cddc3bd16d Merge pull request #265 from upibhalla/master
5856ac1fa7 Fixes for travis.yml
219f474a2e Fix to HSolve to prevent segv during destruction. Update to rdesigneur to not create HSolve when turnOffElec flag is set
9ca16e8246 Merge branch 'master' of https://github.com/BhallaLab/moose-core
58e630b4dc Updates to the Voltage clamp modules. The key thing to note is to use the standalone VClamp object in preference to individually building the circuit with DiffAmp. RC and PID.
12cf83e17a Updates to Hsolve to be able to delete and recreate it. Still problematic for HHChannels. Also added Vclamp to the rdesigneurProtos.
3dc99b53e6 Changes made to object name which had number in starting
3ec52cd9e4 Small bugfix to rdesigneur
241c3d59cb Use sys.executable to execute test. It breaks on python3.
f527490ff0 Fixes to rdesigneur to use the new system for cross-compartment reactions
501ff45939 Major cleanup to get rid of legacy cross-compartment code
f4b4772f0a Numerical improvment for Dsolve::calcJunction done by splitting diffusion and channel calculations into two dt/2 segments bracketing the mass-exchange calculation of calcJnXfer.
35db4b5a31 Major changes to handling of cross-compartment reactions and to the flow of control in Ksolve, during chemical reac-diff simulations. Not yet optimized. Several tests cleared.
1b3b11504b Install pymoose in debug mode as well.
6d911de9fa Test install target with python2 on travis.
ba0bab2206 Fixes to installation prefix (reported by Harsha over email). Chamcham branch patch was not correctly applied.
1a57a54c5b Fixes for Debian.
fab88be5d8 Fix to ConcChan lookup logic
efcb412ff3 Fixes so that CubeMesh can be used with diffusion solver, needed now that Dsolve is required for multi-compartment reactions.
f54acebcb9 PyMOOSE installation directory can work.
fe3061b0a5 temp changes. [skip ci]
b4313cdcca Merge commit 'a039fc3a'
1dc7a63356 Added numProducts field to EnzBase
0f1ecebcb0 Major update so that the diffusion system handles channels across membranes, which are implemented as ConcChans.
53b0e60dc3 Merge branch 'chennapoda' of github.com:BhallaLab/moose
db52562e0b Merge branch 'chennapoda'
f208e2b6fb Merge commit '33bf735f'
ecce024d42 Merge commit 'a1f7f5ea'
643226e2cf Install in debian layout in packages. Added option in setup.cfg file Its delicate solution. Added a note.
c2a574289b Finally. Needs to write setup.cfg file to make /usr/local  and /usr prefix consistent.
ac7e7e5cf4 bdist_egg is more consistent on both RPM and DEB based systems.
c866f9f2d9 Merge commit 'bcf5c52d' into chennapoda
aacb0300ee Fixed typo in command.
d773b400d0 Merge commit 'a1a6faa7' into chennapoda
1e23289141 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.
f2537df577 Use bdist instead of install for creating binay distrution. During installation, untar this to destination.
43891c6900 Tweaks to setup.cmake.py file.
fa4a545df0 Test on travis.
16eea973b1 Merge commit '6d651b60'
ba1065cdb9 Added EndoMesh and updated other meshes to match. Updated diffusion code to do cross-compartment reactions.
545ee72491 Merge commit 'e0b8959c'
ef650c8ec0 On debian/ubuntu install-layout option is set to deb. [skip ci]
2a02c27dc4 Merge commit 'f80ae40d'
f11b189779 This fixes moose but a better solution to install pymoose in moose-core must be found.
635dedf798 Merge commit '6f7697fb'
7687f3c446 Merge commit '627f1ce1'
419d65dd2a Merge commit '7b3c355a'
5cb77cc213 Squashed 'moose-core/' changes from d4417dcffd..2657e3345e (#222)
59bf6585ff Fixed the syntax causing failure.
448fb46d87 Handling MOOSE_VERSION is better way.
cc09546ecf Merge commit 'fba17845'
9bd9c55d3c Merge commit '750df413'
c85e8fc03b Force --install-layout=deb when on debian/ubuntu.
cf20c6c086 Merge commit '99b934e9'
2bc6d025ed Merge commit '2f038f21'
8e8f75f08b Merge commit 'd0e1cee1'
9fd3829997 Merge commit '0014d826'
c39f533796 Follow up fixes to calcium-hsolve  (#221)
c3204e010e Merge branch 'master' into asiaszmek
62b315f08a Merge commit 'e6e83b76' as 'moose-core'
3e88642a5f Calcium hsolve (#218)
a33619039f Merge commit '7fe1c2e7'
4547a9f1d2 Merge commit 'af3c29a4'
fbdaafb332 Fixes to allow moose module to be installed and imported (#220)
42fa11cac2 All changes from previous repository. No new file is added here.
9170767ac7 Merge commit '0f6f5d27'
d9819894f7 Added missing Revision macro file from chamcham branch.
5627ad198f Merge commit 'b4d20b7c'
5ec49526f0 Fixed revision issue.
b3418608f7 Cmake changes from chamcham branch. Build for launchpad.
485c150c85 Do not copy VERSION file for python. Lets find a better and more portable solution.
40bfbf631e Updated default version in setup.py file.
baab7ef505 Merge commit '0ff1b77a'
79e1a65c0d VERSION string is fixed to today's date if not given.
f1adfd3ff9 Fixed for snappy builds.
68e138a565 Let cmake find path of Python.h file.
cf8faf32d8 Merge commit '4489d159'
91a4b30ab1 More changes to snap. Needs to add Python.h path [skip ci]
567c8013ce Removed <<<<, ===  and >>> from improper merge.
435188aa4b Added snapcraft file.
3131b29c76 VERSION conflict file is added
a3a81ace57 Merge commit '628138cb'
4bbbf6ddff Merge commit '7c713058'
a205390e4e Script testing DifShells
0fcafe248d Merge commit 'a5122cfb'
8b1c110945 Fixed docstring on example.
f87a802bdb Merge commit '5bceacfe'
f6f5dd58cd Merge branch 'difshell' of https://github.com/asiaszmek/moose into asiaszmek-difshell
d9d0f6e382 Change order of operations to slightly improve accuracy
d7f378074f Small changes to make the code more alike genesis and other moose objects
4ce676215f Difshells and difbuffers initialize close to equilibrium
ebab1aee87 Add forgotten setting of helper variables to zero after calculations
04d7c5227e Add state in t(i-1)
6779a6e0a4 Fix wrong definitions
10f549bbfd Fix errors in volume calculation
f66bf285a8 Indentation
25feaf08f7 Add MMPump to scheduling and makefiles
c410524b90 Add MMPump to DifShell
2f31fa17cd Implementation of MMPump
f58668f93a Add ticks for DifBufferBase and DifShellBase
372b34f71a Fix bugs: DifShell now compiles and seems to give correct results
efd6ca0bd9 Fix a typo in zombify
4fa3f001bb Rewrite DifShell. Inherit from DifShellBase
82284b9b2c Write base class for DifShell
a3d45d71bd Indentation
e32896701b Implement exponential Euler for DifShell
8d0e9c3ace Move source messages to class. Correctly initialize Faraday's constant
0b2b708d21 Move source messages to class
6c2234bf82 Make DifBuffer look more like other moose classes and fix ticks
0de0b1ba06 Add DifBuffer to clocks
e1586d63a9 Add DifBuffer to compilation
bea1f0a18d Fix no ticks when initializing difshells warning
c986fd8172 Remove useless variable
65e67a0bd5 Reintroduce an old version of DifBuffer from moose
cede2afd61 Moved to cmake folder.
fff821e0d0 Merge commit '0d12ebb0'
ea023b6ae7 master branch.
340c310fea Fixes to BhallaLab/moose#204.
0b083f83d6 Merge commit '04170cb4'
bbd455a47f Updated.
ff2aec915b Fixed, python2 incompatible print function use.
725d2c9c47 Some updates to fix static hdf5 libraries.
b6d80ccd7e This project build pymoose, gui and its examples. TODO: ctest must check each example as well.
44b458500f Builds whole moose project.
bbedb768be Added some sanity tests for both moose and moogli.
32e2226897 Merge commit '1680bac6'
20b1010d24 Changes to cmake file so that we can find the correct static library.
527bc4d489 Fix a development warning in cmake.
30dda99116 Removing shebangs from the python scripts. These scripts were never called as standalone executables.
20641912cd A test commit to package hdf5-devel BhallaLab/moose#201.
077989b4d4 Fixed another typo in FindGSL. Library list was converted to string.
0ddc8bd15f Fixed a typo in FindGSL file.
ebe9a39888 FindGSL also looks for GSL_VERSION now.
07d432d580 Fixes to travis failure.
2c91dddfcc Updated CMake and FindGSL.
11c933e476 Fixes to extension bug.
fff7ce57ab Some fixes to static library dependencies [skip ci]
05856011a9 Cleanup in cmake files. Using bash scripts to generate subprojects. This way I can handle environment variables cleanly.
493c7c49b8 New hdf5 version generates static library with different name. Fix it.
c9f6b7767b This should pass on travis.
d3ac4b814d Merge commit 'd0a6060b'
4d37569e6c Merge commit 'b5a7c2e2'
a39a84acb1 Merge commit '273124ec'
4c79628c60 Merge commit '8bfef2e6'
49c322da4c Merge commit '6c8f2012'
f9e56dd7e3 Merge commit '96580978'
633b9e0503 A test case test_sbml_support.py which inturn calls to write moosewriteSBML which needs networkx which is added as a dependency for travis
f21e02bf7f Oops moment. Fixed the typo in compiler flag for apple-clang
3da3dec81b updated apple-clang flags in compiler. Fix to missing symbols from stl.
70d1a5d90a Merge commit '2af833a0'
24a742712e Moved docs to moose. Removed temp directory.
26f20a818e Merge commit '6b27e69e' as 'moose-core'

git-subtree-dir: moose-core
git-subtree-split: cddc3bd16d3a8e9e3668bdeae524986b0f68b6d4

only assume default.

0cceb29 packaging related changes (#262)
dc861b2 Prepare binary distribution before installing  (#261)

git-subtree-dir: moose-core
git-subtree-split: 0cceb296d06cf021f4fb7120d3f4854c4b219143

f38dc5d On tumbleweed, cmake returns python3 default but python-numpy is python2 version. Won't fix it. Its a upstream problem.
REVERT: f1dcea8 Install in debian layout in packages. Added option in setup.cfg file Its delicate solution. Added a note.
REVERT: 5a73acb Finally. Needs to write setup.cfg file to make /usr/local  and /usr prefix consistent.
REVERT: d7c41e4 bdist_egg is more consistent on both RPM and DEB based systems.
REVERT: be42fd2 Merge commit 'bcf5c52d' into chennapoda
REVERT: d27db9c Do not use -p switch. its not easy to get required info from all linux-distributions.
REVERT: e667953 Fixed message to set in cmake.
REVERT: 8523290 Fixed typo in command.
REVERT: 0b125f6 Fixed typo in cmake file.
REVERT: f3118f0 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.
REVERT: 03d5899 Use bdist instead of install for creating binay distrution. During installation, untar this to destination.
REVERT: a08658e Tweaks to setup.cmake.py file.
REVERT: c5f1d91 Test on travis.
REVERT: 6b32fde Merge commit '6d651b60'
REVERT: 324a20c Merge commit 'e0b8959c'
REVERT: 59f6e9e On debian/ubuntu install-layout option is set to deb. [skip ci]
REVERT: 62201d9 Merge commit 'f80ae40d'
REVERT: 9b81dfc This fixes moose but a better solution to install pymoose in moose-core must be found.
REVERT: 7e27f80 Merge commit '6f7697fb'
REVERT: 939c734 Merge commit '627f1ce1'
REVERT: 4775933 Merge commit '7b3c355a'
REVERT: 43c0674 Squashed 'moose-core/' changes from d4417dcffd..2657e3345e (#222)
REVERT: 8c9ad49 Fixed the syntax causing failure.
REVERT: 397efaf Handling MOOSE_VERSION is better way.

git-subtree-dir: moose-core
git-subtree-split: f38dc5d6b2d6a3bcb5439a2f5ba680adad754ec7

f1dcea8 Install in debian layout in packages. Added option in setup.cfg file Its delicate solution. Added a note.
5a73acb Finally. Needs to write setup.cfg file to make /usr/local  and /usr prefix consistent.
d7c41e4 bdist_egg is more consistent on both RPM and DEB based systems.
be42fd2 Merge commit 'bcf5c52d' into chennapoda
d27db9c Do not use -p switch. its not easy to get required info from all linux-distributions.
e667953 Fixed message to set in cmake.
8523290 Fixed typo in command.
0b125f6 Fixed typo in cmake file.
f3118f0 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.
03d5899 Use bdist instead of install for creating binay distrution. During installation, untar this to destination.
a08658e Tweaks...

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

- 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.

untar this to destination.

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

renamed it.

cmake.

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

268a28862 Merge pull request #224 from upibhalla/master
3ab452e97 Fixed test_nsdf.py. It had relied on the old (and incorrect) function of the spike message to the Table. I have now updated the test_nsdf.py to work with the fixed version of the Table.
616f33a60 Fixed spike timing functionality in Table class. Incorporated into rdesigneur so that tables can record spike times for saving, and users can plot spike times as a dot raster.
7f372b6aa Merge pull request #223 from upibhalla/master
186e91d68 Merge branch 'master' into master
d91a681bf Fix on diffusion scaling in spines, and added Pool::volume field for plotting in rdesigneur.
41c71b147 Merge pull request #221 from upibhalla/master
e27ef8a45 Merge branch 'master' of https://github.com/BhallaLab/moose-core
b07046e15 New Neuron::getSpineIdsFromCompartmentIds function, needed for rdesineur to connect adaptors for spine size and other spine properties.
69d985877 Merge pull request #220 from bhanu151/master
4f67f3338 retracting seqActivation normalization by dt to restore time-step invariance
ca1f36ca6 Merge pull request #219 from hrani/master
be6dc0a28 Hopefully last cleanup
e03c69ddd Hopefully last cleanup
7332ff66b spell correction
d17d383dc absolute import with mtypes just for python3
fb28e1009 Hopefully last one, tested for filepath,moose path and moose object
b782b9552 In merge.py, clean way of cheking the type of path provided, filepath,moose obj, moose path are taken,if source is empty then nothing to copy, if destination was empty list is update with new object
dc0c83027 clean up with in mergeChemModel file
13152346b cleanup in setup file
1f9100b7f cleanup in init file
50cd8feee removed unwanted lines and clean up
e9b88cee7 folder "merge" renamed to "chemMerge", moose.py: func added so that chemMerge can be imported directly,cleanup in test_import.py with the changes made to this commit,merge.py file Neutral object is copied into des path instead of creating and now user have to genesis/SBML format
072913a9c Merge pull request #218 from BhallaLab/missing_merge
fab362fa7 Couple of lines added to moose import test.
064fbea56 Fixed moose.merge import. Added a test which tests moose module import (incomplete).
4211da0e8 Merge pull request #216 from hrani/master
a45e9f0a1 Merge branch 'master' of http://github.com/hrani/moose-core
dacd64039 some more checks made for empty model, empty compartment and for display atleast one reaction should exist for displaying into widget
e0566d476 Merge branch 'master' of https://github.com/BhallaLab/moose-core
2db1b4dac Merge branch 'master' into master
a62961a27 Merge pull request #217 from upibhalla/master
15ee2cc7f Merge branch 'master' of https://github.com/BhallaLab/moose-core
aca164612 Two important fixes for numerics of stochastic solver with diffusion. Affects models using sumtotals and functions.
f5302b08f validator was switched off, which is not correct, so switching ON
87e66a18d if in reaction stoichiometry is not defined then assume 1 and if no unit base unit defined then assume 1 which is mole
38879fd5b Merge pull request #215 from hrani/master
2384657e0 readSBML: explicitly ratio is set to 4, so that e2,e1 is balanced, If units are defined in the rate law for the reaction then checks are made and if not in milli mole the base unit then recalculate, spell correction. writeSBML: instead of printing error msg, saving into string for later use writekkit : instead of printing error msg, saving into string for later use
798c0b6a7 Merge pull request #213 from hrani/master
c1c26f698 Merge branch 'master' into master
aa1cb43e2 Merge pull request #214 from bhanu151/master
b60b73b3a SeqSynHnadler fixes - normalized seqActivation by dt
3d36e7bd1 unwanted print statement is removed
67e026ab8 function definition are read from SBML files, rules which are not read to moose a errorFlag is set out, rateLaw without unit definition, are taken from the substance units and recalculated for all higher reaction, validator checks if model is valid and send out errormsg if not valid, if model doesn't have atleast one compartment, then errormsg is send out
91180c067 Merge pull request #210 from dilawar/master
1f37c10f0 Python3/Python2 import thread has been fixed.
012b5f3ca Preserve the order of plots. Use OrderedDict. Since OrderedDict is not available in python2.6; added implementation.
78f244b0c Utility function to plot tables matching a regular expression.
03dc5a8fc Fixed import error.
2b9e30565 try/except import in moose.py file.
574a12503 Added a test script.
f5202b0cd Merge branch 'master' of github.com:BhallaLab/moose-core
b792838ee Merge pull request #207 from hrani/master
e39c76df2 resolved conflicts
75e289296 all conflict a removed
1e7ebbe3c unwanted statements
98d625b62 Merge branch 'master' into master
cdbe6add9 Fixed clock dt assignment bug in rdesigneur, came up when turnOffElec flag is true (#208)
0da306f5a Fixed clock dt assignment bug in rdesigneur, came up when turnOffElec flag is true
e9526f7c3 Fixes to import plot_util library.
abd664d1e unwanted print statement removed
fd794de74 in print stm space clean up,added findcompartment function to one common place, some space char are allowed in name field, in kkit writer, moose obj which doesn't have compartment are not written, which then appended to error msg for user
5015b14cd Merge branch 'master' of github.com:BhallaLab/moose-core
b32a0bbe9 Fixes to issue204 (#205)
9f88d7c5f Merge pull request #203 from hrani/master
6dbf8bef2 Merge branch 'master' of http://github.com/hrani/moose-core
3c6d41ce4 Restoring contents after bad commit and bad merge
1d34b9b2c Restored some old commit, after the bad commit and after revert fail
f2d3e94ad Restored some old commit, after the bad commit and after revert fail
daa657802 Restoring contents after bad commit and bad merge
30b1c36b2 Merge pull request #202 from upibhalla/master
24c079561 Restoring updates to ksolve including isBuffered flag
d71f6eb53 Merge branch 'master' of https://github.com/BhallaLab/moose-core
eb43e5524 Fixed Rdesigneur verbose flag
5e42df95c Merge branch 'master' of github.com:BhallaLab/moose-core
3c46150a1 Merge branch 'master' of github.com:dilawar/moose-core
b04156b03 Fixes to issue #200. (#201)
1e3bbe04f Merge branch 'master' of github.com:BhallaLab/moose-core
f11ef0a3f Added test script but has not been enabled. This tests the SparseMsg::connectionLists.

git-subtree-dir: moose-core
git-subtree-split: 268a2886219290af163c9c95b755901fa68cfa5d

Conflicts:
	CMakeLists.txt

891f2f8 Removed trailing spaces from code by pre-commit hook utility.
0ed2535 Cherry-pick "Added connectionList field to SparseMsg to allow direct control over connection matrix. Some sanity checks in SparseMatrix to go with this"
d62d10d The bug on travis is still not bypassed. If this does not work, disable DOQCS tests on OSX.
618b4d6 Install moose on osx as well. Prerequisite to test DOQCS.
f717f82 Merge branch 'master' of github.com:BhallaLab/moose-core
908820e Lets see if this is a good workaround travis issue travis-ci/travis-ci#6522.
e251f53 Lets see if is a workaround fixes the OSX bug.
4ff7cff Hopefully this will fix issue on travis-osx build failure. Related to travis-ci/travis-ci#6522.
590c09e Don't use timeout in script. So that we can run on macosx as well. Removed timeout command from script. Now it can run on OSX as well.
e2f8afd Only test doqcs on LinuxOS, not on MacOSX.
dc7b55a Fix to travis-ci/travis-ci#6307.
54b8471 Merge branch 'master' of github.com:BhallaLab/moose-core
18c8759 Test docqs agains gsl version/python2 moose-core.
d6ca9cc Fixes by pre-commit hooks. - Removed trailing whitespaces automatically. - insert * coding - utf8 * line on top of each python script automatically.
d4a6939 Using version v0.8 now.
f944afe Added pre-commit pip install pre-commit --user to activate it.
030bfe0 Merge pull request #195 from dilawar/master
d00a5d1 All tests are passing and new code is protected by appropriate macros.
1959771 Merge branch 'async' of github.com:dilawar/moose-core
0f6aba0 Merge branch 'master' of github.com:BhallaLab/moose-core
ac0a4cd Added note on what to do.
b3bf54e Slower version but results are same.
6bc71c9 Async version is slower (80sec vs 70 sec).
d838267 asyncing clock is not producing great results.
eeaafbf Implemented first parallel version.
166f84e Equivalent serial code which can easily be called from std::async now.
e09a0c1 Merge pull request #194 from dilawar/master
d2d1097 Added MACRO to integrate serial and parallel version.
e68acd6 This is good but do parallelism at Clock.cpp
4cebbca Rdesigneur has python3 default import : absolute_import.
f431cca Merge branch 'master' of github.com:BhallaLab/moose-core
85afa6d Some changes to Ksolve. Still seg-faults.
47e023e Time to test the Gsolve performance when threads are enabled.
2bbfd4f Commented out code appropriately.
91c2da6 moose.test( ) is added not cmake but not enabled. Enable them once all scripts are fixed in moose-examples.
a1699fc Optimized GSolve with default 2 threads.
00a9d9e Removed the debug message. Lets check it now. By default it should be not slower than the default version.
7700c07 Fast Ksolve with 2 default threads.
d154eb3 Parallel ksolve.

git-subtree-dir: moose-core
git-subtree-split: 891f2f8bf7359d61f186c3792c6f12b61d8c0afb