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

14e2d78 Fixes broken Makefile. Object MMPump.o not found error is resolved by commenting out the object. Either source is missing for it was introduced by recent PR.
aeddce7 Fixes to python3 test command in travis script. Previous fixes passed with python2.
00ad9e2 Fixes to recent Travis build failure.  (#170)
3ebc0a5 Merge commit '5bceacfe'
df5ff48 Merge branch 'difshell' of https://github.com/asiaszmek/moose into asiaszmek-difshell
e4a4bcd Change order of operations to slightly improve accuracy
aacebcc Small changes to make the code more alike genesis and other moose objects
4246932 Difshells and difbuffers initialize close to equilibrium
40a200f Add forgotten setting of helper variables to zero after calculations
dad35e6 Add state in t(i-1)
45c2286 Fix wrong definitions
567444a Fix errors in volume calculation
4e0a857 Indentation
cb40719 Add MMPump to scheduling and makefiles
bfc456c Add MMPump to DifShell
be1ceac Implementation of MMPump
c721713 Add ticks for DifBufferBase and DifShellBase
a3bee38 Fix bugs: DifShell now compiles and seems to give correct results
b131c44 Fix a typo in zombify
f1cbfb0 Rewrite DifShell. Inherit from DifShellBase
1486cdd Write base class for DifShell
336cbd1 Indentation
d8ee906 Implement exponential Euler for DifShell
f72d6a1 Move source messages to class. Correctly initialize Faraday's constant
b309dc4 Move source messages to class
5d3b7d2 Make DifBuffer look more like other moose classes and fix ticks
9a1e166 Add DifBuffer to clocks
f949b27 Add DifBuffer to compilation
5418e0b Fix no ticks when initializing difshells warning
5fba26e Remove useless variable
7e29b64 Reintroduce an old version of DifBuffer from moose
8f544e6 Moved to cmake folder.
ae1a5ba Merge commit '0d12ebb0'
3ac6c58 master branch.
65c371c Fixes to BhallaLab/moose#204.

git-subtree-dir: moose-core
git-subtree-split: 14e2d78a7b6e41e67bdce6e3a07fa0d65565744b

1b5b9a9 cspace and genesis model can be merged, yet to check what will happen with co-ordinates
9a405f6 for merging model one can pass file path or the modelpath
51da21a auto-coodinates are not done here, writter(SBML or kkit) will take care
4ba03b7 spell mistake
355e3e6 missing msg definition
3969bcb removed SBML option in Makefile
d1c4119 Merging 2 genesis model
1469b6e clean up in writting plot when file was read from SBML
4894a96 changes made to co-ordinate calculation depending where it comes from (GUI/direct), and type of file (GENESIS,SBML,cspace)
c11fcf0 validation.py is added: common place to validate SBML model before reading and writing, various changes made wrt chemUtil
6e7fa32 changes made to add chemUtil as a package and moose.py spell mistake
4551455 removing pyc files
e6f8c8f chemical based utils like add_delete_ChemicalSolver, chemiConnectionUtil: where chemical objects and connection are searched, graphUtils: used just pygraphviz to layout the model when x and y position are missing e.g for cspace and SBML models

git-subtree-dir: moose-core
git-subtree-split: 1b5b9a9104c0b7f461b569f62abf5f78fd531230

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

bd86fb5 Update INSTALL.md
3602353 Update README.md
f96dbda Merge pull request #155 from dilawar/master
50d720b Merge branch 'master' into master
b408e36 Instead of simple sin/cos use fmod and divide method. Sin/cosine functions gets value of 1 or many points near the maxima when simulation time is large (T for sin/cos). This changes fixes that.

git-subtree-dir: moose-core
git-subtree-split: bd86fb53a865dce7d482e21f959513e5621b1062

6a6bcc1 Python module can also use VERSION file generated by CMAKE. Copy to build directory for not-in-source builds. BhallaLab/moose#200.
7805364 Failsafe mechanism in VERSION reading script.

git-subtree-dir: moose-core
git-subtree-split: 6a6bcc15556a58e08c24203599c3c84837eb65bd

9eeca0c Fixed a typo in setup.py file. Due to which installation was failing without any warning.

git-subtree-dir: moose-core
git-subtree-split: 9eeca0ca8135fbf3c8fe7dd65ce408681b1e4605

14cf2df Fixed the setup.py file. Use absolute path for script to determine absolute path of VERSION file.

git-subtree-dir: moose-core
git-subtree-split: 14cf2df3a65456c6b4ce67b2d34110fd3400c982

343cb02 Fixes to  VERSION issue BhallaLab/moose#200.
835bf9a Added a version file.

git-subtree-dir: moose-core
git-subtree-split: 343cb02705b0874ad0035eea648019420475f7ed

ed5f015 Update README.md
a4a5cc1 Fixed linking error compiling with new gcc.
9a82850 Merge commit '912c550e28d1fccfd310c5968a07ae38dc60c698'
0fb7431 Added option to explicitly set CMAKE_DL_LIBS flag (-ldl).
da5fd97 Merge commit '9296cecdffbe647a929af4792360adbc3768e4bd'
093e681 Disabled unused part of code #86.
c698620 Merge commit '11af2e3b2ecd7b31aefa957412abb5b64ce54014'
57714ae Fixes to VERSION bug. See #BhallaLab/moose#200
59512e1 Merge commit '1d69d002939cc4b270ff4fc51e8a4800a6fbdad1'
3adb8b3 removed a print statement
9aa9405 Use git to generate version when not passed via command line. BhallaLab/moose#200 .
2f8a48e Merge commit '18331bb5a2f6aa2918a4e49b178297a79e3c791b'
c9714fd Merge branch 'master' of github.com:BhallaLab/moose-python-package
df2186a Merge commit 'ec45fa526f0e2de2b49bf05f3f7f8ddb1c7ff463'

git-subtree-dir: moose-core
git-subtree-split: ed5f0151b5c12301b826e47e5a1daaaa7044a714

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 conn...

a15a538 Merge pull request #131 from dilawar/master
1800283 Merge branch 'master' of github.com:dilawar/moose-core
2ad812f Rdesigeur by sarthak,
8e87707 Fixed the streamer test.
e62ec09 Merge remote-tracking branch 'bhallalab/master'
002edb6 Fix to BhallaLab/moose-core#130.
d7ebbe7 No need to have header name in inverted commas.
414a8d9 stimulustable is check and some more correction
343a08a First version of model merging pools and reaction are done
943f96f  clean up in notes field
f2b71f5 Merge branch 'master' of http://github.com/BhallaLab/moose-core
c742934 kkitUtil: check to see if the color goes beyond genesis color Sequence, _main.py: eliminated enzyme cplx pool to genesis under compartment
9aca1c1 Merge pull request #128 from dilawar/master
322093e Streamer uses name of the table whenever possible.
5be9eb4 Added getName, setName to table. If these are set, use them in Streamer class to write the header of csv file.
f9178d2 Merge branch 'master' of github.com:BhallaLab/moose-core
3d420b0 species concentration/amount is calculated depending on the hasOnlySubstanceUnit flag
9188681 Merge branch 'master' of github.com:BhallaLab/moose-core
cf3d4f8 Merge branch 'master' of github.com:dilawar/moose-core
4d98756 Write path without [0] in streamer numpy table instead of table name.
9b143e4 reaction and enzyme are added with the ratelaw
b2fbc15 Merge branch 'master' of http://github.com/BhallaLab/moose-core
0a765fb Rules are added
07a68b9 If -Wno-unused-but-set-variable is supported by compiler, enable it.
d98241c Merge branch 'master' of github.com:BhallaLab/moose-core
d22bfea Moved Doc from here to BhallaLab/moose . In docs folder.
9f18f0a Merge pull request #125 from dilawar/master
a942a4c Fixed the failed build on travis https://travis-ci.org/BhallaLab/moose-core/jobs/134133078
3d6a8cc Added support to float and double to numpy format. Fixed some documentation about Streamer, correct dt is docstring. More assert statements in streamer test script.
aada8c4 Merge branch 'master' of github.com:BhallaLab/moose-core
303ad71 Changes for gcc4.4. on nargis.
1af4a69 Temporary change before switching to another branch.
0018c55 notes are written for species
895766a species added
a7e9509 paremeter and compartment info is read back to moose
2b9076e  update with more details
170739f Put some more utility inside namespace moose. When writing numpy format, do not write whole path in header. Just name would do.
f01727c Merge remote-tracking branch 'bhallalab/master'
7e95a6d A fix to failing unit-tests. When user writes /compt/a/b, inside MOOSE it is represented as /compt[0]/a[0]/b[0] which could be annoying for Streamer user. Just remove [0]. For other [n], don't do anything.
21fe695 Bringing back some changed undone by bad merge strategy. This should now pass on travis.
ca8d55b Merge branch 'master' of https://github.com/BhallaLab/moose-core
c165976 Fixes issue dilawar/moose-core#3  (#123)
c17df70 clean up in filename while writing into SBML
db701fc Enzyme's are written
320b0c3 Function and reaction are written
a8bfc7c compartment and species are written
008e25e moose Annotation like runtime,dts and plots are written
3ba5e33 units are written
bcfa3c7 Merge branch 'master' of http://github.com/BhallaLab/moose-core
d3b3789 firstphase of write file
4418691 For cmake, enable the c++11 support on compiler which supports it. This should fix ">>" to "> >" error in template parameters in boost code which is only supported in cmake build system.
dc9d0c3 Merge branch 'master' of http://github.com/BhallaLab/moose-core
156e762 python readSBML file
2786757 Fixed #124. Not using gsl_rng in global rng. It is not working as expected in class RNG. Using Subha's mtrand() when boost or c++11 is not available.
eecc171 Adding a small print statement about why assert failed in rdesigneur.
6454673 Merge branch 'master' of github.com:BhallaLab/moose-core
270f1d6 Fixed #112. Not using gsl_rng in global rng. It is not working as expected in class RNG. Using Subha's mtrand() when boost or c++11 is not available.
738d9dc Fixed issue #124.  Adding the issue #124 file to repo for reference. Can't reproduce the error with latest commit (this and previous one).
cc85cfb Update README.md
af178bf This fixes the missing time column in streamer. dilawar/moose-core#3.
9faf02e Don't rewrite the table path before writing them to csv in header. dilawar/moose-core#3.
806f6a1 Checks if not of tables added are more than 0 or not. If zero, then disable the streamer. Notify the user. Issue dilawar/moose-core#3
0a93eaa Importing <cstdio> so that it passes with legacy makefiles as well.
4dc2a6c Merge branch 'master' of https://github.com/BhallaLab/moose-core
56fdc36 Fixes to issue #116  (#120)
357b1b5 Fixed the test script. Method rk4 is not good enough when using boost. Use rk5a.
8057a8f Generate h5 name using tmpnam. If tests are run by two different users on the same system, there won't be any issue with permissions. However this makes testing bit harder during development.
b01caf4 Fixes to gcc-5.x on Ubuntu-16.04.
fc98bfc Adding random library to link flags.
ceea4f0 Use RNG object rather than pointer. Can't figure out why pointer did not work well.
ea5529d FIxed -std=c++11 error.
014175d Fixed issue #116. Using real_distribution instead of int_distribution. Let the library take care of scaling to between 0 and 1.
ab91625 Merge branch 'master' of github.com:BhallaLab/moose-core
e23c827 Some temporary changes before merging. I forgot what there are. Probably RNG initialization is changed.
cf73c1f Update of python setup file. (#118)
51bcf63 Disabled part of code which checks for extension . On some platform it reutrns x86_64.so etc, which probably we don't want. In any case, if build fails on open build service, we can bring it back #78.
fb558d8 Modifying SBML_LIBRARY related macros. Since libsbml is now distributed from mosoe repo as well.
487587b test scripts points to directory commited by @subha #issue #94.
e47a492 Update INSTALL.md
13afeaf Update README.md
8b33ae5 Merge branch 'master' of github.com:BhallaLab/moose-core
1268296 Merge branch 'master' of github.com:BhallaLab/moose-core
808ae94 Update INSTALL.md
6316820 Update INSTALL.md
2522f47 Merge branch 'master' of github.com:dilawar/moose-core
3f13efd Temp commit.
347e5b0 Update INSTALL.md
d14e4e8 moved to appropriate doc folder.
5a48285 CheckMOOSECompiler -> CheckCXXCompiler.
5ecd06e Updated INSTALL.md file.
0c42d28 Merge remote-tracking branch 'bhallalab/master'
87c193d Deleted cymoose from master branch.
e77361c Fixed moose building after moving _moose target to subdirectory.
af97ec3 Cymoose remains only in my personal clone branch cymoose. Removing it from master branch.
b3542f6 Cleaned up Cmakefile.
7fec36b Moved pymoose target to its own directory.
7575c55 Update test_ksolve.py
904e32a Added missing cmake file.
1998e27 Using ptr instead of object of RNG.
1ee1427 Added ksolve test.
fbf9d90 Test script for ksolve is modified. Total 40 pools.
2ea5ed1 Separate file to check compiler macro.
c7d3e15 Removed the copy constrcutor from RNG class.
1acec97 GssaVoxelPools gets its won random number generator. Had to remove constantness of a function to be able to use uniform( ) or rng call.
08fa1ed test display is changed a bit. Removed some hanging c++11 auto .
c6bc8c3 Printing tests name during tests.
4116cc5 More verbose output when tests are runnug. Added a macro which runs test.
d1c77ce Replaced simple assert( doubleEq(a, b) ) with ASSERT_DOUBLE_EQ( "", a, b );

git-subtree-dir: moose-core
git-subtree-split: a15a538e22f0cd62de95532c2932156055d58673

git-subtree-dir: moose-core
git-subtree-split: 1318029dc3bc67f182dfe22369929b8abc0c9b52