### Example .env File with Tokens Source: https://docs.nmrium.org/help/zenodo This example shows how to populate your .env file with both production and sandbox Zenodo API tokens, including comments for clarity. ```dotenv # Zenodo production token # Generated from: https://zenodo.org/account/settings/applications/tokens/new/ ACCESS_TOKEN=your_production_token_here # Zenodo sandbox token # Generated from: https://sandbox.zenodo.org/account/settings/applications/tokens/new/ ACCESS_TOKEN_SANDBOX=your_sandbox_token_here ``` -------------------------------- ### Install and run zenodo-nmrium globally Source: https://docs.nmrium.org/help/zenodo Install the package globally via npm and execute it. ```bash npm install -g zenodo-nmrium ``` ```bash zenodo-nmrium [options] ``` -------------------------------- ### Install and run zenodo-nmrium on Linux x64 Source: https://docs.nmrium.org/help/zenodo Download the pre-built binary for Intel-based Linux and execute it. ```bash curl -o zenodo-nmrium https://www.lactame.com/lib/zenodo-nmrium/HEAD/zenodo-nmrium-linux-x64 && chmod 555 zenodo-nmrium ``` ```bash ./zenodo-nmrium [options] ``` -------------------------------- ### Example index.yml Metadata Source: https://docs.nmrium.org/help/zenodo This is an example of the index.yml file required at the root of your dataset folder. It contains metadata about your entire dataset, including title, description, copyright, keywords, and authors. ```yaml title: "My NMR Dataset" description: "

This dataset contains 1H NMR data for compound X.

" copyright: "cc-by-4.0" keywords: - NMR - compound X authors: - family-name: "Doe" given-name: "Jane" affiliation: "University of Example" orcid: "0000-0000-0000-0001" - family-name: "Smith" given-name: "John" affiliation: "Institute of Research" orcid: "0000-0000-0000-0002" ``` -------------------------------- ### Install and run zenodo-nmrium on macOS ARM64 Source: https://docs.nmrium.org/help/zenodo Download the pre-built binary for Apple Silicon and execute it. ```bash curl -o zenodo-nmrium https://www.lactame.com/lib/zenodo-nmrium/HEAD/zenodo-nmrium-darwin-arm64 && chmod 555 zenodo-nmrium ``` ```bash ./zenodo-nmrium [options] ``` -------------------------------- ### Combine Submission Options Source: https://docs.nmrium.org/help/zenodo This example demonstrates combining multiple options for submission, including specifying the access token, enabling production environment, and auto-publishing. ```bash ./zenodo-nmrium ./my-nmr-dataset --access-token YOUR_TOKEN --production --auto-publish ``` -------------------------------- ### Implement HelloDocusaurus Component Source: https://docs.nmrium.org/contribute-to-doc/markdown_features Examples of a simple React component structure for use in documentation. ```javascript function HelloDocusaurus() { return (

Hello, Docusaurus!

) } ``` ```javascript function HelloDocusaurus() { return

Hello, Docusaurus!

; } ``` -------------------------------- ### Example dataset folder structure Source: https://docs.nmrium.org/help/zenodo Required directory layout for organizing NMR samples and metadata before submission. ```text my-nmr-dataset/ ├── index.yml # Dataset metadata (required) ├── sample_1/ # First sample (name will be reused in the table of content) │ ├── structure.mol # Optional: chemical structure file (molfile format) │ ├── 12/ # Experiment number of a native Bruker folder │ │ ├── fid │ │ ├── acqu │ │ ├── acqus │ │ ├── pdata/ # Processed data folder │ │ │ └── 1/ │ │ │ ├── proc │ │ │ ├── procs │ │ │ └── ... │ │ └── ... │ ├── 13/ # Another experiment │ └── ... ├── sample_2.nmrium.zip # Second sample was processed using NMRium. It could contain assignment ├── sample_3/ │ ├── structure.mol # Optional: chemical structure file (molfile format) │ └── spectrum.jdx # JCAMP-DX file (e.g., exported from Topspin using `tojdx` or from MNova with peak assignments) └── ... ``` -------------------------------- ### Run zenodo-nmrium via npx Source: https://docs.nmrium.org/help/zenodo Execute the tool directly without permanent installation using npx. ```bash npx zenodo-nmrium [options] ``` -------------------------------- ### Provide Zenodo Token via Command Line Source: https://docs.nmrium.org/help/zenodo You can provide your Zenodo API token directly using the -t or --access-token option when running the zenodo-nmrium command. ```bash ./zenodo-nmrium ./my-nmr-dataset -t YOUR_SANDBOX_TOKEN ``` -------------------------------- ### Implement Collapsible Details Section Source: https://docs.nmrium.org/contribute-to-doc/details Use the
and tags to create a section that users can expand or collapse. ```html
Epcot Center

Epcot is a theme park at Walt Disney World Resort featuring exciting attractions, international pavilions, award-winning fireworks and seasonal special events.

A second paragraphe

``` -------------------------------- ### Configure Zenodo Tokens via .env File Source: https://docs.nmrium.org/help/zenodo Store your Zenodo API tokens in a .env file for automatic loading. The tool checks for .env files in the current directory, your home directory, or ~/.zenodo-nmrium. ```dotenv ACCESS_TOKEN= ACCESS_TOKEN_SANDBOX= ``` -------------------------------- ### Zenodo Submit Command Line Usage Source: https://docs.nmrium.org/help/zenodo This displays the usage information for the zenodo-submit command, outlining positional arguments and available options for submitting datasets. ```bash Usage: zenodo-submit [options] Positional Arguments: path Path to dataset folder with index.yml and data Options: -t, --access-token Zenodo API access token (required) -s, --sandbox Use sandbox environment (default) -p, --production Use production environment -a, --auto-publish Auto-publish after submission -d, --data-selection Data selection for NMRium visualization Choices: ft, fid, both, preferFT, preferFID Default: ft -l, --log-level Logger level Choices: trace, debug, info, warn, error, fatal, silent Default: info -h, --help Show this help message ``` -------------------------------- ### Submit Data to Production Source: https://docs.nmrium.org/help/zenodo This command submits your NMR dataset to the Zenodo production environment. Ensure you use your production API token and the -p flag. ```bash ./zenodo-nmrium ./my-nmr-dataset -t YOUR_PRODUCTION_TOKEN -p ``` -------------------------------- ### NMRium CLI Configuration Flags Source: https://docs.nmrium.org/help/zenodo Configuration options for the NMRium CLI to manage Zenodo submissions. ```APIDOC ## CLI Configuration Options ### Description Configuration flags for the NMRium CLI to authenticate with Zenodo, select environments, and control submission behavior. ### Parameters #### Options - **--access-token, -t** (string) - Required - API token for Zenodo authentication. Can also be set via ACCESS_TOKEN or ACCESS_TOKEN_SANDBOX environment variables. - **--sandbox, -s** (flag) - Optional - Submit to Zenodo sandbox (default). - **--production, -p** (flag) - Optional - Submit to production environment. - **--auto-publish, -a** (flag) - Optional - Automatically publish the record after submission. If omitted, record is created in draft state. - **--data-selection, -d** (string) - Optional - Controls NMR data types shown. Choices: ft (default), fid, both, preferFT, preferFID. - **--log-level, -l** (string) - Optional - Sets logger verbosity. Choices: trace, debug, info (default), warn, error, fatal, silent. ``` -------------------------------- ### Submit Data Using Environment Variables Source: https://docs.nmrium.org/help/zenodo When using environment variables, you can omit the -t option. The tool will automatically use ACCESS_TOKEN_SANDBOX for sandbox submissions or ACCESS_TOKEN for production if the -p flag is used. ```bash # Uses ACCESS_TOKEN_SANDBOX from .env file ./zenodo-nmrium ./my-nmr-dataset # Uses ACCESS_TOKEN from .env file ./zenodo-nmrium ./my-nmr-dataset -p ``` -------------------------------- ### Create Markdown Links Source: https://docs.nmrium.org/contribute-to-doc/markdown_features Reference other documents using standard Markdown link syntax with relative file paths. ```markdown Let's see how to [Create a document](../20_create/20_create). ``` -------------------------------- ### Auto-Publish Submission to Sandbox Source: https://docs.nmrium.org/help/zenodo This command submits your NMR dataset to the Zenodo sandbox and automatically publishes it after a successful submission. Requires a sandbox API token. ```bash ./zenodo-nmrium ./my-nmr-dataset -t YOUR_SANDBOX_TOKEN -a ``` -------------------------------- ### Create Admonitions with MDX Source: https://docs.nmrium.org/contribute-to-doc/admonitions Use triple colons to define admonition blocks. Titles are optional and content supports standard Markdown formatting. ```markdown :::note The content and title _can_ include markdown. ::: :::note You can specify an optional title Heads up! Here's a pro-tip. ::: :::info Useful information. ::: :::caution Warning! You better pay attention! ::: :::danger Danger danger, mayday! ::: ``` -------------------------------- ### Create a new markdown document Source: https://docs.nmrium.org/contribute-to-doc/create Define the document title using front matter and add content in markdown format. ```markdown --- title: Hello, World! --- ## Hello, World! This is your first document in **Docusaurus**, Congratulations! ``` -------------------------------- ### Embed Markdown Images Source: https://docs.nmrium.org/contribute-to-doc/markdown_features Display images stored in the static directory using standard Markdown image syntax. ```markdown ![Docusaurus logo](/img/docusaurus.png) ``` -------------------------------- ### Define Front Matter Metadata Source: https://docs.nmrium.org/contribute-to-doc/markdown_features Use YAML-formatted metadata at the top of Markdown files to configure document properties like ID, title, and sidebar labels. ```yaml --- id: my-doc title: My document title description: My document description sidebar_label: My doc --- Markdown content ``` -------------------------------- ### Define React Components in MDX Source: https://docs.nmrium.org/contribute-to-doc/markdown_features Use MDX to define and render interactive React components directly within Markdown files. ```jsx export const Highlight = ({children, color}) => ( {children} ); Docusaurus green and Facebook blue are my favorite colors. ```