Code

New Motility interface#82

Code

Merged

mastrof merged 40 commits intomainmastrof/MicrobeAgents.jl:mainfrom motilitymastrof/MicrobeAgents.jl:motilityCopy head branch name to clipboardMay 19, 2024

+739-14,161

Commits

Commits on May 17, 2024

• first draft new motility implementation

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  1fd61ec

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• remove turnrate function and add abmtimestep function

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  de4e717

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• update microbe stepping function

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• update microbe type for new motility interface, no default motility value

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• rename tumblebias to more general bias

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• adapt chemotaxis models (Xie excluded temporarily)

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• add StatsBase dep (for transition sampling), update AbstractMicrobe, comment out Xie model

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  4bd48b7

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• fix step

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• update agent adder to retrieve number of motile states

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• fix docstring

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• fix motility api

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• update turn! function

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• add StatsBase dependency to Project

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• remove CellListMap dependency, add MixedStructTypes

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• add MixedStructTypes, remove neighborlists

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• improve add_agent! methods

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• redefine MotileState using MixedStructTypes

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• update microbe_step!

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• update pathfinder step

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Commits on May 18, 2024

• use nothing for default polar and azimuthal fields in RunState

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• execute turn! only if reorientation components of the motile state are not nothing

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• update model creation and stepping test suites

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  34b7ccb

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• new motility testset

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  24a0d29

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• update analysis and utils tests

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• allow instantaneous turns to happen immediately after a run

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• change default args

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• update validation scripts

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• update tests

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• speed update occurs at the end of step

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• bump minor version

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• update examples

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• update Xie model

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• edit example parameters

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• update exponential drift example

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• update docs

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Commits on May 19, 2024

• rename tumblebias to bias

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• update benchmarks

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• remove unnecessary files

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• add Xie to model creation tests

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• use MVector for transition weights to allow patterns with modulable transitions

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