ChangeLog

0.6.0

• refactoring of MIDAS/CNOGraph data structures.

0.5.3

• use unicode instead of str in cnograph module to prevent error when sppecial character are used as node name
• mapback: implementing the mapback function. Not yet working for the AND gates
• midas: set CellLine to undefined is not set. added normalise function
• normalisation: implementation of the time and control case

0.5.2

• cnograph: add remove_self_loops function ; remove_edge accept key argument (MultiGraph case); split and merge_nodes keep track of colors if any”
• CNOGraphMultiEdges can now plot edges in colors
• fix typo in cnogrpah.CNOGraph.plotdot when using a differnt viewver.
• populate node color when calling cnograph.CNOGraph.rename_node”
• XMIDAS implementation. Written from scratch to make use of Pandas dataframe. No need for makecnolist. the data is stored in a dataframe.
• CNOGraph uses XMIDAS
• CNOGraphMultiEdges seems to work
• Normalisation (on time zero) available for XMIDAS

revision 0.4.2

• fix tests
• add or move modules into ./io directory
• cnograph: fix split_node function for AND gates
• cnograph: prevent compression to compress nodes that would lead to multiedge ambiguity.
• cnograph: can accept as input a networkx graph or any instance that contains reacID attribute.
• cnograph: operator + keeps track of the _stimuli, _signals, _inhibitors attributes.
• nonc: module usees signals and stimuli parameters instead of cnolist
• move SIF files from ./test directory to share/directory and improved test suite
• sif: empty lines may now be present in the SIF. input can be any instance that contains a reacID attriute. ands convertion may now fail (if the input contains incorrect ANDs).

revision 0.4.1

• cnograph: fixed bug in compression to keep orphans if there are stimuli,inhibitors or signals. + Add properties to get stimuli, inhibitors, signals list

revision 0.4.0

• First release of pypi

revision 0.3.0

• cnograph stabalised
• normalisation class added
• tutorial done + documentation

revision 0.2.0

• cnograph and sif modules are still in progress but ready to use
• test coverage of 80%

revision 0.1.0

• add bunch of modules:

  • cnograph, cutnonc, compression

  • converter modules:

    • converter
    • sif2asp
    • adj2sif
    • sop2sif

  • readers:

    • metabolites
    • reactions
    • sif, midas, metabolites
    • kinexus

  • analysis