Getting “Segmentation fault: 11” with Shapely in Python on OSX 10.12.6

Question

I have a number of data processing scripts that worked a few months ago but now getting seg faults. In one script I had to pull out code from a method and embed in the calling method. In this case, I am performing the simplest of tasks. I am trying to use OGR and Shapely to find the nearest street to a point.

OSX 10.12.6
Python 3.5.2 :: Anaconda custom (x86_64)
Shapely 1.6.1

from osgeo import ogr, osr
from shapely.geometry import Point
...
def FilterNearbyStreets (self, logLevel, pntSource):
    shpPoint = Point(pntSource.GetX(), pntSource.GetY())
    enoughSegments = False
    bufferSize = 0.001
    while (enoughSegments != True):
        print ("About to buffer {}".format(bufferSize))
        buffer = shpPoint.buffer(bufferSize)
        print ("Buffered!!!")

We never get to Buffered!!!

Segmentation fault: 11

Answer 1

Shapely is a C extension module and depends on a specific version of the GEOS shared library. The libgeos.dylib that is included with the Shapely wheels on PyPI (tapped into by pip) is incompatible with the libraries from Anaconda or Conda-Forge (https://conda-forge.org/). Importing Shapely from PyPI loads its shared library and can interfere with Conda packages that depend on GEOS like pyproj, osgeo.ogr, etc. As long as you use an environment that is exclusively a Python virtualenv or a conda environment, and source your packages appropriately for those environments, you'll be fine.

Answer 2

I had a segmentation fault as well with shapely on macOS, I had to reinstall shapely to fix it :

pip uninstall shapely; pip install --no-binary :all: shapely