v0.5.1

MicrobeAgents v0.5.1

Diff since v0.5.0

Merged pull requests:

• Remove ValidPos (#96) (@mastrof)

v0.5.0

MicrobeAgents v0.5.0

Diff since v0.4.2

Merged pull requests:

• Fix rotation bug (#93) (@mastrof)
• Motility constructors kwargs (#94) (@mastrof)

Closed issues:

• Motility constructors should take kwargs (#91)
• Fix default distribution of reorientation angles in 3D (#92)

v0.4.2

MicrobeAgents v0.4.2

Diff since v0.4.1

Merged pull requests:

• Use dispatch instead of manual branching (#90) (@Tortar)

v0.4.1

What's Changed

• try workflows update by @mastrof in #84
• Api fixes by @mastrof in #86
• Fix random_velocity by @mastrof in #87
• Chemotaxis tests by @mastrof in #88
• Export abmtimestep function by @mastrof in #89

Full Changelog: v0.4.0...v0.4.1

v0.4.0

MicrobeAgents v0.4.0

Diff since v0.3.0

Merged pull requests:

• New Motility interface (#82) (@mastrof)
• New chemotaxis model: SonMenolascina (#83) (@mastrof)

Closed issues:

• Tumbles of finite duration (#77)
• Better motility implementation (#78)

v0.3.0

MicrobeAgents v0.3.0

Diff since v0.2.0

Merged pull requests:

• fix wrong function call in driftvelocity_point! (#79) (@mastrof)
• Replace :step with :time in dataframes (#81) (@mastrof)

Closed issues:

• Replace :step with :time in analysis submodule (#80)

v0.2.0

MicrobeAgents v0.2.0

Diff since v0.1.0

Merged pull requests:

• Update docs (#48) (@mastrof)
• Use and reexport Agents.jl API functions to access model properties (#52) (@mastrof)
• Update to Agents v6 (#53) (@mastrof)
• Simple stepping benchmarks (#58) (@mastrof)
• Remove leftover tuple conversions (#59) (@mastrof)
• Deprecate UnremovableABM (#60) (@mastrof)
• Use new Agents API function abmtime instead of manual time counter (#61) (@mastrof)
• Simplify motility types (#62) (@mastrof)
• Remove ChainedFunction (#63) (@mastrof)
• Update docs and use Literate.jl (#64) (@mastrof)
• Analysis submodule (#65) (@mastrof)
• Add example: drift in exponential ramp with brumley model (#66) (@mastrof)
• update tests on postprocessing, acf, msd; comment out turn detection … (#67) (@mastrof)
• replace deprecated add_agent_pos! with add_agent_own_pos! (#68) (@mastrof)
• use affect! as ABM property (#69) (@mastrof)
• use abmrng in chemotaxis models (#71) (@mastrof)
• Internally convert ABM propetries to NamedTuple and define chemoattractant as a struct (#72) (@mastrof)
• Use explicit formula for 2D rotations, quaternions for 3D rotations (#73) (@mastrof)
• Export chemoattractant api function (#74) (@mastrof)
• update docstrings and api page of the docs (#75) (@mastrof)
• Agents v6 (#76) (@mastrof)

Closed issues:

• affect! should be passed as argument, not through overloading (#15)
• Example: drift velocity (#16)
• Motion along spherical surfaces (#30)
• Define a velocity function (#34)
• Change symbol for ChainedFunction (#36)
• Support AbstractGridSpace (#39)
• Move analysis routines to submodule? (#42)
• Drop acf in favor of autocor from StatsBase.jl? (#44)
• Rework microbe type definitions using @agent macro (#50)
• Add type parameter for motility (#56)
• Benchmarks (#57)
• Use ABM's random number generator in chemotaxis models (#70)

v0.1.0

MicrobeAgents v0.1.0

Closed issues:

• Example: run statistics (#10)
• Tumble detection (#11)
• Support StandardABM (#13)
• Port and update docs from Bactos.jl (#18)
• Celani shows chemotactic response if initialized from a non-zero concentration (#20)
• Error in the internal state update of BrownBerg (#21)
• Standardize fieldnames across different microbe types (#23)
• Add docstrings to extended Agents.jl functions (#26)
• Implement interface to CellListMap.jl for neighbor lists (#31)
• Docstring of distancevector is unclear (#33)
• Use the space interface from Agents.jl when creating an ABM (#37)
• Define a constant instead of hard-coded value for sensing noise (#38)

Merged pull requests:

• Xie chemotactic model (#1) (@mastrof)
• Use UnremovableABM (#2) (@mastrof)
• Microbe-sphere encounters (#3) (@mastrof)
• Pathfinder (#4) (@mastrof)
• Add spacing keyword to model constructor (#5) (@mastrof)
• Bugfix: MSD for non-cubic domains (#6) (@mastrof)
• Change affect! to unexposed _affect! (#7) (@mastrof)
• Chemotaxis - Celani (#8) (@mastrof)
• unexpose turnrate for Brumley and BrownBerg (#9) (@mastrof)
• Encounters-oldposition (#14) (@mastrof)
• Support both UnremovableABM and StandardABM (#17) (@mastrof)
• Tumble-detection (#19) (@mastrof)
• Bugfix: Error in the internal state update of BrownBerg (#22) (@mastrof)
• Standardize fieldnames (#25) (@mastrof)
• Initialize Celani at steady state (#27) (@mastrof)
• General docs update (#28) (@mastrof)
• Implement barebones interface to CellListMap.jl for neighbor lists (#32) (@mastrof)
• Use ContinuousSpace in ABM constructor (#40) (@mastrof)
• Fix docstrings of distance and distancevector (#41) (@mastrof)
• define CONV_NOISE constant (#43) (@mastrof)
• Chemotaxis (#47) (@mastrof)