Lucian Smith

Runs are getting stuck in the 'processing' phase, e.g. https://run.biosimulations.org/runs/66f1d31f1f1841b171a16e54 which has been running for about 22 hours as of right now with no updates. The site itself should probably...

Uninitialized jump in render's Transformation2D::readAttributes

1

Running stuff through valgrind, I came across the error: ``` ==4973== Conditional jump or move depends on uninitialised value(s) ==4973== at 0xD75631: libsbml::Transformation2D::readAttributes(libsbml::XMLAttributes const&, libsbml::ExpectedAttributes const&) (Transformation2D.cpp:725) ==4973== by 0xD2454F:...

First pass at a fix for #398, which resulted from inappropriately casting an element. Not sure I got all the use cases, but I might have?

The sublist wasn't being deleted, and its contents weren't being transferred.

Fix namespaces in SED-ML output

1

The auto-generated SED-ML that we produce to go with the test suite is invalid: it does not include the SBML core (nor, in some cases, the FBC package) namespaces. The...

For some reason, Windows WSL/Ubuntu didn't work with the older method (which I believe is now deprecated); use the newer 'CMAKE_C_BYTE_ORDER' instead.

Missing child ListOfCurveSegments for RenderCurve

1

In the render spec, fig 11, a 'RenderCurve' object may have a child ListOfCurveSegments. This is, as far as I can tell, not implemented in libsbml at all.

Error messages not complete in 'save as' window.

7

We have an ontology we usually work with in OWL format, but sometimes export to OBO. OBO is more restrictive, so errors can creep in. When you load the OWL...

Another difference in this picture is that the labels in VCell are the IDs of the curves, instead of the names: From the SED-ML: ```xml ```

Use the 'logX' and 'logY' attributes when appropriate: From: ```xml ``` [BIOMD0000000751.omex.zip](https://github.com/user-attachments/files/21845256/BIOMD0000000751.omex.zip)