Merge dev into mpbn #121
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Merge dev into mpbn #121
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feat: added algorithm concepts for eQuilibrator
* Add 'ODE Solver', and move 'CVODE Solver' and 'Livermore solver' to be children of it. * Add 'parameters for' for specifying more-specific parameters for more-specific algorithms.
We use setup.py in an incompatible way with 23.1; fix pip at 23.0.1 for now.
* ODE Solver -> ODE solver * added 'lang' * Moved one-step solvers to be children of new ODE solver.
Add two new terms, change organization.
Also, switch 'ODE solver' to not be 'organizational' since it is indeed intended for use in SED-ML files.
Update for release
* Organize steady-state solvers and give them their own solver category, so solvers that do (say) NLEQ1 can be allowed to also tackle NLEQ2. * Move some SDE solvers out of the ODE branch; give them new SDE branch. * New tests for steadystate group * Let tests be run separately.
A handful of changes:
And make 630 the generic one. The reason is because many existing SED-ML models (and COPASI output) uses 407 to mean 'steady state', not 630.
Make 407 the root-finding steady state algorithm.
Should be used for spatial output.
IDA solvers are ODE solvers plus algebraic rules, not steady state solvers.
KINSOL and the 'method for solving a system of linear equations'. It may be that some of the children of this are actually DAE solvers, but if so, someone with more knowledge than I is going to have to tell us.
Create new 'DAE Solver' category; put IDA-like things in it.
Format md file correctly.
Replace incorrectly-formatted dates, a la #116
* Multiple comments combined into a single comment. * Multiple labels converted to a label and a definition. * The 'has characteristic" reduced to a single domain and range; both this and 'is characteristic of' set to be inverses of each other (instead of just one being flagged as the inverse of the other).
All the numbers for the newly-added logical terms had to be increased. New references to those terms also had to be redirected. But the result should be that all the new logical terms are self-contained and should work. Partway through an update to 2.35
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The mpbn branch has been ignored for too long; it's hard to say what needs to change.