Add Flystem Cells

[Jannetty]

Estimated time to review: Large (sorry)

Summary of changes:
This code adds the fly neuroblast code into the codebase. The changes include:

• Adding fly stem cell classes to the potts cell container convert method so convert can call the PottsCellFlyStem constructor when the stem cell classes are specified in the constructor.
• Adding PottsCellFlyStem class (and test class)
• Adding PottsCellFlyStemProliferation module which includes all plane of division logic, growth rate regulation logic, differentiation logic (and tests)
• Made getUniqueIDs a public function for all implementations so that the PottsCellFlyStemProliferation module can use it to determine the identities of neighboring cells
• Adding parameters needed for PottsCellFlyStem and PottsCellFlyStemProliferationModule

How to verify changes:

• run tests
• Here is a minimal neuroblast setup file which you can run on this branch:

<set prefix="2025-10-23-01">
    <series name="dd" start="1" end="1"
            ds=".3" margin="0" height="1" length="802" width="802"
            dt=".083" ticks="576" interval="4">
        <potts>
            <potts.term id="volume" />
            <potts.term id="adhesion" />
            <potts.term id="surface" />
        </potts>
        <agents>
            <populations>
                <population id="fly-stem-wt" class="fly-stem-wt" init="1" >
                    <population.link id="fly-gmc" weight="1"/>
                    <population.parameter id="proliferation/SIZE_TARGET" value="1.2" />
                    <population.parameter id="CRITICAL_VOLUME" value="52" units="um^3" conversion="DS^-3" />
                    <population.parameter id="proliferation/CELL_GROWTH_RATE" value="5" units="um^3/hour" conversion="DS^-3DT"/>
                    <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
                    <population.parameter id="proliferation/DIV_ROTATION_DISTRIBUTION" value="NORMAL(MU=36,SIGMA=30)" />
                    <population.parameter id="proliferation/DIFFERENTIATION_RULESET" value="location" />
                    <population.parameter id="proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE" value="10" />
                    <population.parameter id="proliferation/APICAL_AXIS_RULESET" value="uniform" />
                    <population.parameter id="proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION" value="UNIFORM(MIN=0,MAX=360)" />
                    <population.parameter id= "proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="0" />
                    <population.parameter id= "proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT" value="0" />
                    <population.parameter id= "proliferation/VOLUME_BASED_CRITICAL_VOLUME" value="1" />
                </population>
                <population id="fly-gmc" class="fly-gmc" init="0">
                 <population.link id="fly-neuron" weight="1"/>
                 <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
                 <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
                 <population.parameter id="proliferation/CELL_GROWTH_RATE" value="1.22" units="um^2/hour" conversion="DS^-2.DT"/>
                 <population.parameter id= "proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="0" />
                </population>
                <population id="fly-neuron" class="fly-neuron" init="0">
                <population.parameter id="proliferation/CELL_GROWTH_RATE" value="0"/>
                <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
                <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
                </population>
            </populations>
        </agents>
    </series>
</set>

resolves #137
resolves #109
resolves #91
resolves #58
resolves #50

[kristaphommatha]

Look great so far! I looked over all the files except for the proliferation module and proliferation module tests, and had a couple of points of confusion for the files I did review!

I'll plan to come back and review the proliferation module and tests within the next couple of days! 🫡

[kristaphommatha]

I see right below these lines there is the exact same import, except static. Why were these non-static imports added/ what is the difference between the static/non-static imports?

[kristaphommatha]

I know that in the PottsCellFlyStem constructor, mudmut and wt cells have a different stemType code that differentiates them. This comment might be nitpicky, but without that context, this implementation could be confusing because it looks like both cases act the exact same way.

Is there a way to specify in the constructor call that you are creating a mudmut or wt cell?

[kristaphommatha]

What is the reasoning behind this check?

From the setStateModule method, I assume that the only module that isn't null is proliferation. I'm just curious about why is it important that the state is undefined instead of proliferative?

[kristaphommatha]

This might be really nitpicky and not even matter, but would there be any unexpected behavior if cellID and the parentID were the same?

[kristaphommatha]

I feel like because of the way the PottsCellFlyStem constructor is implemented, this test and the one above are virtually the same.

I'm not sure if you need both tests here if the class difference between fly-stem-wt and fly-stem-mudmut is tested already in the constructor_validWTStemType_createsInstance() and constructor_validMUDMUTStemType_createsInstance() tests under PottsCellFlyStemTest. I could be wrong though and would love to talk about this more

[kristaphommatha]

Would make on fly-stem-mudmut and fly-stem-wt cells create containers with the exact same parameters?