v0.8.9: Observed graphs, improved PopMaBoSS support

• Added support for Observed State Transition Graphs, a new functionality introduced in MaBoSS 2.6.0
• Improved Lazy loading support for very large PopMaBoSS simulations

Initial PopMaBoSS support, update of cMaBoSS version

• Initial support of PopMaBoSS, using cmaboss or existing simulation files.
• Updated version of cMaBoSS (v1.0.0b24), which comes with numpy 2.0 support and memory improvements on linux
• pipelines.filter_sensitivity not using strict inequalities.
• added option to get last_* data as a series (as_series=True), for now defaulting to False.

Fix PyPI package, SBML import, updated cmaboss dependency

• Fix PyPI package (added missing description.rst, now also producing wheel)
• Fix SBML import (bug in counting the number of nodes)
• Updated cMaBoSS dependency to 1.0.0b21 (better error handling)

Improved documentation, added PyPi description, fix small bugs

• Fix nodes format limitations in initial states
• Fix tracking of mutations, avoiding multiple declarations of $nb_mutants
• Fix simulation of model loaded with cMaBoSS
• Added support for python 3.12
• Improved documentation
• Added long description for PyPi

Fix simulation copy for mutants, fix upmaboss for pandas 2.0

• Fix simulation copy for mutants : mutationTypes was not copied !
• Fix UPMaBoSS for pandas : squeeze argument of read_csv as been retired, not calling .squeeze("columns") after read_csv

Fix nodes plotting, improved sensitivity pipeline, updated cmaboss dependency

• Fix plotting of nodes trajectories : cutoff is now zero by default, fix on empty data
• Improved sensitivity analysis : done on all nodes by default, cmaboss accessible
• Now using cmaboss 1.0.0beta17

New sensitivity analysis API, Bugfixes, Improved documentation

New sensitivity analysis API allowing a quick definition of simulation of single, double mutants and their analysis. The documentation of this API is available at : https://pymaboss.readthedocs.io/en/latest/api/sensitivity_api.html

Bugfixes :

• Fix simulation chaining in UPMaBoSS when using cmaboss
• Fix node count (and maboss MAXNODES selection) when parsing sbml-qual models
• Fix scikit-learn dependency

UPMaBoSS performance improvements

• UPMaBoSS performance improvements
• New functions for sensitivity analysis

Bugfixes

Fix a bug introduced in set_istates, and another in the conda package specification.

SBML-qual compatibility, ensembles of MaBoSS models, bugfixes

• Implementation of SBML-qual compatibility, using cmaboss

sim = maboss.loadSBML(sbml_filename, cfg_filename, use_sbml_names=True)

This will load the sbml file with the given cfg file, or a default one if no cfg filename is given. use_sbml_names chooses if we should use the SBML name of SBML id to name the node in the MaBoSS model.

• Ensembles of MaBoSS models
• Fix FP table for MaBoSS server results
• Added warning when unbinding nodes