0f344909ae SO_REUSEPORT is not always defined. The build fails on centos-5 (#351)
441a66ba82 Issue 342 | TCP/UD Socket based Table Streamer (#345)
c67f8c0672 Travis build failure (#350)
053e256d76 Merge pull request #348 from analkumar2/master
a165432ed2 Corrected the K_AHP z gate and make_Ca y gate
c38c64380f Dec 19 | continuation of NML2 fixes (#344)
e93d391be4 Hotfix: Neuroml2 fixes (#343)
1e426a2c16 Update INSTALL.md
2624d4b190 Continuation to PR #308 (#340)
0997a4623f Merge pull request #341 from hrani/master
4dfac333a3 using existing restoreXreacs function to remove _xfer_ objects before writting into SBML and genesis files
ed7c4d58c3 Merge pull request #339 from upibhalla/master
1b48ce7ff7 Fix to CaConc to factor in valence of 2. Update to rdesigneur to handle SBML files
3aa66d4d34 Merge pull request #338 from hrani/master
356f43ce72 reading and writing diff and motor constant for pool
d6e5711a27 Merge pull request #335 from hrani/master
fac76ad723 groups and subgroups are written to sbml and read from xml files
69f9f33c38 Merge branch 'master' into master
169d0c88b2 Merge pull request #336 from upibhalla/master
d57fa1de92 Merge branch 'master' of https://github.com/BhallaLab/moose-core
b9a51133a3 Fix to Im calculation in HSolve, to include external channels like receptors. Also fix to Neuron.cpp for setting channelDistribution, to always load Ca_concs first, to ensure that any dependent channels are able to find them.
6868716b40 Merge branch 'master' into master
189778c8cd Merge pull request #331 from dilawar/master
7423c39e3b Merge branch 'master' into master
1a9b0f54df Merge branch 'master' into master
23906e50e5 searching for _xfer_
c40c622c0c xref pool are not wirtten and cleaned up if part of Reaction/Enzyme or notes, group are checked under all the mesh
01ebb8461e Merge pull request #333 from hrani/master
d72ad63fc5 Merge branch 'master' of http://github.com/hrani/moose-core
0cd028c047 Added other meshes while searching for groups
2189993593 Merge branch 'master' into master
97913222e9 Reading and creating CylMesh and EndoMesh if specified in the Annotation field
4d1337ae68 Merge branch 'master' of github.com:dilawar/moose-core
f6c4ab39cc Merge pull request #330 from hrani/master
26e966284f Tweaks.
90c97b6599 Fixed the bug caused by previous two commits. Now I need to make sure that ca pool is read at each timepoint.
86522d326e Using built in logging library.
b327ec7d39 xfer cross compartment molecules are not written as species and also for Reaction and Enzyme
e5fbf8c5db For CylMesh, totLength and diffLength is written to Annotation to get number of voxel
d569f56a39 gate with id z is loaded into gateZ in moose now.
b38a4405ae Squashed commit of the following:
ef8e54a15b variable name used in before assignment cleanup
740a7a65b9 CylMesh,EndoMesh,NeuroMesh compartment are written to SBML as compartment with annotation field in which surround,isMembraneBound,numDiffCompts

git-subtree-dir: moose-core
git-subtree-split: 0f344909ae285b147b4bc61089b8ee52aa6b9186

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

d229eba6bb Parallel solvers (#293)

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

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 meant for chemical models only, a check is made to see if modelroot has just cube/CylMesh
3790376c3e Merge pull request #291 from BhallaLab/dilawar-patch-2
c52740323a Update README.md
5843c73ab5 Merge pull request #289 from upibhalla/master
e3baee2dce Merge branch 'master' of https://github.com/BhallaLab/moose-core
7a1b0d8ff6 Test xreacs (#287)
869522d04c Merge branch 'master' of https://github.com/BhallaLab/moose-core
bb274ee43c loadmodel with add_delete_chemSolver (#288)
7d563c7c23 Merge branch 'master' of https://github.com/BhallaLab/moose-core
637d2233a1 setting up dsolver and by passing loadModel from moosemodule.cpp to m… (#277)
9f5a2697f6 Merge branch 'master' of https://github.com/BhallaLab/moose-core
3a8489c475 All random number generators are based on c++11  (#280)
8e29d8eaa7 Minor updates to rdesigneur waveplotting
46718b9c04 Added wavePlot option to rdeisgneur.
506067669c Minor fixes to rdesigneur for setting up stims
5ab1a3c621 Merge branch 'master' of https://github.com/BhallaLab/moose-core
ea487f3ee0 Updated rdesigneur so it can handle a chem system with only a dendrite and spine compartment, no PSD.
7c321bfe94 Merge pull request #284 from upibhalla/master
d9bd29c97d Fix for units of permeability of ConcChan, as computed in Dsolve.cpp. Now it is 1/(mM.sec).
3056c917fe Merge branch 'master' of https://github.com/BhallaLab/moose-core
ae8f2336ce Fixed bug with NeuroMesh
9271d0ba22 Fixes to ReadKkit, Dsolve, rdesigneur to handle EndoMesh to insert in neuronal geometries.
f4ba9362e4 Intermediate save of rdesigneur with partial changes for handling endoMesh. Works with old examples, not tested for EndoMeshes

git-subtree-dir: moose-core
git-subtree-split: d5b330dc02ed938fcb7cff95d8ae0e2cd388d0ea

2657e3345e Merge pull request #199 from dilawar/master
973dd380ba Deleted Makefile.
545b4241c8 Restore synapse folder back to 933b259 . synapseOrder is now working.
90711a865c execute_process is now used to get the extension of python module. See http://bugs.python.org/issue16754 in case build fails on some unix because of 'SO'.
5b0a529c4e We do not reply on VERSION file to create version. TODO: Use config.h.in file to populate VERSION information.
2749918927 Accessing an existing object (#198)
220128f284 Do not run DOQCS with moose-core. Test DOQCS with released package only. Do so in moose-examples repo.
ad2c63da12 Use QUIET_MODE=ON on travis.

git-subtree-dir: moose-core
git-subtree-split: 2657e3345e8b783cf22634680c7561f8dbd9f127

891f2f8 Removed trailing spaces from code by pre-commit hook utility.
0ed2535 Cherry-pick "Added connectionList field to SparseMsg to allow direct control over connection matrix. Some sanity checks in SparseMatrix to go with this"
d62d10d The bug on travis is still not bypassed. If this does not work, disable DOQCS tests on OSX.
618b4d6 Install moose on osx as well. Prerequisite to test DOQCS.
f717f82 Merge branch 'master' of github.com:BhallaLab/moose-core
908820e Lets see if this is a good workaround travis issue travis-ci/travis-ci#6522.
e251f53 Lets see if is a workaround fixes the OSX bug.
4ff7cff Hopefully this will fix issue on travis-osx build failure. Related to travis-ci/travis-ci#6522.
590c09e Don't use timeout in script. So that we can run on macosx as well. Removed timeout command from script. Now it can run on OSX as well.
e2f8afd Only test doqcs on LinuxOS, not on MacOSX.
dc7b55a Fix to travis-ci/travis-ci#6307.
54b8471 Merge branch 'master' of github.com:BhallaLab/moose-core
18c8759 Test docqs agains gsl version/python2 moose-core.
d6ca9cc Fixes by pre-commit hooks. - Removed trailing whitespaces automatically. - insert * coding - utf8 * line on top of each python script automatically.
d4a6939 Using version v0.8 now.
f944afe Added pre-commit pip install pre-commit --user to activate it.
030bfe0 Merge pull request #195 from dilawar/master
d00a5d1 All tests are passing and new code is protected by appropriate macros.
1959771 Merge branch 'async' of github.com:dilawar/moose-core
0f6aba0 Merge branch 'master' of github.com:BhallaLab/moose-core
ac0a4cd Added note on what to do.
b3bf54e Slower version but results are same.
6bc71c9 Async version is slower (80sec vs 70 sec).
d838267 asyncing clock is not producing great results.
eeaafbf Implemented first parallel version.
166f84e Equivalent serial code which can easily be called from std::async now.
e09a0c1 Merge pull request #194 from dilawar/master
d2d1097 Added MACRO to integrate serial and parallel version.
e68acd6 This is good but do parallelism at Clock.cpp
4cebbca Rdesigneur has python3 default import : absolute_import.
f431cca Merge branch 'master' of github.com:BhallaLab/moose-core
85afa6d Some changes to Ksolve. Still seg-faults.
47e023e Time to test the Gsolve performance when threads are enabled.
2bbfd4f Commented out code appropriately.
91c2da6 moose.test( ) is added not cmake but not enabled. Enable them once all scripts are fixed in moose-examples.
a1699fc Optimized GSolve with default 2 threads.
00a9d9e Removed the debug message. Lets check it now. By default it should be not slower than the default version.
7700c07 Fast Ksolve with 2 default threads.
d154eb3 Parallel ksolve.

git-subtree-dir: moose-core
git-subtree-split: 891f2f8bf7359d61f186c3792c6f12b61d8c0afb

052318cb4 [skip ci] Moved git precommit script into script. if someone wants to activate it in her repo, rename it to .pre-commit-config.yaml and enable it
d15e77649 Removed legacy makefile #180. These appeared again because of push from subtree in moose repo. Sigh!
ed708e01b No-longer supporting Makefile based old flow on travis.
bea1f4a9d Integrated test script from PR BhallaLab/moose#218 . I need to confirm if results are correct.

git-subtree-dir: moose-core
git-subtree-split: 052318cb48027ca0c401a13be9fddd2b0d5a66b7

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