Skip to content
Snippets Groups Projects
  1. Nov 16, 2016
  2. Nov 14, 2016
    • Dilawar Singh's avatar
      This should pass on travis. · f1d6aba3
      Dilawar Singh authored
      f1d6aba3
    • Dilawar Singh's avatar
      Merge commit 'd0a6060b' · 7143a53a
      Dilawar Singh authored
      7143a53a
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from 9eeca0c..6a6bcc1 · d0a6060b
      Dilawar Singh authored
      6a6bcc1 Python module can also use VERSION file generated by CMAKE. Copy to build directory for not-in-source builds. BhallaLab/moose#200.
      7805364 Failsafe mechanism in VERSION reading script.
      
      git-subtree-dir: moose-core
      git-subtree-split: 6a6bcc15556a58e08c24203599c3c84837eb65bd
      d0a6060b
    • Dilawar Singh's avatar
      Merge commit 'b5a7c2e2' · 15f18b90
      Dilawar Singh authored
      15f18b90
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from 14cf2df..9eeca0c · b5a7c2e2
      Dilawar Singh authored
      9eeca0c Fixed a typo in setup.py file. Due to which installation was failing without any warning.
      
      git-subtree-dir: moose-core
      git-subtree-split: 9eeca0ca8135fbf3c8fe7dd65ce408681b1e4605
      b5a7c2e2
    • Dilawar Singh's avatar
      Merge commit '273124ec' · fef5e24c
      Dilawar Singh authored
      fef5e24c
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from 343cb02..14cf2df · 273124ec
      Dilawar Singh authored
      14cf2df Fixed the setup.py file. Use absolute path for script to determine absolute path of VERSION file.
      
      git-subtree-dir: moose-core
      git-subtree-split: 14cf2df3a65456c6b4ce67b2d34110fd3400c982
      273124ec
    • Dilawar Singh's avatar
      Merge commit '8bfef2e6' · 7822c60b
      Dilawar Singh authored
      7822c60b
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from ed5f015..343cb02 · 8bfef2e6
      Dilawar Singh authored
      343cb02 Fixes to  VERSION issue BhallaLab/moose#200.
      835bf9a Added a version file.
      
      git-subtree-dir: moose-core
      git-subtree-split: 343cb02705b0874ad0035eea648019420475f7ed
      8bfef2e6
    • Dilawar Singh's avatar
      Merge commit 'aca40347' · fb9fba5e
      Dilawar Singh authored
      fb9fba5e
    • Dilawar Singh's avatar
      Squashed 'moose-gui/' changes from 1e5f537..e49ca7d · aca40347
      Dilawar Singh authored
      e49ca7d Changes Function symbol to summation symbol, objectedit.py function expr is not editable as this summation of pools, some cleanup with colors selection,Function which is now just summation object, set's up setN for output as input is nout
      328b8f5 for now function output connected to pool via setConc message, but there is "increment" which depend on the function input this will be fixed later
      16075b3 cleanup with colormap string from genesis file
      aa377ed resetup for multicompartment model before setting up the solver
      26d2be7 Changes made are related to functions which now doesn't need parent as pool but if exist like in case of genesis then it displays as its, setsolver: setting ticks to table, 18 is not required as its set default when table is created
      7ad2bb9 plot are saved to csv forms
      20a76af some more cleanup
      653b464 added units for Km, kcat is added which display in object editor
      cbf2c5e added units for volume which display in object editor, vector data for stimulusTable is editable for enz_cplx delete and move is not allowed so removed the icons
      6882e0b some more colors to ignore which are light
      faad938 If compartment is moved,then object is move then, movement of object with respect to qtscenecoro-ordinates was not moving correctly that is correctly, in KKitOrdinateUtil: pygraphviz:- instead of larrow for reaction I have circle for now, if one needs to save the image of the model loaded
      0f0674d small cleanup
      0ab70d7 cleaner way to set co-ordinate with round trip
      49a3f9c time being removing import sbml
      0622266 instead of pygraphviz_layout which was dependent on pygrapviz installation using graphviz_layot from networkx itself
      a62e275 MMENZ and cplx connection exist, if MMEnz is moved then arrow to cplx is updated
      ad437db saved sbmlfile return to calling function
      a108d2c Instead of spring_layout using pygraphviz_layout which can be further used for saving the layout image to png format
      624f52b 1.Getting layout co-ordinates to Genesis co-ordinates 2.Automaticlayout done using pyqgraphviz for files for sbml and cspace. 3.Separate messge if missing output for StimulusTable and Function
      db36afc Size of the compartment is cleanedup
      1ef13c9 QGraphicsRectItem when no children, then setRect size is fixed to default size
      
      git-subtree-dir: moose-gui
      git-subtree-split: e49ca7da411f0cc7ad8b62ff077522ef92ba2390
      aca40347
    • Dilawar Singh's avatar
      Merge commit '3c9138df' · 2f085e3e
      Dilawar Singh authored
      2f085e3e
    • Dilawar Singh's avatar
      Squashed 'moose-examples/' changes from 0494d05..d7e9a97 · 3c9138df
      Dilawar Singh authored
      d7e9a97 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
      0def9bd correction with function names
      e9950fe Merge pull request #7 from rahulgayatri23/master
      0e7cef8 Contains a readme file.
      282955a clean up in checking the file name and runtime
      ed2198f Merge branch 'master' of https://github.com/BhallaLab/moose-examples
      37ad100 mooseReadSBML is corrected
      64565e9 parallelSolver folder has a script to try the parallelization of the solvers.
      bdc5c95 Added spine calcium diffusion chemical model example files
      344f73c traub 2005 gui: switched to networkx for drawing morphology
      747bbee Partial fix to traub 2005 demo.
      d458ca8 fixed a work around for small bug in the draw_grapviz function in networkx-1.11 which no longer import toplevel namespace
      599d976 Updated traub2005 example.
      70b3389 New examples for axon and myelinated axon
      
      git-subtree-dir: moose-examples
      git-subtree-split: d7e9a9791cf267811eaac827e0915cc021309ee5
      3c9138df
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from c2c32b9..ed5f015 · 6c8f2012
      Dilawar Singh authored
      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
      6c8f2012
    • Dilawar Singh's avatar
      Merge commit '6c8f2012' · 58de93dd
      Dilawar Singh authored
      58de93dd
    • Dilawar Singh's avatar
      Update README.md · 9e7e1fa6
      Dilawar Singh authored
      9e7e1fa6
  3. Nov 11, 2016
  4. Nov 09, 2016
  5. Nov 08, 2016
  6. Nov 07, 2016
    • Dilawar Singh's avatar
      fdca7481
    • Dilawar Singh's avatar
    • HarshaRani's avatar
      Update README.md · eca66f7f
      HarshaRani authored
      eca66f7f
    • HarshaRani's avatar
      Update README.md · b33e7096
      HarshaRani authored
      b33e7096
    • Dilawar Singh's avatar
      No need of dpkg and sbml c++. · a77c09fa
      Dilawar Singh authored
      a77c09fa
    • Dilawar Singh's avatar
      Merge commit '96580978' · e5ac4a01
      Dilawar Singh authored
      2 tags
      e5ac4a01
    • Dilawar Singh's avatar
      Squashed 'moose-core/' changes from a15a538..c2c32b9 · 96580978
      Dilawar Singh authored
      c2c32b9 Before tagging runing with clang.
      1cc19f1 updated runtime to annotation field in moose
      3ad9558 runTime and solver type is read from xml file to moose, cleaning in names
      5de1f05 function output to pool object set's "setN" as input is "nOut"
      ae24a3d Merge branch 'master' of https://github.com/BhallaLab/moose-core
      7b43f70 Fixed Function unzombification for increment messages. Added update for time in Zombie Functions.
      f4310e6 for now function output connected to pool via setConc message, but there is "increment" which depend on the function input this will be fixed later
      f286dca removed writekkit.py duplicate file
      6d299eb replace all the obj under /kinetics or /kinetics/group which is required by genesis format
      a6dad52 Merge branch 'master' of https://github.com/BhallaLab/moose-core
      0ddbd21 Gsolve updates to monitor number of reac events. Stoich updates to avoid crashes when handling edge cases without objects in model.
      2ab410d function can be connected to pool,bufpool and reaction
      086ef95 using networkX spring_layout rather than grapviz dot layout
      0000d51 Ids begining with numbers needed to processed with dash for sbml compartability,No substrate, no product enzymes are not written down, function are now placed under compartment and for backwarcs compartability with genesis they are placed under BufPool
      f0f1444 Merge branch 'master' of github.com:BhallaLab/moose-core
      e0c6c1a Allow failure with clang. I could not reproduce the error on my local machine.
      9e4db61 First skeleton changes to the Gsolver to track the number of reaction firings for each reaction. Also some fixes to the SeqSynHandler.
      cff32e4 Fixes to include path of muparsers. This is passing on openSUSE.
      2117969 Added missing SeqSynHandler source file to CMake.
      58ddb2b Added SeqSynHandler class to deal with single-neuron sequence recognition models
      1e42ece Merge branch 'master' of https://github.com/BhallaLab/moose-core
      659a908 Fixes for Ksolve accuracy, and some ReadKkit edge cases
      7c3e72e small correction
      0d7f908 clean up for Annotation, plots, reactions, enz
      a2f6a95 Merge branch 'master' of http://github.com/BhallaLab/moose-core
      fb70792 empty reaction are not written,units corrections, plot paths are written from compartment level unlike before from model level
      a1593e9 Disabled pip install python-sbml with clang.
      13acd0f Disabled SBML test for time being till issue #145 and #152 are resolved.
      f3b42fd Merge branch 'master' of https://github.com/BhallaLab/moose-core
      b16311e Fixed unicode conversion for docstrings Put in sorting of fields in showfields.
      793ae62 Added pygraphviz to pip3 install list. pygraphviz is a dependency for SBML.
      396e607 Both python2-networkx and python3-networkx can't be installed simultaneously. Fixes that on travis.
      ac02cea Added python-networkx to python3 dependency. Test run on travis.
      dd4fc4e Removed option WITH_SBML deprecated warning [skip ci]
      c6c60e6 Removed c++ sbml support code. Test run on travis.
      c73e4cd Removed C++ sbml code.
      68ea7c2 Changed SBML script to make them compatible with python3.
      8614680 Fixed Leakage class
      8b15511 Merge branch 'master' of https://github.com/BhallaLab/moose-core
      24a01e8 Added ICa for NMDA channel to known plot variables for rdesigneur
      52ae361 Fix to issue #147.
      c251c0d reaction rateLaw and enz's km is corrected
      a03cb6a initial concentration is set if hasOnlySubstanceUnit=false with correct units
      7018230 Fixes for SynChan modulation, added a couple of synaptic channel prototypes
      66bfcff Upi fixed the scaling factor
      b6532e8 Merge branch 'master' of http://github.com/BhallaLab/moose-core
      b7a3ad4 MMEnz is created
      37c5312 Deprecating sbml related code on travis. Don't download SBML debian package and install.
      791762a plots populated to moose if defined in the sBML file
      b05a983 Adding python-networkx as dependency in travis.     python-networkx seems to be required to run SBML related code (needs confirmation?)     python-networkx is a dependency for moose-gui.
      76c5381 print statement needed paranthese
      d52bd19 fixed a work around for small bug in the draw_grapviz function in networkx-1.11 which no longer import toplevel namespace, readSBML:cleanup
      2fd15b6 updated to read SBML file into moose
      422bbc0 One of the testcase where model loaded in moose are written to SBML file
      dbc5412 Removing sbml build from cmake. SBML test is failing.
      8876581 Merge branch 'master' of https://github.com/BhallaLab/moose-core
      66f55c2 A check made to see if python-libsbml modules is installed if yes then reading and writing to SBML is done, else a warning message to install module is done
      073ef60 Merge pull request #144 from dilawar/master
      94b686a Fix to BhallaLab/moose-core#143.
      b460557 Removing c++ depenedency of libsbml and its files
      fea73c3 Merge pull request #141 from subhacom/master
      7644e69 Fixed adding spike generators in ReadCell dotp.
      3928fae Merge remote-tracking branch 'upstream/master'
      5822181 Merge branch 'master' of https://github.com/subhacom/moose-core
      79d5a5c Updated generated neuroml2 module and test file.
      5a4197c Merge branch 'master' of https://github.com/BhallaLab/moose-core
      06aea5b SBML is removed from the make file
      2a5bc46 Merge branch 'master' of https://github.com/BhallaLab/moose-core
      1a55310 Fixes for enzyme rate scaling when reading kkit files
      8f44029 Merge pull request #140 from dilawar/master
      f9e8720 Merge branch 'master' of github.com:BhallaLab/moose-core
      1aee89a When WITH_SBML=OFF is given from command line, do not compile its support.
      c959613 Merge branch 'master' of https://github.com/BhallaLab/moose-core
      00a9171 Fixed access functions for kinetic objects and solvers
      d70da97 some more colors to ignore which are light
      4d89fd6 color if not defined in genesis then random color from pyqt Qcolor matplotlib files are taken as saved, matplotlib
      5ecd2b1 all the co-ordinate are calculated and pass from kkit to this file and only we run in commandline then auto-coordinates are calculated with appropriate zoom factor
      27bfae9 using graphviz_layout instead of pygraphviz_layout to get the position for auto-coordinates for layout the moodels
      1f93ddb Removing pygraphviz lib dependency and using pygraphviz_layout to get the position of spring_layout
      2c421a0 readSBML gets x and y co-ordinates from the file and loads it
      eba7d75 cleanup in layout co-ordinates to save the model from moose to genesis
      17863ee Layout co-ordinates from GUI is saved into SBML file, 2.Automatic Layout done using pyqgraphviz when model saved from command line to SBML file. InitialConc are saved with mole as default units
      395daa7 Fix for muParser for C++ 10
      ef2196e Adding quot operator in muparser.
      6deb249 Merge branch 'master' of github.com:BhallaLab/moose-core
      a6f8bab Updates to rdesigneur
      b922890 Fix dependency on hdf5
      6f7e46d cleanup
      b943072 added networkx's Graph for layout the co-ordinates when model is save to SBML at commandline, if model saved at GUI level then pyqt's scenepos which is used for layout in GUI, those co-ordinates are used
      8b1a05d Co-ordinates,group,textcolor and background color are written to SBML file in Annotation field
      2718470 auto co-ordinates if one saves model from commandline and also cleanup with co-ordinates for genesis
      41b6bfb color index is cleanedup according to genesis requirement and co-ordinates calculation is removed, since I am sending ScenePos
      ce6b740 cleanup in writing genesis file with scene co-ordinates and few other clean up
      8f2a3e1 Added compiler macros for AppleClang.
      076ecf6 libsbml-5.9.0 is not available on brew. Build breaks with sbml 5.11.0
      2976483 Fix apple build. adding -stdlib=libc++ to cmake.
      530d69b Merge branch 'master' of https://github.com/BhallaLab/moose-core
      d8cd4bd Updated python setup script to include streaming classes
      5d6ee59 Actual fix for issue #110
      5df0a7f Merge branch 'master' of https://github.com/BhallaLab/moose-core
      39145e3 Merge branch 'master' of https://github.com/BhallaLab/moose-core
      2634422 Merge branch 'master' of https://github.com/subhacom/moose-core
      ddbdd8c Removed mgui and moogli from Python setup.py
      c2fa2cf Added hsolve test comparing to NEURON
      
      git-subtree-dir: moose-core
      git-subtree-split: c2c32b97caecd422d6bc9398094073ce9f1b7492
      96580978
  7. Aug 24, 2016
  8. Aug 23, 2016
  9. Aug 16, 2016
  10. Aug 11, 2016
  11. Jul 08, 2016