GitHub PushEvent at 2014-03-20 17:30:54
Repository: cobrapy
Actor: danielhyduke
Payload: {"shas":[["98bdd17f812b5bd5f21366ed7d2c94928296ce8a","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","begin separating glpk for cpython and jython","Ali Ebrahim",false],["6abaacca1418879c3c6c1cf946ac124da24d9f4b","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","glpk solver uses comprehensions in format solution","Ali Ebrahim",false],["df6ce013c01c4d01ffe9378fd9f2df8c073804bd","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","split cplex and gurobi java solvers off","Ali Ebrahim",false],["fa2e529c265fa0bfbf0db9b25617998e2a1bf3d9","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","glpk solver uses izip in create_problem\n\nspeeds up problem_creation by 9% while using less memory","Ali Ebrahim",false],["7e84352202a352a7aae873023bb53a2a00e59f4a","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","gurobi_solver now has change_variable_bounds\n\ngurobipy does not allow getting variables by index, but does by name\n(for some strange reason). Therefore, this now uses the index as the\nname (ugh) so we can get this functionality. Otherwise, we would need to\nindex the specific variable out of the entire list of lp.getVars(),\nwhich takes nearly 500us every time.","Ali Ebrahim",false],["f7fc31d0d77addcf9440da6cb0acde1bbb617c8d","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","add change_variable_bounds to cplex","Ali Ebrahim",false],["f0e510d4a267304238e87df1261ccc0fd6d12fad","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","small bugfix for glpk and glpk_java","Ali Ebrahim",false],["072cbfe39bafa58c037ba75e3711aaaa41ff036a","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","single deletion fba fast method\n\nSingle reaction deletions with this function are 20x faster\n\nThis speedup comes from using the solver specific functions","Ali Ebrahim",false],["f881ec442c845ebaf2ecae8c3537c6dd64cc587a","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","add change_variable_objective to cpython solvers","Ali Ebrahim",false],["b6a9c59838138d6bce0e86f0c59c886a5c2eca94","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","implement fva using optimized solver functions\n\nspeedup of 3.5x","Ali Ebrahim",false],["ccd60fd2aec0f8145c1f4ecfafa608c9144b5fca","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","small cleanup for new fva and single rxn deletion","Ali Ebrahim",false],["b14b17e13599dfdf2f7eb30b61986ec9021f0da2","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","gene deletion computed in separate function\n\nThe logic used to determine which reactions are inactivated by a gene\ndeletion has been moved from delete_model_genes into a standalone\nfunction find_gene_knockout_reactions","Ali Ebrahim",false],["12f202bb1199ba84ba778a51efb67a51845150cb","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","single_gene_deletion_fba with new solver speedup\n\nUsing lower level solver control enalbles 2.4x speedup with iJO1366\nmodel single gene deletions.","Ali Ebrahim",false],["83b5c1c8e547b748eb6ef11af948265d1f173e68","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","identify possible numeric fva isssue with new speedup","Ali Ebrahim",false],["ce0a0dc1c00788328d5f5fca74f14a50d11f929e","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","fast fva no longer assumes objectives sum to 1","Ali Ebrahim",false],["ac6cddb733d38ce8a696ea9d42f0079e7b0c3f0d","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","glpk sets constraints from reaction._metabolites\n\ninstead of from metabolite._reaction","Ali Ebrahim",false],["d042d75b8287c01b2063b45bcc7bb9140145424c","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","solver unit tests for low level control","Ali Ebrahim",false],["d0061c5437fc561605894867f8e8d942e1f0f81b","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","SMatrix works with both lil and dok","Ali Ebrahim",false],["3ab53eb880a797b5a1d3019948e25dc8ebf67961","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","revert arraybasedmodel default to lil","Ali Ebrahim",false],["908273a07e69a658c234eff09fc248b5f5495b6b","9932eb6ef1488c3d87a122f4753473956aa29430@ucsd.edu","implement LinkedArray, add for model.reactions\n\nLinkedArray is an ndarray which updates model.reactions (or metabolites)\nappropriately if it is changed. For example, model.lower_bounds[4] = 10\nwill cause model.reactions[10].lower_bound = 10 to be automatically\nexecuted as well.","Ali Ebrahim",false]],"size":85,"ref":"refs/heads/species","head":"5041528bc2119dccc4617668e6d7b115e13fddc1"}