jupyter

Command-line tool subcommand

Creates and runs a Jupyter notebook for the loaded pipeline. The pipeline is made easily available within the notebook, providing a way to load the modules and get their outputs.

This is a useful way to explore the data or analyses coming out of your modules. Once a module has been run, you can load it from a notebook and manipulate, explore, visualize, etc to results.

A new directory is automatically created in your project root to contain the pipeline’s notebooks. (You can override the location of this using --notebook-dir). An example notebook is created there, to show you how to load the pipeline.

From within a notebook, load a pipeline like so:

from pimlico import get_jupyter_pipeline
pipeline = get_jupyter_pipeline()

Now you can access the modules of the pipeline through this pipeline object:

mod = pipeline["my_module"]

And get data from its outputs (provided the module’s been run):

print(mod.status)
output = mod.get_output("output_name").

Usage:

pimlico.sh [...] jupyter [-h] [--notebook-dir NOTEBOOK_DIR]

Options

Option	Description
--notebook-dir	Use a custom directory as the notebook directory. By default, a directory will be created according to: <pimlico_root>/../notebooks/<pipeline_name>/