Parameterize and execute notebooks
complete
S
Silky Porpoise
We want to parameterize, (inspect), and execute notebooks using Papermill.
Rob Newman
marked this post as
complete
This is available via custom environments in Data Studios, using the following example YAML:
name: papermill-env
channels:
- conda-forge
dependencies:
- papermill=2.6.0
G
Glacier Goat
Silky Porpoise is your intent to incorporate a parameterized notebook as a step in a nextflow workflow?
Rob Newman
marked this post as
in progress
We are actively working on Custom Environment support in Data Studios.
Rob Newman
Silky Porpoise: This will be resolved by the implementation of Custom Environments (the next Data Studios milestone). In the interim, you can run the following in your Jupyter notebook to install
papermill
:!pip install papermill
With session persistence, this library will always be available once executed in the Data Studio session.
Rob Newman
marked this post as
acknowledged