Maboss

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.

- Fix Mersenne Twister pseudo-random number generator support
- Fix BNet support
- Fix compilation of cmaboss without SBML support
- New tests and deployment architecture
- Now using cibuildwheel to build cmaboss wheels
- Added cmaboss support for macosx ARM64

Fix memory bug in MaBEstEngine and EnsembleEngine destructors.

This new version comes with support for parallelization using MPI. This allows the simulation to run on multiple machines and to split the computational load.
To compile MaBoSS with MPI support, use :

make MPI_COMPAT=1 CXX=mpic++ install


More information can be found on the new tutorial on Montagud's newly released Prostate model : https://github.com/sysbio-curie/MaBoSS-env-2.0/tree/master/tutorial/Montagud_2022_Prostate_Cancer

- Improved memory management
- Logarithmic cumulator merging algorithm
- Bugfixes in cmaboss object structure
- Automatic generation of compiled binaries and libraries for linux, mac, windows.

MaBoSS is now compatible with [SBML-qual](http://www.colomoto.org/formats/sbml-qual.html) model files.

Usage: MaBoSS [--use-sbml-names] [-c|--config CONF_FILE] -o|--output OUTPUT BOOLEAN_NETWORK_FILE

Where :
- CONF_FILE is a classic CFG file.
- OUTPUT is the prefix of the output files.
- BOOLEAN_NETWORK_FILE is the network file, in BND, SBML-Qual or BNet format.
- --use-sbml-names indicate that MaBoSS should use SBML names for naming nodes instead of SBML ids.

To compile it with SBML-qual compatibility, install libsbml and then use :
make install SBML_COMPAT=1

Version of MaBoSS available on Conda is compatible, with a new dependency on libsbml.
Version of cmaboss available on Conda and PyPi is compatible.