feat: use pip dependencies instead of system packages, make lxml mandatory #1175
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This PR removes the system installs of certain packages in the dockerfiles as these were not using the correct python version. Instead the setup.py now includes the needed libraries and they will always be installed via pip. This also removes the need to install these packages if doing a custom install on ubuntu. Additionally shapely, lxml, geos, gdal and pyproj are no longer optional.
This also makes it easier to rely on a certain version of the dependencies.