[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

[allison-li-1016]

I have a couple clarification questions -- will take a deeper look into the tests after clarification.

[allison-li-1016]

Looks good to me !

[kristaphommatha]

Everything LGTM!