nemar-cli

library0.7.26jsnpmunverified

The nemar-cli package provides a command-line interface for managing datasets within NEMAR (Neuroelectromagnetic Data Archive and Tools Resource), an initiative focused on curating and sharing human neuroelectromagnetic (EEG, MEG, iEEG) data. It facilitates interaction with BIDS-formatted datasets, often leveraging DataLad for version control and data management, and integrating with resources like OpenNeuro. This CLI is designed to help researchers create, update, and manage neuroimaging datasets, particularly those with restrictive licenses that prevent hosting on fully public repositories, while still ensuring free access for academic use. The current stable version is 0.7.26, indicating active development with potential for frequent updates and feature enhancements before a 1.0 release. Its key differentiators include specialized support for neuroimaging data standards (BIDS), integration with advanced data versioning systems (DataLad), and its role in an ecosystem that provides high-performance computing resources via the Neuroscience Gateway. It aims to streamline data management workflows for neuroscientists.

data devops workflow

npm install nemar-cli

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · NEMAR-CLI

nemar-cli

datajavascriptv0.7.26

Install

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Import

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Disk

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Pass rate

0/ 6

Env Coverage0 / 6

glibc

18–22

musl

18–22

Install & Compatibility

Where this runs

tested against v? · npm install

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

node 18–226 runs

build_error

glibc

node 18–226 runs

build_error

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

nemar-cli

✓ npm install -g nemar-cli nemar-cli --version

✗ import nemarCli from 'nemar-cli'

As a CLI tool, nemar-cli is typically installed globally or executed via npx/bunx. It does not export JavaScript modules for direct import into other applications. The primary interaction is through shell commands.

nemar-cli

✓ npx nemar-cli --help

✗ node nemar-cli.js --help

Using `npx` (or `bunx`) allows executing the CLI without a global installation, ensuring the correct version from `node_modules` is used or fetching it if not locally available. Direct `node` execution is only for development or specific package structures.

nemar-cli dataset create

✓ nemar-cli dataset create --name 'MyNewDataset' --bids --datalad

✗ nemar-cli createdataset MyNewDataset

Commands typically follow a hierarchical structure (e.g., `command subcommand [options]`). Refer to `nemar-cli --help` or specific subcommand help for exact syntax and available flags.

This quickstart demonstrates how to install `nemar-cli` globally using Bun and verify its installation and basic functionality by checking the version and displaying the main help message. It emphasizes the Bun engine requirement and shows how to explore available commands.

#!/bin/bash # Ensure Bun is installed and meets the engine requirement. if ! command -v bun &> /dev/null || ! bun --version | grep -q "^1\."; then echo "Error: Bun (version >=1.0.0) is required but not found or not compatible." echo "Please install Bun: https://bun.sh/docs/installation" exit 1 fi # Install the nemar-cli globally using Bun bun install -g nemar-cli echo "\nNEMAR CLI installed. Verifying installation:" nemar-cli --version echo "\nListing available commands:" nemar-cli --help echo "\nExample: Initializing a new NEMAR dataset (interactive, requires user input):" # This command initiates an interactive process for dataset creation. # For automated scripts, specific subcommands and flags would be used. # nemar-cli dataset create echo "\nTo clean up the global installation (optional):" # bun uninstall -g nemar-cli

nemar --version

Debug

Known issues

breakingThe package requires Bun runtime version >=1.0.0. Using Node.js or an older Bun version will result in errors and prevent the CLI from running.

fix

Ensure Bun is installed globally and updated to at least version 1.0.0. Use `bun install -g nemar-cli` to leverage Bun's package management.

affects: <=0.7.26

gotchaAs a pre-1.0.0 release, `nemar-cli` may introduce breaking changes in minor or patch versions. Command syntax, options, or output formats can change without a major version bump, requiring frequent review of release notes.

fix

Pin the exact version of `nemar-cli` in your project dependencies (`package.json`) and review the GitHub repository's release notes or changelog before updating to a newer version.

affects: >=0.0.0

gotcha`nemar-cli` integrates with DataLad for dataset management. Proper functioning requires DataLad and its dependencies (like git-annex) to be installed and configured correctly on the user's system, which are external to npm.

fix

Install DataLad and git-annex via your system's package manager (e.g., `apt`, `brew`, `conda`). Refer to the DataLad documentation for detailed installation instructions and system requirements.

affects: >=0.0.0

gotchaWhen running `nemar-cli` commands that interact with cloud storage (e.g., AWS S3 for DataLad datasets), appropriate authentication and authorization credentials must be configured in your environment.

fix

Ensure your AWS CLI is configured with valid credentials (`aws configure`) or that environment variables (e.g., `AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY`) are set, as DataLad often relies on these for cloud access.

affects: >=0.0.0

Errors

Common errors & fixes

nemar-cli: command not found

The `nemar-cli` executable is not in your system's PATH, either because it wasn't installed globally or `npx`/`bunx` was not used.

fix

Install globally: `bun install -g nemar-cli`. Or use `npx nemar-cli [command]` or `bunx nemar-cli [command]`.

Error: Bun (version >=1.0.0) is required but not found or not compatible.

The `nemar-cli` package specifies a `bun` engine requirement (>=1.0.0) which is not met by the current runtime.

fix

Install Bun or update it to the latest version (e.g., `curl -fsSL https://bun.sh/install | bash`) and ensure your shell is configured to use it.

DataLadError: 'git-annex' is not available in PATH

DataLad, which `nemar-cli` depends on for certain operations, requires `git-annex` to be installed and accessible in your system's PATH.

fix

Install `git-annex` using your system's package manager (e.g., `sudo apt install git-annex`, `brew install git-annex`) and verify it's in your PATH (`which git-annex`).

BIDSValidationError: Subject 'sub-01' is missing required file 'sub-01_ses-01_task-rest_eeg.bids.json'

A dataset operation failed due to non-compliance with the Brain Imaging Data Structure (BIDS) specification, often related to missing or incorrectly named files/metadata.

fix

Review the BIDS specification for the required file structure and naming conventions. Use BIDS validators to check your dataset before using `nemar-cli` commands that rely on BIDS compliance.

Upgrade

Version history

0.7.26latest on npm

Audit

Dependencies

dataladrequiredCore data management functionality, especially for versioning and accessing large datasets stored on platforms like AWS S3. DataLad itself relies on git-annex.

git-annexrequiredUnderpins DataLad's ability to manage large files efficiently by storing file contents outside of Git's primary repository, using symlinks. Essential for DataLad functionality.

Agent activity

23 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/nemarOrg/nemar-cli ↗

packagehttps://www.npmjs.com/package/nemar-cli ↗

homepagehttps://nemar.org ↗