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  1. Feb 02, 2017
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from 14e2d78..f3d0477 · 7c713058
      Dilawar Singh authored
      f3d0477 Merge branch 'master' of https://github.com/BhallaLab/moose-core
      176a5f0 solver's short form should also be taken
      8624e24 Merge branch 'master' of https://github.com/BhallaLab/moose-core
      6c964b1 Added isBuffered field to Pool to let users convert the object class to BufPool, and vice versa.
      97db69e moose::Neuron uses global RNG object. Global RNG object behaviour is following. - moose.seed(0) or moose.seed( ) assign a random value to seed. Use   random_device if avaible else time(NULL) is used. - moose.seed( x) set moose.seed to x.
      c1dec94 Fixed long argument for mtseed in moosemodule.cpp
      54c94f7 Modified travis scripts and reenabled developers to the list.
      31dd779 Fixed import error with python3. No module should be imported in python/moose/__init__.py . Added a note for developers. This should fix the travis.
      
      git-subtree-dir: moose-core
      git-subtree-split: f3d0477a3ea5045db044aaae94b46a133527dbc7
      7c713058
  2. Jan 23, 2017
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from 1b5b9a9..14e2d78 · a5122cfb
      Dilawar Singh authored
      14e2d78 Fixes broken Makefile. Object MMPump.o not found error is resolved by commenting out the object. Either source is missing for it was introduced by recent PR.
      aeddce7 Fixes to python3 test command in travis script. Previous fixes passed with python2.
      00ad9e2 Fixes to recent Travis build failure.  (#170)
      3ebc0a5 Merge commit '5bceacfe'
      df5ff48 Merge branch 'difshell' of https://github.com/asiaszmek/moose into asiaszmek-difshell
      e4a4bcd Change order of operations to slightly improve accuracy
      aacebcc Small changes to make the code more alike genesis and other moose objects
      4246932 Difshells and difbuffers initialize close to equilibrium
      40a200f Add forgotten setting of helper variables to zero after calculations
      dad35e6 Add state in t(i-1)
      45c2286 Fix wrong definitions
      567444a Fix errors in volume calculation
      4e0a857 Indentation
      cb40719 Add MMPump to scheduling and makefiles
      bfc456c Add MMPump to DifShell
      be1ceac Implementation of MMPump
      c721713 Add ticks for DifBufferBase and DifShellBase
      a3bee38 Fix bugs: DifShell now compiles and seems to give correct results
      b131c44 Fix a typo in zombify
      f1cbfb0 Rewrite DifShell. Inherit from DifShellBase
      1486cdd Write base class for DifShell
      336cbd1 Indentation
      d8ee906 Implement exponential Euler for DifShell
      f72d6a1 Move source messages to class. Correctly initialize Faraday's constant
      b309dc4 Move source messages to class
      5d3b7d2 Make DifBuffer look more like other moose classes and fix ticks
      9a1e166 Add DifBuffer to clocks
      f949b27 Add DifBuffer to compilation
      5418e0b Fix no ticks when initializing difshells warning
      5fba26e Remove useless variable
      7e29b64 Reintroduce an old version of DifBuffer from moose
      8f544e6 Moved to cmake folder.
      ae1a5ba Merge commit '0d12ebb0'
      3ac6c58 master branch.
      65c371c Fixes to BhallaLab/moose#204.
      
      git-subtree-dir: moose-core
      git-subtree-split: 14e2d78a7b6e41e67bdce6e3a07fa0d65565744b
      a5122cfb
  3. Jan 05, 2017
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from 3f8c345..7c9fe23 · 0d12ebb0
      Dilawar Singh authored
      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 fixes in travis script.
      429420b Cleanup, osx related travis macros.
      e287118 Disable OSX build here on master brach. Created issue #165 to build and test for MacOSX.
      87aeb1a Travis build scripts for macosx and linux are in ./scripts folder.
      24643bc Some more fixes to travis build failure on OSX.
      a05826e Fixing brew taps and build dependencies.
      ea0ede1 This commit is just to test the OSX build on travis. Unfortunately there is no way to test it offline.
      1b6f42a Fixes to travis scripts.
      b0baaab Excluded linux and osx build from config file.
      626fd30 Testing with OsX support on travis. xcode-8.1. Most likely to break
      ab933ad Fixes to recent travis build failure. make all python files python3 compatible in addition to #164.
      72afc02 Enabled macosx build on travis. Though allowing failure for now.
      bedb51e Fixes for issue #164. Also hotfix for branch chamcham.
      e821a9d Fixes due to API change in SBML support.
      bb8c850 Fixes to #164.
      806605d Fixed the prog -> position. Hotfix for release.
      2cba78a Merge branch '3.1.1' of github.com:BhallaLab/moose-core into 3.1.1
      82c3024 Fixes to #163.
      598433e Related to BhallaLab/moose#204.
      48c5535 formating
      0cec9d2 spell correction
      6d66bc1 function to add and delete solvers to Chemical solver
      eefafa9 filename changed
      c9208a9 added mooseWriteKkit, moosedeleteChemSolver,mooseaddChemSolver and cleaned up write/ReadSBML as mooseWriteSBML, mooseReadSBML for consistency in moose.py
      d462c7e Removed saveModel which doesn't exists anymore
      8c5af82 Fixes to issue 129 (#162)
      eee822b Fixes to recent build failure on travis.
      bdc1436 Alternative implementation of moose.Streamer  (#161)
      94444f9 Notify user if python-libsbml is not found.
      db41ad5 Merge pull request #157 from dilawar/master
      c11cb03 Added recently added C++ files in synapses folder.
      5868a2f Added libsbml test. Runs only when python2 is used.
      716305c Fixes to boost build failure on travis.
      4355f02 Various fixes to libsbml related part.
      acf46ff Fixes to lintian errors [ skip ci ]
      75c8f34 Similar fixes to writeSBML file.
      54f127e Cleanup and fixed pylint error     power( ) -> pow( )     Instead of try catch, check for libsbml at the begining and warn user.
      d24b389 Fixes to test_sbml scripts. The basic functions are working.
      0430732 BhallaLab/moose-core#156 .  Created writeSBML and readBSML functions in moose.py
      c56b347 BhallaLab/moose-core#156 . Removed deprecated sbml functions.
      0e09e0b VERSION is a temp file.
      29190b6 Merge branch 'master' of github.com:BhallaLab/moose-core
      2c8156a Changed the environement variable which cmake uses to search for GSL.
      ee4ae8a Merge branch 'master' of github.com:dilawar/moose-core
      da93767 Fixes to recent travis failure. All files are now compile with python2 and python3.
      0ec89d2 Added test to make sure each python script compiles with python2 as well.
      98d6c31 Merge branch 'master' of github.com:BhallaLab/moose-core
      3bc4e6c Update .travis.yml
      c1f4c84 Adding pre-commit hooks. BhallaLab/moose#189 .
      8847b26 Update .travis.yml
      6b2fa39 Disabling libsbml on travis. It does not build with clang.
      12a72da python-libsbml doesn't build with clang. Allowing failure for clang compiler on travis (test commit).
      be83da8 Fixed import statement in genesis. Related to python3 import.
      ac29a99 Enable QUIET_MODE for Release. No information is printed onto console when moosemodule is loaded.
      6e871fa Changes : 0. Mixed tabs and spaces are turned into 4 spaces. 1. Python code is python3 compatible. 2. Removed libmumbl from source tree. Not in active development.
      5916f7f Fixed a typo in travis.
      246bc58 Merge commit '04170cb4'
      0390d6a Updated.
      993f8f7 Fixed, python2 incompatible print function use.
      030aea3 Some updates to fix static hdf5 libraries.
      4255ecf This project build pymoose, gui and its examples. TODO: ctest must check each example as well.
      c92e761 Builds whole moose project.
      d40fbe6 Added some sanity tests for both moose and moogli.
      29fd242 Even when format is set, stream!
      f96fe68 One test failing on nargis (centos-6). Try it locally.
      eb61ab7 ctest script setups its environment. No need to have set environment for each tests.
      1b43dc7 This fixes python3 linking problem on openSUSE-Leap. Not sure about travis.
      ec15bd2 Linking error with boost-filesystem.
      0847eb2 This might or might now work with python3. Taking a shot.
      e7a87b8 Some changes in Makefile. Protected some boost related code with USE_BOOST macros.
      
      git-subtree-dir: moose-core
      git-subtree-split: 7c9fe237abfcd49b45a3c843567f2c2ddcd67d65
      0d12ebb0