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The "console scripts" entry points must point to a function in an installed python module.
tomocupy_cli:main
was not a python module, it was a script located in /bin, so it is not a valid entry point. Pip creates a bash/cmd script (depends on the platform) that wraps the function listed in "console scripts" and installs it.The files listed in "scripts" are copied directly to the /bin folder, so they are not cross-platform because Windows and Unix handle scripts in different ways.
In this PR, I have moved the tomocupy_cli script into the the tomocupy package, so it is installed with the rest of the module and now the console_scripts entry point points to a function that actually exists.