Why do I have "ModuleNotFoundError: No module named 'scipy.special.cython_special'" when I don't even use cython?

I had this error after freezing a program that used scipy version 1.5.0 but I changed the version to 1.4.1 (which I had used with an earlier virtual environment) and the error disappeared.

I'm getting the same error, and not exactly sure what causes it or why pyinstaller doesn't find that dependency, but you can fix it by adding 'scipy.special.cython_special' to your pyinstaller myapp.spec file like this:

a = Analysis(['/Users/Name/path/to/mystartupfile.py'],
             pathex=['/Users/Name/...'],
             binaries=[],
             datas=[('data')],
             hiddenimports=['scipy.special.cython_special'],
             hookspath=['/Users/Name..../hooks'],
             runtime_hooks=[],
             excludes=['IPython', 'FixTk', 'tcl', 'tk', '_tkinter', 'tkinter', 'Tkinter'],
             win_no_prefer_redirects=False,
             win_private_assemblies=False,
             cipher=block_cipher,
             noarchive=False)

Add --hidden-import="scipy.special.cython_special" to your pyinstaller command.

I just solved this problem by copying the cython_special.cp37-win_amd64.pyd file from MyEnv>Lib>site-packages>scipy>special into the same directory of the compiled pyinstaller program.

I had the same problem, turns out I was using Python 3.8 which isn't supported by Pyinstaller. Try using 3.7.

I also had this issue.

Downgrading scipy package to 1.4.1 solved the issue as @profTC said.

Alternatively, one can upgrade to PyInstaller 4.0 where they have added a new hook file to deal with this. See: https://pyinstaller.readthedocs.io/en/v4.0/CHANGES.html#hooks

Another solution is to use to directly copy the hook file and include it as an additional hook when building with PyInstaller.