REVERT: 69e0354705 Create CONTRIBUTING.md

git-subtree-dir: moose-core
git-subtree-split: b09650323312b56d2cfb777947f5db45f44b578a

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

2ecab963b Merge commit 'af3c29a4'
ad3ec12ec Fixes to allow moose module to be installed and imported (#220)
0fb32dec5 All changes from previous repository. No new file is added here.

git-subtree-dir: moose-core
git-subtree-split: 2ecab963b249229174cfef1fafd282977a7920c3

b3b597f41 Removed legacy Makefile based build flow. CMake is only build-system now. #180.
20dc0a598 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
9373d1bc1 python Counter function removed, just to give backward compatibility for Centos6 for python 2.6
e8300d7e9 added to ask User if merged model to be saved
933b25971 Made ReadSwc less verbose. Fixed bug in SeqSynHandler in application of sequencePower.
662eaa2e1 Added sequencePower term to SeqSynHandler to achieve greater specificity for sequences vs all inputs on at once.
7ccc8a2b1 Merge branch 'master' of https://github.com/BhallaLab/moose-core
fe5765ca7 More fixes to plot_utils
6a9a618e7 Fixed the error in plot_tables utility.
658af76a4 Fix for Table.vector bug (#179)
423dc9dc6 Merge branch 'master' of https://github.com/BhallaLab/moose-core
200871a9f Added in hack for rmoogli to display time
157c501b9 reaction or enzyme name is empty then id is taken as name while reading files from SBML
43a235040 color and textcolor inchanged for enzyme
02de4c37e Bugfix for SparseMsg, corrects allocation of synapses when setting connectionList

git-subtree-dir: moose-core
git-subtree-split: b3b597f411500f5956976349f4d56b1cbc94f734

ef066f704 Fixes to violation of mass-conservation when Dsolve and Gsolve run for very long time (#176)
46ea47260 Local Documentation (#177)
852819875 Added connectionList field to SparseMsg to allow direct control over connection matrix. Some sanity checks in SparseMatrix to go with this.

git-subtree-dir: moose-core
git-subtree-split: ef066f70493fe05fe05393af48449b264c8f4bc0

6099142 Added missing Revision macro file from chamcham branch.
d0a81a4 Merge commit 'b4d20b7c'
79d7a4c Fixed revision issue.
985e8b5 Cmake changes from chamcham branch. Build for launchpad.

git-subtree-dir: moose-core
git-subtree-split: 6099142d63632177056c3077d6d84035388cb93f

4f391e1 --std=c++11 is must now. Fixes BhallaLab/moose#214.
718252a Do not copy VERSION file for python. Lets find a better and more portable solution.
f26225d Updated default version in setup.py file.
1476ea1 Merge commit '0ff1b77a'
0da1cc4 VERSION string is fixed to today's date if not given.

git-subtree-dir: moose-core
git-subtree-split: 4f391e1ef906eacb103bb85d723ee98453f06d5b

eb878dd Merge branch 'master' of https://github.com/BhallaLab/moose-core
68ef2ed Less verbose ReadSwc and rdesigneur. Fix to SeqSynHandler
2c93c52 return type from None to moose.shell
07fc0f9 Ignore /opt/bin/python3 on travis. Numpy is not available for this path. Try /usr/bin/python3.
45fb960 mtseed and mtrand are under moose namespace and defined in global.h file. Fixes for travis failure with BOOST.
dfa0ab1 Explicitly naming the source file in synapse directory.
cd32764 old makefile based flow is deprecated. Recent commit fixed the test faillure.
c0f5469 Merge branch 'master' of https://github.com/BhallaLab/moose-core
fd96222 Verbose flag for rdesigneur; added synapseOrder to SeqSynHandler, fixes to testSynapse
e7d57cf plot_tables can plot on user given axis.
43faa23 mu.plot_records is renamed to mu.plot_tables.
99f5ee7 Merge branch 'master' of github.com:BhallaLab/moose-core
953142d Fixed for snappy builds.
6931e80 Let cmake find path of Python.h fi...

270c880 Search numpy path in cmake are fixed for snapcraft.

git-subtree-dir: moose-core
git-subtree-split: 270c880c3a3005c3ed1000a87069a0f6bb1bdb0f

669b981 VERSION conflict file is added
29362b6 Merge commit '628138cb'

git-subtree-dir: moose-core
git-subtree-split: 669b981fd06bf9b0919dca08cf87505c2f411802

c15c1b1 Changes to testSynapse so it can compile in DEBUG mode. Issue #175.
e4caa2f Merge branch 'master' of github.com:BhallaLab/moose-core
f99cd77 Removed VERSION file .. again.
7646e6b Python3/python2 compatible import statements.
b77448d Removed VERSION file from source.
97e1a25 Fixed broken test in synapse/testSynapse.cpp file
eb4eeb2 Install python3-numpy using pip on travis. Another failure is with synapse tests setResponseScale and setWeightScale ; these functions are not available.
1998b5f Fixes to python3 import .
22849ab Find python3 on travis.
f5870c9 missing parentheses for print stm
17462d1 Merge branch 'master' of https://github.com/BhallaLab/moose-core
9471341 Group's with annotation is written and read from SBML model
5ab33ad Put SparseMatrix access functions into SparseMsg
46d80cc All default units are added, as some of the simulator requires all the units to be specfied, km unit is defined, group and annotation to the group (compartme...

434c478 qMerge branch 'master' of https://github.com/BhallaLab/moose-core
425d8c8 writeKKit: checked if matplotlib is install before importing, moose.py:removed all unwanted check's on genesis_support and sbml_support
0791eb5 Fixes to SeqSynHandler
51a3a30 Moved Pool::increment, decrement and nIn to PoolBase for uniformity with Solvers. Dummy functions except in Pool and BufPool
1c9a9df group info is added to plot
03dbc2c While connecting table for plotting, a check is made to see if its pool
fdc4924 Cleaner way to replace the string
4f92820 libsbml spell corrected
22a276d unwanted print statement cleanup
2c48b1c reading group information from the SBML if exist into moose
e68a509 spell correction
8deaed8 switched from new to old to old to new while providing the files for mergering
ef9edd1 clenup while loading model and solvers are deleted
c2383e2 python3 compatibility with print statement
4ac79b1 Function cleanup while mergering and path cleanup
6fd5ed6 chemUtil and merge folders also needed to copied while using "make install" while using cmake
caaafc9 Fixed test script for python3. Removed VERSION file. Pull request BhallaLab/moose#206 .
a9a8344 Merge commit '7c713058'
6d907ee Script testing DifShells
0dd5cd6 Merge commit 'a5122cfb'
4fc5760 Fixed docstring on example.

git-subtree-dir: moose-core
git-subtree-split: 434c47885637c72d820f92914660a679b34c0301

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 Impl...

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 f...

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 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

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