Activity for Antimony

  • Lucian Smith Lucian Smith committed [r3751]

    Move source repository to https://github.com/sys-bio/antimony/

  • Lucian Smith Lucian Smith committed [r3750]

    Disallow non-ASCII characters when otherwise not a part of a string or anything else.

  • Lucian Smith Lucian Smith committed [r3749]

    Update local python installation rules so that it will create explicit 'wheel' files.

  • Lucian Smith Lucian Smith committed [r3748]

    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.

  • Lucian Smith Lucian Smith committed [r3747]

    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.

  • Lucian Smith Lucian Smith committed [r3746]

    Updates to make antimony compile and install on unix.

  • Lucian Smith Lucian Smith committed [r3745]

    Can't use '_strdup' on linux/gcc.

  • Lucian Smith Lucian Smith committed [r3744]

    Update python binding and CMake system.

  • Lucian Smith Lucian Smith committed [r3743]

    Add API test.

  • Lucian Smith Lucian Smith committed [r3742]

    Install libantimony file with python bindings.

  • Lucian Smith Lucian Smith committed [r3741]

    Create new Antimony python bindings based on ctypes instead of swig. Remove the old python stuff.

  • Lucian Smith Lucian Smith committed [r3740]

    Various fixes:

  • Lucian Smith Lucian Smith committed [r3739]

    Update installer files.

  • Lucian Smith Lucian Smith committed [r3738]

    Remove warnings, and fix one warning that was actually a bug.

  • Lucian Smith Lucian Smith committed [r3737]

    Various fixes:

  • Lucian Smith Lucian Smith posted a comment on ticket #50

    Solved via https://stackoverflow.com/questions/39689162/qt-project-in-visual-studio-2015-unresolved-external-symbol-wwinmain and https://stackoverflow.com/questions/18067870/what-option-do-i-set-to-use-main-instead-of-wmain namely: add 'mainCRTStartup' to Visual Studio/QTAntimony/Properties/Linker/Advanced/Entry point Still need to figure out how to do this in CMake, so others don't run into the issue.

  • Lucian Smith Lucian Smith created ticket #50

    QTAntimony won't compile in Release mode

  • Lucian Smith Lucian Smith committed [r3736]

    Remove Boolean errors from setLevelAndVersion, since we already were removing them from the base version.

  • Lucian Smith Lucian Smith committed [r3735]

    Update to allow compilation on latest experimental release of libsbml, instead of latest SVN only.

  • Lucian Smith Lucian Smith committed [r3734]

    Fix warnings.

  • Lucian Smith Lucian Smith committed [r3733]

    Update to v2.12; update documentation.

  • Lucian Smith Lucian Smith committed [r3732]

    More memory leak fixes (for error conditions).

  • Lucian Smith Lucian Smith committed [r3731]

    Fix memory leak, plus mismatched free/delete.

  • Lucian Smith Lucian Smith committed [r3730]

    Fix wrong way to get the module name.

  • Lucian Smith Lucian Smith committed [r3729]

    Change includes to be correct format with correct slash for unix.

  • Lucian Smith Lucian Smith committed [r3728]

    Initialize member variables that need values.

  • Lucian Smith Lucian Smith committed [r3727]

    Add the ability to read/write 'distrib' style annotations (mean, stdev, etc.) Many tests added as well. Removed ability to define units in curly brackets, since that interfered with libsbml's vector reading for arrays, but I don't think anyone was using it, anyway.

  • Lucian Smith Lucian Smith committed [r3726]

    Add test for unary negative of parentheticals, which had been broken.

  • Lucian Smith Lucian Smith committed [r3725]

    Antimony now saves function names, so they're preserved across the translations.

  • Kyle Medley Kyle Medley committed [r3724]

    removed BECOMESMOD token, which prevented parsing of unary negation + parentheses; -( reaction divider can still be parsed as separate tokens

  • Lucian Smith Lucian Smith committed [r3723]

    Clean up parsing of module/function names, and make function names actually work.

  • Lucian Smith Lucian Smith committed [r3722]

    Error out if functionname.something = 3 is used, if 'something' isn't 'sboTerm'.

  • Lucian Smith Lucian Smith committed [r3721]

    Error out if modulename.something = 3 is used, if 'something' isn't 'sboTerm'.

  • Lucian Smith Lucian Smith committed [r3720]

    Adjust error messages; update tests.

  • Lucian Smith Lucian Smith committed [r3719]

    * Check the type of reactants as we add them.

  • Lucian Smith Lucian Smith committed [r3718]

    Disallow synchronizing an SBO term with something.

  • Lucian Smith Lucian Smith committed [r3717]

    * Add restriction that variables without mathematical meaning cannot be used in equations.

  • Lucian Smith Lucian Smith committed [r3716]

    More memory leak fixes on erroring.

  • Lucian Smith Lucian Smith committed [r3715]

    If a submodel has both an sbo term and a variable named 'sboTerm', try other names to set the term.

  • Lucian Smith Lucian Smith committed [r3714]

    Fix memory leaks for errors.

  • Lucian Smith Lucian Smith committed [r3713]

    Add missing files.

  • Lucian Smith Lucian Smith committed [r3712]

    A model's sbo term may fall after 'end', so replace that, too.

  • Lucian Smith Lucian Smith committed [r3711]

    Add new files.

  • Lucian Smith Lucian Smith committed [r3710]

    Revert this--broke tests.

  • Lucian Smith Lucian Smith committed [r3709]

    * Consolidate getting/setting annotation information.

  • Lucian Smith Lucian Smith committed [r3708]

    Add reaction/SBO test.

  • Lucian Smith Lucian Smith committed [r3707]

    Add function/sbo test.

  • Lucian Smith Lucian Smith committed [r3706]

    Various fixes for setting SBO terms, plus added tests for everything:

  • Lucian Smith Lucian Smith committed [r3705]

    Fix some issues with setting the SBO term, including making it caseless (when it's clearly not anything else), and moving the sboTermWrapper class to its own files.

  • Lucian Smith Lucian Smith committed [r3704]

    Fix naming modules so it actually works. Add tests for this and for incorrect CV terms.

  • Lucian Smith Lucian Smith committed [r3703]

    Update version number for tests.

  • Lucian Smith Lucian Smith committed [r3702]

    Revert commenting the tests.

  • Lucian Smith Lucian Smith committed [r3701]

    Add tests for Kyle's new CV Terms syntax.

  • Matthias König Matthias König created ticket #49

    Support for python 3.7 (pip packages)

  • Kyle Medley Kyle Medley committed [r3700]

    pass second string arg to new module

  • Lucian Smith Lucian Smith committed [r3699]

    Bump version number to 2.11.0

  • Lucian Smith Lucian Smith committed [r3698]

    Remove some shift/reduce conflicts by centralizing inequalities to be similar to mathThings, and pushing some parsing to the lexer.

  • Lucian Smith Lucian Smith committed [r3697]

    Change parsing so that right-side-only reactions work! Add tests for it and everything.

  • Lucian Smith Lucian Smith committed [r3696]

    Protect against future oddnesses with metaid differences; make test more similar across types.

  • Lucian Smith Lucian Smith committed [r3695]

    More leaks fixes in tests.

  • Lucian Smith Lucian Smith committed [r3694]

    More leaks fixes in tests.

  • Lucian Smith Lucian Smith committed [r3693]

    More leaks fixes in tests.

  • Lucian Smith Lucian Smith committed [r3692]

    More leaks fixes in tests.

  • Lucian Smith Lucian Smith committed [r3691]

    More leaks fixes in tests.

  • Lucian Smith Lucian Smith committed [r3690]

    * Fix more leaks, UnitDef's in particular. Cleaner architecture where there used to be leaks.

  • Lucian Smith Lucian Smith committed [r3689]

    Fix leaks in test code.

  • Lucian Smith Lucian Smith committed [r3688]

    Add required includes.

  • Lucian Smith Lucian Smith committed [r3687]

    Pull in libsbml's new 'WITH_CHECK' system for linux, so the right libraries are included.

  • Lucian Smith Lucian Smith committed [r3686]

    Fix memory leak of ASTNode.

  • Lucian Smith Lucian Smith committed [r3685]

    Update libcheck bit of CMakeLists to match libsbml. Still doesn't solve the linking issue, but hey.

  • Lucian Smith Lucian Smith committed [r3684]

    Memory leak plugging: delete the SBML document after we're done with it.

  • Lucian Smith Lucian Smith committed [r3683]

    Fix memory leak when updating the level/version of an SBML model.

  • Lucian Smith Lucian Smith committed [r3682]

    Fix for unix compiler, so we don't take address of temp variable.

  • Lucian Smith Lucian Smith committed [r3681]

    Change how default units are stored so they don't leak like a sieve.

  • Lucian Smith Lucian Smith committed [r3680]

    Fix module copy constructors so they copy the new 'm_displayname' member variable. Fix tests so they match.

  • Kyle Medley Kyle Medley committed [r3679]

    revert test-breaking changes

  • Lucian Smith Lucian Smith committed [r3678]

    Fix memory leak: delete SBML document after reading it.

  • Lucian Smith Lucian Smith committed [r3677]

    Fix memory leak of ASTNodes.

  • Lucian Smith Lucian Smith committed [r3676]

    Fix memory leak of converter.

  • Lucian Smith Lucian Smith committed [r3675]

    Fix memory leaks of 'AllElements' lists.

  • Lucian Smith Lucian Smith committed [r3674]

    Fix memory leak when we get an error string.

  • Lucian Smith Lucian Smith committed [r3673]

    Fix memory leak when we get an error string.

  • Kyle Medley Kyle Medley committed [r3672]

    sync api ver to 2.10.0

  • Kyle Medley Kyle Medley committed [r3671]

    pass display name to module ctor

  • Kyle Medley Kyle Medley committed [r3670]

    clean up

  • Kyle Medley Kyle Medley committed [r3669]

    use comma separators for rdf resources

  • Kyle Medley Kyle Medley committed [r3668]

    fix object parsing

  • Kyle Medley Kyle Medley committed [r3667]

    use new-style annot parser to add cv terms

  • Kyle Medley Kyle Medley committed [r3666]

    fix eof return

  • Kyle Medley Kyle Medley committed [r3665]

    add first impl of composite annot parser, will clean up (21 errors in tests)

  • Kyle Medley Kyle Medley committed [r3664]

    merge cv term work; all tests passing

  • Kyle Medley Kyle Medley committed [r3663]

    add metaids to distrib test files

  • Kyle Medley Kyle Medley committed [r3662]

    perform metaid-less comparisons in tests

  • Kyle Medley Kyle Medley committed [r3661]

    add names to sbml tests

  • Kyle Medley Kyle Medley committed [r3660]

    don't add built-in units to flattening

  • Kyle Medley Kyle Medley committed [r3659]

    add name attr to fixname_test

  • Kyle Medley Kyle Medley committed [r3658]

    elide metaids from comparison of flattened model

  • Kyle Medley Kyle Medley committed [r3657]

    update expected syntax error

  • Kyle Medley Kyle Medley committed [r3656]

    add git diff utility function

  • Kyle Medley Kyle Medley committed [r3655]

    add elideMetaIds and elideMetaIdsFromSBMLstring SBML utility functions to allow testing for compliance sans metaids

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