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jhkorhonen / MOODS

MOODS: Motif Occurrence Detection Suite
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install MOODS python extention module for python3 #4

Closed joshuabhk closed 6 years ago

joshuabhk commented 8 years ago

Hello,

First thank you very much for your great module! Your work helped me a lot! But when I tried to move onto python3, the python interface cannot be built. It is not your bug but python's change of module extension rules. https://docs.python.org/3/howto/cporting.html If you can port for python3 that would be great! If you do not have time, I might chip in!

Thanks.

Bong-Hyun

jhkorhonen commented 8 years ago

This should be fixed already in develop branch version, though I have not tested that the new SWIG-generated python interfaces actually work also with python3 as promised. The develop branch is also already in a state where it could be used to replace MOODS 1.0, though using it will require some edits to the calling scripts at the moment -- the development has been really sluggish, unfortunately.

I'll try to put up a semi-usable beta package ("version 1.9") of the new python interfaces later this week, assuming I can find the time to do that properly.

If you are feeling particularly adventurous, you can try using the current develop head (3ed3c010da06064761d777f747be2ba8361af1cb). You'll need SWIG 3 installed (try swig -version), but assuming you have that, you can just symlink/copy the MOODS/core/ under MOODS/python/ and run build.sh under MOODS/python/ to compile everything. The example scripts won't necessarily work with python3 directly, but should get you started.

joshuabhk commented 8 years ago

Thank you so much for your help!! I will try and let you know the result.

Best,

Bong-Hyun

On Tue, Nov 17, 2015 at 7:17 AM jhkorhonen notifications@github.com wrote:

This should be fixed already in develop branch version, though I have not tested that the new SWIG-generated python interfaces actually work also with python3 as promised. The develop branch is also already in a state where it could be used to replace MOODS 1.0, though using it will require some edits to the calling scripts at the moment -- the development has been really sluggish, unfortunately.

I'll try to put up a semi-usable beta package ("version 1.9") of the new python interfaces later this week, assuming I can find the time to do that properly.

If you are feeling particularly adventurous, you can try using the current develop head (3ed3c01 https://github.com/jhkorhonen/MOODS/commit/3ed3c010da06064761d777f747be2ba8361af1cb). You'll need SWIG 3 installed (try swig -version), but assuming you have that, you can just symlink/copy the MOODS/core/ under MOODS/python/ and run build.sh under MOODS/python/ to compile everything. The example scripts won't necessarily work with python3 directly, but should get you started.

— Reply to this email directly or view it on GitHub https://github.com/jhkorhonen/MOODS/issues/4#issuecomment-157352874.

jhkorhonen commented 8 years ago

There's now a cleanly packaged 1.9 release, though I have not yet had time to test it with python3.

jhkorhonen commented 6 years ago

For reference, everything should be Python 3 compatible as of version 1.9.3.