Make `nipoppy init` run `git init` in the code directory

nipoppy / nipoppy

Lightweight framework for neuroimaging-clinical data organization/processing

https://nipoppy.readthedocs.io/en/stable/

MIT License

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Make `nipoppy init` run `git init` in the code directory #234

Open michellewang opened 5 months ago

michellewang commented 5 months ago

From a discussion with @nikhil153 today.

The user would specify both a DATASET_ROOT and a CODE_ROOT (for example). The code directory should have a structure that mirrors the dataset structure, except they should contain code/scripts instead of data:
- tabular: for manifest-generation, tabular bagel generation
- dicom_reorg: for wrangling raw, pre-BIDS imaging data
- analysis: for downstream analyses
- Others?
Maybe also a requirements.txt file pre-populated with Nipoppy
Maybe also run git init if the user has Git installed

I think the idea would be that this is a starting point for "good practices", but that users are not obligated to use these directory names exactly. Unlike the dataset layout which is mandatory since the Nipoppy tools expect it.

michellewang commented 5 months ago

Alternative: follow abstractions/"steps" listed in the slides

curation
processing
tracking
extraction
analysis etc.

Remi-Gau commented 4 months ago

Maybe also run git init if the user has Git installed

related to this:

I already have the cohort creator turning the nipoppy "hierarchy of folders" into a datalad sub-datasets with a code diretory.

Maybe this could be an option of the init CLI to create datalad datasets if datalad is installed and if requested by the user.

michellewang commented 3 months ago

Just discussed this again with @nikhil153 and @mathdugre:

We can do nipoppy init which will attempt to run git init in the code directory (which will now be inside the study directory, to be closer to BIDS)
- The user can optionally specify a remote URL to be added to the repo
- The Git thing can be opted-out of since some systems don't have (or do not like) Git

nikhil153 commented 1 month ago

Notes after enigma-pd roll out plan:

Need: central dashboard to track progress of multiple remote nipoppy deployments Proposal: Use this code repo to push bagels. Implication: May need a field in global_config

Thoughts @michellewang, @mathdugre?

michellewang commented 1 month ago

@nikhil153 can we clarify (tomorrow maybe?) what we want the dashboard to look like? For example would a Kanban board be enough? And what do we want to do with the pushed bagels?