The cell_typist_model downloading is not working properly

[AlbertPlaPlanas]

Discussed in #52

^{Originally posted by Lyeleyl June 13, 2025}
I tried to use Adult_Human_Skin.pkl. The codes below cannot properly download models from the website, so I can only download models by myself and put them in the directory.

Check if the model file exists on disk

    if os.path.isfile(self.cell_typist_model):
        # The model file already exists on disk; no further action is required.
        pass
    else:
        # The model file does not exist on disk;
        if not self.cell_typist_model.endswith(".pkl"):
            # Append '.pkl' if not already present
            self.cell_typist_model = self.cell_typist_model + ".pkl"
        if not os.path.isfile(self.cell_typist_model):
            # Download model if it does not exist
            models.download_models(model=self.cell_typist_model)</div>

[AlbertPlaPlanas]

Lyeleyl

Can you please

Can you check if this code works for you (and paste the error log if it does not?)?

from celltypist import models
import os

cell_typist_model = "Adult_Human_Skin"


if os.path.isfile(models.get_model_path(cell_typist_model)):
    print("model available locally")
    # The model file already exists on disk; no further action is required.
    pass
else:
    # The model file does not exist on disk;
    if not cell_typist_model.endswith(".pkl"):
        print("Model name lacks .pkl. Adding it.")
        # Append '.pkl' if not already present
        cell_typist_model = cell_typist_model + ".pkl"
    if not os.path.isfile(models.get_model_path(cell_typist_model)):
        # Download model if it does not exist
        print("Downloading")
        models.download_models(model=cell_typist_model)
        print("Downloaded")
    else:
        print("Model not downloaded. Already available")

It may fail if you are behind a proxy or if you have any issues with SSL certification.

[Lyeleyl]

Thank you for the response, I think I made wrong issue about the model. I think the actual problem is just the Fetal_Human_Skin.pkl, I've tried Pan_Fetal_Human, Adult_Human_Skin, Human_Colorectal_Cancer, they worked fine but Fetal_Human_Skin.pkl is still not working. Even when I downloaded the model from https://www.celltypist.org/models.

The output of your code was:
Model name lacks .pkl. Adding it.
Downloading
Downloaded

[AlbertPlaPlanas]

From what you describe seems to be a Celltypist issue and not an Enact problem.
Is the model working when using celltypist as a standalone library/application?

[Lyeleyl]

Not working well, as I forgot to say when using ENACT, although there is output,
it also reports: celltypist.logger:⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate.

When I upload the filtered feature matrix to celltypist online analysis, it also reports error: Invalid expression matrix in .X, expect log1p normalized expression to 10000 counts per cell. So Im not sure if it is the cause.