Datalad Subdatasets

Skill: datalad-subdatasets

Inspect the subdataset tree and manage subdataset properties. Lists all registered subdatasets, their state (present/absent), and the commit SHA they are pinned to.

Steps

1. Verify DataLad context — check for .datalad/ in the current directory or a

parent: ``bash ls .datalad/ 2>/dev/null `` If no dataset is found, inform the user and stop.

1. Determine action — read from $ARGUMENTS or conversation context:

• inspect (default): list all subdatasets
• recursive listing: list the full tree
• filter absent: show only uninitialized subdatasets
• set property: modify a .gitmodules entry for a specific subdataset

1. Construct and run command:

### inspect (default) ``bash datalad subdatasets ``

### recursive listing ``bash datalad subdatasets -r ``

### filter absent ``bash datalad subdatasets --state absent ``

### set property Show the command and confirm before running — this modifies .gitmodules: `` datalad subdatasets --set-property ` Common properties: url` (change where the subdataset is fetched from).

### run a command across subdatasets (datalad foreach-dataset) When the user wants to execute a command on every subdataset in the tree, use datalad foreach-dataset. Gather:

• The command or DataLad command to run (as a string)
• Whether to recurse (-r) into nested subdatasets
• Whether to include the superdataset (--include-super)

``bash datalad foreach-dataset [-r] [--include-super] -- ``

Examples: ```bash # Run datalad status on every subdataset datalad foreach-dataset -r -- datalad status

# Update all subdatasets datalad foreach-dataset -r -- datalad update --how=merge

# Check annex usage in every subdataset datalad foreach-dataset -r -- git annex info --fast ```

Always show the full command before executing and warn that errors in one subdataset will be reported but processing continues for the rest.

1. Interpret output — explain the results to the user:

• state: present — the subdataset is cloned and accessible locally
• state: absent — the subdataset is registered in .gitmodules but not yet cloned;

files are not accessible

• gitshasum — the exact commit the superdataset has pinned for this subdataset

1. Suggest follow-up based on what's found:

• For absent subdatasets:

> "Run datalad get -n to initialize the subdataset handle without > downloading content, or datalad get to initialize and retrieve all files."

• For present subdatasets that appear out-of-date:

> "Run datalad update -s origin --how=merge to pull the latest state."

• For a large tree with many absent subdatasets:

> "Run datalad get -r . to initialize and retrieve all absent subdatasets and > their content at once."

Reference

Load ${CLAUDE_PLUGIN_ROOT}/../references/subdataset-patterns.md for the absent/present model, neuroimaging layout examples, recursive get patterns, and .gitmodules structure.

Constraints

• The query actions are read-only — datalad subdatasets and --state filters do

not modify any state.

• For --set-property: always show the command and ask the user to confirm before

running — it modifies .gitmodules, which is a tracked file that requires a subsequent datalad save to record the change.

• Never edit .gitmodules directly — use datalad subdatasets --set-property or

DataLad's other subdataset management commands.

• Never use git submodule commands directly inside a DataLad dataset unless explicitly

debugging at the git level — DataLad's abstraction layer must be kept consistent.

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: neuroanalytics
• Source: neuroanalytics/data-science-harness
• License: MIT

Install and usage instructions live in the source repository linked above.