Latest Kappa repo changes

[JamesPino]

For future reference, when using the newest version of kappa (direct from git repo master), kappa now appends ".dot" to the output for contact maps and influence maps. PySB does this also, causing pygraphviz to fail on loading.

For example when running the unit test, It looks for
./tmpKappa_test_run_static_analysis_cmap_vzMlaD/test_run_static_analysis_cmap_cm.dot
but the file is
./tmpKappa_test_run_static_analysis_cmap_vzMlaD/test_run_static_analysis_cmap_cm.dot.dot

Simple fix is to remove '.dot' from the file names we write, then add it when read back in from pysb.

Just wanted to point this out. Not sure if it is documented anywhere and if it is I didn't finding when installing Kappa for PySB.

[jmuhlich]

@bgyori @johnbachman did this get fixed through your work on the kappa module?

[alubbock]

@JamesPino Are you still having problems with this? I think everything's working with PySB 1.6.0 and Kappa 4.0RC1.

[JamesPino]

Yep!