For some reason, codesign is allergic to names with . in them in the Contents/MacOS/ subdirectory. Normally the hacky workaround is to move shapely to Contents/Resources then create a symlink (using ln -s) from Contents/MaOS/shapely to Contents/Resources/shapely. See also the same issue here <https://github.com/pyinstaller/pyinstaller/issues/6612#issuecomment-1047241220> .
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