v.2.0.2

improved plots

v.2.0.1

Larger refactor. Main goal was to ensure better type safety of simulation parameters and a better compatibility of multimm package with the multimm web server. Main changes:

added ruff, black, isort, docformatter. Fixed all ruff warnings.
moved to modern pyproject instead of setup py
updated openmm and numpy to newest versions
added pydantic for type safety of configuration parameters
added a bridge.py that exposes the multimm config, and simulation through functions that are easy to consume by multimm server (reducing a big amount of boilerplate code required in multimm server)
changed the main package import name from 'simulation' to 'multimm' for more intuitive usage
various bugfixes regarding empty parameters, such as empty region when chromosome modeling is selected
a couple of tests with fixtures for easier bug reproducibility
updated the publishing github workflow to newest version
added 'uv' support
replaced all print statements with a dedicated logger

Multimm server is already using this version of multimm package, it has been tested with genomewide 150k beads simulation and a smaller single chromosome simulation

v.1.1.0.0.1

Fixed 200 exit error.

v.1.1.0.0.0

Fixed plots

v.1.0.24

Improved the region around gene.

v.1.0.23

Added CPU threads.

v.1.0.22

Added gene visualization, more organized output and some magic argument that makes modeling easier.

v.1.0.21

Fixed setup.py

MultiMM: v.1.0.16

Added some tests to make it more user-friendly.

MultiMM: v.1.0.15

Added option for downsampling.