Merge version 3.2 - #176
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Update the Escher style, with help from libsbmlnetwork.
Need to change antimony_api.h to antimony_api.h.in so that CMake can put in the current version into a string.
Also, get the latest dependencies, to get the latest VS version for Windows.
We don't need the generated .h file; the .h.in file is fine. We're parsing it ourselves, and don't care about the @name@ bits.
The layout test had a premature ';': removed it, changed the values, and tested against the new values.
Add a 'getVersionStr' function to the API.
NSBML was removed from the antimony source yonks ago; this cleans it out of auxiliary files.
Required for the latest google test, but probably a good idea in general.
Also compile that with debug info, so any error message will be at least somewhat informative. Also allow manual running of valgrind on the debug branch when we need more diagnostic information.
Also upload all of them as an artifact, and split into groups of 20 so we see them before waiting the entire time.
We were inconsistently deleting a passed-around vector<string>* object from antimony.ypp. Now we pass it as a const reference instead, and delete it inside antimony.ypp directly, instead of inside the functions it passed to. Also actually delete the removed rateOf function definition when it was found in the SBML model.
Fixed dependency leaks in libsbml (and a now-unused fix in libsbmlnetwork). Also only upload memory test results, not all of them, and give them unique names.
Add CI that runs things through valgrind.
Test roundtrip test suite v2
added build from source instructions to the README.md
Had to update maddy to use standard table formats instead of its own bespoke version.
We only need to make sure they're unique IDs when we translate to (and from) SBML.
Implement support for stoichiometries with the same name.
Pull from develop
Re-activate the Inno installer of QTAntimony on windows.
Noticed there was text in the docs about how well Antimony supported round-tripped SBML models. Need to regularly test this.
* Allow negative values when setting species amount/concentration a la '-3/C' or '-3*C' * Don't remove SBO-410 flagged compartments that aren't default and antimony-named.
Also, call four biomodels models 'fragile', and not reproducible on a roundtrip.
Also, add a warning when this happens.
Also roundtrip biomodels through Antimony.
Also the antimony installer, which now needs to install different example files.
Update docs.
added runtime evaluation
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Merge everything from version 3.2