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

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

Conflicts:
	CMakeLists.txt

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

95fe1a7 Force --install-layout=deb when on debian/ubuntu.

git-subtree-dir: moose-core
git-subtree-split: 95fe1a7b8f24b50d600d5e7c3a1d0171a809b9aa

a13dbd9 Better formatted output on running tests. These tests are moose-examples scripts which are known to pass.
1409792 Fixes to debian related python install. When --prefix=/usr is given, its installs in site-packages rather than dist-pacakges.
4f3e773 If for some reason matplotlib is not imported successfully, disable kkit import.
4f6f8b1 Fixes to debian related python install. When --prefix=/usr is given, its installs in site-packages rather than dist-pacakges.
7771173 Merge branch 'master' of github.com:BhallaLab/moose-core
8fff67d Refactoring in cmake file.
3e1e043 Minor changes to test script: Dont wait till test is over to print which test is being executed.

git-subtree-dir: moose-core
git-subtree-split: a13dbd9f31f93d915faee59f440cfe6bbc8ce428

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

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

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

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

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

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 (compartment and color) is added
b76929f Find gsl header as well.
4df3c47 If user set the GSL_ROOT_DIR then do not search in system dir.
1ef020e Always use private muparser.
abfa2c8 Merge branch 'master' of https://github.com/BhallaLab/moose-core
ff7bf04 Moved isBuffered field from Pool to PoolBase.
c470f10 group information is populated as per SBML rules under listofGroups instead of annotation
70c1e8b clean up in documention
98c5a76 Hopefully description given for merging the files will be clear to user

git-subtree-dir: moose-core
git-subtree-split: c15c1b1b41e429e96ea769c85c105e6167c68ffa

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

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.

TODO: ctest must check each example as well.

can handle environment variables cleanly.

can handle environment variables cleanly.

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

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