml 5.11.0
2976483 Fix apple build. adding -stdlib=libc++ to cmake.
530d69b Merge branch 'master' of https://github.com/BhallaLab/moose-core
d8cd4bd Updated python setup script to include streaming classes
5d6ee59 Actual fix for issue #110
5df0a7f Merge branch 'master' of https://github.com/BhallaLab/moose-core
39145e3 Merge branch 'master' of https://github.com/BhallaLab/moose-core
2634422 Merge branch 'master' of https://github.com/subhacom/moose-core
ddbdd8c Removed mgui and moogli from Python setup.py
c2fa2cf Added hsolve test comparing to NEURON

git-subtree-dir: moose-core
git-subtree-split: c2c32b97caecd422d6bc9398094073ce9f1b7492

build environment from precise to trusty.

Added clang compiler also to travis.

path.

git-subtree-dir: moose-examples
git-subtree-split: 0494d058023aca7e6ffefd414fb3c7e6b4397dc1