bumped version.

49d5b3ef6b Merge pull request #255 from dilawar/master
f498d7c6a4 Merge branch 'master' of github.com:dilawar/moose-core
c09dd9936f Cut down on unneccessary looping. It is logically equivalent to original block.
aab34e125d Merge branch 'master' into master
3568083113 replace has_key with python3 compatible statement.
026d0a39b1 updated pre-commit config.
b811def3bd Merge branch 'master' of github.com:BhallaLab/moose-core
5bc1e1410a Merge pull request #254 from upibhalla/master
b08b888f56 Merge branch 'master' of https://github.com/BhallaLab/moose-core
945fb6b961 Added funcDt to rdesigneur arguments, set sensible defaults
760f554966 Update Function.cpp
8e9bcb58ac Merge pull request #253 from upibhalla/master
2f8dc9fcfe Merge branch 'master' of https://github.com/BhallaLab/moose-core
b55e1a74ea Update to Synapse to permit set/get access to addSpike. Cascaded onto all SynHandlers. Update to rdesigneur to permit fullscreen display of Moogli.
6eca687a68 Added deploy section in travis. Deploy on PyPi. Needs to add script t… (#251)
c8f9101621 Fixed cmake error on osx when not compiled in debug mode. Affect only >=cmake-3.6
f6ab07d0ef Update README.md
0d3f850fe5 Update README.md
cc94e3bd61 Set VERSION_MOOSE only
948406bc17 Marked as release candidate 3.2.0rc1.
b675c4d1bf Fixed build failure due to newline in output variable.
bf8d39351e Add git hash to version.
d95e58650f Python wheel for pymoose (#250)
edbb4ce966 Fixing VERSION; MOOSE_VERSION; project name is moose-core.
e245ef6a4d call project moose-core.
9061927ca7 Build GSL with fPIC.
230466ff32 updated dockerfile. Added missing gsl library.
69bc228b34 rename to pymoose.
41ef965e75 Heredocs are not supported in docker.
f370b4aa19 Docker file has the script inline.
b8b9679943 Time to merge into master branch.
9c7241f1bd Wheels are built. Now use manylinux docker file to build them.
c439f55046 Build in manylinux environment.
108f71809d Wheel is created.
d08ddf290f removed file.
9d654b4cba no need to link with PYTHON_LIBS.

git-subtree-dir: moose-core
git-subtree-split: 49d5b3ef6b585ff1c64734f447ac08cd67d9996a

Created links to CREDIT and INSTALL  file in README file.

Moved authors/credits to separate file 'CREDITS'.

better formatting at the top of readme.

Quick link to packages and documents.

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

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

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

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

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

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

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

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

Fixed typos.

removed url. URL is listed on the project page.

Added readthedoc link.

cmake 2.8 which is now the minimum version required to build moose.
Revered back Makefile in moose-core.
Update README.md
Fixed indentation.

Fixed indentation.

git-subtree-dir: moose-gui
git-subtree-split: a3d3a067901ee0f1f183f50f667a98bebf3e447f

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

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

Added few more instructions on how to install moose.