.dockstore.yml for Notebooks Templates (version 1.2)
Two templates are provided here, one for you to quickly copy-paste into your repository, and one with a complete explanation of the possible fields and values you can use.
Simple template
version: 1.2
notebooks:
- format: <JUPYTER>
language: <PYTHON | R | JAVASCRIPT | SCALA | JULIA | OTHER>
path: <String>
kernel: <String>
otherFiles:
- <String>
- <String>
testParameterFiles:
- <String>
- <String>
readMePath: <String>
authors:
- name: <String>
email: <String>
topic: <String>
Full template with explanation of all available fields
# The first line refers to the version 1.2 of the .dockstore.yml schema
version: 1.2
# An array of notebooks. Each element corresponds to a notebook on Dockstore.
notebooks:
# The optional notebook name for a notebook, which may only consist of alphanumerics
# and internal underscores and hyphens, but no spaces or other characters. Names may not exceed 256 characters.
# If using a .dockstore.yml with multiple notebooks, this field is required
# to uniquely identify notebooks in the repository.
#
# It should be noted that having the name come first is an arbitrary decision.
# You could use subclass instead, for instance. Provided arrays are not broken
# up, the order of fields within a .dockstore.yml is not important.
- name: <String>
# The format used for the notebook. This cannot be changed once the notebook is registered.
# Currently, only Jupyter is supported.
# If not provided, the format will default to Jupyter.
format: <Jupyter>
# The programming language of the code contained in the notebook. This cannot be changed once the notebook is registered.
# If not provided, the language will default to Python.
language: <Python | R | Javascript | Scala | Julia | other>
# The absolute path to the notebook file in the Git repository.
# - For Jupyter notebooks, the notebook is a .ipynb file.
path: <String>
# Notebook-wide setting that will affect ALL branches/tags; only set this as needed in a main branch.
# Set to true to publish an unpublished notebook, or false to unpublish a published notebook.
# Omitting the publish setting leaves the publish-state unchanged (recommended for all non-primary branches).
publish: <Boolean>
# An optional array of absolute paths to other files in the Git repository that should be read and included with the notebook.
otherFiles:
- <String>
- <String>
# An optional path to a notebook-specific readme in the Git repository. If not provided, Dockstore will show
# the readme.md present at the root of the Git repository if it is present.
# If you have multiple notebooks in a single Git repository, it is recommend to give each one a readme.
readMePath: <String>
# An optional array of authorship information.
# Note that if orcid is present, then all other fields will be ignored, as information will be taken from orcid.
# If orcid is not present, make sure to at a minimum include the name field for each author.
authors:
- orcid: <String>
- name: <String>
email: <String>
role: <String>
affiliation: <String>
# An optional short text description of the notebook, 150 characters or less in length.
# Useful to specify unique topics for multiple notebooks in the same repository, or a topic that differs from the default.
# If not provided, Dockstore will use the repository's "About" description as the topic.
# Set this field to the empty string to reset the topic to the repository's "About" description.
# Notebook-wide setting that will affect ALL branches/tags; only set this as needed in a main branch.
topic: <String>
# A boolean that will change the default version to be displayed on Dockstore. Default: False.
# A value of true will automatically display the latest tag updated as default.
# A value of false will retain the default version that has been specified via the Dockstore UI.
latestTagAsDefault: <Boolean>
# The optional filters section allow specifying sets of Git branches and tags to include for the notebook.
# If no filters are given, all branches and tags are included.
# Branches and tags are arrays of pattern-strings.
# Pattern-strings use Unix-style Glob syntax by default (Ex: `develop`, `mynotebook/**`)
# https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/FileSystem.html#getPathMatcher(java.lang.String)
# or RegEx when the string is surrounded by / (Ex: `/develop/`, `/mynotebook\/.*/`).
filters:
branches:
- <String>
- <String>
tags:
- <String>
- <String>