kipoi package has a config file located at ~/.kipoi/config.yaml. By default, it will look like this (without comments):

  kipoi: # source name 
    type: git  # git repository
    remote_url: [email protected]:kipoi/models.git  # git remote
    local_path: /home/avsec/.kipoi/models/ # local storage path

  # special model source storing models accessed via github permalinks
    type: github-permalink
    local_path: /home/avsec/.kipoi/github-permalink/

model_sources defines all the places where kipoi will search for models and pull them to a local directory.

By default, it contains the model-zoo from github.com/kipoi/models which is a normal git repository,

All possible model source types

In addition to the default kipoi source, you can modify ~/.kipoi/config.yaml and add additional (private or public) model sources. Available model source types are:

  • git - Normal git repository, all the files will be downloaded on checkout. This is the source type used by the public kipoi repository.
  • git-lfs - Model weights will get downloaded from git-lfs upon request.
  • local - Local directory.


    type: git
    remote_url: [email protected]:kipoi/models.git
    local_path: /home/avsec/.kipoi/models/

    type: git
    remote_url: [email protected]:asd/other_models.git
    local_path: ~/.kipoi/other_models/

    type: local
    local_path: /data/mymodels/

About model definition

A particular model is defined by its source (key under model_sources, say kipoi) and the relative path of the desired model directory from the model source root (say Basset).

A directory is considered a model if it contains a model.yaml file.