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

Added docker image info.

Fixed typo.

Added PIP package.

67f02feb7e qgraGrp declaration at kineticswidget

git-subtree-dir: moose-gui
git-subtree-split: 67f02feb7e7cb621c45de0cabfd04dbb07d0b693

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 DEBUG mode.
2e6524b9cf if libneuroml and pyneuroml is not found, do not load NML2 support .     Ignore silently. Print help message when user call NML2 related function.
30fc7d0636 Turned it into a module so 'absolute_import' can work.
d9853b5322 Merge branch 'chennapoda'
00170beb15 Merge pull request #247 from dilawar/master
b0adf404cc Added libneuroml and pyneuroml in dependencies on travis.
0d831227cd renamed tests/python/neuroml to test/python/_neuroml so it does not clash with import neuroml. Ready to be a PR. Integrate BhallaLab/moose-core#246 into moose import system. Exposed moose.mooseReadNML2 function for gui etc. Added dummy docstring. Deleted redundant files.
792b4e7d43 Added nml2 test script.
1e3413349e Integrated NML2 support BhallaLab/moose-core#246 Made is compatible with python2/python3. Needs testing before merging into upstream.
596b9d2e1a Merge branch 'master' of github.com:BhallaLab/moose-core
740f9c6eb4 Added jenkinsfile for local testing over jenkins.
7dcd970481 Merge pull request #246 from pgleeson/master
bb8c8a94b3 Minor edits
c2872f7d4e Merge pull request #2 from BhallaLab/master
a520f8aed8 t test script to test BhallaLab/moose-core#242 .
d6ba37e003 Merge pull request #244 from upibhalla/master
d8ad6d6e53 Exposed field Stoich::allowNegative to control whether the solver permits negative values in simulations.
0e460485e5 Merge pull request #243 from upibhalla/master
f2553db028 Merge branch 'master' of https://github.com/BhallaLab/moose-core
32430d1f1d Oops, another silly error in the negative concentration test.
a2fee560b8 Merge pull request #242 from upibhalla/master
53244691c4 Merge branch 'master' of https://github.com/BhallaLab/moose-core
369b26c369 Fixed major error in GSL solver in VoxelPools. I had introduced this when putting in check for negative concs, for some reason first set of tests didn't identify this bug. Works for several tests now.
394032dcfe Merge pull request #241 from hrani/master
bce317e34c Few clean up while reading and writing from/to SBML
d7dbc9997a Added flag Stoich::allowNegative. This defaults to False. If true it allows pools to take negative concs, needed for general ODE solutions but illegal for chemical systems.
158db52f1f Merge pull request #238 from BhallaLab/brew
8c93330ca3 Improved temperature dep
afd925b101 Merge branch 'master' into brew
818ad2df5f Improved unit handling
54b505d6da Merge pull request #237 from hrani/master
fe628d39ae Test homebrew formula as well on travis.
337bab4ce5 Update .travis.yml
2b54325545 clean up in print stm
a592ec8875 existence of model path is checked, clean check is made for enzyme and function before writting into file
1398206c9d Merge branch 'master' of https://github.com/BhallaLab/moose-core
3b920f3fc4 Improvements
3cc29d3fe5 Improved saving of rates
24710aa103 More general
2a1b06477f Installable
f2188a3903 Read populations/inputs from nml
fc689f018f Allowing -nogui
1bc8a23cfc qMerge branch 'master' of https://github.com/BhallaLab/moose-core
abf8e5465a Now works with libNeuroML
2ec562cba7 Working HH example!
010b0f9db8 Passive test on new cell
2cb3edaf20 Working passive example
cdfb8e1fc7 More tests
3f6de38f50 Not completely failing...
152857db78 Ignore build dir
2b36a6b4d8 Update example files
f7228682d4 Merge branch 'BhallaLab-master'
61453b8a9c Merge branch 'master' of https://github.com/BhallaLab/moose-core into BhallaLab-master
9cc0e101d0 Merge branch 'master' of https://github.com/BhallaLab/moose-core
f3c6a71b9c added python3 for compliation which was removed
0920cfaf1b instead of importing rmoogli in init file replaced in rdesigneur.py,checking if travis passes for python3
6a4b102099 Updated pre-commit hooks in chamcham branch.
411a71798a Updated moose_test module. Function test( ) can accept timeout parameter.
226e8662c4 Force --install-layout=deb when on debian/ubuntu.
7032ffdfe7 Fixed kkit tests.
f0ec0c3759 No inbuild test should depends on matplotlib.
ccb43d16a7 Fixes to debian related python install. When --prefix=/usr is given, its installs in site-packages rather than dist-pacakges.
65954b71e8 Minor changes to test script: Dont wait till test is over to print which test is being executed.
327d0aa4ff Updated sanity test with version information in ctest.
8bc1994345 __version__ = version( ) is both python2 and python3 compatible.
fac27902c2 Added __version__ string in __init__.py file.
ab03233775 Merge branch 'chamcham' of github.com:BhallaLab/moose-core into chamcham
a567aa1d5b Added __version__ and version( ) info.
85f1f1ef2f Added `moose.test` to test `moose-examples` online (#189)
6fe5f5c7c4 Using absolute imports in 3.1.3  (#190)
027e40bfdb Fixes absolute import in chamcham branch as well.
474faafe51 Python3 compatible import mechanism,  NML parser fixes (#188)
4e915e0b0f Fixes to chemUtil import.
13e3cb8ad8 More import fixes.
25d3c43252 Merge branch 'chamcham' of github.com:BhallaLab/moose-core into chamcham
2ed651fc37 Fixed the plot util function (again).
4d4b275958 Deleted old/junk functions. Force python2 to honor python3 style import.
b899ada38b More fixes in plot utility library. If some function breaks on python3/python2, do not import the whole utility library.
f2a6d7b8d1 Removed junk utility functions. Forced python3 import style (PEP8).
a7a03c7852 Some renames.
ff84f3d0dd Added another function plotTables wrapper on plotRecords .
2fb7676353 Fixed error in plotRecords functions.
b32a39b444 Merge commit '9355916f' into chamcham
1eb8ca281c More changes to NetworkML BhallaLab/moose-core#218 .
0e0615c816 Fixes to #186 are integrated into chamcham release.
4a0d4f37df Fixed a typo in install instructions.
3498c1801a Bumped version to 3.1.2
fc14920945 Added AUTHOR and bumped the version up.
b5898ac306 Added missing 'moose.chemUtil' module.
d7c938283e Fixed revision issue.
1c1bbe059d Added GetRevision macro to get current timestamp.
ba9ec990eb Write the version to VERSION file so setup.py file can use it.
4e9aa317f2 Not reading version file anymore.
315837d775 Changes from master branch.
557184389c Packaging related changes from master branch to chamcham branch.
4d5c6a5d87 NO version file should be in-source.
de25310563 Merge commit 'efa006c9' into chamcham
52eeb541ef CMake related bugfixes from master branch.
9df1ba7fad Merge commit 'efc1324a' into chamcham
815a79a9db Fixed the VERSION file creation.
726e71c063 cleanup in demo, filemenu links
d5c5391949 adding missing files
5291f7c4fc missing folder/files
760274cbcc Changes made to gui to work with moose-core
be92816c83 Merge commit '36ca236d' into chamcham
74b43c3ef6 Enabled travis emails to developers for this release branch.
76bf85476e Related to #169 Dropped the support for VERSION file. 1) It would cause lot of merge issues if VERSION file is left in source tree.
00ea9d3c10 Close #169. Renamed MOOSE_VERSION to _MOOSE_VERSION.
da0db901b4 Changed MOOSE_VERSION to __VERSION__ since new cmake 3.7.1 sets it to empty. See cmake policy CMP0048.
a6a05eff71 Merge commit '41be11d5' into chamcham
b8a8b6d150 hotfix from branch issue167.
8a6346d029 Merge branch 'chamcham' of github.com:BhallaLab/moose-core into chamcham
7d4cf8b84b Changes from master branch. Test on macosx as well as linux. Quantified import to avoid self-recursion. Ran autopep8 on files.
de3d964f65 Changes from master branch. Test on macosx as well as linux.
9156b897da Fixes for issue #164. Also hotfix for branch chamcham.
34429e228e Using correct import
e2574fb25f Uses the MOOSE_VERSION value from CMakeLists.txt in setup.py

git-subtree-dir: moose-core
git-subtree-split: 0c33b2c3339d8a43f9de1fb31573cbea621739f6

Added binder functionality (interactive tutorials online) to documentation

Added links to interactive moose binder environment on main website. See tutorials, 'getting started with python scripting for moose', and the new 'interactive tutorials' tab in quickstart

Arch linux package has been created. Needs to be added to OBS.

Added instruction to pull the docker image. #234 .

Addition of Help.png. Related to #225 

Created links to CREDIT and INSTALL  file in README file.

Moved authors/credits to separate file 'CREDITS'.

Documentation update 2

git are converted to pdf in pdf #232.
Using `libertine` font in pdf doc.

Added short hidden section at beginning of cookbook snippet sections explaining how to run the snippets

tweaking pehaps a listing environment for codeblock.
Related to BhallaLab/moose#225 .