Maboss

- Introducing Observed State Transition Graphs, based on a selected list of nodes
- MPI Support for PopMaBoSS
- Support of HDF5 export (experimental)
- Granular pop size in PopMaBoSS (experimental)
- Python 3.13 support in PyPi (experimental)
- Tests now using latest libSBML version (5.20.4)

MaBoSS:
- Fix a few memory leaks in PopMaBoSS model parsing

cMaBoSS:
- Added support for numpy 2.0
- Now forcing malloc to release memory
- Added support for PopMaBoSS

This release comes with two main improvements :
- Better compatibility with arm64 on macOS: We now are providing a universal binary for macOS, and native arm64 python wheels and conda packages.
- Beta version of SBML-qual export of MaBoSS model:
`MaBoSS model.bnd -c model.cfg -x model.sbml`
will export the model defined by model.bnd into SBML-qual, as a pure Boolean model. Please test and report issues !

- Now automatically producing arm64 libMaBoSS
- Added more error checking to cMaBoSS
- Fix support of unary boolean operator in SBML-qual
- MaBoSS MPI version now with a .MPI suffix
- MaBoSS docker image now available via GitHub packages
- Code cleanup

- Adding compatibility with python 3.12 in cMaBoSS
- Updating libSBML version to 5.20.2

This release comes with two performance improvements :
- Evaluation of boolean formulas allowing for short-circuiting of boolean expressions (11), thanks exaexa !
- nodesTransitionRates is now represented as a vector, initialized only once, thanks PopCoE !

Also included is the beta release of PopMaBoSS, a new multicellular pathway modeling framework (thanks vincent-noel , gautierstoll eviara). Manuscript is in preparation !
To test it, run :

cd engine/src
make popmaboss


Examples are available in the `engine/examples/popmaboss` directory.

This release also include new pypi and conda packages for cmaboss with python 3.11.