vigra.cmake: Eliminated extra spaces.
geos.cmake: Added geo, which is a dependency of shapely.
geos.cmake: Added a patch to geos to bypass a broken test.
patches/geos-CoordinateArraySequenceFactoryTest.cpp.patch: Patches the broken test.
shapely.cmake: Added shapely, which is a dependency of sima.
sima.cmake: Added sima, which is a tool for "analysis of time-series imaging data arising from fluorescence microscopy".
sima.cmake: Skipped OpenCV as it does not appear to be absolutely necessary for sima and currently OpenCV has build errors.
sima.cmake: Added a patch to sima due to an incorrect import from scipy.
patches/sima-segment.py.patch: Patches sima to make correct import.