find: zscore-normalize: No such file or directory

[Jkgarciam]

Hi, I recently changed laptop and now i cant run the intensity normalization package from the terminal.

macOS Sonoma 14.4.1
2.6 GHz 6-Core Intel Core i7
Radeon Pro 560X 4 GB
Intel UHD Graphics 630 1536 MB
16 GB 2400 MHz DDR4

[jcreinhold]

Can you import intensity_normalization in the Python REPL in which it's installed? If not, you probably need to activate the virtual environment in which you installed it.

If that's not the case, please provide the following information:

• intensity-normalization version (e.g., 0.3.8):
• numpy version (e.g., 1.0):
• OS (e.g., Linux):
• How you installed intensity-normalization (conda, pip, source):
• Build command you used (if installed from source):
• Python version:

[Jkgarciam]

Yes, I can import intensity_normalization in python REPL

Intensity_normalization version 2.2.4, installed with pip
numpy version 1.26.4
macOS Sonoma 14.4.1
python version 3.9

[jcreinhold]

I can't replicate the error. Can you try reinstalling the package? For example, use pip install --upgrade --no-cache-dir --force-reinstall intensity-normalization==2.2.4. Or create a new virtual environment/use conda. If that doesn't work, let me know.

[jcreinhold]

You probably need to add the path where the CLIs are installed to your PATH environment variable. When you pip install the package, I believe it'll list where the entrypoints are installed. Just prepend that directory to PATH; perhaps set it in .zshrc or whatever, so you don't have to set it each time you open a new terminal.

[jcreinhold]

FYI you should install brew, conda, do user installs of packages, or use a virtual environment. You don't want to be using or modifying the system Python.

[Jkgarciam]

Thank you I fixed the problem creating a virtual environment.
Best,

Josefa