archivotron: a python suite for naming and organizing data

[jbteves]

Title

archivotron: a project to help people organize their data

Leaders

• Joshua Teves
• Anthony Galassi

Collaborators

No response

Brainhack Global 2021 Event

Brainhack Washington DC

Project Description

• What are you doing, for whom, and why?

We are building a suite of python tools to help people generate BIDS or similar datasets by helping to facilitate name generation and attribute decomposition from large filenames.

• What makes your project special and exciting?

This is not a good pitch but honestly it's kind of boring but really should get done.

• How to get started?

Show up and ask lots of questions about how we're going to achieve our goals.

• Where to find key resources?

Show up to the brainhack, GitHub repository is here:

Link to project repository/sources

https://github.com/jbteves/archivotron

Goals for Brainhack Global

Skeleton of a functional path generator for BIDS datasets

Good first issues

1. issue one: Help sketch out goals

2. issue two: Help sketch out documentation

Communication channels

DC Brainhack slack

Skills

• Python: intermediate to advanced
• Documentation: sphinx/readthedocs
• Communication skill is a must

Onboarding documentation

We'll be making it at the hack as we figure out more about how to achieve the project goals.

What will participants learn?

If not existing, PyTest and object-oriented design, some experience developing configuration files.

Data to use

No response

Number of collaborators

1

Credit to collaborators

Project contributors will get listed on the README

Image

Leave this text if you don't have an image yet.

Type

data_management, other

Development status

1_basic structure

Topic

other

Tools

other

Programming language

Python

Modalities

not_applicable

Git skills

2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.

[jbteves]

Hi @brainhackorg/project-monitors my project is ready!

Pitch: right now we do not have tools to automatically generate names for standardized brain imaging data standards such as BIDS. This tool seeks to help users flexibly create and ingest filenames using an attribute-based rather than string-manipulation approach, and allow them to make easy modifications to standards while still retaining machine-readability.

[Remi-Gau]

Looks good to me.

[Remi-Gau]

Will ping @JuliaSprenger as this is close to some of the tools you are working on BIDS BEP32
https://github.com/INT-NIT/BEP032tools#general-usage-for-the-templater-script

I believe that @effigies also mentioned some similar templating initiatives.

And @rwblair had a cookie cutter set for some of this.
https://github.com/rwblair/cookiecutter-bids

And because I can't mind my own business, you might want to keep an eye on pybids for constructing filenames (see Path construction in this notebook)
https://github.com/bids-standard/pybids/blob/master/examples/pybids_tutorial.ipynb

[jbteves]

There is high overlap with the pyBIDS example, but this package will endeavor to allow non-BIDS outputs as well, so long as it is completely specified. This will allow things to pivot more quickly if BIDS changes, or if somebody has needs which are not met by BIDS, as well as potentially be of interest outside of the neuroimaging community.
I do appreciate your linked examples of similar software projects.

[Remi-Gau]

Having something more general than BIDS would be awesome.

As keep telling everone, having some standard is better than no standard.