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

portable solution.

d282884 specific math functions are imported
16439cc checked for Qt_Version and icon takes config.settings
cecb74c resize qObject if change in text size

git-subtree-dir: moose-gui
git-subtree-split: d282884250997aa6cc1154b6ba93fee6c3ccc630

8c7c00c can pass command line arguments also
70f83d0 cleanup in return type from None to moose.shell
fe4238b indentation for python3
3e81764 indentation fixes for python3
66f1bb0 Removed <<<<, ===  and >>> from improper merge.
0719a5d Merge commit '349abe7e'
864776c added deleted files
87a6963 temp deleted

git-subtree-dir: moose-examples
git-subtree-split: 8c7c00c0e29c3c02c1e20f82f8baba5206ea913d

eb878dd Merge branch 'master' of https://github.com/BhallaLab/moose-core
68ef2ed Less verbose ReadSwc and rdesigneur. Fix to SeqSynHandler
2c93c52 return type from None to moose.shell
07fc0f9 Ignore /opt/bin/python3 on travis. Numpy is not available for this path. Try /usr/bin/python3.
45fb960 mtseed and mtrand are under moose namespace and defined in global.h file. Fixes for travis failure with BOOST.
dfa0ab1 Explicitly naming the source file in synapse directory.
cd32764 old makefile based flow is deprecated. Recent commit fixed the test faillure.
c0f5469 Merge branch 'master' of https://github.com/BhallaLab/moose-core
fd96222 Verbose flag for rdesigneur; added synapseOrder to SeqSynHandler, fixes to testSynapse
e7d57cf plot_tables can plot on user given axis.
43faa23 mu.plot_records is renamed to mu.plot_tables.
99f5ee7 Merge branch 'master' of github.com:BhallaLab/moose-core
953142d Fixed for snappy builds.
6931e80 Let cmake find path of Python.h fi...