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

* 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. 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: 8463cc73e5d837ade8e191404359bc278f377b9d

* Fixes to build system.

* Some test only runs on travis only.

* Don't run moose.test()

* 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 centos5 (manylinux docker image).

git-subtree-dir: moose-core
git-subtree-split: 406fee2a068f43af14be9918825e6fa88cc7377e

* Squashed 'moose-examples/' changes from 2d98492..1502a55

1502a55 removed old script.

git-subtree-dir: moose-examples
git-subtree-split: 1502a550706e049ee726f8adb4694a77feb63bbd

* Squashed 'moose-gui/' changes from d226931..8dae832

8dae832 kkitViewcontrol both the groups size are updated if moved from-to is different
44b53bc default: addSolver->mooseAddChemSolver, kkitViewcontrol: while rubberbandselection if entire group is selected then delete if partly selected then delete all the items under the selection
80b599f 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: 8dae832c3513bac92b3fba9601e9a77b4ec36653

* Install gsl-dev on travis.

* Build chhennapoda branch.

* Run tests as well.

* Squashed 'moose-core/' changes from 406fee2..b608810

b608810 Fixes for linux.

git-subtree-dir: moose-core
git-subtree-split: b6088109bf8ba75cb072d97dd306bec9ab2b0e9a

* Squashed 'moose-core/' changes from d229eba..3420928

3420928 Update moose_test.py (#301)

git-subtree-dir: moose-core
git-subtree-split: 342092829ca21e457c785a5ce791429d403b79e7

* Squashed 'moose-examples/' changes from 2d98492..1502a55

1502a55 removed old script.

git-subtree-dir: moose-examples
git-subtree-split: 1502a550706e049ee726f8adb4694a77feb63bbd

* Squashed 'moose-gui/' changes from d226931..8dae832

8dae832 kkitViewcontrol both the groups size are updated if moved from-to is different
44b53bc default: addSolver->mooseAddChemSolver, kkitViewcontrol: while rubberbandselection if entire group is selected then delete if partly selected then delete all the items under the selection
80b599f 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: 8dae832c3513bac92b3fba9601e9a77b4ec36653

* Build nightly version.

49d5b3ef6b Merge pull request #255 from dilawar/master
f498d7c6a4 Merge branch 'master' of github.com:dilawar/moose-core
c09dd9936f Cut down on unneccessary looping. It is logically equivalent to original block.
aab34e125d Merge branch 'master' into master
3568083113 replace has_key with python3 compatible statement.
026d0a39b1 updated pre-commit config.
b811def3bd Merge branch 'master' of github.com:BhallaLab/moose-core
5bc1e1410a Merge pull request #254 from upibhalla/master
b08b888f56 Merge branch 'master' of https://github.com/BhallaLab/moose-core
945fb6b961 Added funcDt to rdesigneur arguments, set sensible defaults
760f554966 Update Function.cpp
8e9bcb58ac Merge pull request #253 from upibhalla/master
2f8dc9fcfe Merge branch 'master' of https://github.com/BhallaLab/moose-core
b55e1a74ea Update to Synapse to permit set/get access to addSpike. Cascaded onto all SynHandlers. Update to rdesigneur to permit fullscreen display of Moogli.
6eca687a68 Added deploy section in travis. Deploy on PyPi. Needs to add script t… (#251)
c8f9101621 Fixed cmake error on osx when not compiled in debug mode. Affect only >=cmake-3.6
f6ab07d0ef Update README.md
0d3f850fe5 Update README.md
cc94e3bd61 Set VERSION_MOOSE only
948406bc17 Marked as release candidate 3.2.0rc1.
b675c4d1bf Fixed build failure due to newline in output variable.
bf8d39351e Add git hash to version.
d95e58650f Python wheel for pymoose (#250)
edbb4ce966 Fixing VERSION; MOOSE_VERSION; project name is moose-core.
e245ef6a4d call project moose-core.
9061927ca7 Build GSL with fPIC.
230466ff32 updated dockerfile. Added missing gsl library.
69bc228b34 rename to pymoose.
41ef965e75 Heredocs are not supported in docker.
f370b4aa19 Docker file has the script inline.
b8b9679943 Time to merge into master branch.
9c7241f1bd Wheels are built. Now use manylinux docker file to build them.
c439f55046 Build in manylinux environment.
108f71809d Wheel is created.
d08ddf290f removed file.
9d654b4cba no need to link with PYTHON_LIBS.

git-subtree-dir: moose-core
git-subtree-split: 49d5b3ef6b585ff1c64734f447ac08cd67d9996a

0c33b2c333 remove setup.py. It has been renamed to setup.cmake.py to avoid confusion. This file is to be used only by cmake.
079730d06d Added missing package data.
59d374fa48 removed deprecated setup.py file.
9d3f7439f6 Merge remote-tracking branch 'origin/chamcham'
28ded4be72 matplotlib is not essential dependencies in tests or in any moose import. If NSDF support is not found, do not fail the test.
b7294b2814 More informative message if plot utilities are not loaded.
4678f1a263 Merge branch 'master' of github.com:BhallaLab/moose-core
667a3d254f more detailed error message if neuroml2 import fails.
5d504a5a1e Merge branch 'master' of https://github.com/BhallaLab/moose-core
c5c5854fe8 Added extra args to setup.py.
07f19011c8 install using debian layout.
0c3c2b7416 Merge pull request #249 from dilawar/master
03951bd314 When build in DEBUG mode, we never go to negative values in this test script. This causes test to fail on some unix platform in DEB...

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 'mast...

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

7c9fe23 Fixes to issue #167. (#168)
3f077c1 Resolved merge conflict with Table.h
9b175c8 Major bugfix for Table and derived class Streamer, to fix error introduced by duplicating the 'name' field which is already defined for Neutral. Minor bugfix for melement.cpp
f0d4c02 Update INSTALL.md
2737220 Fixes to issue165 (#166)
a934676 Update .travis.yml
601d06a Fixes to PYTHON3 build failure on travis.
9d9d925 Tested locally for linux. The scripts seems to be fine on openSUSE-42.2
93bbd4f By default travis pick up /opt/bin/python when `which python` is used. Do not use this construct in script. Moved travis related scripts to a hidden folder .travis.
c0d3871 If python3 exists (installed on travis), then check for the compatibility otherwise don't.
65a85da Almost there. Calling script from top of directory.
0db2016 Make trusty default build environment. python3-matplotlib is not available by default.
d8c1c6a setuid to root for linux script.
4c90f04 Some more f...

[ skip ci ]

[ skip ci ]

ed5f015 Update README.md
a4a5cc1 Fixed linking error compiling with new gcc.
9a82850 Merge commit '912c550e28d1fccfd310c5968a07ae38dc60c698'
0fb7431 Added option to explicitly set CMAKE_DL_LIBS flag (-ldl).
da5fd97 Merge commit '9296cecdffbe647a929af4792360adbc3768e4bd'
093e681 Disabled unused part of code #86.
c698620 Merge commit '11af2e3b2ecd7b31aefa957412abb5b64ce54014'
57714ae Fixes to VERSION bug. See #BhallaLab/moose#200
59512e1 Merge commit '1d69d002939cc4b270ff4fc51e8a4800a6fbdad1'
3adb8b3 removed a print statement
9aa9405 Use git to generate version when not passed via command line. BhallaLab/moose#200 .
2f8a48e Merge commit '18331bb5a2f6aa2918a4e49b178297a79e3c791b'
c9714fd Merge branch 'master' of github.com:BhallaLab/moose-python-package
df2186a Merge commit 'ec45fa526f0e2de2b49bf05f3f7f8ddb1c7ff463'

git-subtree-dir: moose-core
git-subtree-split: ed5f0151b5c12301b826e47e5a1daaaa7044a714

"

a15a538 Merge pull request #131 from dilawar/master
1800283 Merge branch 'master' of github.com:dilawar/moose-core
2ad812f Rdesigeur by sarthak,
8e87707 Fixed the streamer test.
e62ec09 Merge remote-tracking branch 'bhallalab/master'
002edb6 Fix to BhallaLab/moose-core#130.
d7ebbe7 No need to have header name in inverted commas.
414a8d9 stimulustable is check and some more correction
343a08a First version of model merging pools and reaction are done
943f96f  clean up in notes field
f2b71f5 Merge branch 'master' of http://github.com/BhallaLab/moose-core
c742934 kkitUtil: check to see if the color goes beyond genesis color Sequence, _main.py: eliminated enzyme cplx pool to genesis under compartment
9aca1c1 Merge pull request #128 from dilawar/master
322093e Streamer uses name of the table whenever possible.
5be9eb4 Added getName, setName to table. If these are set, use them in Streamer class to write the header of csv file.
f9178d2 Merge branch 'master' of github.com:BhallaLab/moose-core
3d420b0 species concentration/amount is calculated depending on the hasOnlySubstanceUnit flag
9188681 Merge branch 'master' of github.com:BhallaLab/moose-core
cf3d4f8 Merge branch 'master' of github.com:dilawar/moose-core
4d98756 Write path without [0] in streamer numpy table instead of table name.
9b143e4 reaction and enzyme are added with the ratelaw
b2fbc15 Merge branch 'master' of http://github.com/BhallaLab/moose-core
0a765fb Rules are added
07a68b9 If -Wno-unused-but-set-variable is supported by compiler, enable it.
d98241c Merge branch 'master' of github.com:BhallaLab/moose-core
d22bfea Moved Doc from here to BhallaLab/moose . In docs folder.
9f18f0a Merge pull request #125 from dilawar/master
a942a4c Fixed the failed build on travis https://travis-ci.org/BhallaLab/moose-core/jobs/134133078
3d6a8cc Added support to float and double to numpy format. Fixed some documentation about Streamer, correct dt is docstring. More assert statements in streamer test script.
aada8c4 Merge branch 'master' of github.com:BhallaLab/moose-core
303ad71 Changes for gcc4.4. on nargis.
1af4a69 Temporary change before switching to another branch.
0018c55 notes are written for species
895766a species added
a7e9509 paremeter and compartment info is read back to moose
2b9076e  update with more details
170739f Put some more utility inside namespace moose. When writing numpy format, do not write whole path in header. Just name would do.
f01727c Merge remote-tracking branch 'bhallalab/master'
7e95a6d A fix to failing unit-tests. When user writes /compt/a/b, inside MOOSE it is represented as /compt[0]/a[0]/b[0] which could be annoying for Streamer user. Just remove [0]. For other [n], don't do anything.
21fe695 Bringing back some changed undone by bad merge strategy. This should now pass on travis.
ca8d55b Merge branch 'master' of https://github.com/BhallaLab/moose-core
c165976 Fixes issue dilawar/moose-core#3  (#123)
c17df70 clean up in filename while writing into SBML
db701fc Enzyme's are written
320b0c3 Function and reaction are written
a8bfc7c compartment and species are written
008e25e moose Annotation like runtime,dts and plots are written
3ba5e33 units are written
bcfa3c7 Merge branch 'master' of http://github.com/BhallaLab/moose-core
d3b3789 firstphase of write file
4418691 For cmake, enable the c++11 support on compiler which supports it. This should fix ">>" to "> >" error in template parameters in boost code which is only supported in cmake build system.
dc9d0c3 Merge branch 'master' of http://github.com/BhallaLab/moose-core
156e762 python readSBML file
2786757 Fixed #124. Not using gsl_rng in global rng. It is not working as expected in class RNG. Using Subha's mtrand() when boost or c++11 is not available.
eecc171 Adding a small print statement about why assert failed in rdesigneur.
6454673 Merge branch 'master' of github.com:BhallaLab/moose-core
270f1d6 Fixed #112. Not using gsl_rng in global rng. It is not working as expected in class RNG. Using Subha's mtrand() when boost or c++11 is not available.
738d9dc Fixed issue #124.  Adding the issue #124 file to repo for reference. Can't reproduce the error with latest commit (this and previous one).
cc85cfb Update README.md
af178bf This fixes the missing time column in streamer. dilawar/moose-core#3.
9faf02e Don't rewrite the table path before writing them to csv in header. dilawar/moose-core#3.
806f6a1 Checks if not of tables added are more than 0 or not. If zero, then disable the streamer. Notify the user. Issue dilawar/moose-core#3
0a93eaa Importing <cstdio> so that it passes with legacy makefiles as well.
4dc2a6c Merge branch 'master' of https://github.com/BhallaLab/moose-core
56fdc36 Fixes to issue #116  (#120)
357b1b5 Fixed the test script. Method rk4 is not good enough when using boost. Use rk5a.
8057a8f Generate h5 name using tmpnam. If tests are run by two different users on the same system, there won't be any issue with permissions. However this makes testing bit harder during development.
b01caf4 Fixes to gcc-5.x on Ubuntu-16.04.
fc98bfc Adding random library to link flags.
ceea4f0 Use RNG object rather than pointer. Can't figure out why pointer did not work well.
ea5529d FIxed -std=c++11 error.
014175d Fixed issue #116. Using real_distribution instead of int_distribution. Let the library take care of scaling to between 0 and 1.
ab91625 Merge branch 'master' of github.com:BhallaLab/moose-core
e23c827 Some temporary changes before merging. I forgot what there are. Probably RNG initialization is changed.
cf73c1f Update of python setup file. (#118)
51bcf63 Disabled part of code which checks for extension . On some platform it reutrns x86_64.so etc, which probably we don't want. In any case, if build fails on open build service, we can bring it back #78.
fb558d8 Modifying SBML_LIBRARY related macros. Since libsbml is now distributed from mosoe repo as well.
487587b test scripts points to directory commited by @subha #issue #94.
e47a492 Update INSTALL.md
13afeaf Update README.md
8b33ae5 Merge branch 'master' of github.com:BhallaLab/moose-core
1268296 Merge branch 'master' of github.com:BhallaLab/moose-core
808ae94 Update INSTALL.md
6316820 Update INSTALL.md
2522f47 Merge branch 'master' of github.com:dilawar/moose-core
3f13efd Temp commit.
347e5b0 Update INSTALL.md
d14e4e8 moved to appropriate doc folder.
5a48285 CheckMOOSECompiler -> CheckCXXCompiler.
5ecd06e Updated INSTALL.md file.
0c42d28 Merge remote-tracking branch 'bhallalab/master'
87c193d Deleted cymoose from master branch.
e77361c Fixed moose building after moving _moose target to subdirectory.
af97ec3 Cymoose remains only in my personal clone branch cymoose. Removing it from master branch.
b3542f6 Cleaned up Cmakefile.
7fec36b Moved pymoose target to its own directory.
7575c55 Update test_ksolve.py
904e32a Added missing cmake file.
1998e27 Using ptr instead of object of RNG.
1ee1427 Added ksolve test.
fbf9d90 Test script for ksolve is modified. Total 40 pools.
2ea5ed1 Separate file to check compiler macro.
c7d3e15 Removed the copy constrcutor from RNG class.
1acec97 GssaVoxelPools gets its won random number generator. Had to remove constantness of a function to be able to use uniform( ) or rng call.
08fa1ed test display is changed a bit. Removed some hanging c++11 auto .
c6bc8c3 Printing tests name during tests.
4116cc5 More verbose output when tests are runnug. Added a macro which runs test.
d1c77ce Replaced simple assert( doubleEq(a, b) ) with ASSERT_DOUBLE_EQ( "", a, b );

git-subtree-dir: moose-core
git-subtree-split: a15a538e22f0cd62de95532c2932156055d58673

git-subtree-dir: moose-core
git-subtree-split: 1318029dc3bc67f182dfe22369929b8abc0c9b52

be written on INSTALL.md file on how to build using this repository.