v2.6.0: Observed State Transition Graphs, PopMaBoSS MPI

• 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)

Added numpy 2.0 support for cMaBoSS, improved memory management.

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

Improved compatibility with arm64 on macos (universal binary, python wheels, conda packages), SBML-qual export draft

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 !

libMaBoSS for arm64 now part of the release assets

• 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

Python 3.12 cMaBoSS compatibility, libSBML 5.20.2

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

MaBoSS performance improvements, PopMaBoSS beta release

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 PRNG, BNet support, Added cmaboss support for macosx ARM64

• 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 in MaBEstEngine and EnsembleEngine

Fix memory bug in MaBEstEngine and EnsembleEngine destructors.

MPI Parallelization

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

Memory, Parallelization improvements

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