0.2.0

Release notes for sbmlode 0.2.0

sbmlode 0.2.0 writes the ODE system in the native quantities of the SBML state variables: a species is a state in amount or in concentration as the model declares it, also in a compartment whose size changes. This changes the system and its typed target, see the breaking changes.

New features

• a species in concentration in a compartment whose size changes stays in concentration: its ODE is the one of SBML Level 3 Version 2, section 3.4.6, the reaction terms divided by the size minus the dilution S/V dV/dt (Ode.size_rate); a boundary, constant or not reacting species in such a compartment keeps its amount and is diluted alone (origin dilution) (matthiaskoenig/sbml4humans#114)
• the rate of the size of a compartment dV/dt is an assignment of its own (origin size_rate, OdeSystem.size_rates, a symbol of kind rate whose source is the compartment, typeset as the derivative of the compartment): the right hand side of its rate rule, or the derivative of its assignment rule by the chain rule; a size with an assignment rule of constants only is constant, a rule which cannot be differentiated is the unsupported construct rate of an assigned size
• astutil.derivative(ast, variable), the symbolic derivative of a math, simplified
• an event which changes a size rescales every species in concentration of the compartment with the size after the event, also when it changes a parameter of the assignment rule of the size; the code writes the function event_sizes_<id> of these sizes
• rateOf of a species in concentration in a variable compartment and of a size with an assignment rule

Documentation

• the logo of sbmlode in the README, the documentation, the release notes and as favicon

Breaking changes

• OdeSystem.amounts, Quantity.amount_of, Ode.amount_of, the origin concentration and the section amounts of the typed target and of the documents are removed, a species is never replaced by its amount n_S
• TypesetEventAssignment has no field species, its conversion is None or resized
• the code context of an event assignment has divisor_index into the new list sizes of the event instead of divisor_position

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