biotope

| | | | ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Package | | | Meta | | | Automation | |

CLI integration for BioCypher ecosystem packages

Status: early alpha, volatile, partly vibe-coded

Documentation here, may be incomplete.

Currently discussed here.

Metadata Management — Main Usage

The biotope CLI provides a unified interface for managing scientific datasets and metadata in the BioCypher ecosystem. It supports project initialization, data staging, metadata annotation, version control, and more. Here we describe the metadata management functionality, the most mature aspect of the package. Most other functionality is in prototype stage.

Typical Workflow

```bash

1. Initialize a new biotope project (with Git integration)

biotope init

2. Add local data files for annotation and tracking

biotope add data/raw/experiment.csv

Or add all new files in a folder recursively

biotope add -r data

Or download and stage remote files (will call add once finished)

biotope get https://example.com/data/experiment.csv

3. Check project status and staged files

biotope status

4. Create or complete metadata annotations

biotope annotate interactive --staged

Or complete incomplete annotations

biotope annotate interactive --incomplete

5. Commit metadata changes to version control

biotope commit -m "Add experiment dataset"

6. View project history

biotope log --oneline

7. Push or pull metadata to/from remote repositories

biotope push biotope pull

8. Verify data integrity

biotope check-data ```

Available Commands

• biotope init – Initialize a new project with Git integration.
• biotope add – Stage local data files for annotation and version control.
• biotope get – Download and stage remote files for annotation.
• biotope status – Show the current status of your project and staged files.
• biotope annotate – Create, complete, or validate metadata using the Croissant ML schema.
• biotope commit – Commit metadata changes using Git.
• biotope log – View the commit history of your project.
• biotope push / biotope pull – Share metadata with remote repositories.
• biotope check-data – Verify data integrity using checksums.
• biotope build, biotope chat, biotope read, biotope view – Additional tools for building knowledge representations, chatting with your project, extracting information, and visual analysis.

For more details and advanced usage, see the full documentation.

Copyright

• Copyright © 2025 BioCypher Team.
• Free software distributed under the MIT License.