Changelog

cr_mech_coli 0.8.0 (22.09.2025)

  • Improve results of crm_amir script

  • Allow to explicitly set growth rates for new cells

  • Fix functionality of crm_divide script

cr_mech_coli 0.7.1 (19.09.2025)

  • Exclude some files in distribution release due to large file sizes

cr_mech_coli 0.7.0 (19.09.2025)

  • Extend methods of CellContainer

  • Use rayon as default parallelizer

  • Adjust to new cellular_raza version

  • New script crm_divide to fit model to dividing bacteria

  • Calculate profiles more efficiently for crm_fit

  • Improve type hints of Rust-based code

cr_mech_coli 0.6.0 (19.06.2025)

  • Modularize crm_fit script

  • Adjust to new cellular_raza version

cr_mech_coli 0.5.3 (12.05.2025)

cr_mech_coli 0.5.2 (09.05.2025)

  • Update dependencies

  • Add performance metrics in documentation

  • Allow picking new growth rates from distribution

  • New script crm_amir to fit model to bent rod

  • New script crm_perf_plots to plot performance of simulations

  • Update plots of crm_multilayer script

cr_mech_coli 0.5.1 (01.05.2025)

  • New script crm_fit for fitting microscopig images

  • New script crm_multilayer for calculating multilayer behaviour of a colony.

  • Use BTreeMap instead of HashMap in CellContainer to preserve order in CellContainer.

  • New functions to (de)serialize and load a CellContainer from stored results

  • Implement growth rate reduction depending on neighbors

  • Rewrite main run_simulation function to take list of agents instead of only parameters.

  • Add new data sources for crm_fit script

cr_mech_coli 0.5.0 (14.02.2025)

  • Include presentation from Jeti Seminar 02.02.2025

  • Generalize Interaction to use either Morse or Mie Potential

  • First attempt at estimating parameters ref~692b7899

  • Enhance scripts for fitting model to data

  • Extend extract_positions function

cr_mech_coli 0.4.3 (31.01.2025 19:42)

  • Release first version to pypi

cr_mech_coli 0.4.2 (31.01.2025 19:08)

  • Get Github actions testing to work

cr_mech_coli 0.4.1 (31.01.2025 11:17)

  • Short intermediate release to publish initial version to pypi See release 0.5.0 for more in-depth notes.

cr_mech_coli 0.4.0 (19.11.2024)

  • Added first iteration of preprint

  • Improved position extraction algorithm

cr_mech_coli 0.3.0 (31.10.2024)

  • Added fitting methods

    • Extend documentation

    • Conversion between pixel and length-positions

  • Introduction of the CellContainer class which bundles information about a time series of cellular agents.

  • Small improvements in Imaging

  • Remove unused jupyter scripts

cr_mech_coli 0.2.0 (23.10.2024)

cr_mech_coli 0.1.0 (14.10.2024)

  • Initial commit