sys-bio/roadrunner: v2.11.0

Updates:

• Now released for python 3.15 (and three previous python versions, through 3.12)
• Use latest SWIG for python bindings.
• Update Sundials library
• The absolute tolerance vector is now scaled from the initial values of the model, not the current values. This leads to more stable bugfixing when searching out 'what are good tolerances for this model', and allows you to break up a long simulation into simulated sections without (hopefully) as many things changing.
• CVODE warnings now tied to roadrunner's own warning system, so they're off by default.
• Now allow setting init(x) even if x has an existing initial assignment (this now overrides the old assignment).

Bug fixes:

• Many memory bugs fixed, including many from the plugins; plugins now work on ubuntu without crashing after finishing!
• Updated SBML test suite 1511, whose steps were too wide to properly test what it was supposed to be testing.
• Now pass all VolumeConcentrationRate tests from the test suite.
• Fix the 'last step' of variable step size runs to actually end where we're supposed to end to the correct tolerance.
• Correctly update tolerances for finding event triggers.
• Fix RK45 bugs
• Update rules about conserved moieties to allow assignment rules but not rate rules.
• Fix steady state assessment in models with conserved moieties so we no longer change total mass.
• Flatten comp models when reading from a string (used only flatten comp-enabled files)
• Various cleanup bugs discovered by AI fixed.