git clone https://github.com/pygeos/pygeos.git pygeos-clean
cd pygeos-clean
# update commit messages
git-filter-repo --message-callback 'return re.sub(b"#([0-9]+)", b"pygeos/pygeos#\\1", message)'
git-filter-repo --message-callback 'return message.removeprefix(b"[Done] ")'
# rename conflicting files / dirs
git mv MANIFEST.in MANIFEST_pygeos.in 
git mv pyproject.toml pyproject_pygeos.toml 
git mv README.rst README_pygeos.rst 
git mv setup.cfg setup_pygeos.cfg
git mv setup.py setup_pygeos.py
git mv .gitignore .gitignore_pygeos
git mv docs/ docs_pygeos
git mv ci/install_geos.cmd ci/install_geos_pygeos.cmd
git mv ci/install_geos.sh ci/install_geos_pygeos.sh
git commit -am "Migration to Shapely: rename conflicting files"

git clone https://github.com/Toblerity/Shapely.git shapely-clean
cd shapely-clean
# adding pygeos as a remote and fetching it
git remote add pygeos ../pygeos-clean
git fetch pygeos --tags
git merge --allow-unrelated-histories -m "Merge PyGEOS source code into Shapely" pygeos/master
# this is now pushed to my fork, when final this is pushed to shapely:main
git push https://github.com/jorisvandenbossche/Shapely.git HEAD:merge-pygeos