warn when a transformation hands an attack to a non-attacking type

[drbergman]

Draft. Stacks on #341 — the first two commits here are that PR's; the new work is the last commit. Review/merge #341 first and this will shrink to one commit.

Why

#341 makes an in-progress attack survive the attacker's transformation. That attack can land on a cell definition that would never have started it, which is the concern raised on #341:

• attack_rates default to 0, so a type the user never wrote attack parameters for inherits the attack anyway
• attack_damage_rate defaults to 1.0 and attack_duration to 30 min, so those defaults — not the model — decide how much damage gets done

This is easy to arrive at by accident: it needs no attack configuration on the new type at all.

What this does

Nothing to the simulation. Whether such an attack should continue is a modelling question, and every automatic answer I could come up with (drop the attack when the new type's attack rate is zero, add a conserved-style flag, re-roll the duration) decides something on the user's behalf. So this only warns, and leaves the call to them.

The warning fires when the new type's attack rate against the target's cell type is zero — i.e. the cell is now continuing an attack it could not itself have begun:

Warning: a 'CD8+ T cell' transformed into a 'neutrophil' while attacking a 'bacteria',
	but 'neutrophil' has an attack rate of 0 against 'bacteria', i.e. it would never start this attack itself.
	The attack continues regardless, for up to attack_duration = 0.1 min at attack_damage_rate = 1.
	If that is not what you intend, set the attack parameters for 'neutrophil' explicitly, or end the attack in a custom function.
	(reported once per combination of transformation and target type)

Reported once per (old type, new type, target type) combination — the same transformation recurs constantly in a real model, and per-cell-per-step output would bury everything else.

Notes for review

• Thread safety. convert_to_cell_definition runs inside the parallel phenotype loop. The dedupe list is guarded by a named critical: detach_cells_as_spring() and the attacked_by helpers take the unnamed one, and OpenMP criticals are not reentrant.
• The target's type is read as an int through find_cell_definition_index() rather than reading pTarget->type_name, since a target transforming on another thread in the same step would be rewriting that string. find_cell_definition_index only calls find() on a map that is fixed after setup.
• attack_rates is indexed via find_cell_definition_index, not by type directly — Cell::type is the XML ID, which is not necessarily the definition index. (Cell_Interactions::attack_rate(name) was not reused here: it does unordered_map::operator[], which inserts on a miss and so is not safe to call concurrently.)

Verification

Built and ran interaction-sample with CD8+ T cell -> neutrophil transformation enabled and a 30 min attack duration:

• warning fires once across multiple qualifying transformations
• silent when neutrophil's attack rate against bacteria is set > 0
• clean at OMP_NUM_THREADS=8

interactions and rules_sample are the only sample configs with both nonzero attack and transformation rates. Both run to completion on their stock configs with zero warnings, so this does not add noise to existing models.

Open question

Should this be suppressible from the config, or is once-per-combination quiet enough?

[rheiland]

I wonder if we should adopt the creation/use of a std::ofstream warnings.log file? The concern has always been that warnings from cout will simply fly by the user. There will likely be more warnings that could go into such a .log file. At least users could check it post-sim. Unfortunately this feature would affect all sample projects... or else we just show it's possible in the template project.

[drbergman]

I think that's a great idea. If we can build it entirely apart from user files, then we don't need this to touch sample projects. We could demonstrate how to hook into it for main.cpp and custom_modules in the template project.