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datalad-boutiques

OHBM 2023 hackathon Project

Boutiques Integration to Datalad

Description and the goals for the OHBM BrainHack

The idea is to create a datalad plugin for boutiques functionality.

Datalad has a lot of useful functionality already, specifically: rerunning commands or scripts and "installing" containers to a dataset.

Boutiques is a tool for annotating an analysis script. It documents the inputs, outputs, and container to run a specific script. It's basically a .json sidecar for your analysis.

The goal of the plugin will be to create a datalad boutiques command that can streamline:

  • installing a boutiques command / container from zenodo to a datalad dataset
  • call the installed container on data within the dataset
  • provide useful ways of tracking the outputs
  • stringing multiple pipelines together

Participants

Project Proposer (lead?)

  • Brent McPherson (bcmcpher)

Contributors

  • Jacob Sanz-Robinson

Skills

  • python (both tools are python based)

some experience (or interest in learning the mechanics of)

  • datalad
  • boutiques

Short name for the Discord chat channel (~15 chars)

dl-boutiques

DataLad Extension Template

Build status codecov.io crippled-filesystems docs

This repository contains an extension template that can serve as a starting point for implementing a DataLad extension. An extension can provide any number of additional DataLad commands that are automatically included in DataLad's command line and Python API.

For a demo, clone this repository and install the demo extension via

pip install -e .

DataLad will now expose a new command suite with a hello... command.

% datalad --help |grep -B2 -A2 hello
*Demo DataLad command suite*

  hello-cmd
      Short description of the command

To start implementing your own extension, use this template, and adjust as necessary. A good approach is to

  • Pick a name for the new extension.
  • Look through the sources and replace helloworld with <newname> (hint: git grep helloworld should find all spots).
  • Delete the example command implementation in datalad_helloworld/hello_cmd.py.
  • Implement a new command, and adjust the command_suite in datalad_helloworld/__init__.py to point to it.
  • Replace hello_cmd with the name of the new command in datalad_helloworld/tests/test_register.py to automatically test whether the new extension installs correctly.
  • Adjust the documentation in docs/source/index.rst. Refer to docs/README.md for more information on documentation building, testing and publishing.
  • Replace this README, and/or update the links in the badges at the top.
  • Update setup.cfg with appropriate metadata on the new extension.
  • Generate GitHub labels for use by the "Add changelog.d snippet" and "Auto-release on PR merge" workflows by using the code in the datalad/release-action repository as described in its README.

You can consider filling in the provided .zenodo.json file with contributor information and meta data to acknowledge contributors and describe the publication record that is created when you make your code citeable by archiving it using zenodo.org. You may also want to consider acknowledging contributors with the allcontributors bot.

Contributing

See CONTRIBUTING.md if you are interested in internals or contributing to the project.