these files are meant to be pulled all at once and then symlinked where needed
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init.vim already has its own neovim python environment, project specific python modules should be installed in every project
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pip install -U black mypy
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you should then activate the project virtual environment before starting vim because deoplete will look on the path for executables, not in the neovim environment. The executables need to be in the same environment as the project requirements in order to find them
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deoplete-jedi and jedi-vim work by some vendored jedi version in their respective neovim packages, I am not sure how it works exaclty, but it doesn't need to be installed anywhere by hand