* Remove zombification from DifShell and DifBuffer

* Add sending out current message to hsolve

Fix externalCalcium_ iteration in advanceChannels.

* Test for hsolve handling external calcium.

Slightly rewrote functions shared with test_difshells.py

49779ba730 As per Upi suggestion, co-ordinates are reprocessed for genesis file (yaxis is negated) at loading time so that, at the interface level co-ordinate are played around independently and while saving scene co-ordinates are save.
1f32b418d2 Kd is calculated for second order reaction only and value is displayed in object editor,Notes header is added, and unit for Kd is added in default.py
254d1f077a Enzyme can't be connected for second order reaction
3038c31d1a missing import math
355d721e4f added libsbml and moogli is removed
0343ce3e11 Added a Model information, like number of compartment,group,pool,function,reaction etc when model is loaded for the first time

git-subtree-dir: moose-gui
git-subtree-split: 49779ba730bbbb214728c86d3550fc2b27d8ef24

69e0354705 Create CONTRIBUTING.md
b096503233 Added travis related setttings update.
REVERT: 2ecab963b2 Merge commit 'af3c29a4'
REVERT: b3b597f411 Removed legacy Makefile based build flow. CMake is only build-system now. #180.
REVERT: 20dc0a5989 a warning message is sent out \n 1.if function is not connected to output and \n 2.yet to write back StimulusTable is to genesis. \n No more transformation with y axis as it has already taken care in kkit.py file
REVERT: 9373d1bc16 python Counter function removed, just to give backward compatibility for Centos6 for python 2.6
REVERT: e8300d7e92 added to ask User if merged model to be saved
REVERT: 933b259710 Made ReadSwc less verbose. Fixed bug in SeqSynHandler in application of sequencePower.
REVERT: 662eaa2e13 Added sequencePower term to SeqSynHandler to achieve greater specificity for sequences vs all inputs on at once.
REVERT: 7ccc8a2b1e Merge branch 'master' of https://github.com/BhallaLab/moose-core
REVERT: fe5765ca7b More fixes to plot_utils
REVERT: 6a9a618e72 Fixed the error in plot_tables utility.
REVERT: 658af76a47 Fix for Table.vector bug (#179)
REVERT: 423dc9dc69 Merge branch 'master' of https://github.com/BhallaLab/moose-core
REVERT: 200871a9f7 Added in hack for rmoogli to display time
REVERT: 157c501b98 reaction or enzyme name is empty then id is taken as name while reading files from SBML
REVERT: 43a2350406 color and textcolor inchanged for enzyme
REVERT: 02de4c37ee Bugfix for SparseMsg, corrects allocation of synapses when setting connectionList

git-subtree-dir: moose-core
git-subtree-split: 69e0354705cd27d3dad42ba33610f960d270660e

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

https://github.com/BhallaLab/moose-examples.

2ecab963b Merge commit 'af3c29a4'
ad3ec12ec Fixes to allow moose module to be installed and imported (#220)
0fb32dec5 All changes from previous repository. No new file is added here.

git-subtree-dir: moose-core
git-subtree-split: 2ecab963b249229174cfef1fafd282977a7920c3

b3b597f41 Removed legacy Makefile based build flow. CMake is only build-system now. #180.
20dc0a598 a warning message is sent out \n 1.if function is not connected to output and \n 2.yet to write back StimulusTable is to genesis. \n No more transformation with y axis as it has already taken care in kkit.py file
9373d1bc1 python Counter function removed, just to give backward compatibility for Centos6 for python 2.6
e8300d7e9 added to ask User if merged model to be saved
933b25971 Made ReadSwc less verbose. Fixed bug in SeqSynHandler in application of sequencePower.
662eaa2e1 Added sequencePower term to SeqSynHandler to achieve greater specificity for sequences vs all inputs on at once.
7ccc8a2b1 Merge branch 'master' of https://github.com/BhallaLab/moose-core
fe5765ca7 More fixes to plot_utils
6a9a618e7 Fixed the error in plot_tables utility.
658af76a4 Fix for Table.vector bug (#179)
423dc9dc6 Merge branch 'master' of https://github.com/BhallaLab/moose-core
200871a9f Added in hack for rmoogli to display time
157c501b9 reaction or enzyme name is empty then id is taken as name while reading files from SBML
43a235040 color and textcolor inchanged for enzyme
02de4c37e Bugfix for SparseMsg, corrects allocation of synapses when setting connectionList

git-subtree-dir: moose-core
git-subtree-split: b3b597f411500f5956976349f4d56b1cbc94f734

* pymoose: unbreak installation under Python 3

Commit 24ebac50 removed the setting
of the suffix of the binary python module. Unfortunately no explanation
was provided…
Anyway, 'python3 setup.py build' and 'python3 setup.py install' stopped
working because setup.py is expecting a file like
_moose.cpython-36m-x86_64-linux-gnu.so, and it simply ignored _moose.so.
As a result the binary module was not installed.

* .gitignore: ignore "moose" only in the top-level directories

Just "moose" would also match python/moose, with predictably bad
consequences.

* .gitignore: ignore VERSION

It's a generated file.

* Restore moose/moose.py

It was removed in 24dea426. No
explanation was provided, but it seems to have been a mistake, because
without this file, 'import moose' has little chances of succeeding,
since __init__.py includes 'from .moose import *'.

* Fix a bunch of local imports

* changed files in docs folder for final version of documentation

* changed the README.txt file.

* changed the path to moose-examples in conf.py and formatting in chem_GUI

* removed docs/source/user/py/introduction/index.rst, and /install/index.rst due to redundency

* Changed some moose-example files as online readthedocs was generating some issues, and added Makefile in docs/ directory.

* a couple of more changes..

* changed files in docs folder for final version of documentation

* changed the README.txt file.

* changed the path to moose-examples in conf.py and formatting in chem_GUI

* removed docs/source/user/py/introduction/index.rst, and /install/index.rst due to redundency

strict about formatting of time.

installing openscenegraph-dev error-prone.

ef066f704 Fixes to violation of mass-conservation when Dsolve and Gsolve run for very long time (#176)
46ea47260 Local Documentation (#177)
852819875 Added connectionList field to SparseMsg to allow direct control over connection matrix. Some sanity checks in SparseMatrix to go with this.

git-subtree-dir: moose-core
git-subtree-split: ef066f70493fe05fe05393af48449b264c8f4bc0

6099142 Added missing Revision macro file from chamcham branch.
d0a81a4 Merge commit 'b4d20b7c'
79d7a4c Fixed revision issue.
985e8b5 Cmake changes from chamcham branch. Build for launchpad.

git-subtree-dir: moose-core
git-subtree-split: 6099142d63632177056c3077d6d84035388cb93f

Conflicts:
	moose-core/CMakeLists.txt

4f391e1 --std=c++11 is must now. Fixes BhallaLab/moose#214.
718252a Do not copy VERSION file for python. Lets find a better and more portable solution.
f26225d Updated default version in setup.py file.
1476ea1 Merge commit '0ff1b77a'
0da1cc4 VERSION string is fixed to today's date if not given.

git-subtree-dir: moose-core
git-subtree-split: 4f391e1ef906eacb103bb85d723ee98453f06d5b

Conflicts:
	moose-core/CMakeLists.txt