SBOL_TEST requires linking to Python libraries

[kirichoi]

SBOL_TEST requires linking to Python libraries which should not happen.
This issue was introduced by commit 41ad477 and was temporarily circumvented in commit 4eec728 by linking Python libraries.

[kirichoi]

It segfaults now when it tries to run sbol_test executable.
@bbartley: Please take a look at this if you can. I will also try to find what's causing the issue.

[kirichoi]

I believe this issue occurs because C++ library now has Python specific code embedded to it. When both SBOL_BUILD_TEST and SBOL_BUILD_PYTHON2 flags are TRUE, C++ library is practically useless by itself, leading to failure in test executable.

[bbartley]

 I believe this issue occurs because C++ library now has Python specific code embedded to it. When both SBOL_BUILD_TEST and SBOL_BUILD_PYTHON2 flags are TRUE, C++ library is practically useless by itself, leading to failure in test executable.

It's true, I embedded Python specific code.  But wasn't there already Python specific code embedded? The error messages make me think that the SBOL_BUILD_PYTHON2  flag is not being passed to SWIG when compiling the wrapper library.  Previously, I had similar problem on Mac.  This line fixed it:     set(CMAKE_SWIG_FLAGS -DSBOL_BUILD_PYTHON2) Is something similar going on with Linux builds?

[kirichoi]

I don't think Python specific code was ever tested through Travis. This seems like a linking problem specific to test executable and any other projects that depends on libSBOL. I think the issue is that SBOL_BUILD_PYTHON2 enables Python specific code creating libSBOL library that will only work when Python library is linked. I think Mac should have similar problem when trying to build test and wrapper at the same time.

[bbartley]

I think this is Linux specific. On Mac I can link and execute a test application without linking Python library. Also I can import libsbol bindings into the python interpreter. I didn't get any about missing symbols.

…

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On Sep 10, 2017, at 11:34 AM, Kiri Choi ***@***.***> wrote: I don't think Python specific code was ever tested through Travis. This seems like a linking problem specific to test executable and any other projects that depends on libSBOL. I think the issue is that SBOL_BUILD_PYTHON2 enables Python specific code creating libSBOL library that will only work when Python library is linked. I think Mac should have similar problem when trying to build test and wrapper at the same time. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[kirichoi]

Hmm, I will check what's going on.

[kirichoi]

This could be also gcc specific. @bbartley: could you test gcc?

[kirichoi]

I think this is gcc specific issue. In clang it seems like you are using weak linking? I did got this working by linking all appropriate libraries and include directories. I will push out and let you see whether it's appropriate fix or not.