f3d0477 Merge branch 'master' of https://github.com/BhallaLab/moose-core
176a5f0 solver's short form should also be taken
8624e24 Merge branch 'master' of https://github.com/BhallaLab/moose-core
6c964b1 Added isBuffered field to Pool to let users convert the object class to BufPool, and vice versa.
97db69e moose::Neuron uses global RNG object. Global RNG object behaviour is following. - moose.seed(0) or moose.seed( ) assign a random value to seed. Use   random_device if avaible else time(NULL) is used. - moose.seed( x) set moose.seed to x.
c1dec94 Fixed long argument for mtseed in moosemodule.cpp
54c94f7 Modified travis scripts and reenabled developers to the list.
31dd779 Fixed import error with python3. No module should be imported in python/moose/__init__.py . Added a note for developers. This should fix the travis.

git-subtree-dir: moose-core
git-subtree-split: f3d0477a3ea5045db044aaae94b46a133527dbc7

Script testing DifShells

Script creates a test model of a dendrite segment with one Ca
channel. DifShells are created. DifBuffers are created. DifShells are
connected to provide diffusion. DifBuffers are connected to provide
diffusion. DifBuffers are connected with DifShells to provide
buffer. MMPumps are created and connected to the outer DifShell. Ca
channel is connected to the outer Difshell to provide Ca influx and
outer DifShell is connected to Ca channel to provide ion
concentration. Segment's Vm, channel's Gk and Ik, DifShell's C and
DifBuffer's bBound are connected with output to save simulation
results.

14e2d78 Fixes broken Makefile. Object MMPump.o not found error is resolved by commenting out the object. Either source is missing for it was introduced by recent PR.
aeddce7 Fixes to python3 test command in travis script. Previous fixes passed with python2.
00ad9e2 Fixes to recent Travis build failure.  (#170)
3ebc0a5 Merge commit '5bceacfe'
df5ff48 Merge branch 'difshell' of https://github.com/asiaszmek/moose into asiaszmek-difshell
e4a4bcd Change order of operations to slightly improve accuracy
aacebcc Small changes to make the code more alike genesis and other moose objects
4246932 Difshells and difbuffers initialize close to equilibrium
40a200f Add forgotten setting of helper variables to zero after calculations
dad35e6 Add state in t(i-1)
45c2286 Fix wrong definitions
567444a Fix errors in volume calculation
4e0a857 Indentation
cb40719 Add MMPump to scheduling and makefiles
bfc456c Add MMPump to DifShell
be1ceac Implementation of MMPump
c721713 Add ticks for DifBufferBase and DifShellBase
a3bee38 Fix bugs: DifShell now compiles and seems to give correct results
b131c44 Fix a typo in zombify
f1cbfb0 Rewrite DifShell. Inherit from DifShellBase
1486cdd Write base class for DifShell
336cbd1 Indentation
d8ee906 Implement exponential Euler for DifShell
f72d6a1 Move source messages to class. Correctly initialize Faraday's constant
b309dc4 Move source messages to class
5d3b7d2 Make DifBuffer look more like other moose classes and fix ticks
9a1e166 Add DifBuffer to clocks
f949b27 Add DifBuffer to compilation
5418e0b Fix no ticks when initializing difshells warning
5fba26e Remove useless variable
7e29b64 Reintroduce an old version of DifBuffer from moose
8f544e6 Moved to cmake folder.
ae1a5ba Merge commit '0d12ebb0'
3ac6c58 master branch.
65c371c Fixes to BhallaLab/moose#204.

git-subtree-dir: moose-core
git-subtree-split: 14e2d78a7b6e41e67bdce6e3a07fa0d65565744b

2ba6bd5 cleanup
d0f5918 replace writeKkit to moosewriteKkit
cb067ac correct from writeKkit to mooseWriteKkit
6b1bff4 Ubuntu16.04 with networkx and pygraphviz has some bug, for now small fix, automatic layout will be done spring_layout format
dbe6875 Update .travis.yml
8a71426 Update README.md
fcbacd5 Added travis file to moose-gui.
ddcfbdc Removed shebangs from python scripts.
d5cf170 Fixed the address of Free Software Foundation Inc.
b88d5cc Merge commit 'aca40347'
e0cea9f Squashed 'moose-gui/' changes from 1ef13c9-1ef13c9

git-subtree-dir: moose-gui
git-subtree-split: 2ba6bd5d8e6b022edf3f3aa1a567462ab7ddf6ed

8038f56 documentation is moved under main function
6ebca4d Corrected kkitwrite function
1726122 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
fbcaef7 added line to show how to set solver to sbml files
07a11d3 Merge pull request #11 from dilawar/master
536b53e Construct absolute path relative to script directory.
f5a7d84 All files must be python2 and python3 compatible [skip ci]
6895e56 All compiles with python2 and python3.
d9cb5b7 This version compiles with python2.
d80ec97 print_statement is the first statement of file.
74c70bc Custom fixes to print end='' statement on python2. Whenever possible import from __future__.
8977107 python-qt4 instead of python-pyqt4 is valid name package.
5e47fd8 Install and do not use moogli.
7b8c680 Fixed all files breaking with python3 compielall module.
e00a845 Fixed two more files.
3f789a1 Fixed one more script.
54f9549 Fixed syntax of this file as well.
63b9c43 Fix some more syntax issues.
5446b0e All scripts are now python3 compatible.
e5e259f This script is broken.
3e420f0 Merge remote-tracking branch 'bhallalab/master'
92ba920 Merge branch 'master' of github.com:dilawar/moose-examples
8a47205 Fixed print( , end='' ) with python2
f756065 Fixed print_function in couple of scripts.
3c6fbe0 Converted files to be campatible with python3 with tool 2to3.
da8c0dc Ran 2to3 on all examples. See which scripts are failing on travis.
469e3f3 These scripts were not chmod to executable. Removed hashbang from header.
3429792 Merge branch 'master' of github.com:BhallaLab/moose-examples
d34c8df Merge branch 'master' of github.com:BhallaLab/moose-examples
d56f575 Changelog:     - No python3 incompatible file should be added to repo.     - moose contains moogli now. No need to install it separately.
31137eb Fixed, python2 incompatible print function use.
a5375cc Merge commit '00a12e20'
15de0ce Since none of the following files was executable, removed shebangs.
4a20952 To run this file libsbml needs to be installed and not compile with moose as its at python level
092eec8 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
bee94a1 Merge commit '3c9138df'
4590e9e Merge branch 'master' of https://github.com/BhallaLab/moose-examples
62e3218 Moved docs to moose. Removed temp directory.
dc5a230 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
c8f96c5 Once simulation is done, store the results in png file.
5c36c87 Used 2to3 tool to make these scripts python3 compatibles. Also saving results to a png file after run is over.

git-subtree-dir: moose-examples
git-subtree-split: 8038f56ec24965353de70fb460ceccff3861f7b1

1b5b9a9 cspace and genesis model can be merged, yet to check what will happen with co-ordinates
9a405f6 for merging model one can pass file path or the modelpath
51da21a auto-coodinates are not done here, writter(SBML or kkit) will take care
4ba03b7 spell mistake
355e3e6 missing msg definition
3969bcb removed SBML option in Makefile
d1c4119 Merging 2 genesis model
1469b6e clean up in writting plot when file was read from SBML
4894a96 changes made to co-ordinate calculation depending where it comes from (GUI/direct), and type of file (GENESIS,SBML,cspace)
c11fcf0 validation.py is added: common place to validate SBML model before reading and writing, various changes made wrt chemUtil
6e7fa32 changes made to add chemUtil as a package and moose.py spell mistake
4551455 removing pyc files
e6f8c8f chemical based utils like add_delete_ChemicalSolver, chemiConnectionUtil: where chemical objects and connection are searched, graphUtils: used just pygraphviz to layout the model when x and y position are missing e.g for cspace and SBML models

git-subtree-dir: moose-core
git-subtree-split: 1b5b9a9104c0b7f461b569f62abf5f78fd531230

Make sure that innerArea is not negative. Move sending out of messages
to the bottom of the process function. Add sending out of
concentration to the buffer and diffusion to other difshells in
DifShell and diffusion to other buffers in DifBuffer in reinit. This
matches genesis implementation.

In DifShell reinit set C (calcium) to Ceq. In DifBuffer reinit
calculate bFree (free buffer) and bBound (bound buffer) to steady
state value. This matches genesis implementation.

Integration results were incorrect, because the helper variables were
not reset after every iteration.

Most of Cinfo code is moved to DifShellBase, so it got deleted from
DifShell. Method's names are changed, because they are now inherited
from DifShellBase.

Base classes are necessary for implementing hsolve.

Reintroduced implementation of Difbuffer used moose objects that have
been since rewritten and renamed.  Change used moose objects to
current version.

Change process_0 to proc, to match other classes which need to be
driven by ticks.