NEWS.md
In saezlab/CARNIVAL: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

CARNIVAL 2.3.0

bug fix: parsing the output of ILP solvers were incorrect, especially building the nodesAttributes. The bug resulted in inconsistencies between the reported nodes and interactions
bug fix: empty workdir and outputFolder resulted in unhandled errors. From now on, current working directory is used for temporary and result files if not specified otherwise in the options
bug fix: the function defaultCbcSolveCarnivalOptions() had a undefined variable.
bug fix: lpSolve has a non-negativity constraint which was ignored so far. Now this issue is handled. lpSolve can be used for small networks and in tests.
tests added: added many small-medium, general tests for lpSolve, CPLEX and CbC

Changed API: introduced separate functions for different flavours of CARNIVAL.
A more convenient way to work with CARNIVAL parameters. Parameters setup is possible through jsons and function calls.
Better file naming to prevent concurrent file writing when running several instances of CARNIVAL.
An easy way to add more solvers.
A possibility to tune CARNIVAL setups for cplex: manual addition of parameters is possible through jsons.
General improvements and refactoring of the code, removed multiple duplications.
Removed multiple experimental conditions in a matrix form (was not used).
Inputs are transformed to vectors (except prior knowledge network).
MetaInfo is saved: runId, parsed data (internal data representation), start time, CARNIVAL flavour.
Reading from preparsed data and/or lp file is possible.

saezlab/CARNIVAL documentation built on Jan. 17, 2024, 5:10 p.m.

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