38da92b048 Fixes to bad-merging.
812d2d97f8 Merge commit '320e525a'
6fc726e560 All changes from previous repository. No new file is added here.

git-subtree-dir: moose-gui
git-subtree-split: 38da92b0481f53ffd2cdc75d8f7aec49408dc4ae

0c5527e77d Why docs were here?
16ef3f4444 Merge branch 'master' of github.com:BhallaLab/moose-examples
a47d702034 Merge commit '48fc9733'
37d94cb38e Fixed the script. Runs with moose-3.1.2.
fcf47109e5 Merge commit 'edd901da' as 'moose-examples'
423c4759 Removed moose-examples due to screwed up history with https://github.com/BhallaLab/moose-examples.
7b366bcb Merge commit '45f9e9b9'
45f9e9b9 Squashed 'moose-core/' changes from b3b597f41..2ecab963b
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...

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

80169bcc5c Resolved a merge error.
d5caa39361 use moose.element over  moose.HHChannel.
26e9aac794 Merge branch 'master' of github.com:BhallaLab/moose-examples
9b83291de6 Merge branch 'master' of github.com:BhallaLab/moose-examples
2f46ad096d Convert u'ABCD' to 'ABCD' to probably fix the python3 issue on travis. Works fine with python3 on ubuntu 16.04/Debian8.
6232b3a888 Send email to malav if build fails.
4a92db239b Merge branch 'master' of github.com:BhallaLab/moose-examples
4800cd62df Adding python-libsbml to dependencies.
c045972c2e Fixed second script as well.
e927a88875 Merge branch 'master' of github.com:BhallaLab/moose-examples
626afb8242 Added a hack to make this script work with both python3 and python2.
24fdc9e1b7 Indentation for python3
e9e5d92828  Using force-yes with -y
3c60a8263a Upi fix the assert error
ca2d4090e7 Upi cleaned up the file
a9ddced2bc Merge branch 'master' of https://github.com/BhallaLab/moose-examples
b4715d09ba F...

REVERT: 69e0354705 Create CONTRIBUTING.md

git-subtree-dir: moose-core
git-subtree-split: b09650323312b56d2cfb777947f5db45f44b578a

* 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 *'.

* F...

* 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.