Working with GIS is fun. Maps! This project is so fun. No brains though. 
GeoJSON files in Python and shape files in QGIS. Will I come up against nasties soon?
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I am using this in Python: https://uscensusbureau.github.io/citysdk/developers/gettingstarted/ …
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In the terrible times before I could get an ESRI licence ;) I usually ended up using Shapely/Fiona/GeoAlchemy2/PostGIS
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I actually have a wrapper around some arcpy functions to make them work more like Shapely and Fiona. It's not very pretty.
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I know nothing of what you speak!

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Shapely/Fiona are nice python libraries for geometry manipulation/IO. GeoAlchemy2 is a SQLAlchemy Geometry extension.
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ahhh I see
shapely has a hilarious name
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