Segmentation faults may be a result of mixing libraries from different versions. When installing packages with Anaconda (and conda-forge), you should install via conda install shapely to ensure that the correct libraries are used for that environment. Installing via pip install shapely in a conda environment might use incompatible binary wheels from PyPI, so you could try pip uninstall shapely to undo these changes. Or re-create the conda environment using conda packages. There are some instances where "pip install ..." can be used in conda environments, but usually these are for pure-Python libraries.