Periodic merge of subprojects : Nov 11, 2018

e5868beb9 Merge pull request #329 from upibhalla/master
a56b7e883 Fix to rdesigneurProtos so that the classic HH Na and K_DR channels now work properly.
0bdebdf6f Merge pull request #328 from upibhalla/master
bc3ff9ccd Got rid of printf debug line
788bce98b Merge branch 'master' of https://github.com/upibhalla/moose-core
b8eeb9d5f Merge branch 'master' of https://github.com/BhallaLab/moose-core
47ee21c36 Fixes to rdesigneur so that chemProto without chemDistrib will not fail confusingly.
50f03b860 Fixes to EndoMesh (#327)
552ca01a1 Merge branch 'master' into master
905c98332 Merge pull request #323 from hrani/master
aca01be2e Fixed numDimentions to 3
12e429d47 Merge branch 'master' of https://github.com/BhallaLab/moose-core
1f91c76fc Added dummy CubeMesh as default parent for EndoMesh to avert segvs on several methods
5a8ec044e Merge branch 'master' into master
e4c19935e Merge pull request #324 from upibhalla/master
0327eb9e7 Fixed test_Xchan1.py to match bugfix for Dsolve.
2e2227649 Merge branch 'master' of https://github.com/BhallaLab/moose-core
182e95c52 Bugfix for ConcChan to correct scaling for permeability to SI units of millimolar
865e99dbb Merge branch 'master' of http://github.com/hrani/moose-core
70f116ad9 cleanup in print statement
83afd0fe3 Merge branch 'master' into master
9b0569b93 while reading the sbml model validator can be switched off
5b0bbe1be Merge pull request #322 from hrani/master
05eba8faa Channel are written back to genesis and zeroth voxel moose object is written for both cubeMesh or CylMesh
53cbe3656 reading info field for channel from kkit file (#321)
ba88932fb CylMesh are written to SBML with annotation field and only zeroth ele… (#318)
f917df152 Merge pull request #319 from dilawar/master
637583439 Works after disabling alpha and beta properties.
0b208c8c9 Now user can pass verbose option to mooseReadNML2
556ebef64 Hotfix. If self.network not found, sett the temperate to 25 deg C.
7c86d4ebc Merge branch 'master' of https://github.com/BhallaLab/moose-core
3a655cd06 Minor typo in warning report for Dsolve
b4637b21a Merge pull request #317 from upibhalla/master
d6e35de32 Merge branch 'master' into master
ecfca8401 Update README.md (#312)
f66ba9003 Merge branch 'master' of https://github.com/BhallaLab/moose-core
51dd77625 Rdesigneur passiveDistrib modified to handle legacy commands
5d20e0433 corrected the spell of CyclMesh-->CylMesh, negating the yaxis for kkit is corrected as now saving the value of scene coOrdinates (#313)
a8769f2c4 Update CMakeLists.txt
f0e4db0e9 Fixes to build failure on OSX because cmake does not MACOSX but APPLE on (#316)
2fb51c9a5 Hotfix: Neuroml2 fixes. (#315)
e46429530 Merge pull request #314 from upibhalla/master
b57a6d0df Merge branch 'master' into master
d2749931d Build System Tweaks  (#309)
293d44144 Some fixes to Ca-dependent channel prototypes in rdesigneur.
88bcf0797 Merge pull request #311 from upibhalla/master
aaf589ab2 Merge branch 'master' of https://github.com/BhallaLab/moose-core
0909ceb32 Fixes as suggested by PyLint. Added a target pylint in cmake file. (#308)
cdbf917b2 Merge branch 'master' of https://github.com/BhallaLab/moose-core
79e2d65f5 hotfix for running Boost, Added NMDAR to rdesigneurProtos.
eb4e83662 Fixed boost segfault with dense solver.  Also remove GSL specific attrib from the test. (#310)
8463cc73e Update setup.cmake.py (#307)
8c38fc6d6 Removed deprecated warnings from neuroml2 reader (#305)
6df4332d2 Fixes to BOOST based steadystate solver (#306)
99dd7d250 Merge pull request #302 from BhallaLab/chhennapoda
86c424452 Merge branch 'master' into chhennapoda
ec06b242a HotFix: Fix regression in StreadyState solver caused by #293. (#304)
6b79f6701 prefer .so suffix over CPython version specific suffix . this way a wheel compiled by any version of python3 will work with any python3.
92da6a7fb removed python-libsbml from install dependencies; added matplotlib. sbml and neuroml packages should be installed by user and not automatically. They may not be available for all distribution of python on all OSes.
e2bc19c0e Merge branch 'master' into chhennapoda
385a5cf0a Merge pull request #303 from upibhalla/master
080767c5a Fixes to rdesigneur due to bad merge. Cleanup on rmoogli
62f8bc89e Tweak to Neuron.cpp so it can handle insertion of spines with uniform spacing.
b6088109b Fixes for linux.
406fee2a0 Temp commit to test on OSX.
cc3c604b9 Merge branch 'master' into chhennapoda
342092829 Update moose_test.py (#301)
61f4f6684 show timeout in moose.test() .
abf822c4a with python2, just test with GSL. Build python3 first.
088c61673 Made changes to build system so that pymoose directory can be built in isolation. Build system is bit more module. Ideally I should make sure that each subdirectory can built in isolation.
3c0ff2790 Few changes to build with python3.6.
5d688f63d Use option --relative in setup.py and tell cmake not to look into usr prefix anymore.
1f3fe9fc3 Merge branch 'chhennapoda' of github.com:BhallaLab/moose-core into chhennapoda
3e19983c8 removed unneeded library which is never used.
c2fbab872 cmake related changes to build on centos5 (manylinux docker image).
f1230f151 Merge branch 'master' of https://github.com/upibhalla/moose-core
23a2892cc Merge branch 'master' of https://github.com/BhallaLab/moose-core
8a835c133 minor bugfix to rdesigneur
6ef1d567e Merge branch 'master' into master
a9a2e758f Merge branch 'master' of https://github.com/BhallaLab/moose-core
5e1294d99 Further updates to rdesigneur for argument handling
a702bded5 Put in kwargs based specification of plotList, stimList and moogList. Folded savePlots into plotList but not yet tested.

git-subtree-dir: moose-core
git-subtree-split: e5868beb97afcb778d6a945c38e80300c953b39a

uploaded updated Rdesignuer files from Upi

* Pull subtree to master branch.

* Squashed 'moose-core/' changes from d229eba6bb..b4637b21a0

b4637b21a0 Merge pull request #317 from upibhalla/master
d6e35de324 Merge branch 'master' into master
ecfca84012 Update README.md (#312)
f66ba90038 Merge branch 'master' of https://github.com/BhallaLab/moose-core
51dd776253 Rdesigneur passiveDistrib modified to handle legacy commands
5d20e04333 corrected the spell of CyclMesh-->CylMesh, negating the yaxis for kkit is corrected as now saving the value of scene coOrdinates (#313)
a8769f2c48 Update CMakeLists.txt
f0e4db0e98 Fixes to build failure on OSX because cmake does not MACOSX but APPLE on (#316)
2fb51c9a56 Hotfix: Neuroml2 fixes. (#315)
e46429530f Merge pull request #314 from upibhalla/master
b57a6d0df0 Merge branch 'master' into master
d2749931d0 Build System Tweaks  (#309)
293d441443 Some fixes to Ca-dependent channel prototypes in rdesigneur.
88bcf0797c Merge pull request #311 from upibhalla/master
aaf589ab23 Merge branch 'master' of https://github.com/BhallaLab/moose-core
0909ceb328 Fixes as suggested by PyLint. Added a target pylint in cmake file. (#308)
cdbf917b21 Merge branch 'master' of https://github.com/BhallaLab/moose-core
79e2d65f58 hotfix for running Boost, Added NMDAR to rdesigneurProtos.
eb4e836623 Fixed boost segfault with dense solver.  Also remove GSL specific attrib from the test. (#310)
8463cc73e5 Update setup.cmake.py (#307)
8c38fc6d60 Removed deprecated warnings from neuroml2 reader (#305)
6df4332d2d Fixes to BOOST based steadystate solver (#306)
99dd7d2503 Merge pull request #302 from BhallaLab/chhennapoda
86c4244522 Merge branch 'master' into chhennapoda
ec06b242ae HotFix: Fix regression in StreadyState solver caused by #293. (#304)
6b79f6701c prefer .so suffix over CPython version specific suffix . this way a wheel compiled by any version of python3 will work with any python3.
92da6a7fb8 removed python-libsbml from install dependencies; added matplotlib. sbml and neuroml packages should be installed by user and not automatically. They may not be available for all distribution of python on all OSes.
e2bc19c0e4 Merge branch 'master' into chhennapoda
385a5cf0a1 Merge pull request #303 from upibhalla/master
080767c5aa Fixes to rdesigneur due to bad merge. Cleanup on rmoogli
62f8bc89e0 Tweak to Neuron.cpp so it can handle insertion of spines with uniform spacing.
b6088109bf Fixes for linux.
406fee2a06 Temp commit to test on OSX.
cc3c604b9f Merge branch 'master' into chhennapoda
342092829c Update moose_test.py (#301)
61f4f66843 show timeout in moose.test() .
abf822c4a6 with python2, just test with GSL. Build python3 first.
088c61673c Made changes to build system so that pymoose directory can be built in isolation. Build system is bit more module. Ideally I should make sure that each subdirectory can built in isolation.
3c0ff27903 Few changes to build with python3.6.
5d688f63d8 Use option --relative in setup.py and tell cmake not to look into usr prefix anymore.
1f3fe9fc35 Merge branch 'chhennapoda' of github.com:BhallaLab/moose-core into chhennapoda
3e19983c83 removed unneeded library which is never used.
c2fbab8726 cmake related changes to build on centos5 (manylinux docker image).
f1230f1518 Merge branch 'master' of https://github.com/upibhalla/moose-core
23a2892cc8 Merge branch 'master' of https://github.com/BhallaLab/moose-core
8a835c1332 minor bugfix to rdesigneur
6ef1d567ec Merge branch 'master' into master
a9a2e758ff Merge branch 'master' of https://github.com/BhallaLab/moose-core
5e1294d991 Further updates to rdesigneur for argument handling
a702bded54 Put in kwargs based specification of plotList, stimList and moogList. Folded savePlots into plotList but not yet tested.

git-subtree-dir: moose-core
git-subtree-split: b4637b21a04e37e3358867c2327d636369990e15

* Pull subtree to master branch.

* Squashed 'moose-core/' changes from d229eba6bb..8463cc73e5

8463cc73e5 Update setup.cmake.py (#307)
8c38fc6d60 Removed deprecated warnings from neuroml2 reader (#305)
6df4332d2d Fixes to BOOST based steadystate solver (#306)
99dd7d2503 Merge pull request #302 from BhallaLab/chhennapoda
86c4244522 Merge branch 'master' into chhennapoda
ec06b242ae HotFix: Fix regression in StreadyState solver caused by #293. (#304)
6b79f6701c prefer .so suffix over CPython version specific suffix . this way a wheel compiled by any version of python3 will work with any python3.
92da6a7fb8 removed python-libsbml from install dependencies; added matplotlib. sbml and neuroml packages should be installed by user and not automatically. They may not be available for all distribution of python on all OSes.
e2bc19c0e4 Merge branch 'master' into chhennapoda
385a5cf0a1 Merge pull request #303 from upibhalla/master
080767c5aa Fixes to rdesigneur due to bad merge. Clean...

* Squashed 'moose-core/' changes from d229eba6bb..ec06b242ae

ec06b242ae HotFix: Fix regression in StreadyState solver caused by #293. (#304)
385a5cf0a1 Merge pull request #303 from upibhalla/master
080767c5aa Fixes to rdesigneur due to bad merge. Cleanup on rmoogli
62f8bc89e0 Tweak to Neuron.cpp so it can handle insertion of spines with uniform spacing.
342092829c Update moose_test.py (#301)
f1230f1518 Merge branch 'master' of https://github.com/upibhalla/moose-core
23a2892cc8 Merge branch 'master' of https://github.com/BhallaLab/moose-core
8a835c1332 minor bugfix to rdesigneur
6ef1d567ec Merge branch 'master' into master
a9a2e758ff Merge branch 'master' of https://github.com/BhallaLab/moose-core
5e1294d991 Further updates to rdesigneur for argument handling
a702bded54 Put in kwargs based specification of plotList, stimList and moogList. Folded savePlots into plotList but not yet tested.

git-subtree-dir: moose-core
git-subtree-split: ec06b242ae650f413d50b9c22b76381a94efcba4

* Squashed 'moose-examples/' changes from 2d9849222d..e30d87a637

e30d87a637 Merge pull request #47 from BhallaLab/nml2
e350e8a801 Fixed path in script.
1602f54763 Added missing NML files and removed unneccessary files.
6d6c27e051 nml2 snippets.
3963e7969a Merge pull request #46 from upibhalla/master
4165c53e4a Merge branch 'master' of https://github.com/BhallaLab/moose-examples
2c0afa8fcc Clean up of ephys1 and ephys2 tutorials
9793e59f6c Merge branch 'master' of https://github.com/BhallaLab/moose-examples
2e91700547 Merge pull request #45 from upibhalla/master
7420933455 Added missing image file
70a3b3fc1c Test with python2.7, python3.6 and python3.7 .
bf6c180ee1 Use pypi nightly version to test.
075d01c1af Merge pull request #44 from upibhalla/master
13da78cfc0 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
e3cd31b515 Added Ephys demo for Rall's Law
2e12a9b42a Added squid demo with pyqt5.
410103e36a Use moose.element to get the element.
8f71469d17 Merge pull request #42 from upibhalla/master
77f6694e0e cleanup of some rdesigneur tutorials
9a6f8e214e Merge branch 'master' of https://github.com/BhallaLab/moose-examples
cc44a7e4fb Added demo for uniform spine placement, and putting them in a spiral
3a25620865 First commit for Electrophys tutorial directory
1502a55070 removed old script.
3b7a109b5e Merge branch 'master' of https://github.com/BhallaLab/moose-examples
4336dc3ae8 Fixed passiveDistrib argument list, got rid of unused '.' argument in a few examples
c5e895f30e Updated ex7.5 and README
9f95a87909 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
9ce8913fa5 Added 3 demos for dendritic transport

git-subtree-dir: moose-examples
git-subtree-split: e30d87a6374107d7f0494587dd3d868a22a58e20

* Squashed 'moose-gui/' changes from d226931e0b..c29cede420

c29cede420 hen vertical or horizontal layout is applied for group, compartment size is recalculated
d76d66af1d Function moved to place other than parentpool location its pullback
d03482329c color field is not editable for compartment, enzcplxpool and reaction
0a4b1cab43 compartment boundary is selected if its inside another compartment interior
02b9d3964f comparment size is calculated based on group sceneBoundingRect
8dae832c35 kkitViewcontrol both the groups size are updated if moved from-to is different
44b53bc56d default: addSolver->mooseAddChemSolver, kkitViewcontrol: while rubberbandselection if entire group is selected then delete if partly selected then delete all the items under the selection
80b599f85d mgui: is popup exist then close, objectedit: objectwindowTitle is updated with name when changed, kkit: in positionChange all the neutral is updated with size, kkitViewcontrol:when moose object is moved from Compt/group to group/compartment then mooseobject path is set and for qgraphicalItem and qlineitem objects the parentItem is set which will be grpItem or comptItem

git-subtree-dir: moose-gui
git-subtree-split: c29cede4201bd25dfe868aaaa9d227ea455410ae

* Build using Travis.

* Scripts to test OSX and Linux packages.

* Pull from branch chhennapoda.

* No clang.

* Made scripts executable.

* New version.

* Squashed 'moose-core/' changes from d229eba..406fee2

406fee2 Temp commit to test on OSX.
cc3c604 Merge branch 'master' into chhennapoda
3420928 Update moose_test.py (#301)
61f4f66 show timeout in moose.test() .
abf822c with python2, just test with GSL. Build python3 first.
088c616 Made changes to build system so that pymoose directory can be built in isolation. Build system is bit more module. Ideally I should make sure that each subdirectory can built in isolation.
3c0ff27 Few changes to build with python3.6.
5d688f6 Use option --relative in setup.py and tell cmake not to look into usr prefix anymore.
1f3fe9f Merge branch 'chhennapoda' of github.com:BhallaLab/moose-core into chhennapoda
3e19983 removed unneeded library which is never used.
c2fbab8 cmake related changes to build on cen...

d229eba6bb Parallel solvers (#293)

git-subtree-dir: moose-core
git-subtree-split: d229eba6bbc957c97bac44d24d513543956942c1

the test.

test.

d226931e0b while deleting the group a warning box is set,deleteSolve is now mooseDeleteChemSolver, while saving to sbml model scenepos is picked up, hopefully this works for others. Tested for single compartment multiple group
c1a3949a3e adding/deleting the solvers are picked from the python/chemUtil folder instead of local setsolver file and addsolver is now mooseAddChemSolver
2f8fcab25f in disableModel function added dsolve also
b4d5376ae8 From command line if filename is passed it load into moose-gui
a82842f683 group border color can be editable
395d5f0a9c if moose object is moved from compartment to group or from group to another group/compartment, then mooseobject path and qt object parentItem are updated

git-subtree-dir: moose-gui
git-subtree-split: d226931e0b932407ecea7863588b1f3d9e8721a7

2d9849222d Add 3 new demos for rdesigneur (#41)
f25999106c update sbml file to store scenepos
2f78a07958 Fixed testHSolve script.
c537773939 Use python based relpath. The realpath utility is too old on travis.
5dbee3920d Merge pull request #39 from upibhalla/master
5a2af75f90 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
fda496c533 minor fix to scaleVolumes demo
0fe42549ce Added ex8.1 for CICR in a multiscale model. Some updates to ex8.2 and the README
2e1b2035f4 Added rdesigneur tutorial for synaptic-input triggered CICR
59a458b611 Fix to units for permeability for ConcChan, affects ex7.2_CICR.py
2b026c5ab5 Updated some demos, added new ex7.2 which demonstrates CICR, endo-compartments, and the operation of ConcChans.
a6adb6acc1 mooseaddChemSolver changed to mooseAddChemSolver, commented buildXreac and filterXreac
27855bb699 Renamed the file. First argument takes the method name.
12f57e76ba Update test_ksolve_lsode.py
63...

d5b330dc02 Merge pull request #296 from hrani/master
5a606df86c Merge remote-tracking branch 'upstream/master'
ce545cf507 Rdesigneur updates (#295)
9869046490 Merge branch 'master' into master
753b189063 changes made after fixXreacs is moved from python to python/moose for package
5eca1a3620 moved fixXreacs.py from python to python/moose for packaging, changes made to get fixXreacs files
3a519cec39 mooseAddChemSolver and mooseDeleteChemSolver is meant for chemical models only (#292)
9ba0e85532 check for enz parent is done by neighbors['enzDes'] rather than enz.parent and if enzyme parent is not pool then raise an exception
161c475e2c Merge branch 'master' into master
f9d869da24 Merge pull request #294 from upibhalla/master
a76dd524b4 Merge branch 'master' of https://github.com/BhallaLab/moose-core
c0d5ba6d9b Added plot y limits to rdesigneur
5fa7226e60 clean up modelRoot while printing
3c6972aae3 mooseAddChemSolver and mooseDeleteChemSolver is mea...