Activity for Brett Olivier
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Brett Olivier committed [r1303]
cleanup
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Update to release 1.01
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updated readme
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Updated to release 1.01
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Seconded. Jannie Hofmeyr also noted this and suggested the change in a personal communication.
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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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new conda files
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version bump to dev 0.9.9
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release 0.9.8
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cleanup
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0.9.8 release
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pysces 0.9.8 release
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updated FBC proposal text
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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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update svn to 2020 codebase
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Suggested change to SBML multi-compartment model example
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continue implementing group pointers
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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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updated correct fallback directory listings
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fixed minor issues related to merging
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added custom information message
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fixed mismatched closing arguments issue
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added CMAKE based directory scanning for R source build
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added CMAKE based directory scanning for Python source build
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update package directories
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added missing l3v2extendedmath directory
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added getXObjects to Model, removed boundary option from getSpecies and fixed bug in getGeneLabels substring search
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cmake tests if check compiles on linux, fixes #163641055
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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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Updated v3 specification proposal document
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Updated FBC v3 harmony proposal with new charge definition.
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fixed typos in proposal example text
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updated build-python for Python 3.7, vs14 and fixed build to add correct Python 2/3 wrapper to packages
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Updated official build-python to include Python 3.7 and vs14 support line end
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Updated official build-python to include Python 3.7 and vs14 support.
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Removed "make install_with_setup Python 3 friendly" that was causing issues with cpack under certain conditions
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Fixed syntax error in Python template file.
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Slightly modified description of get/set/unset Python modification to include activation options.
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fixed syntax in setup template
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Added automatic network update on if change in gene activity detected
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implemented a Python2/3 compatible fix for the autoproperty metaclass, removing deprecation warning in Python 3.6
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changed keep-me-alive label to __parent_ref__
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fixed cmake to create Python 3 aware wrappers when using INSTALL_IN_PREFIX or INSTALL_WITH_SETUP options
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Fixed some Python3 compatibility issues
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PythonAPI: prototype implementation of model to document reference based on FB suggestion.
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Updated unittests to match new getCVTerms behaviour
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PythonAPI getCVTerms returns an empty list instead of None when no terms.
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Python warning framework to get/set/add methods.
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New branch for python changes, replaces api2 branch
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merged trunk to 25619
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fixed potential operator isssue in user constraints
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refactor docs
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cleaned text in fbc proposal and addressed TP comments
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fixed text issues and suggestions from TP
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incorporated comments from TP into proposal
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Added DistribASTPlugin definition for swig
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updates to test code
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testing new test code
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