Merge branch 'gdevelop' into gfeature-llvm

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/feature-llvm@1085 c0027639-9190-0b57-01eb-f09a03790dae
cleaned up cmakefile

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/feature-llvm@1086 c0027639-9190-0b57-01eb-f09a03790dae
clean up LLVM CXX options

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/feature-llvm@1087 c0027639-9190-0b57-01eb-f09a03790dae
Merge branch 'gfeature-llvm' into gdevelop

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/develop@1088 c0027639-9190-0b57-01eb-f09a03790dae
Added 120 tests, mainly l3v1 ones, to reach a total of 1069 tests.
Still quite a few, above 980 that are failing..

Added getImplementationLanguage to plugin interface
Removed some obsolete files


git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/create_code_for_C_plugins@1089 c0027639-9190-0b57-01eb-f09a03790dae
Added getEigenvaluesVector to VS def file

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/create_code_for_C_plugins@1090 c0027639-9190-0b57-01eb-f09a03790dae
Merged revision(s) 1047-1090 from branches/create_code_for_C_plugins:
Branch to setup code to allow plugins written in C to be loaded by the plugin manager
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Merge branch 'gdevelop' into gfeature-llvm
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initial LLVM stubs
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Created RRComplexVector struct

Other utility additions
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Cleaned up rrc_api.cpp
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Ran the tests
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Working on getting a framework setup for roadrunner C plugins.
Created plugin descendants, CPP and C.

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Merge branch 'gfeature-llvm' of github.com:AndySomogyi/roadrunner into gfeature-llvm
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updated cmake build to optionally find llvm
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tell the ModelGeneeratorFactor if we have llvm
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tell the ModelGeneeratorFactor if we have llvm
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cleaned up LLVM build, fixed some bad const casts
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removed autogenerated file from source control
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improve LLVM finding
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Got C plugins going
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Ran the visual studio tests
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Cleaning up some docs
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Keep docs in the root of the repository
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Deleted some obsolete docs
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More cleaning
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fixed include capitalization and Linux linking without BUILT_TESTS
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fixed Linux linking issue
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merged llvm changes
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clean up cmake, make finding LLVM includes more reliable on different platforms
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Merge branch 'gfeature-llvm' into gdevelop
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Added 120 tests, mainly l3v1 ones, to reach a total of 1069 tests.
Still quite a few, above 980 that are failing..

Added getImplementationLanguage to plugin interface
Removed some obsolete files

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Added getEigenvaluesVector to VS def file
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git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/develop@1091 c0027639-9190-0b57-01eb-f09a03790dae
Ran the tests

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/develop@1092 c0027639-9190-0b57-01eb-f09a03790dae
Added c plugin demo files

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/create_code_for_C_plugins@1093 c0027639-9190-0b57-01eb-f09a03790dae
fixed switch fallthough global assignment bug

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/develop@1095 c0027639-9190-0b57-01eb-f09a03790dae
Merge branch 'gdevelop' into gfeature-llvm

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/feature-llvm@1096 c0027639-9190-0b57-01eb-f09a03790dae
documentation updtes
Merge documentation updates from feature-llvm

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/develop@1097 c0027639-9190-0b57-01eb-f09a03790dae
documentation updtes

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/feature-llvm@1098 c0027639-9190-0b57-01eb-f09a03790dae
added documentation, added const correctness and setup LibStruct so we don't have to re-parse sbml, fixed bug in currently unused code branch of lmcurve

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/develop@1103 c0027639-9190-0b57-01eb-f09a03790dae
merge changes from develop

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/feature-llvm@1104 c0027639-9190-0b57-01eb-f09a03790dae
The LLVM generator will have little shared internal functionality with the code generating ones, so moved all the string / symbol manipulation to CompiledModelGenerator

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/develop@1105 c0027639-9190-0b57-01eb-f09a03790dae
updtes

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/feature-llvm@1106 c0027639-9190-0b57-01eb-f09a03790dae
Merge branch 'gdevelop' into gfeature-llvm

git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/feature-llvm@1107 c0027639-9190-0b57-01eb-f09a03790dae
Refactoring:
loadSBMLE - > loadSBMLEx
RRInstanceListHandle -> RRInstanceListPtr
RRVectorHandle -> RRVectorPtr
RRStringArrayHandle -> RRStringArrayPtr
RRMatrixHandle -> RRDoubleMatrixPtr
RRListItemHandle - > RRListItemPtr
RRListItemHandle -> RRListPtr





git-svn-id: https://roadrunnerlib.googlecode.com/svn/branches/create_code_for_C_plugins@1108 c0027639-9190-0b57-01eb-f09a03790dae