Jain/prospero#212

Draft

Jannetty wants to merge 28 commits into

feature/add-flystemcellsfrom

Commits on Feb 25, 2026

broken & unupdated prospero preliminary code
navyacodes
committed

Commits on Mar 4, 2026

broken code with prospero changed to be more biologically accurate
navyacodes
committed

Commits on Mar 6, 2026

Modified 1.xml file and removed PottsCellFlyNeuron inheritance change

Alice Fu
authored and
Alice Fu
committed
Modified PottsCellContainer, PottsOutputSerializer, and PottsCellFly to optionally incorporate prospero so prospero values will print in the output files

Alice Fu
authored and
Alice Fu
committed
Factored out logic determining prospero inheritance for makeDaughterStemCell method into splitStemProspero

Alice Fu
authored and
Alice Fu
committed
Merge branch 'feature/add-flystemcells' into jain/prospero

Alice Fu
authored and
Alice Fu
committed
Attempted to write a small test, but it is not being run when ./gradlew test is called

Alice Fu
authored and
Alice Fu
committed

Commits on Mar 11, 2026

Commits on Mar 18, 2026

Added javadoc comments for PottsCellFly class
navyacodes
committed
Added tests for getAllProspero, splitStemProspero; fixed step test.
navyacodes
committed
added a test for ProsperoSerializer's serialize method
navyacodes
committed
Added saveProspero test

Alice Fu
authored and
Alice Fu
committed
Merge branch 'jain/prospero' of https://github.com/bagherilab/ARCADE into jain/prospero

Alice Fu
authored and
Alice Fu
committed
making copyJar run after other jobs in build.gradle
Jannetty
committed
Reverted prospero saving changes in PottsCellContainer

Alice Fu
authored and
Alice Fu
committed
Merge branch 'jain/prospero' of https://github.com/bagherilab/ARCADE into jain/prospero

Alice Fu
authored and
Alice Fu
committed
updating PDE like test to have correct number of mocked neuroblasts
Jannetty
committed

Commits on Apr 8, 2026

Added error when degradation rate pulled from parameters is negative

Alice Fu
authored and
Alice Fu
committed
Flipped the sign of prospero degradation so the positive degradation rate is subtracted from the current prospero in GMCs

Alice Fu
authored and
Alice Fu
committed
Tests exception for negative Prospero degradation rate is thrown

Alice Fu
authored and
Alice Fu
committed

Commits on Apr 27, 2026

Added test for step function in PottsModuleFlyGMCDiffferentiationTest

Alice Fu
authored and
Alice Fu
committed