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Activity for Kyle Medley

  • Kyle Medley Kyle Medley committed [r105]

    disable swigdoc

  • Kyle Medley Kyle Medley committed [r104]

    use namespaces for libsbml and libsedml

  • 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

  • Kyle Medley Kyle Medley committed [r3700]

    pass second string arg to new module

  • Kyle Medley Kyle Medley committed [r3679]

    revert test-breaking changes

  • Kyle Medley Kyle Medley committed [r3672]

    sync api ver to 2.10.0

  • Kyle Medley Kyle Medley committed [r103]

    bump ver to 1.0.10

  • 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

  • Kyle Medley Kyle Medley committed [r3654]

    update test data to use names and metaids where applicable to pass tests

  • Kyle Medley Kyle Medley committed [r3653]

    update basic test data to expect meta ids; update basic test data to not expect implicit sbml model display name

  • Kyle Medley Kyle Medley committed [r3652]

    remove inline module display name rule; update basic test data to expect meta ids; update basic test data to not expect implicit sbml model display name

  • Kyle Medley Kyle Medley committed [r3651]

    move copy ctor to .cpp

  • Kyle Medley Kyle Medley committed [r3650]

    variable: manually add copy ctor, don't copy m_sboTermWrapper

  • Kyle Medley Kyle Medley committed [r3649]

    allow naming module in declaration; fix some s/r conflicts by specially parsing reaction dividers; always set meta ids for elements

  • Kyle Medley Kyle Medley committed [r3648]

    add syntax for setting display id of modules and functions

  • Kyle Medley Kyle Medley committed [r3647]

    add optional enableAnnotations parameter to functions which return antimony strings

  • Kyle Medley Kyle Medley committed [r3645]

    parse module sboTerm assignments inside module body

  • Kyle Medley Kyle Medley committed [r3644]

    allow parsing top-level sbo terms for modules

  • Kyle Medley Kyle Medley committed [r3643]

    parse and write SBO terms; subclass Variable to provide a proxy object for using SBO terms with dot syntax

  • Kyle Medley Kyle Medley committed [r3642]

    add functions to write out cv terms in Antimony syntax when converting SBML -> Antimony

  • Kyle Medley Kyle Medley committed [r3641]

    Update test suite to fix most failing tests (only 3 are still failing).

  • Kyle Medley Kyle Medley committed [r3640]

    add initial grammar for cv terms; expand Annotation base class to store list of cv terms

  • Kyle Medley Kyle Medley committed [r3639]

    branch for miriam annotations

  • Kyle Medley Kyle Medley committed [r102]

    Squashed commit of the following:

  • Kyle Medley Kyle Medley committed [r101]

    Squashed commit of the following:

  • Kyle Medley Kyle Medley committed [r100]

    Squashed commit of the following:

  • Kyle Medley Kyle Medley committed [r99]

    Squashed commit of the following:

  • Kyle Medley Kyle Medley posted a comment on ticket #46

    The SBO term was added by Tellurium, can be deleted

  • Kyle Medley Kyle Medley created ticket #46

    Antimony Round-tripping Bug

  • Kyle Medley Kyle Medley posted a comment on ticket #24

    I just made a commit to this repo that should fix this. The fix is available in PhraSEDML 1.0.8, just uploaded to PyPI for win/mac/lin 64-bit.

  • Kyle Medley Kyle Medley committed [r98]

    bump ver to 1.0.8

  • Kyle Medley Kyle Medley committed [r97]

    fix https://sourceforge.net/p/phrasedml/tickets/24/

  • Kyle Medley Kyle Medley committed [r96]

    lsoda is 88

  • Kyle Medley Kyle Medley committed [r95]

    bump ver to 1.0.7

  • Kyle Medley Kyle Medley committed [r94]

    add initialConcentration selector

  • Kyle Medley Kyle Medley committed [r93]

    add lsoda phrasedml name

  • Kyle Medley Kyle Medley committed [r92]

    add lsoda to phrasedml algo names

  • Kyle Medley Kyle Medley committed [r3637]

    fix .gitignore

  • Kyle Medley Kyle Medley committed [r3636]

    bump ver to 2.9.4

  • Kyle Medley Kyle Medley committed [r3635]

    add .gitignore

  • Kyle Medley Kyle Medley committed [r91]

    add else block

  • Kyle Medley Kyle Medley committed [r90]

    fix xml extension not being applied in some cases

  • Kyle Medley Kyle Medley committed [r89]

    fix for jws quirks

  • Kyle Medley Kyle Medley committed [r3634]

    bump ver to 2.9.3

  • Kyle Medley Kyle Medley committed [r3633]

    change back to l3v1 as workaround for https://www.pivotaltracker.com/story/show/146893141

  • Kyle Medley Kyle Medley committed [r88]

    bump ver to 1.0.6

  • Kyle Medley Kyle Medley committed [r87]

    Add functional range support for pulse experiment

  • Kyle Medley Kyle Medley committed [r86]

    add .gitignore

  • Kyle Medley Kyle Medley committed [r3632]

    bump ver to 2.9.2

  • Kyle Medley Kyle Medley committed [r3628]

    install runtime libs on windows

  • Kyle Medley Kyle Medley posted a comment on ticket #21

    I fixed this in phrasedml 1.0.5 via a string substitution hack. There doesn't seem...

  • Kyle Medley Kyle Medley committed [r85]

    add hack to fix min/max symbol encodings. see h...

  • Kyle Medley Kyle Medley committed [r84]

    bump ver to 1.0.5

  • Kyle Medley Kyle Medley committed [r83]

    allow making model changes via xpath

  • Kyle Medley Kyle Medley posted a comment on ticket #21

    Matthias, are you able to read SED-ML with the special csymbol definitions using...

  • 0u812 0u812 committed [r82]

    fix version

  • 0u812 0u812 committed [r81]

    add linux/osx shared libs to python package

  • 0u812 0u812 committed [r80]

    remove v from __version__ and add myself to aut...

  • 0u812 0u812 committed [r79]

    bump version to 1.0.4

  • 0u812 0u812 committed [r3627]

    apparently there are multiple places the versio...

  • 0u812 0u812 committed [r3626]

    antimony.__version__ should not contain 'v'; bu...

  • 0u812 0u812 posted a comment on ticket #430

    Thanks for your reply, Frank. The "undefined dynamic lookup" option does not exist...

  • 0u812 0u812 created ticket #430

    PYTHON_USE_DYNAMIC_LOOKUP not working on Linux

  • 0u812 0u812 committed [r78]

    use relative imports (should work for py2/3)

  • 0u812 0u812 committed [r77]

    use correct flags for linux

  • 0u812 0u812 committed [r76]

    dyn binding on osx/linux

  • 0u812 0u812 committed [r75]

    add my name to authors since I am creating the ...

  • 0u812 0u812 committed [r3623]

    resolve isnan

  • 0u812 0u812 committed [r3622]

    specify full (relative) path so import works ac...

  • 0u812 0u812 committed [r3621]

    do not link to python lib on non-windows platforms

  • 0u812 0u812 committed [r3620]

    include versioned .so files in python package

  • 0u812 0u812 committed [r3619]

    include .dylibs and .so files in python package

  • 0u812 0u812 created ticket #6

    Include the word "experimental" in the name of the experimental source archive

  • 0u812 0u812 created ticket #23

    Get rid of .pth file

  • 0u812 0u812 committed [r72]

    add conda files

  • 0u812 0u812 posted a comment on ticket #19

    Thanks! Tested on Mac and works.

  • 0u812 0u812 created ticket #19

    Undefined functions break Python API

  • 0u812 0u812 committed [r69]

    comment undefined function setPhrasedWriteSBMLT...

  • 0u812 0u812 committed [r59]

    fix late bindings on Mac

  • 0u812 0u812 committed [r52]

    make swig output dependency of command to copy ...

  • 0u812 0u812 committed [r3612]

    Make antimony_wrap.cpp a dependency of custom c...

  • 0u812 0u812 committed [r3611]

    Add missing install target for binding_python_l...

  • 0u812 0u812 committed [r3610]

    Need to specify setuptools in meta.yaml

  • 0u812 0u812 committed [r3609]

    Add WITH_CONDA_BUILDER CMake option

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