d27db9c8e7 Do not use -p switch. its not easy to get required info from all linux-distributions.
e667953634 Fixed message to set in cmake.

git-subtree-dir: moose-core
git-subtree-split: d27db9c8e732a8b7a34f7670a19d16e6ccaa6118

0b125f6940 Fixed typo in cmake file.
f3118f0115 multiple fix to build system. - dont use python setup.py install . It does not work anymore if --prefix   directory is not in PYTHONPATH. - Use python setup.py bdist -d INSTALL_DIR and let cmake unarchive and copy it   to desired location. This is much better solution.
03d589931f Use bdist instead of install for creating binay distrution. During installation, untar this to destination.
a08658e990 Tweaks to setup.cmake.py file.
c5f1d919f4 Test on travis.
6b32fde2bd Merge commit '6d651b60'
324a20c1be Merge commit 'e0b8959c'
59f6e9ed1a On debian/ubuntu install-layout option is set to deb. [skip ci]
62201d9f65 Merge commit 'f80ae40d'
9b81dfc5d9 This fixes moose but a better solution to install pymoose in moose-core must be found.
7e27f809de Merge commit '6f7697fb'
939c734c36 Merge commit '627f1ce1'
4775933d2b Merge commit '7b3c355a'
43c06745f8 Squashed 'moose-core/' changes from d4417dcffd..2657e3345e (#222)
8c9ad49b79 Fixed the syntax causing failure.
397efafe2a Handling MOOSE_VERSION is better way.

git-subtree-dir: moose-core
git-subtree-split: 0b125f694049577a63cefd5d2259edb24889073c

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

0c33b2c333 remove setup.py. It has been renamed to setup.cmake.py to avoid confusion. This file is to be used only by cmake.
079730d06d Added missing package data.
59d374fa48 removed deprecated setup.py file.
9d3f7439f6 Merge remote-tracking branch 'origin/chamcham'
28ded4be72 matplotlib is not essential dependencies in tests or in any moose import. If NSDF support is not found, do not fail the test.
b7294b2814 More informative message if plot utilities are not loaded.
4678f1a263 Merge branch 'master' of github.com:BhallaLab/moose-core
667a3d254f more detailed error message if neuroml2 import fails.
5d504a5a1e Merge branch 'master' of https://github.com/BhallaLab/moose-core
c5c5854fe8 Added extra args to setup.py.
07f19011c8 install using debian layout.
0c3c2b7416 Merge pull request #249 from dilawar/master
03951bd314 When build in DEBUG mode, we never go to negative values in this test script. This causes test to fail on some unix platform in DEBUG mode.
2e6524b9cf if libneuroml and pyneuroml is not found, do not load NML2 support .     Ignore silently. Print help message when user call NML2 related function.
30fc7d0636 Turned it into a module so 'absolute_import' can work.
d9853b5322 Merge branch 'chennapoda'
00170beb15 Merge pull request #247 from dilawar/master
b0adf404cc Added libneuroml and pyneuroml in dependencies on travis.
0d831227cd renamed tests/python/neuroml to test/python/_neuroml so it does not clash with import neuroml. Ready to be a PR. Integrate BhallaLab/moose-core#246 into moose import system. Exposed moose.mooseReadNML2 function for gui etc. Added dummy docstring. Deleted redundant files.
792b4e7d43 Added nml2 test script.
1e3413349e Integrated NML2 support BhallaLab/moose-core#246 Made is compatible with python2/python3. Needs testing before merging into upstream.
596b9d2e1a Merge branch 'master' of github.com:BhallaLab/moose-core
740f9c6eb4 Added jenkinsfile for local testing over jenkins.
7dcd970481 Merge pull request #246 from pgleeson/master
bb8c8a94b3 Minor edits
c2872f7d4e Merge pull request #2 from BhallaLab/master
a520f8aed8 t test script to test BhallaLab/moose-core#242 .
d6ba37e003 Merge pull request #244 from upibhalla/master
d8ad6d6e53 Exposed field Stoich::allowNegative to control whether the solver permits negative values in simulations.
0e460485e5 Merge pull request #243 from upibhalla/master
f2553db028 Merge branch 'master' of https://github.com/BhallaLab/moose-core
32430d1f1d Oops, another silly error in the negative concentration test.
a2fee560b8 Merge pull request #242 from upibhalla/master
53244691c4 Merge branch 'master' of https://github.com/BhallaLab/moose-core
369b26c369 Fixed major error in GSL solver in VoxelPools. I had introduced this when putting in check for negative concs, for some reason first set of tests didn't identify this bug. Works for several tests now.
394032dcfe Merge pull request #241 from hrani/master
bce317e34c Few clean up while reading and writing from/to SBML
d7dbc9997a Added flag Stoich::allowNegative. This defaults to False. If true it allows pools to take negative concs, needed for general ODE solutions but illegal for chemical systems.
158db52f1f Merge pull request #238 from BhallaLab/brew
8c93330ca3 Improved temperature dep
afd925b101 Merge branch 'master' into brew
818ad2df5f Improved unit handling
54b505d6da Merge pull request #237 from hrani/master
fe628d39ae Test homebrew formula as well on travis.
337bab4ce5 Update .travis.yml
2b54325545 clean up in print stm
a592ec8875 existence of model path is checked, clean check is made for enzyme and function before writting into file
1398206c9d Merge branch 'master' of https://github.com/BhallaLab/moose-core
3b920f3fc4 Improvements
3cc29d3fe5 Improved saving of rates
24710aa103 More general
2a1b06477f Installable
f2188a3903 Read populations/inputs from nml
fc689f018f Allowing -nogui
1bc8a23cfc qMerge branch 'master' of https://github.com/BhallaLab/moose-core
abf8e5465a Now works with libNeuroML
2ec562cba7 Working HH example!
010b0f9db8 Passive test on new cell
2cb3edaf20 Working passive example
cdfb8e1fc7 More tests
3f6de38f50 Not completely failing...
152857db78 Ignore build dir
2b36a6b4d8 Update example files
f7228682d4 Merge branch 'BhallaLab-master'
61453b8a9c Merge branch 'master' of https://github.com/BhallaLab/moose-core into BhallaLab-master
9cc0e101d0 Merge branch 'master' of https://github.com/BhallaLab/moose-core
f3c6a71b9c added python3 for compliation which was removed
0920cfaf1b instead of importing rmoogli in init file replaced in rdesigneur.py,checking if travis passes for python3
6a4b102099 Updated pre-commit hooks in chamcham branch.
411a71798a Updated moose_test module. Function test( ) can accept timeout parameter.
226e8662c4 Force --install-layout=deb when on debian/ubuntu.
7032ffdfe7 Fixed kkit tests.
f0ec0c3759 No inbuild test should depends on matplotlib.
ccb43d16a7 Fixes to debian related python install. When --prefix=/usr is given, its installs in site-packages rather than dist-pacakges.
65954b71e8 Minor changes to test script: Dont wait till test is over to print which test is being executed.
327d0aa4ff Updated sanity test with version information in ctest.
8bc1994345 __version__ = version( ) is both python2 and python3 compatible.
fac27902c2 Added __version__ string in __init__.py file.
ab03233775 Merge branch 'chamcham' of github.com:BhallaLab/moose-core into chamcham
a567aa1d5b Added __version__ and version( ) info.
85f1f1ef2f Added `moose.test` to test `moose-examples` online (#189)
6fe5f5c7c4 Using absolute imports in 3.1.3  (#190)
027e40bfdb Fixes absolute import in chamcham branch as well.
474faafe51 Python3 compatible import mechanism,  NML parser fixes (#188)
4e915e0b0f Fixes to chemUtil import.
13e3cb8ad8 More import fixes.
25d3c43252 Merge branch 'chamcham' of github.com:BhallaLab/moose-core into chamcham
2ed651fc37 Fixed the plot util function (again).
4d4b275958 Deleted old/junk functions. Force python2 to honor python3 style import.
b899ada38b More fixes in plot utility library. If some function breaks on python3/python2, do not import the whole utility library.
f2a6d7b8d1 Removed junk utility functions. Forced python3 import style (PEP8).
a7a03c7852 Some renames.
ff84f3d0dd Added another function plotTables wrapper on plotRecords .
2fb7676353 Fixed error in plotRecords functions.
b32a39b444 Merge commit '9355916f' into chamcham
1eb8ca281c More changes to NetworkML BhallaLab/moose-core#218 .
0e0615c816 Fixes to #186 are integrated into chamcham release.
4a0d4f37df Fixed a typo in install instructions.
3498c1801a Bumped version to 3.1.2
fc14920945 Added AUTHOR and bumped the version up.
b5898ac306 Added missing 'moose.chemUtil' module.
d7c938283e Fixed revision issue.
1c1bbe059d Added GetRevision macro to get current timestamp.
ba9ec990eb Write the version to VERSION file so setup.py file can use it.
4e9aa317f2 Not reading version file anymore.
315837d775 Changes from master branch.
557184389c Packaging related changes from master branch to chamcham branch.
4d5c6a5d87 NO version file should be in-source.
de25310563 Merge commit 'efa006c9' into chamcham
52eeb541ef CMake related bugfixes from master branch.
9df1ba7fad Merge commit 'efc1324a' into chamcham
815a79a9db Fixed the VERSION file creation.
726e71c063 cleanup in demo, filemenu links
d5c5391949 adding missing files
5291f7c4fc missing folder/files
760274cbcc Changes made to gui to work with moose-core
be92816c83 Merge commit '36ca236d' into chamcham
74b43c3ef6 Enabled travis emails to developers for this release branch.
76bf85476e Related to #169 Dropped the support for VERSION file. 1) It would cause lot of merge issues if VERSION file is left in source tree.
00ea9d3c10 Close #169. Renamed MOOSE_VERSION to _MOOSE_VERSION.
da0db901b4 Changed MOOSE_VERSION to __VERSION__ since new cmake 3.7.1 sets it to empty. See cmake policy CMP0048.
a6a05eff71 Merge commit '41be11d5' into chamcham
b8a8b6d150 hotfix from branch issue167.
8a6346d029 Merge branch 'chamcham' of github.com:BhallaLab/moose-core into chamcham
7d4cf8b84b Changes from master branch. Test on macosx as well as linux. Quantified import to avoid self-recursion. Ran autopep8 on files.
de3d964f65 Changes from master branch. Test on macosx as well as linux.
9156b897da Fixes for issue #164. Also hotfix for branch chamcham.
34429e228e Using correct import
e2574fb25f Uses the MOOSE_VERSION value from CMakeLists.txt in setup.py

git-subtree-dir: moose-core
git-subtree-split: 0c33b2c3339d8a43f9de1fb31573cbea621739f6

bda9742 Merge pull request #236 from upibhalla/master
86751f2 Added more accurate error messages to ZombieEnz for reporting missing messages during solver setup
5d93f75 Merge pull request #233 from upibhalla/master
cc47a2d Merge branch 'master' into master
a7ac8f4 Merge pull request #234 from BhallaLab/fix_travis_nov_30
5a08c96 pip is renamed to pip2. This commit passes on local machine.
bf8585d Possible fixes to travis build failure on osx.
f61a591 Added hack for channel not scaling when compartment size is scaled. Checks for child object called scaleFormula.
dff5731 Merge branch 'master' of https://github.com/BhallaLab/moose-core
7f0eb4b Merge pull request #231 from BhallaLab/prefix_python3
1d99906 Fix for spine ordering. Added capability to do unordered_map which may help with some of the performance issues during setup.
296c030 moose-core does not handle debian layout anymore. This should be handled in BhallaLab/moose.
0433574 commenting out changes introduced by 985af4e. Reopened BhallaLab/moose#224.

git-subtree-dir: moose-core
git-subtree-split: bda97426c899b2f366d08bdf30cf0f69876c9567

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

e5ba823ba Merge pull request #227 from dilawar/master
9742b9e87 auto_ptr -> unique_ptr .
6f6015e46 scaled down chemDt and diffDt.
68c7001fc Added test.
c57990604 Fixed import issues in rdesigneur.

git-subtree-dir: moose-core
git-subtree-split: e5ba823ba8abd740f2d3323a5dd0c29f727309d0

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

2657e3345e Merge pull request #199 from dilawar/master
973dd380ba Deleted Makefile.
545b4241c8 Restore synapse folder back to 933b259 . synapseOrder is now working.
90711a865c execute_process is now used to get the extension of python module. See http://bugs.python.org/issue16754 in case build fails on some unix because of 'SO'.
5b0a529c4e We do not reply on VERSION file to create version. TODO: Use config.h.in file to populate VERSION information.
2749918927 Accessing an existing object (#198)
220128f284 Do not run DOQCS with moose-core. Test DOQCS with released package only. Do so in moose-examples repo.
ad2c63da12 Use QUIET_MODE=ON on travis.

git-subtree-dir: moose-core
git-subtree-split: 2657e3345e8b783cf22634680c7561f8dbd9f127

d4417dcffd Fixes to missing function declaration, post cherry-pick.

git-subtree-dir: moose-core
git-subtree-split: d4417dcffdd939de91bebf447ad776945c2fcc65

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

1cbe2f063 __version__ = version( ) is both python2 and python3 compatible.

git-subtree-dir: moose-core
git-subtree-split: 1cbe2f06372d760333681952d6f81e2087c90aac

d1130b7 Merge branch 'master' of github.com:BhallaLab/moose-core
967ac3b Added VERSION info moose.version( ) or moose.__version__ returns the version. It was lost somewhere in rrefactoring the code.
457850e Added version( ) and __version__ string.
2625fd0 Added `moose.test` to test `moose-examples` online (#189)
2a822a2 Added assertion in test case and remove import of matplotlib. BhallaLab/moose#221.
2484214 absolute imports are forced with python2 as well.
6c92901 All tests passes locally with python3.
bd78e14 Fixes to import statements.
5c3811e Print time information as well.
a7e715c Inbuilt moose.test( ) functions to run moose-examples. BhallaLab/moose-core#184.
c424e0d Fixes to chemUtil import.
f29e35e Merge branch 'master' of github.com:BhallaLab/moose-core
087aad0 moose.Compartment -> moose.element( ) in couple of more place. One more (#187)
d618fe6 Merge branch 'master' into master
4aca08a Merge branch 'master' of github.com:BhallaLab/moose-core...

ba97d4cc0 Merge commit '0014d826'
6aac85bad Follow up fixes to calcium-hsolve  (#221)

git-subtree-dir: moose-core
git-subtree-split: ba97d4cc05425dc8b8b42ee6f8976989e229a144

052318cb4 [skip ci] Moved git precommit script into script. if someone wants to activate it in her repo, rename it to .pre-commit-config.yaml and enable it
d15e77649 Removed legacy makefile #180. These appeared again because of push from subtree in moose repo. Sigh!
ed708e01b No-longer supporting Makefile based old flow on travis.
bea1f4a9d Integrated test script from PR BhallaLab/moose#218 . I need to confirm if results are correct.

git-subtree-dir: moose-core
git-subtree-split: 052318cb48027ca0c401a13be9fddd2b0d5a66b7

2c3fe7516a Merge branch 'master' into asiaszmek
9f3ffcb261 Merge commit 'e6e83b76' as 'moose-core'
be87aea0 Deleted moose-core due to dirty history in upstream moose-core.
1051706f Merge commit '48fc9733'
48fc9733 Squashed 'moose-examples/' changes from 2eb5fa888f..80169bcc5c
304173cc Merge commit 'd27e942f'
d27e942f Squashed 'moose-core/' changes from 69e0354705..b096503233
0f741382 Calcium hsolve (#218)
fbf9dbd4 Fixes to bad-merging.
2ea8560e Travis required changes after yesterday upgrade.
849103d0 Merge commit '320e525a'
320e525a Squashed 'moose-gui/' changes from d282884250..49779ba730
7fe1c2e7 Squashed 'moose-core/' changes from 2ecab963b2..69e0354705
faf993a1 Merge commit '7fe1c2e7'
edd901da Squashed 'moose-examples/' content from commit 2eb5fa888
be2d4ec3 Merge commit 'edd901da' as 'moose-examples'
423c4759 Removed moose-examples due to screwed up history with https://github.com/BhallaLab/moose-examples.
45f9e9b9 Squashed 'moose-core/' changes from b3b597f41..2ecab963b
7b366bcb Merge commit '45f9e9b9'
4c60725d Merge commit 'af3c29a4'
af3c29a4 Squashed 'moose-core/' changes from ef066f704..b3b597f41
60f3632e Fixes to allow moose module to be installed and imported (#220)
7ffff42d documentation branch merge request (#219)
ec194c8a Documentation final PR (#217)
0318bd7e Added python-lxml in dependencies.
226eb630 Added --git-ignore-branch option.
42cb3feb Fixes in timeformat of debina changelog. The debian parser has gotten very strict about formatting of time.
94e2ff2c git buildpackage is renamed to gbp buildpackage.
0fcf8252 Using dist:trusty by default on travis. Recent updated in travis Trusty's image has made installing openscenegraph-dev error-prone.
18ec171e Fixes to launcher.
6d0693d7 Changes from PR by Malav.
6e6051e4 Gettting docs from Malav pull request. Pull request is revered back.
a843c585 Local .gitignore. If exists, merge please!
813f7bc4 Adding doxygen file.
0cf3a18c Adding rst files.
24ebac50 All changes from previous repository. No new file is added here.
0f6f5d27 Squashed 'moose-core/' changes from 6099142d6..ef066f704
ec32a6f5 Merge commit '0f6f5d27'
57ffc864 Adding local changes.
cc8759c2 Squashed 'moose-core/' changes from 4f391e1..6099142
a9798ffc Merge commit 'cc8759c2'
b2fda562 Added missing Revision macro file from chamcham branch.
cc540278 Merge commit 'b4d20b7c'
b4d20b7c Squashed 'moose-core/' changes from eb878dd..4f391e1
2b8d61d3 Fixed revision issue.
5805bdf3 Added missing file after merging branches.
64799ebd Travis fixes.
b8673be3 Fixed to cmake which were causing launchpad failure.
5ace57ba Cmake changes from chamcham branch. Build for launchpad.
7bef269a Do not copy VERSION file for python. Lets find a better and more portable solution.
2ebd41f9 Updated default version in setup.py file.
25a907eb Squashed 'moose-gui/' changes from 6104940..d282884
224487f4 Merge commit '25a907eb'
02fcf721 Merge commit 'c37dddbf'
c37dddbf Squashed 'moose-examples/' changes from 7054325..8c7c00c
0ff1b77a Squashed 'moose-core/' changes from 270c880..eb878dd
2bd23400 Merge commit '0ff1b77a'
b498916c VERSION string is fixed to today's date if not given.
8287330a Enable chamcham branch on travis.
9cb49e27 Fixed for snappy builds.
debc6e63 Let cmake find path of Python.h file.
2ae2b209 Merge commit '4489d159'
4489d159 Squashed 'moose-core/' changes from 669b981..270c880
9e888548 More changes to snap. Needs to add Python.h path [skip ci]
0d29983a On master branch, the snap channel is edge [skip ci].
70fbb707 launched script is now snap friendly.
503c9ade Removed <<<<, ===  and >>> from improper merge.
de659651 Merge commit '349abe7e'
349abe7e Squashed 'moose-examples/' changes from 69062d9..7054325
7088b0c5 Added snapcraft file.
de4e03f5 added deleted files
7cb7cc7a temp deleted
0015fd23 Resolved merge conflict
15733245 temp deletion
6ed2f701 Squashed 'moose-examples/' changes from 7318878..69062d9
f890fa08 deleted unwanted files and added new files
0e491aa4 Squashed 'moose-examples/' changes from 8038f56..7318878
ccf3e614 Squashed 'moose-core/' changes from c15c1b1..669b981
593b3f73 Merge commit 'ccf3e614'
e565756c Squashed 'moose-gui/' changes from 2a1f94f..6104940
50279060 Merge commit 'e565756c'
c50a82a9 VERSION conflict file is added
24dea426 Squashed 'moose-core/' changes from 434c478..c15c1b1
ae611181 Create LICENCE
83152c5a Fixed assert by Upi
0e5351e9 Merge branch 'master' of github.com:BhallaLab/moose
9f653729 Removed generated doc from source tree.
0208d06a Merge pull request #210 from malav4994/master
ae36bc57 little bit change in docs/
55a2f09e Merge commit '628138cb'
628138cb Squashed 'moose-core/' changes from f3d0477..434c478
acafba2c Merge commit 'edb505a7'
edb505a7 Squashed 'moose-gui/' changes from 2ba6bd5..2a1f94f
fe2d8940 Deleted temp files.
88e9ca95 Merge pull request #208 from malav4994/master
12b07199 khali khali
30a89548 to put documentation in BhallaLab/moose
2936ba85 Merge commit '7c713058'
7c713058 Squashed 'moose-core/' changes from 14e2d78..f3d0477
f2b5cfdc Merge pull request #206 from asiaszmek/difshell-tests
3618469d Script testing DifShells
ac0b8002 Merge commit 'a5122cfb'
a5122cfb Squashed 'moose-core/' changes from 1b5b9a9..14e2d78
2edfcf15 Fixed docstring on example.
f95d827b Merge commit 'f0fd0e53'
f0fd0e53 Squashed 'moose-gui/' changes from e49ca7d..2ba6bd5
3324aa5a Merge commit '07ef36e1'
07ef36e1 Squashed 'moose-examples/' changes from ed3253d..8038f56
5bceacfe Squashed 'moose-core/' changes from 7c9fe23..1b5b9a9
d92afeeb Merge commit '5bceacfe'
1effa957 Merge branch 'asiaszmek-difshell'
bb650ae8 Merge branch 'difshell' of https://github.com/asiaszmek/moose into asiaszmek-difshell
6aa27cac Change order of operations to slightly improve accuracy
bc28246b Small changes to make the code more alike genesis and other moose objects
a4d7de8f Difshells and difbuffers initialize close to equilibrium
f6805f17 Add forgotten setting of helper variables to zero after calculations
f32bef60 Add state in t(i-1)
a7bf1414 Fix wrong definitions
118484ec Fix errors in volume calculation
08f2e43a Indentation
d0c7b374 Add MMPump to scheduling and makefiles
e5152fe3 Add MMPump to DifShell
91d10224 Implementation of MMPump
8cb32de5 Add ticks for DifBufferBase and DifShellBase
a56de071 Fix bugs: DifShell now compiles and seems to give correct results
4a99131d Fix a typo in zombify
7537d1c7 Rewrite DifShell. Inherit from DifShellBase
7b9b3174 Write base class for DifShell
c4bcadef Indentation
8cd96163 Implement exponential Euler for DifShell
5d2cb8a8 Move source messages to class. Correctly initialize Faraday's constant
41b15f25 Move source messages to class
1a014489 Make DifBuffer look more like other moose classes and fix ticks
8d67d853 Add DifBuffer to clocks
2dbbc214 Add DifBuffer to compilation
f411dc8e Fix no ticks when initializing difshells warning
65569a6d Remove useless variable
e4146c12 Reintroduce an old version of DifBuffer from moose
2feb865c Merge branch 'master' of github.com:BhallaLab/moose
f6df6f4d moose-core is tested on osx. No need to test this repo with osx.
a853687d Update index.rst
d9223838 Merge branch 'master' of github.com:BhallaLab/moose
88562db0 - Removed multiple conf.py file. Only a single file at top-level directory. If neccessary, this can be symlinked to other folders as well. - Cleanup in index.rst to make sure whole document build as whole one. - Cleanup toplevel index.rst. Removed non-existing entries. - Section numbers is currently disabled. It can be enabled in top-level `index.rst` file by putting `:numbered:` in ::toc.
10f313d3 Removed multiple conf.py file. Only a single file at top-level directory. If neccessary, this can be symlinked to other folders as well. Cleanup in index.rst to make sure whole document build as whole one.
be6e7176 Moved to cmake folder.
b94543d4 Merge commit '0d12ebb0'
0d12ebb0 Squashed 'moose-core/' changes from 3f8c345..7c9fe23
51b53b52 master branch.
4d697e96 Fixes to BhallaLab/moose#204.
ea50d83b BhallaLab/moose#204.
c0e1ef95 documentation gets picked up for some of the python class
d184c46d Set theme jekyll-theme-minimal
5304fbe8 Update index.rst
25a35d08 Instead of moosegui, install moose.
9aa87c84 Do not run gui tests.
f71343d4 Merge commit '04170cb4'
04170cb4 Squashed 'moose-core/' changes from bd86fb5..3f8c345
028b5cfc Updated.
1c9726ca Fixed, python2 incompatible print function use.
1aeca36e Some updates to fix static hdf5 libraries.
a844183e Added missing file.
46ca6d52 This project build pymoose, gui and its examples. TODO: ctest must check each example as well.
6baece11 Builds whole moose project.
625917a7 Added some sanity tests for both moose and moogli.
00a12e20 Squashed 'moose-examples/' changes from d7e9a97..ed3253d
bb393507 Merge commit '00a12e20'
1680bac6 Squashed 'moose-core/' changes from 6a6bcc1..bd86fb5
0e3c74d8 Merge commit '1680bac6'
ba8772f1 Changes to cmake file so that we can find the correct static library.
6bc4ced8 Fix a development warning in cmake.
8b3f4807 Removing shebangs from the python scripts. These scripts were never called as standalone executables.
03d15d00 Since none of the following files was executable, removed shebangs.
7ab6aa49 Removed shebangs from python scripts.
e3c8a188 Fixed the address of Free Software Foundation Inc.
2f9a0597 A test commit to package hdf5-devel BhallaLab/moose#201.
85a3b245 To run this file libsbml needs to be installed and not compile with moose as its at python level
909169d7 Merge branch 'master' of https://github.com/BhallaLab/moose
c5e7e5a3 Update README.md
15d6475d Fixed another typo in FindGSL. Library list was converted to string.
efd282df Fixed a typo in FindGSL file.
10e3fee1 sourceforge mailing is depreciated
68ca4c9b FindGSL also looks for GSL_VERSION now.
079927d7 Fixes to travis failure.
cbee1629 Update index.rst
eeb6e80d Updated CMake and FindGSL.
284b9e3c Fixes to extension bug.
7a560392 duplicate rdesigneur folder exists one level above
28caf3bb removing duplicate folder
da83bc1f rearrange python documentation as per website
64ec9591 Some fixes to static library dependencies [skip ci]
3bb481d5 Added script to merge changes from this repo to all subtrees. [ skip ci ]
4286c436 Cleanup in cmake files. Using bash scripts to generate subprojects. This way I can handle environment variables cleanly.
21f5e65e Clean up in README file and deleted unwanted files and folders
ff37cca1 Merge commit '76b621'
76b621c0 New hdf5 version generates static library with different name. Fix it.
78fe32b7 clean up
6f5289fc removing rst file which can be generated from "markdown" folder
474cbb26 deleting this folder
fe82fab1 Merge branch 'master' of https://github.com/BhallaLab/moose
7613fc1b Doxygen_1.8.9 is added which should be used to generate doxygen files,Rdesigneur folder is creater under "user" folder and corrected index.rst file is updated, deleted "html" folder,Rdesigneur markdown file with correct date,"snippet " and "tutorial"folder is created with relevant files to generate html files
f1d6aba3 This should pass on travis.
d0a6060b Squashed 'moose-core/' changes from 9eeca0c..6a6bcc1
7143a53a Merge commit 'd0a6060b'
b5a7c2e2 Squashed 'moose-core/' changes from 14cf2df..9eeca0c
15f18b90 Merge commit 'b5a7c2e2'
fef5e24c Merge commit '273124ec'
273124ec Squashed 'moose-core/' changes from 343cb02..14cf2df
7822c60b Merge commit '8bfef2e6'
8bfef2e6 Squashed 'moose-core/' changes from ed5f015..343cb02
fb9fba5e Merge commit 'aca40347'
aca40347 Squashed 'moose-gui/' changes from 1e5f537..e49ca7d
3c9138df Squashed 'moose-examples/' changes from 0494d05..d7e9a97
2f085e3e Merge commit '3c9138df'
6c8f2012 Squashed 'moose-core/' changes from c2c32b9..ed5f015
58de93dd Merge commit '6c8f2012'
9e7e1fa6 Update README.md
5bbb12f8 clean up, all markdown files will be placed under docs/user/markdown, images under /docs/images one can use markdown2rst.py to convert Rdesigner,MooseGui and Kkit docs which places the file under docs/user/GUI and docs/user/Rdesigneur and further one can use makefile to convert to rst to html which will be placed under _build folder in respective folders
5bdccdaf various cleanup in doc folder
d3dbb49e Cleanup in the images
ad5e43e0 function is replaced with summatation
fdca7481 Merge branch 'master' of github.com:BhallaLab/moose
f54fffde Pass moose version from command line BhallaLab/moose#200 .
eca66f7f Update README.md
b33e7096 Update README.md
a77c09fa No need of dpkg and sbml c++.
e5ac4a01 Merge commit '96580978'
96580978 Squashed 'moose-core/' changes from a15a538..c2c32b9
bcbc1c1a Added documentation sent by Upi.
e3fb24b3 Added documentation from Rahul.
7467592c removed USE_SBML=1 from the file "
5fddb6d2 removed all libsbml dependency
66617caa Changed build number to match all gsl packages. This should fix the build.
223ce2fa Fixed the link of gsl binary package version 1.16. Later I should upgrade the build environment from precise to trusty.
459dc9cf Fixing the upstream link of gsl debian package.
b53f9021 A test case test_sbml_support.py which inturn calls to write moosewriteSBML which needs networkx which is added as a dependency for travis
65960cdf fixed broken path which was due to doc folder moved from moose-core to moose
6b07347e update date correction
3cc12841 update date correction
0c31b014 Clean up in the document
df31522a Added axon model and documentation for rdesigneur
1628fa03 Squashed 'moose-gui/' changes from 1ef13c9-1ef13c9
f0054556 Oops moment. Fixed the typo in compiler flag for apple-clang
0d098851 updated apple-clang flags in compiler. Fix to missing symbols from stl.
2c8c4dcd Squashed 'moose-gui/' changes from c21a557..1e5f537
f68eadb5 Merge commit '2c8c4dcd'
5cf6177c Squashed 'moose-gui/' changes from bc510df..c21a557
65698f84 Merge commit '5cf6177c'
d2a4eeed Merge branch 'master' of https://github.com/BhallaLab/moose
382e5d39 Fixing version.
dbb2ab99 Use rsync instead of cp.
3d82717f Merge branch 'master' of https://github.com/BhallaLab/moose
9a7917a1 better script.
2247ee17 Updated. Try on strudel.
ca9c7ff8 Updated script.
5e5b17f8 Fixing scripts to build DMG file.
2fed9a35 Added packaging script for mac.
63601c5b Added scripts to build packages for MaC.
c8e99801 Squashed 'moose-gui/' changes from a3d3a06..bc510df
498a2aee Merge commit 'c8e99801'
2af833a0 Squashed 'moose-core/' changes from 1318029..a15a538
1eb469f6 Merge commit '2af833a0'
c31c9eb8 Scripts to pull the subtree into moose working tree.
e402660f Update index.rst
ba5c43de Merge branch 'master' of github.com:BhallaLab/moose
61754bb9 Needs more cleaning. This is for testing how document looks on RTD.
9db92946 Added streamer class to list
a83a2caf Fixed some more image links.
f6be0690 Fixed author and date directive. Integrated with other docs.
930a7955 Added images.
7e7d77a3 Added Rdesigneur documentation also.
30f4f342 Update index.rst
8637590a Merge branch 'master' of github.com:BhallaLab/moose
13ca5cc1 INstallation page is almost over.
eb128ef1 Update INSTALL.md
66a50a05 Update README.md
147301f6 Added links to issue in rst.
b7416fbf Update README.md
6db7335e Merge branch 'master' of github.com:BhallaLab/moose
0e0b838c Fixed formatting and added issue page.
7856aa34 Update .travis.yml
b305d886 Fixed formatting and added more install instructions.
b7327320 Merge pull request #196 from BhallaLab/dilawar-patch-2
6f5ceea5 Some more changes to make formatting consistent with RST
7d9c3f84 Update index.rst
f8908825 Formatting can be fixed on github now.
6d3d8491 Fixed the link to documentation on RTD
e9d20501 Changes from md to rst
d4ba03e0 Added markdown install instructions, need to update on github with proper rst formatting.
67fea2d3 Layed out the structure of documentation for installation, changelog, known_issues and release notes.
6b6828a2 Added missing file which should have installation instructions.
36c23d2e Merge branch 'master' of github.com:BhallaLab/moose
8012451a Enabling todo.ext with sphinx.
84cfe95d Fixed typo. Added a todo not.
cd5ea17c deleted unneccessary file.
dce53aa8 Some more rearranging to make sure the <no title> does not appear in final documentation.
266aec94 Rearraged documentation a bit to suit the latest directory sturcture.
ed088fcb Few more changes for local build testing.
ff035060 Fixed a typo in readthedocs-pip-requirements.txt file. Added file with instruction to install.
a49282d6 Added numpydoc as a dependency on rtd.
f5515c92 Started template for building and installing moose.
9e4bc321 Fixed logo path for latex latex build on rtd.
790a32df Moved docs to moose. Removed temp directory.
aa2deb82 Adding docs from moose-core.
a72f52bb Adding document folder to test building on read-the-docs.
7f43a2ec typo in WITH_CUDA [skip ci]
008a3f19 Added /usr/lib64 to ldconfig. SBML installs its library to this non-standard path.
edccf663 Making test command empty.
7d355710 Passes on ghevar.
d1d5740d Merge branch 'master' of github.com:BhallaLab/moose
1f4535a6 Don't run ctest before install. Needs to find a better way to integrate test.
79c42058 Update INSTALL.md
847cd59c Update README.md
bdf8b8c3 Update README.md
b9d2394b Added file to install.
a7eacd0c Updated readme file.
082ae66c Merge branch 'master' of github.com:BhallaLab/moose
bcbd49a6 Issue #195. Using external project to simplify the maintainence. centos-6 has cmake 2.8 which is now the minimum version required to build moose. Revered back Makefile in moose-core. Update README.md Fixed indentation.
513ccd28 Update README.md
894f881e Update README.md
0cda31e2 Squashed 'moose-gui/' content from commit a3d3a06
69456794 Merge commit '0cda31e2' as 'moose-gui'
e8f7e79c Squashed 'moose-examples/' content from commit 0494d05
c376ead0 Merge commit 'e8f7e79c' as 'moose-examples'
6b27e69e Squashed 'moose-core/' content from commit 1318029
64e5323b Merge commit '6b27e69e' as 'moose-core'
658e5413 Added scripts to pull subtree.
0a90e72d Removed submodules. Need to add subtree
8e0759fc After package is built, run the post-package tests. #BhallaLab/moose#194
39a577d2 Added python-nose as missing dependency. It shouldn't be there. I think it is needed to run python test
d64ae69f Merge branch 'master' of github.com:BhallaLab/moose
be28ed89 Don't check for gpg key and don't sign the package. This should fix the gpg key related exceptions.
47f92cf4 Don't pack libmoose.so. The lintian was complaining. libmoose.so is only used with moose.bin (for running unit-test in debug mode).
f691dc82 Do no install libmoose.so in package. Just install python interface and moosegui binary.
f58259ce Added cdbs to build dependency Travis was failing
25ae3229 Added wget to dependencies Fixed formatting error in yml file.
48dd2bc5 Install deb package instead of building from source code. --git-ignore-new  to git-buildpackage.
98579ee9 Added two very basic tests. Just import moose and moogli.
44b05aa9 Merge branch 'master' of github.com:BhallaLab/moose
d43d60e6 Instead of building source code using cmake, build the debian package whenever there is a commit.
00c90e68 Added debian folder to create debian on travis.
a7379219 Update README.md
63eab148 I should add packaing script to this repo. Ideally each merge to this repo must be tested for packaging.
1898ed1c Test pacakging.
9f2113f2 Submodules updated.
86089da2 cleanup folder too
7c25eb2e cleanup in setting up the pythonpath after the scripts where moved from moose to moose/scripts
5f77e25d update-repository is moved from scripts to moose folder which pull the code from submodule recursive
88a089d6 - moved the port file to package repo. Removing it from here. - Initialize git lfs support to add large files to repo without increasing its   size.
af869d41 Moving various install related scripts to ./scripts folder. Instructions are to be written on INSTALL.md file on how to build using this repository.
6e0544b9 make clean is also need
1afe9e87 Cleaned up readme. Added link to wiki.
58a0ad66 Updated submodules.
13dec237 Each submodule gets its own portfile.
6acd3e97 Added port file. Needs to improve the long description.
31bb3981 script to install dependencies on debian systems
99c11d77 Added build script to build all code in one go, modified update-repository to alleviate detached head issue in submodules
9c60afa1 The script now checkouts the correct branch
087fd797 Changed bootstrap to a logically correct and sensible name, modified it to checkout moogli correctly
fb851a95 Merge branch 'master' of https://github.com/BhallaLab/moose
8aeca9e4 Added new moogli, renamed old moogli
d4863ac8 Added port file [skip ci]
a7e79c66 Script to build mac bundle using cmake [skip ci]
341fab30 Added more instruction on how to build and install.
0da8d805 Added information about packages.
cee4e0e3 Update README.md
1dc477d0 merging submodules
f9e96888 Integrating changes from submodules.
77d497a7 Merged changes, fixed the build, updated readme.
479227a0 Updated submodules.
fbb7586c Merged submodules.
08c86ac8 Updating submodules.
3f84a9dd Updated submodule.
5e052a24 Merge branch 'master' of github.com:BhallaLab/moose
1ea6378c Merge branch 'master' of github.com:BhallaLab/moose
c49218ca Replaced tab with spaces, travis file now validates
a1091478 Corrected travis file format, removed the comment.
be72340a libsbml5.9.0 is support not libsbml-5.11.4
2f0111b3 Fixed travis. Doxygen and python-sphinx are in.
ff5f2177 readme with WITH_DOC option explained.
f60abf55 Updated submodules.
33e9ce9e Script which runs all demo and snippets in non-blocking mode.
4411e091 Updated readme file with details about subprojects and location of packages.
7a13e693 Updated readme.
0e1147cc Using pip to uninstall the moose-python. Also using cmake -P to install generated target rather than running make install.
1cf48e5b The uninstall happens successfully. Need to test if make install aslo runs make again.
df41948a make install also runs the target build. This should be fixed.
33418bff Still does not uninstall.
2bb84736 removed temp file.
76f75655 Added simple makefile to automate the process of installing, uninstalling the submodules. Testing needs to be done.
5a2e1536 make install instead of cmake install in cmake file now.
ac2b19f1 Merge branch 'master' of https://github.com/BhallaLab/moose
9be7ccd4 uninstsall does not work yet.
684f5183 make uninstall still not workinng.
f7fc67dc Updated readme file with installtion details.
ca1055fd A bootstrap script to pull the submodules and init them properly.
90d47d85 Fixed a typo in travis file.
cbb80549 Fix the typo in travis.
ed95e307 The install prefix in travis is changed to alocal path.
f2d679ac ctest --output-on-failure
1779f618 integrating new checkin.
a6f10072 This installs and build fine.
846f27c2 moosegui script.
876dc6be No point in making local package. Use launchpad and osc for that.
20fbde5e Added debian folder for launchpad.
26e6bbe5 Tiny changes. Paths of installation.
f706a4a6 Added moosegui scipt.
9d5c34ef moose-gui is installed to <prefix>/share/moose/gui folder.
eccc5bb2 Added travis for meta repo.
8a4afb1f Added readme file.
92919e07 Added submodules.

git-subtree-dir: moose-core
git-subtree-split: 2c3fe7516a3a462c6e408a0e8b3b8f0254c5e903

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