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

v0.7.19

• fix get_initial_state with joined nodes (#48)

Restrictions in variables' names

• Remove restriction in the variables' name preventing them to contain boolean operators.
• Introduction of a list of reserved names, which can't be used (True, False, And, Or, Xor, Not, Node)
• Fix bug in plotting entropy

Fixing bug in parsing initial states

Fixed a bug in the parser for initial states, where a formula was refused if it contained spaces.

Added plotting options

• Added an optional nil_label to replace in piechart, PCA chart
• Added an argument to PCA plot to highlight a model
• Fix arrow and text size
• Added option to label PCA comparison
• Fixing comparison colors
• Saving the PCA figure as self._pcafig
• Saving the 3D figure as self._3dfig