After merging in the https://github.com/pygeos/pygeos repo into Shapely, this are some minimal changes to get a the shapely package in a "working state":

• First commit: move /pygeos/* directory into /shapely/*. The only conflict is strtree.py, so the pygeos version is temporarily named strtree_pygeos.py (and in a follow-up we need to merge both strtree files)
• Second commit: replacing "pygeos" with "shapely" in the package source and tests (not yet in docs, CI, etc, also not yet in docstring examples (for doctests))
• Third commit: minimal changes to get a working package:
  • minimal setup.py (I kept the old one as setup_shapely.py for now, we can in a follow-up consolidate the setup files (the exact setup arguments, author, maintainer, description, etc)
  • renamed geometry.py to _geometry.py, because it otherwise conflicts with geometry/__init__.py submodule (and therefore also renamed _geometry.pyx to _geometry_helpers.pyx). If there are other suggestions for names, that's certainly welcome.

With those changes, building and installing the new shapely package works (python setup.py build_ext -i / python setup.py develop / pip install -e . --no-build-isolation), and the package is in a working state: it imports, most functionality works, the tests run (but there are still a bunch of failures)

(it's probably easiest to check the commits separately)

cc @sgillies @caspervdw