Related to moving out Rdesignuer from cookbook as a seperate section add files and update Rdes.rst and related images which is updated by Upi

1271dcd Merge pull request #278 from upibhalla/master
c400af3 Minor extension to rdesigneur to handle display of the passive electrical parameters of compartments: Rm, Ra, Cm. These will be scaled if spine geometry changes.
a77c611 Fixes to rdesigneur for NeuroMesh models. Key bugfix to Dsolve for NeuroMesh models. Some code cleanup to eliminate compiler warnings about uninitialized variables.
840021f Added lots of channel prototypes to rdesigneurProtos. Small fixes to rdesigneur for multiscale models.
c4f9fa5 Updates to Rdesigneur to handle synaptic input stimulus. Modified RandSpike with a doPeriodic flag, so it can be used for periodic stimuli as well.
cb2dd4b Merge branch 'master' of https://github.com/BhallaLab/moose-core
fc6ca10 Updates to rdesigneur to handle voltage clamp specification as a stimulus. Added doEvalAtReinit flag to Function so that it can initialize at a precomputed value rather than zero.
0445da5 Merge pull request #276 from upibhalla/master
48d1d4c Updates to rdesigneur to handle soma parameters and ball-and-stick model in cellProto argument
694fe5e Merge branch 'master' of https://github.com/BhallaLab/moose-core
180109a Changed Enz number-rate scaling to use the volume of the enzyme molecule, rather than the volume of the substrate. This usage gives results consistent with Genesis/kkit
f9de66e Merge pull request #273 from upibhalla/master
c2d1a6f Fixed grotesque bug with Dsolve.cpp which manifested only if pool names were of length 13 and they were diffusing.
b9448c0 Merge branch 'master' of https://github.com/BhallaLab/moose-core
bcd9ddb Fixes to Enz so that kcat of zero doesn't set up NaNs in Km and K1. Display updates to rdesigneur, rmoogli, moogul.
eeea183 Merge pull request #270 from upibhalla/master
5e840d2 Merge branch 'master' into master
9ac8d79 Merge pull request #272 from BhallaLab/dilawar-patch-2
8f276ef Update travis_prepare_osx.sh
2d00294 Update rmoogli.py
5e793c3 Update moogul.py
5108d7e Update rmoogli.py
42a4f3b Merge branch 'master' of https://github.com/BhallaLab/moose-core
8ea8b2e Fixes to moogli when run from outside the rdesigneur directory
c411242 minor cleanup on rdesigneur
ea99dcc Updated version of moogul, integrated now with rdesigneur
d81e796 Merge pull request #264 from hrani/master
bf0119b Update test_negative_value_flag.py
6e71d8e Update test_kkit.py
fdc7d66 cleaned up print stm
51dfc2c cleaned up print stm
b055a5c cleaned up wrt to python3 compilation problem
09da84b indentation corrected
00bc557 indentation corrected
b55acd9 Cleaned wrt to diffusion,clean up to remove in ReadKKit removed the setting up of solver, in mooseaddsolver() cleaned up in setting and deleting the solver, added utils.loadmodel function to call loadmodel function with setting for solver
9441bf9 Merge branch 'master' into master
08f0804 Merge pull request #266 from upibhalla/master
0ad961c Update rdesigneur.py
3ec65d7 Update rdesigneur.py
b6b58a4 Moved fixXreacs.py from python/rdesigneur directory to python directory
736f7f5 Merge branch 'master' of https://github.com/BhallaLab/moose-core
38a1d03 Bugfix for fixXreacs so that it works properly if there was already some text in the notes.
b8fcd11 Merge branch 'master' of http://github.com/hrani/moose-core
ad6925f Merge branch 'master' of https://github.com/BhallaLab/moose-core
9d5be9d Merge branch 'master' into master
cc13c50 travis failing with libgfortran not found, hopefully this should fix it
b246358 rename modelA and modelB to modelS and modelD, cleanup while copying the object at Neutral level
ad7236b enzcomplex pool cleaned-up
8fce41c indentation corrected while writting annotation for enzymecomplex

git-subtree-dir: moose-core
git-subtree-split: 1271dcd74baf95a973debcdef0fc8b348010bb78

Highlighted pip section.

Added instructions.

Fixed typo.

3fd3739e86 From Editor Widget add plot of n or conc
a15524b05e from runWidget plot can be added either n or conc and function can have Neutral as parent as compared to pool

git-subtree-dir: moose-gui
git-subtree-split: 3fd3739e86802afb217c540b0cf72cb268dd6242

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.

Testing on travis.

bumped version.