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name: model-management description: "Manage CellTypist built-in model discovery, local cache behavior, model pickle inspection, conversion, subsetting, markers, and offline test fixtures." disable-model-invocation: true metadata: disco-role: operating license: MIT

CellTypist Model Management

Use this sub-skill when a task is about locating, downloading, loading, writing, inspecting, converting, subsetting, or smoke-testing CellTypist models.

Route Quickly

• Read model reference for cache paths, remote downloads, Model.load, Model.write, prediction labels/probabilities, and marker extraction.
• Read conversion and subsetting before changing species, gene identifiers, or retained cell types; these methods mutate the loaded model in place.
• Use troubleshooting for cache/network surprises, invalid pickle files, missing map files, conversion column mistakes, invalid collapse modes, and subset constraints.
• Run model_cache_check.py to inspect the active CELLTYPIST_FOLDER model cache or verify a local model pickle without downloading anything.
• Run tiny_model_factory.py to create a tiny offline-compatible CellTypist model pickle for smoke tests and examples.

Stay In Scope

• Stay here for celltypist.models, built-in model inventory/download/cache behavior, Model object persistence and metadata, marker extraction, Model.convert, and Model.subset.
• Route annotation with a selected model to annotation-workflows.
• Route training a new real reference model to training-and-custom-models.
• Route result tables, AnnData insertion, UMAPs, dotplots, or interpretation of finished predictions to visualization-and-results.

Offline-First Pattern

For offline work, avoid implicit default-model resolution and pass an explicit local model path containing a forward slash, such as ./local_model.pkl or Path("local_model.pkl").resolve().as_posix().

from pathlib import Path
from celltypist import models

model_path = Path("local_model.pkl").resolve().as_posix()
model = models.Model.load(model_path)
print(model.cell_types)
print(model.features[:5])

If a task may run without network access, inspect cache state first:

python scripts/model_cache_check.py --verify-model ./local_model.pkl