Activity for CBMPy
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Brett Olivier committed [r715]
resynch to git move
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moving to git primary
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continuing update to swiglpk
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started rewrite of GLPK to take advantage of swiglpk
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added new CBSolve module
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line-ends and format fixes
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synched to new git repo structure
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cleanup src
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cleanup src
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continue implementing group pointers
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CBMPy released /release/0.7/cbmpy-0.7.25-py3-none-any.whl
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hacked some form of serialization support into new group structure that allows models to be serialized
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first attempt at switching groups over to use weakrefs rather than references
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cloneing and serialization of FluxBound classes using weakrefs for _parent links and also "new style" extended reactions now implemented.
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trimmed oldsolver
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tweaked new FluxBound
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improved ReactionNew class and FluxBoundBase integration
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version bump
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added new reaction class that has integrated fluxbounds
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Refactered FluxBoundBase and crreated tow subclasses FluxBoundLower and FluxBoundUpper
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Adding new FluxBound class
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tweaked docstring
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extended docstring
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fixed docstring
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refactored addFluxBound 2X speedup using fbexists
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added deleteCompartment function to Model
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version bump
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fixed bugs in internal __deleteGeneFromTree__ and added __pruneTree__ functionality to GPR
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version update in setup
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updated version
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standardised use of setId across all model componenents
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update model component constructors to check for a valid id
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fixed setId function to deal with setting existing id
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added getFluxesAssociatedWithCompartments function
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py2 vs 3 again
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added support for runtime model extension
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first attempt at a model extension mechanism
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added getXObjects to Model, removed boundary option from getSpecies and fixed bug in getGeneLabels substring search
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put in place a workaround for the P3 utf-8 issue
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resolving conflicts
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resolving conflicts
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fixed new changes for Py27
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fixed bug where notes were not being added to reactions and rewrote note getters ands setters
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Added getGPRassociationString to reaction
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updated setup with new default model layout
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removed unit tests from source
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removed tests from source and refactored default models into CBDefaultModels.py
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removed test module installation
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Added automatic network update on if change in gene activity detected
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Fixed some Python3 compatibility issues
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fixed potential operator isssue in user constraints
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refactor docs
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updates to test code
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testing new test code
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fixed gpr import issue with fbcv1 files
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updated year
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version bump
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version bump
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added automatic file validation
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fixed idless model error
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Added mergeGroups function
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took out unnecessary debug lp writer
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tweaked cplex return status reporting
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allow SBML export of models with incomplete GPR's
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allow SBML export of models with incomplete GPR's
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tweaked error message in setId
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added getGPRIds() to model, new __checkId__() code optimized, all setId() methods now check for Id validity and raise a RuntimeWarning if not.
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added user friendly loadModel() and saveModel() methods.
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fix strange p3 behaviour
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fixed for solver refactor
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fixed W.G. corner case with GLPK
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made the setChemFormula more intuitive
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added protection from invalid empty GPR elements
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Starting refactoring of solver modules
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tweaked userconstraint importUserConstraints
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added user constraint input/output and unit tests, including generic write tests
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added user constraint import/export
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sync
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version set
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setId does nothing if the old and new id are the same
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updated buggy BiGG model without objective function
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new version tag
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tweaks for build system
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0.7.19b
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0.7.19
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fixed GPRfromString bug
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updated Python 3 compatibility
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