We've provided an overview of the most important open source packages for processing and analyzing geospatial data. The question then becomes when to use a certain package and why. GDAL, OGR, and GEOS are indispensable for geospatial processing and analyzing, but were not written in Python, and so they require Python binaries for Python developers. Fiona, Shapely, and pyproj were written to solve these problems, as well as the newer Rasterio library. For a more Pythonic approach, these newer packages are preferable to the older C++ packages with Python binaries (although they're used under the hood).
However, it's good to know the origins and history of all of these packages as they're all so widely used (and for ...
