Activity for SloppyCell
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Bryan Daniels created merge request #1
fix crash in newer versions of scipy
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Keeyan S Ghoreshi committed [a0b474]
Fixed optimization routine passing iterations parameter in the wrong place
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Changed backslash to forward slash and sleep before showing graphs
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Changed backslashes to forward
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Merge remote-tracking branch 'origin/master'
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Ryan Gutenkunst committed [2ab615]
Merge commit '1b4fd6f16413a01d2443e52606fbe1f888635e38'
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Ryan Gutenkunst committed [a200a5]
Add pdf version of user documentation to repository.
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Updated format to match parsing changes
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Updated saving methods and added ability to output .CSV for trajectories (not ensembleTrajectories yet)
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Ryan Gutenkunst committed [df35a8]
Bug fix for developer documentation
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Ryan Gutenkunst committed [4efb86]
Remove parallelization and graphviz discussion from user manual, which aren't really supported anymore.
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Ryan Gutenkunst committed [417b65]
Fix two small bugs in developer documentation
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Ryan Gutenkunst committed [a198b6]
Updates to user manual. Adding pdf files so it always compiles.
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Updated command line input module
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Re-added temp foler
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Emptied temp folder
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Capitalized "example"
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Added temp folder to put saved data in.
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Added forgotten input statement
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Updated XML examples
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Changed to the updated version
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Ryan Gutenkunst committed [2fd53b]
Merge select files from XML_Interface development branch
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Ryan Gutenkunst committed [f02a27]
Correct issue arising from Keeyan changing capitalization of directory names
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Ryan Gutenkunst committed [9dd9a2]
Simplify naming of XML examples
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Remodeling project structure
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Ryan Gutenkunst committed [b35e8b]
Add README and setup for PyPI submission
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Ryan Gutenkunst committed [9113ce]
Further simplify setup.py
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Ryan Gutenkunst committed [02d9e9]
Add PyPI info to setup.py
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Ryan Gutenkunst committed [b04d05]
Add copy of BSD license
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Ryan Gutenkunst committed [64aa30]
Reorganize package to match standard distutils layout (for future submission to PyPI)
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Testing
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Testing
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Added files for testing on other machine
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Added preliminary command line handler and .scell file parser
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Added example constructor, prior defining functionality, and csv data parsing
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Updated some small things before merging
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Small changes to syntax
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Adding the jak_stat xml file back to the repository. Don't know why it wasn't there anymore.
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Switched to XML file parsing, but kept .scell file parsing just in case
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copied from dropbox
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Created source folder and root package
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Added network creation/modification support
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Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
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Switched over to full xml implementation, added new experiment constructor
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added debugging lines
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GitHub committed [08e60d]
Adding the jak-stat example xml file back
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ddaskr changes (fortran removal)
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Merge remote-tracking branch 'sloppy/Development' into Development
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Added trajectory plotting action routine
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Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
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Small changes to ensure file deletion
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Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
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Took care of all the TODOs, mostly small fixes and getting rid of any hard-coding
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(Mostly) Fixed C compiling issue in NetworkMod
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Streamlined saving process, added ensemble action routine, and fixed various bugs related to saving/loading data. Made everything much more modular.
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Redid method for action routine parsing. Also modified Network_Mod to delete generated code even in the event of DLL failure.
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Removing duplicates of ddaskr directory
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Fixed various syntax/compiler errors
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Attempt to post updated code to development
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Added new files and tweaked existing ones slightly
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Finished ensemble trajectory routine, completing all graphs for Tyson Example
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Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
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Small changes for debugging and to show graphs
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Added network creation handling
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Small changes to ensure compatibility with jak-stat and autocorrelation graphing from cache
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Created xml file to run specified example, recreates related reproduction .py file.
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Added a quick workaround to avoid .pyd file buildup in main directory
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Added sophisticated trajectory calculation and graphing functions
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Example updates, added anvin's model
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Some quick bug fixes and an override functionality
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Updates to example Scell files for new Optimization routine
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Fixed mysterious bug related to failure to import c modules
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Added piecewise dynamics testing
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Redid optimization routine and added a "replace" option to overwrite cache
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Merge branch 'master' of git://git.code.sf.net/p/sloppycell/git into Development
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Updated to include network creation
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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
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Modified files to work with new test construction features
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Fixed mysterious residual adding bug & added Hessian routine
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Ryan Gutenkunst committed [d0ab0d]
Fix typo bug
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Ryan Gutenkunst committed [7024ce]
Fix careless bug in SBMLInterface
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Ryan Gutenkunst committed [330c7f]
Protect atexit removal of build directory from empty directory issue
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Ryan Gutenkunst committed [6493c6]
Delay remove of build directory until python session closes. This was causing mysterious problems with compilation.
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Ryan Gutenkunst committed [628302]
More complete conversion of SBML formula to Python syntax
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Ryan Gutenkunst committed [ab8298]
Add basic test for piecewise in dynamical equations
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Ryan Gutenkunst committed [77c093]
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)]
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Ryan Gutenkunst committed [22c625]
More thorough cleanup of files from C compilation
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Ryan Gutenkunst committed [4b17bc]
Remove hiding of specific compiler warnings.
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Ryan Gutenkunst committed [b54950]
Improve error reporting in run_distutils
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Ryan Gutenkunst committed [1090eb]
Make alg_res, don't generated empty C declaration.
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Ryan Gutenkunst committed [0d61ff]
C89 compatibility for integrate_stochastic_tidbit
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Ryan Gutenkunst committed [9ab907]
Fix error in test_Stochastic, by limiting seed range (which is still huge enough.)
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Ryan Gutenkunst committed [a6ea2c]
Fix ddaskr_jac signature inconsitency
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Ryan Gutenkunst committed [3bbc64]
More C89 compatibility
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Ryan Gutenkunst committed [f8d6f0]
Ignore some visual c++ warnings, for clarity
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Ryan Gutenkunst committed [cbac5a]
Use binary file write, to get line endings proper on Windows.
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Ryan Gutenkunst committed [697171]
Typo fix
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Ryan Gutenkunst committed [376b6b]
In dynamic C functions, declare all variables before any computations, because Visual C++ only supports C89.
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Ryan Gutenkunst committed [5f2f3e]
More line ending fixes
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Ryan Gutenkunst committed [7742c8]
Network_mod, replace \n with os.linesep
