~/.kipoi/config.yaml

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

model_sources:
  kipoi: # source name 
    type: git-lfs  # git repository with large file storage (lfs)
    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
  github-permalink:
    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. It is not a normal git repository, since bigger files are stored with git large file storage (git-lfs). This repository will be stored locally under local_path. Advantage of using git-lfs is that only the files tracked by git will be downloaded first. Larger files stored in git-lfs will be downloaded individually for each model upon request (say when a user invokes a kipoi predict command).

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-lfs - As for kipoi model source. Model weights will get downloaded upon request (say when running kipoi predict).
  • git - Normal git repository, all the files will be downloaded on checkout.
  • local - Local directory.

Example:

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

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

  my_local_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 rbp_eclip/UPF1).

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