cleanup
Update to release 1.01
updated readme
Updated to release 1.01
Seconded. Jannie Hofmeyr also noted this and suggested the change in a personal communication.
resynch to git move
moving to git primary
continuing update to swiglpk
started rewrite of GLPK to take advantage of swiglpk
new conda files
version bump to dev 0.9.9
release 0.9.8
cleanup
0.9.8 release
pysces 0.9.8 release
updated FBC proposal text
added new CBSolve module
line-ends and format fixes
synched to new git repo structure
cleanup src
cleanup src
update svn to 2020 codebase
Suggested change to SBML multi-compartment model example
continue implementing group pointers
hacked some form of serialization support into new group structure that allows models to be serialized
first attempt at switching groups over to use weakrefs rather than references
cloneing and serialization of FluxBound classes using weakrefs for _parent links and also "new style" extended reactions now implemented.
trimmed oldsolver
tweaked new FluxBound
improved ReactionNew class and FluxBoundBase integration
version bump
added new reaction class that has integrated fluxbounds
Refactered FluxBoundBase and crreated tow subclasses FluxBoundLower and FluxBoundUpper
Adding new FluxBound class
tweaked docstring
extended docstring
fixed docstring
refactored addFluxBound 2X speedup using fbexists
added deleteCompartment function to Model
version bump
fixed bugs in internal __deleteGeneFromTree__ and added __pruneTree__ functionality to GPR
version update in setup
updated version
standardised use of setId across all model componenents
update model component constructors to check for a valid id
fixed setId function to deal with setting existing id
added getFluxesAssociatedWithCompartments function
py2 vs 3 again
added support for runtime model extension
first attempt at a model extension mechanism
updated correct fallback directory listings
fixed minor issues related to merging
added custom information message
fixed mismatched closing arguments issue
added CMAKE based directory scanning for R source build
added CMAKE based directory scanning for Python source build
update package directories
added missing l3v2extendedmath directory
added getXObjects to Model, removed boundary option from getSpecies and fixed bug in getGeneLabels substring search
cmake tests if check compiles on linux, fixes #163641055
put in place a workaround for the P3 utf-8 issue
resolving conflicts
resolving conflicts
fixed new changes for Py27
fixed bug where notes were not being added to reactions and rewrote note getters ands setters
Added getGPRassociationString to reaction
updated setup with new default model layout
removed unit tests from source
removed tests from source and refactored default models into CBDefaultModels.py
removed test module installation
Updated v3 specification proposal document
Updated FBC v3 harmony proposal with new charge definition.
fixed typos in proposal example text
updated build-python for Python 3.7, vs14 and fixed build to add correct Python 2/3 wrapper to packages
Updated official build-python to include Python 3.7 and vs14 support line end
Updated official build-python to include Python 3.7 and vs14 support.
Removed "make install_with_setup Python 3 friendly" that was causing issues with cpack under certain conditions
Fixed syntax error in Python template file.
Slightly modified description of get/set/unset Python modification to include activation options.
fixed syntax in setup template
Added automatic network update on if change in gene activity detected
implemented a Python2/3 compatible fix for the autoproperty metaclass, removing deprecation warning in Python 3.6
changed keep-me-alive label to __parent_ref__
fixed cmake to create Python 3 aware wrappers when using INSTALL_IN_PREFIX or INSTALL_WITH_SETUP options
Fixed some Python3 compatibility issues
PythonAPI: prototype implementation of model to document reference based on FB suggestion.
Updated unittests to match new getCVTerms behaviour
PythonAPI getCVTerms returns an empty list instead of None when no terms.
Python warning framework to get/set/add methods.
New branch for python changes, replaces api2 branch
merged trunk to 25619
fixed potential operator isssue in user constraints
refactor docs
cleaned text in fbc proposal and addressed TP comments
fixed text issues and suggestions from TP
incorporated comments from TP into proposal
Added DistribASTPlugin definition for swig
updates to test code
testing new test code