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Catchup merge from main into SED#27

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dmitrisvetlov wants to merge 657 commits intoSequentialExperimentDesignfrom
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Open

Catchup merge from main into SED#27
dmitrisvetlov wants to merge 657 commits intoSequentialExperimentDesignfrom
main

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@dmitrisvetlov
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@dmitrisvetlov dmitrisvetlov commented Jun 16, 2025

My changes on the SequentialExperimentDesign branch are intended to build upon the existing code without modifying the latter in any way, so conflicts should never arise. As this is just a "catchup" merge, and it can be automatically made, I will go ahead and approve the PR myself.

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dmitrisvetlov commented Jun 16, 2025

@Munsky,

There are several (trivial) conflicts that occur in trying to merge main into my branch; all of them can be resolved by simply taking the version on main, since any changes I have made to existing code (e.g. to Examples/Cook_etal_2024_Sequential_Design/) were only for testing and debugging purposes.

However, even when I resolve the conflicts, GitHub does not allow the pull request to be merged, because it tries to reverse the merge, making it from SequentialExperimentDesign into main. Do you know why this is occurring? It seems like a pretty severe GitHub bug, if that is where the fault lies.

image

If we can't resolve this, I can try to merge this via the command line, or make a fresh branch from main and simply copy-and-paste my changes over there.

- Dmitri

alexpopinga and others added 28 commits December 10, 2025 16:59
@alexpopinga
Fix improper FSP bounds on simple models
ec0a33a 
Revert bounds to what were initially specified.  The changed bounds lead to incorrect solutions.
@alexpopinga
Let the SSIT set default FSP bounds for simple models
fadb7a0 
-until we work out what is going awry
@alexpopinga
Allow for time point selection in plotFits
652d2e9
@alexpopinga
Add ability to specify subset of model parameters for scatter plots i…
f1be5a0 
…n plotMHResults
@alexpopinga
Read model parameter names in plotMHResults
3673065
@alexpopinga
Revert plotMH changes
0849a25
@Munsky
Fix bug in propensity functions for ode models when multiple logicals…
afcd91f 
… are used.
@Munsky
Fix bug to prevent re-use of stale state space when model reactions/s…
2d48b38 
…pecies are changed.
@Munsky
Add pipeline example and scSeq data.
ba4ba97
@Munsky
Update defaults to suppress figure sin multi-model. Update cluster ex…
8511b7b 
…ample.
@Munsky
Add shortened example of codes to run on cluster.
2e588f4
@Munsky
Update ClusteScriptOnly.m
e708375
@Munsky
Update pipeline for fitting to allow for multiple rounds.
b663a57
@Munsky
Update fittingPipelineExample.m
3b24dc0
@Munsky
Update ClusteScriptOnly.m
defae3f
@alexpopinga
Add lossy binomial PDO as selectable case
b278690
@alexpopinga
Store solutions inside model in examples
7997af3
Add scSeq data and models
fed1536
@alexpopinga
Change plot defaults and update PDO examples
e5639f9
@Munsky
Update scSeq Model Definitions.
bcdca45
@Munsky
Update ClusteScriptOnly.m
1de61f8
@Munsky
Update ClusteScriptOnly.m
d5d8cc3
@Munsky
Update ClusteScriptOnly.m
439e227
@Munsky
Update ClusteScriptOnly.m
4e90745
Fix Cluster run code
f5311b3
update scSeq model fits
45546f0
update scSeq fits
15e53bf
@Munsky
Add draft for a little post-fit analysis for scSEQ data.
a1041a7
@alexpopinga
Fix cases for string input
5282579 
Switch case for plotType in plotFSP assumed characters rather than strings so therefore always used default plotType "means"
@Munsky Munsky temporarily deployed to github-pages March 3, 2026 21:05 — with GitHub Pages Inactive
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