Usage

Installation

The DSO Python API is part of the DSO CLI package. See installation for more details.

Typical usage

The purpose of the Python API is to provide covenient access to stage parameters from Python scripts or notebooks. Using read_params() the params.yaml file of the specified stage is compiled and loaded into a dictionary. The path must be specified relative to the project root – this ensures that the correct stage is found irrespective of the current working directory, as long as it the project root or any subdirectory thereof. Only parameters that are declared as params, dep, or output in dvc.yaml are loaded to ensure that one does not forget to keep the dvc.yaml updated.

from dso import read_params

params = read_params("subfolder/my_stage")

By default, DSO compiles paths in configuration files to paths relative to each stage (see configuration). From Python, you can use stage_here() to resolve paths relative to the current stage independent of your current working directory, e.g.

import pandas as pd
from dso import stage_here

pd.read_csv(stage_here(params["samplesheet"]))

This works, because read_params has stored the path of the current stage in a configuration object that persists in the current Python session. stage_here can use this information to resolve relative paths.