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For reference, just in case someone finds this issue in the future: FBC package issues can now be found at https://github.com/sbmlteam/sbml-specifications/labels/L3%20Package%3A%20fbc
DO NOT POST NEW ISSUES HERE
Add NSF/Google/Volkswagen to Acknowledgements of Funding
Moved to https://github.com/sbmlteam/sbml-org-website/issues/42
Multiple entries for SBSCL within the Simulation Database
Moved to https://github.com/sbmlteam/sbml-org-website/issues/41
DO NOT POST NEW ISSUES HERE
DO NOT POST NEW ISSUES HERE
DO NOT POST NEW ISSUES HERE
SBML validator registration for API key not working
I think this has been addressed? If not, please file a new issue at https://github.com/sbmlteam/libsbml/issues/
libsbml doesn't work with vckpg libraries
Moved to https://github.com/sbmlteam/libsbml/issues/245
Issue with installation of R interface of libSBML 5.18.0
This has been addressed. Note that any new tickets should be posted to the new github site, at https://github.com/sbmlteam/libsbml/issues
DO NOT POST NEW ISSUES HERE
FBC V2 typos section 2
Moved to https://github.com/sbmlteam/sbml-specifications/issues/289
wrong namespace used for the protein modification ontology
Moved to https://github.com/sbmlteam/sbml-specifications/issues/291
MathML package: Allow n-ary function definitions?
Moved to https://github.com/sbmlteam/sbml-specifications/issues/292
Layout: no validation rule for must-be-positive attributes
Moved to https://github.com/sbmlteam/sbml-specifications/issues/331
Render: UML diagram for GraphicalPrimitive2D class incorrect
Moved to https://github.com/sbmlteam/sbml-specifications/issues/348
Render: Style is abstract base class: should be italicized in UML
Moved to https://github.com/sbmlteam/sbml-specifications/issues/349
Render: Figure 2 doesn't say versionMajor and versionMinor are optional
Moved to https://github.com/sbmlteam/sbml-specifications/issues/350
Layout: Figure 5 has a 'ListOfLineSegments' class, which should be 'ListOfCurveSegments'.
Moved to https://github.com/sbmlteam/sbml-specifications/issues/352
Render: fix examples that switch namespaces.
Moved to https://github.com/sbmlteam/sbml-specifications/issues/353
Multi: Syntax errors in the examples
Moved to https://github.com/sbmlteam/sbml-specifications/issues/357
Allow l3v1 packages in l3v2 documents to inherit 'id' and 'name'?
Moved to https://github.com/sbmlteam/sbml-specifications/issues/358
spatial spec example problematic
Moved to https://github.com/sbmlteam/sbml-specifications/issues/362
Possible typo in the value of the "persistent" attribute
Moved to https://github.com/sbmlteam/sbml-specifications/issues/363
Suggested change to SBML multi-compartment model example
Moved to https://github.com/sbmlteam/sbml-specifications/issues/364
Moved to https://github.com/sbmlteam/sbml-specifications/issues/365
Update identifiers.org URLs
qual: Input Species not in FunctionTerm
Moved to https://github.com/sbmlteam/sbml-specifications/issues/366
SBML L3V2 units UML is incorrect (arrow direction)
Moved to https://github.com/sbmlteam/sbml-specifications/issues/367
Extensive/Intensive reversed
Moved to https://github.com/sbmlteam/sbml-specifications/issues/368
Remove everything and point to new locations on github.
Remove everything and point to new locations on github.
Remove everything and point to new locations on github.
Remove everything and point to new locations on github.
Remove everything and leave a note pointing people to the new source repository.
'mi' and 'mim' annotations not converted
Change non-ASCII character to double dash.
Extensive/Intensive reversed
Clarify use of bvar in lambda element of FunctionDefinition
Released.
Be explicit about rateOf at times < 0
Released.
l3v1r2 mentions 'rateOf' in validation rule 10205
Released.
Min and max are not generally discouraged, only no-argument
Released.
Update unit validation rules for compartments
Released.
Mention metaid syntax is from XML spec 1.0, not 1.1
Released.
Update URLs to use https if possible
Released.
Clarify attribute namespace rules for packages
Released!
Add new SBML Editors to latest spec
Released!
Update mathml-related validation rules to reflect the ability of packages to override them.
Released!
"Species with negative or zero values" section not red; has stray paragraph
Fixed in latest release.
I found the problem and have submitted a fix. The situation you describe was indeed anticipated in the code, but it clearly was never tested: it checked whether the root ASTNode had the id of the element to be converted... but ASTNodes use 'name' instead. Sorry about that! https://github.com/sbmlteam/libsbml/pull/47
Comp flattening drops conversion_factors for assignment rules of the form "p1 = p2"
Move source repository to https://github.com/sys-bio/antimony/
Move to github
Disallow non-ASCII characters when otherwise not a part of a string or anything else.
Update python setup so that the wheel file it creates will be platform-specific.
Update local python installation rules so that it will create explicit 'wheel' files.
Change installation defaults: turn on libsbml compression, since that's on by default in libsbml, and do the local Python install instead of the global one by default.
Fix warnings from mac build, most of which involved the fact that 'varConstraint' wasn't in a bunch of 'switch' statements. This actually fixed a bug that I hadn't realized was there, when flattening models with constraints.
Updates to make antimony compile and install on unix.
Can't use '_strdup' on linux/gcc.
Update python binding and CMake system.
Run the example files through the new validator and fix the results:
Add API test.
Install libantimony file with python bindings.
Create new Antimony python bindings based on ctypes instead of swig. Remove the old python stuff.
Various fixes: