Activity for Lucian Smith
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Lucian Smith posted a comment on ticket #130
Whoops, forgot to log in. That was me!
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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
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DO NOT POST NEW ISSUES HERE
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Add NSF/Google/Volkswagen to Acknowledgements of Funding
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Moved to https://github.com/sbmlteam/sbml-org-website/issues/42
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Multiple entries for SBSCL within the Simulation Database
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Moved to https://github.com/sbmlteam/sbml-org-website/issues/41
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DO NOT POST NEW ISSUES HERE
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DO NOT POST NEW ISSUES HERE
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DO NOT POST NEW ISSUES HERE
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SBML validator registration for API key not working
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I think this has been addressed? If not, please file a new issue at https://github.com/sbmlteam/libsbml/issues/
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libsbml doesn't work with vckpg libraries
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Moved to https://github.com/sbmlteam/libsbml/issues/245
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Issue with installation of R interface of libSBML 5.18.0
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This has been addressed. Note that any new tickets should be posted to the new github site, at https://github.com/sbmlteam/libsbml/issues
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DO NOT POST NEW ISSUES HERE
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FBC V2 typos section 2
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/289
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wrong namespace used for the protein modification ontology
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/291
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MathML package: Allow n-ary function definitions?
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/292
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Layout: no validation rule for must-be-positive attributes
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/331
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Render: UML diagram for GraphicalPrimitive2D class incorrect
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/348
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Render: Style is abstract base class: should be italicized in UML
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/349
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Render: Figure 2 doesn't say versionMajor and versionMinor are optional
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/350
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Layout: Figure 5 has a 'ListOfLineSegments' class, which should be 'ListOfCurveSegments'.
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/352
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Render: fix examples that switch namespaces.
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/353
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Multi: Syntax errors in the examples
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/357
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Allow l3v1 packages in l3v2 documents to inherit 'id' and 'name'?
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/358
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spatial spec example problematic
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/362
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Possible typo in the value of the "persistent" attribute
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/363
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Suggested change to SBML multi-compartment model example
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/364
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/365
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Update identifiers.org URLs
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qual: Input Species not in FunctionTerm
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/366
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SBML L3V2 units UML is incorrect (arrow direction)
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/367
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Extensive/Intensive reversed
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Moved to https://github.com/sbmlteam/sbml-specifications/issues/368
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Remove everything and point to new locations on github.
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Remove everything and point to new locations on github.
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Remove everything and point to new locations on github.
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Remove everything and point to new locations on github.
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Remove everything and leave a note pointing people to the new source repository.
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'mi' and 'mim' annotations not converted
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Change non-ASCII character to double dash.
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Extensive/Intensive reversed
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Clarify use of bvar in lambda element of FunctionDefinition
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Released.
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Be explicit about rateOf at times < 0
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Released.
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l3v1r2 mentions 'rateOf' in validation rule 10205
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Released.
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Min and max are not generally discouraged, only no-argument
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Released.
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Update unit validation rules for compartments
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Released.
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Mention metaid syntax is from XML spec 1.0, not 1.1
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Released.
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Update URLs to use https if possible
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Released.
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Clarify attribute namespace rules for packages
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Released!
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Add new SBML Editors to latest spec
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Released!
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Update mathml-related validation rules to reflect the ability of packages to override them.
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Released!
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"Species with negative or zero values" section not red; has stray paragraph
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Fixed in latest release.
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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
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Comp flattening drops conversion_factors for assignment rules of the form "p1 = p2"
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Move source repository to https://github.com/sys-bio/antimony/
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Move to github
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Disallow non-ASCII characters when otherwise not a part of a string or anything else.
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Update python setup so that the wheel file it creates will be platform-specific.
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Update local python installation rules so that it will create explicit 'wheel' files.
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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.
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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.
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Updates to make antimony compile and install on unix.
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Can't use '_strdup' on linux/gcc.
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Update python binding and CMake system.
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Run the example files through the new validator and fix the results:
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Add API test.
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Install libantimony file with python bindings.
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Create new Antimony python bindings based on ctypes instead of swig. Remove the old python stuff.
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Various fixes:
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