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