update intracellular in first time step

[drbergman]

Low priority PR that fixes bug causing intracellular updates to skip the first diffusion time step at t=0. I don't believe that PhysiBoSS or PhysiCelldFBA require this step to be skipped, but please inform if it is necessary :)

It is possible that rules that depend on variables expected to be set in a post_intracellular_update function could receive unexpected inputs causing unintended behavior in the first advance_bundled_phenotype_functions and subsequent mechanics updates.

• this change allows intracellular updates to occur in the first diffusion step
• before, they had to wait one diffusion step to update (if there's a reason for this, it's lost on me)
• removed need for initialzed [sic] field in Cell_Container class
• also make easier-to-parse logic and variable names for when to update phenotype and mechanics

[Copilot]

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

[vincent-noel]

I don't think there is a reason, and I don't see how.
In the case of PhysiBoSS, if there is a need to wait, there is a special parameter which can be set (start_time) for example to allow for a gradient to reach equilibrium.

[drbergman]

Merge once conflict is resolved.

[drbergman]

waiting for checks to past before merging. had to bring in the change to pre-update intracellular first