fix crash in newer versions of scipy
Fixed optimization routine passing iterations parameter in the wrong place
Changed backslash to forward slash and sleep before showing graphs
Changed backslashes to forward
Merge remote-tracking branch 'origin/master'
Merge commit '1b4fd6f16413a01d2443e52606fbe1f888635e38'
Add pdf version of user documentation to repository.
Updated format to match parsing changes
Updated saving methods and added ability to output .CSV for trajectories (not ensembleTrajectories yet)
Bug fix for developer documentation
Remove parallelization and graphviz discussion from user manual, which aren't really supported anymore.
Fix two small bugs in developer documentation
Updates to user manual. Adding pdf files so it always compiles.
Updated command line input module
Re-added temp foler
Emptied temp folder
Capitalized "example"
Added temp folder to put saved data in.
Added forgotten input statement
Updated XML examples
Changed to the updated version
Merge select files from XML_Interface development branch
Correct issue arising from Keeyan changing capitalization of directory names
Simplify naming of XML examples
Remodeling project structure
Add README and setup for PyPI submission
Further simplify setup.py
Add PyPI info to setup.py
Add copy of BSD license
Reorganize package to match standard distutils layout (for future submission to PyPI)
Testing
Testing
Added files for testing on other machine
Added preliminary command line handler and .scell file parser
Added example constructor, prior defining functionality, and csv data parsing
Updated some small things before merging
Small changes to syntax
Adding the jak_stat xml file back to the repository. Don't know why it wasn't there anymore.
Switched to XML file parsing, but kept .scell file parsing just in case
copied from dropbox
Created source folder and root package
Added network creation/modification support
Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
Switched over to full xml implementation, added new experiment constructor
added debugging lines
Adding the jak-stat example xml file back
ddaskr changes (fortran removal)
Merge remote-tracking branch 'sloppy/Development' into Development
Added trajectory plotting action routine
Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
Small changes to ensure file deletion
Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
Took care of all the TODOs, mostly small fixes and getting rid of any hard-coding
(Mostly) Fixed C compiling issue in NetworkMod
Streamlined saving process, added ensemble action routine, and fixed various bugs related to saving/loading data. Made everything much more modular.
Redid method for action routine parsing. Also modified Network_Mod to delete generated code even in the event of DLL failure.
Removing duplicates of ddaskr directory
Fixed various syntax/compiler errors
Attempt to post updated code to development
Added new files and tweaked existing ones slightly
Finished ensemble trajectory routine, completing all graphs for Tyson Example
Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
Small changes for debugging and to show graphs
Added network creation handling
Small changes to ensure compatibility with jak-stat and autocorrelation graphing from cache
Created xml file to run specified example, recreates related reproduction .py file.
Added a quick workaround to avoid .pyd file buildup in main directory
Added sophisticated trajectory calculation and graphing functions
Example updates, added anvin's model
Some quick bug fixes and an override functionality
Updates to example Scell files for new Optimization routine
Fixed mysterious bug related to failure to import c modules
Added piecewise dynamics testing
Redid optimization routine and added a "replace" option to overwrite cache
Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
Updated to include network creation
Finished up most examples, left out ones that are too similar to other examples and ones that are too complicated to be done with the current framework
Modified files to work with new test construction features
Fixed mysterious residual adding bug & added Hessian routine
Fix typo bug
Fix careless bug in SBMLInterface
Protect atexit removal of build directory from empty directory issue
Delay remove of build directory until python session closes. This was causing mysterious problems with compilation.
More complete conversion of SBML formula to Python syntax
Add basic test for piecewise in dynamical equations
Add preliminary support for piecewise in equations. Note that this requires manually disabling derivative functions and C compilation. [net.disable_deriv_funcs(); net.compile(disable_c=True)]
More thorough cleanup of files from C compilation
Remove hiding of specific compiler warnings.
Improve error reporting in run_distutils
Make alg_res, don't generated empty C declaration.
C89 compatibility for integrate_stochastic_tidbit
Fix error in test_Stochastic, by limiting seed range (which is still huge enough.)
Fix ddaskr_jac signature inconsitency
More C89 compatibility
Ignore some visual c++ warnings, for clarity
Use binary file write, to get line endings proper on Windows.
Typo fix
In dynamic C functions, declare all variables before any computations, because Visual C++ only supports C89.
More line ending fixes
Network_mod, replace \n with os.linesep