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This commit restores the last\r\nversion of simulate.py for continued development internally.\r\n\r\n* Add classmethod simulate() to run a single simulation\r\n\r\n* ComplexPattern.is_equivalent_to() now works on Python 3\r\n\r\nThe ComplexPattern.is_equivalent_to() method relied on sorting a tuple\r\ncontaining (str, dict, int). dicts are no longer sortable in Python 3\r\nwithout specifying a sort order. The problem is fixed using a lambda\r\nfunction to specify the sort order, replicating the Python 2 behaviour.\r\n\r\n* First draft of ScipyOdeSimulator() class\r\n\r\n* Cache simulator trajectory array internally for concs_all() calls\r\n\r\n* Simulator class now allows initial condition overrides as a dict\r\n\r\nPrevious behaviour was that the entire list of initial conditions had\r\nto be specified as a list, matching the order of model.species. This\r\ncommit allows simulation-specific initial condition overrides to be\r\nspecified using a dict with a MonomerPattern or ComplexPattern for each\r\nkey.\r\n\r\nExample:\r\n```\r\nScipyOdeSolver.execute(model,\r\n                       tspan=linspace(0, 100, 10),\r\n                       initials={A(a=1) % B(b=1): 10})\r\n```\r\n\r\n* Fix Simulator class with initial conditions specified in a list\r\n\r\nThis was previously broken due to a bug. Thanks to @michael-irvin\r\nfor the catch. A unit test has also been implemented to catch the\r\nerror.\r\n\r\n* Simulator class: setting initials or parameters using numpy arrays now works\r\n\r\nPreviously this would fail silently without updating the initials/parameters\r\n(oops).\r\n\r\n* Simulator class: add more unit tests and increase coverage\r\n\r\n* Adding default options for lsoda\r\n\r\n* Add setter for Solver._use_inline\r\n\r\n* Use relative import for .scipyode\r\n\r\n* Refactor Simulator class _clear_outputs to _init_outputs\r\n\r\n* Allow tspan, initials and param_values to be set im Simulator constructor\r\n\r\n* Tweaks to Simulator initials setter (thanks @jmuhlich)\r\n\r\n* Simulator.run() now returns SimulationResult; execute() classmethod removed\r\n\r\nThe Simulator class `run()` method now returns a SimulationResult object\r\ninstead of no return type. 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