{"push_id":1041923139,"size":12,"distinct_size":12,"ref":"refs/heads/master","head":"2aca3ae8d86b61240d6c23b61d73e38c57138d11","before":"442a09de5727af0d9577752ea665ce9c5c2962eb","commits":[{"sha":"3b46a85fd36c39bd27c0109bb491e6525934be9f","author":{"email":"aa743a0aaec8f7d7a1f01442503957f4d7a2d634@drhagen.com","name":"David Hagen"},"message":"Fixed Update. Cleared more symbolic variables in finalizeModelAnalytic.\n\nSymbolic variables in the don't save well and are not needed to run the model, so they are cleared before the function handles are constructed.","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/3b46a85fd36c39bd27c0109bb491e6525934be9f"},{"sha":"5b32b1fdc89779721f72a5bbdf4cd00a91b7bcc4","author":{"email":"aa743a0aaec8f7d7a1f01442503957f4d7a2d634@drhagen.com","name":"David Hagen"},"message":"Refactor code that checks conditions, observations, and objectives\n\nThis should improve the error messages in this arena. There is still some ambiguity about the inheritance relationship between observations and objectives, so the type check in those instances has been commented out. Closes #78.","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/5b32b1fdc89779721f72a5bbdf4cd00a91b7bcc4"},{"sha":"3ed72ab50ba215c670d93cd756ecbc28a23ef4ed","author":{"email":"aa743a0aaec8f7d7a1f01442503957f4d7a2d634@drhagen.com","name":"David Hagen"},"message":"Allow dot between compartment and species in expressions\n\nThis implements #70. It also fixes a bug with simbio models that have symbols in their names.","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/3ed72ab50ba215c670d93cd756ecbc28a23ef4ed"},{"sha":"a24e2326fc7c2fd829224011e235768aca1fd6a1","author":{"email":"aa743a0aaec8f7d7a1f01442503957f4d7a2d634@drhagen.com","name":"David Hagen"},"message":"Move files to Tutorial folder and fix up some of the tutorials","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/a24e2326fc7c2fd829224011e235768aca1fd6a1"},{"sha":"a9afa595e9b9e29857a1ca2605e2aa5f4e17b1b7","author":{"email":"df3cd239cf3b5e0b996b5f6db8b1d2747e06c27b@gmail.com","name":"Kevin Shi"},"message":"Analytic models: ICsAsSeeds, Inf2Big+Nan2Zero opts\nAdded back some important functionality to analytic model building and loading that was lost in previous commits over the last year. Default behavior isn't changed from current master - readded features are optional.\n- Option to import state initial conditions as seeds instead of hardcoded ICs. Specify opts.ICsAsSeeds in LoadModelSbmlAnalytic. Default is false.\n- Readded inf2big and nan2zero hacks onto expressions in analytic models. These are technically incorrect but sometimes necessary for models where, for example, symbolic calculations fail to handle removable discontinuities properly. An example is the derivative of a Hill function w.r.t. the Hill coefficient n. Specify opts.Inf2Big and opts.Nan2Zero in FinalizeModel. Default is to not do this.","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/a9afa595e9b9e29857a1ca2605e2aa5f4e17b1b7"},{"sha":"8d3761d26d2038f35929413acdeb873c20027cf9","author":{"email":"df3cd239cf3b5e0b996b5f6db8b1d2747e06c27b@gmail.com","name":"Kevin Shi"},"message":"Bugfixes to LoadSBML/ICsAsSeeds from last commit\n- Fixed 3 bugs with opts.ICsAsSeeds in LoadModelSbmlAnalytic\n   - Made default opts.ICsAsSeeds = false in sbml2analytic, in accordance with documentation/expected behavior\n   - The seed name in the state's initial condition value field is now surrounded by parentheses to be safe when compartment/state name has invalid characters.\n   - When opts.ICsAsSeeds = true, only states whose initial condition is not already an expression from a substituted rule get seeds. This makes it compatible with changes above that do rule substitution first.","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/8d3761d26d2038f35929413acdeb873c20027cf9"},{"sha":"32a759a82e20e95aa7263fddb7203e530e938b9f","author":{"email":"0b2f470f27561c20f520b42a0075132417673a16@mit.edu","name":"dflowers7"},"message":"Fixed hang occurring when steady state experiment starts at steady state\n\nThe steady state event function checks for a zero-crossing event that never occurs when the steady state is the initial condition. Now a check is done before simulation to determine whether the initial condition is a steady state.","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/32a759a82e20e95aa7263fddb7203e530e938b9f"},{"sha":"f017a5ad9ed74931d8fcbaa01ac54ccb1938a747","author":{"email":"df3cd239cf3b5e0b996b5f6db8b1d2747e06c27b@gmail.com","name":"Kevin Shi"},"message":"Merge drhagen's Tutorial reorg into master\nMerge branch 'master' of https://github.com/drhagen/kroneckertoolbox into current 'master' of https://github.com/kroneckerbio/kroneckerbio. Resolve conflicts in updated options when loading models.","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/f017a5ad9ed74931d8fcbaa01ac54ccb1938a747"},{"sha":"c396a6bcb6497ed032c7fd6c760f61a8e5280573","author":{"email":"df3cd239cf3b5e0b996b5f6db8b1d2747e06c27b@gmail.com","name":"Kevin Shi"},"message":"Merge branch 'drhagen-master'","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/c396a6bcb6497ed032c7fd6c760f61a8e5280573"},{"sha":"07f4d75db8206cc6d7d3f74f5ef962550a597d29","author":{"email":"df3cd239cf3b5e0b996b5f6db8b1d2747e06c27b@gmail.com","name":"Kevin Shi"},"message":"Started dedicated published documentation\nBuilt the overall framework and tutorial pages. See PubDocs' help comments for more details. The main landing page is in the webroot/index.html. It's made by interpreting and publishing Docs/index.m. These docs refer to the current unstable dev branch since we've made lots of changes since 0.5.0.\n\nSome features:\n- Call the function PubDocs.m in the root dir to generate all the documentation. The default location is the subdir Docs/html. This can be changed.\n- Basic templating system to augment Matlab's publishing markup. Basically, replace the string '%${X}' with the value of a vars.X struct in the sub_template function.\n- Started a versioning system for the website, where the current unstable dev version is in a dir called 'current' and tagged releases are in their respective named dirs. Right now, this isn't fully implemented yet (don't have links to each version of each tutorial, for example), and I'll hold off on it until after some discussion nearer to the next release.\n- Cleaned up the tutorials - added titles, etc. Had to change the paths/filenames of the model loading functions to be absoute paths (autogenerated from pwd) so get them to publish.\n\nMain TODO:\n- Function help. Still thinking of the best way to do this.\n- Frontmatter like FAQs, contribution copyrights, etc.\n\nThis will go into a kroneckerbio organization Github Pages website. Some minor tweaks may be necessary to get it fully displaying.\n\nI felt like I was reinventing the wheel some here, but I still like this better than heavily modifying something else + introducing too many extra dependencies for a 3rd party solution.","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/07f4d75db8206cc6d7d3f74f5ef962550a597d29"},{"sha":"a1bd93164667d73f5f550081f8212e74ca15ccba","author":{"email":"df3cd239cf3b5e0b996b5f6db8b1d2747e06c27b@gmail.com","name":"Kevin Shi"},"message":"Merge pull request #81 from kroneckerbio/pub-docs\n\nStarted dedicated published documentation","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/a1bd93164667d73f5f550081f8212e74ca15ccba"},{"sha":"2aca3ae8d86b61240d6c23b61d73e38c57138d11","author":{"email":"aa743a0aaec8f7d7a1f01442503957f4d7a2d634@drhagen.com","name":"David Hagen"},"message":"Added doseList and fixed some bugs in ut_vectorized\n\nCloses #83","distinct":true,"url":"https://api.github.com/repos/xpspectre/kroneckerbio/commits/2aca3ae8d86b61240d6c23b61d73e38c57138d11"}]}