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
kipoimodel source. Model weights will get downloaded upon request (say when running
git- Normal git repository, all the files will be downloaded on checkout.
local- Local directory.
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
kipoi) and the relative path of the desired model directory from the model source root (say
A directory is considered a model if it contains a