Code Ocean User Guide
v3.3.0
v2.5.0v2.6.0v2.7.0v2.8.0v2.9.0v2.10.0v2.11.0v2.12.0v2.13.0v2.14.0v2.15.0v2.16.0v2.17.0v2.18.0v2.19.0v2.20.0v2.21.0v2.22.0v3.0.0v3.1.0v3.2.0v3.3.0v3.4.0Release Notes
v3.3.0
v2.5.0v2.6.0v2.7.0v2.8.0v2.9.0v2.10.0v2.11.0v2.12.0v2.13.0v2.14.0v2.15.0v2.16.0v2.17.0v2.18.0v2.19.0v2.20.0v2.21.0v2.22.0v3.0.0v3.1.0v3.2.0v3.3.0v3.4.0Release Notes
  • Welcome to Code Ocean
  • Onboarding
    • Quick Start Guides
      • Create a Capsule in 5 minutes
      • Create a Pipeline in 5 minutes
    • Video Library
  • Key Concepts
  • Capsule Guide
    • The Capsule Interface
      • File Navigation/App Builder Panel
      • Editor Panel
      • Reproducibility Panel
    • The Structure of a Capsule
      • Metadata
      • Environment
      • Code
      • Data
      • .codeocean
      • Scratch
      • Results
    • Reproducible Runs
    • Version Control
      • Importing a Capsule from a Git Provider
      • Clone via Git...
    • Managing Capsules
      • Sharing a Capsule with Secrets
      • Exporting Capsules to your Local Machine
    • Secret Management Guide
      • Setting a Secret in the Account Settings Page
      • Accessing a Secret in a Capsule
  • Setting up the Environment
    • Selecting a Starter Environment
    • Package Managers and Adding Packages
    • Installing R packages
    • Environment Variables
    • Build Log
    • Post-Install Script
    • Compute Resources
  • Working in a Cloud Workstation
    • Launching a Cloud Workstation
      • Running RShiny in Code Ocean
      • Running Streamlit in Code Ocean
      • Using Terminal in Code Ocean
      • Using Ubuntu Desktop in Code Ocean
      • Using MATLAB in Code Ocean
      • Using VS Code in Code Ocean
    • Exiting a Cloud Workstation Session
  • Data Assets Guide
    • Types of Data Assets
    • Creating a New Data Asset
    • Capturing a Result
      • Provenance of the Result Data Asset
    • Using Data Assets in a Capsule
    • Managing Data Assets
      • Finding Data Assets
        • Custom Metadata
  • Pipeline Guide
    • The Pipeline UI
      • File Tree System
      • Pipeline App Panel
      • Timeline
    • Components of a Pipeline
      • Nextflow File
      • Capsules
      • Data
      • Results Bucket
      • Map Paths
      • Capsule Settings
      • Pipeline Settings
      • .codeocean
    • Managing Pipelines
      • Exporting Pipelines to your Local Machine
    • Capsule vs Pipeline Differences
    • How to Run Code in Parallel
    • Nextflow Configurations
    • Pipeline Monitoring
      • Monitoring Dashboard
      • Task Details
    • Nextflow Artifacts
    • nf-core Pipelines
      • Import nf-core pipelines
      • nf-core RNASeq Tutorial
        • iGenomes
    • Pipeline Tutorial
  • Release Capsules and Pipelines
    • Creating and Using Release Capsules
    • Creating Release Pipelines
    • Internal Releases
  • Collections
  • Code Ocean Apps
    • Genomics
    • Cheminformatics
    • Visualization
    • Machine Learning
    • Data Connectors
    • Quality Control
    • Use Cases and Examples
      • CombFold Pipeline
      • Data Connector Example
      • Gene Set Enrichment Overview
      • RNASeq Quantification Pipeline
  • App Panel Guide
    • App Builder User Interface
      • Validation pattern for strings
    • Passing App Panel's Parameters to the Script
    • Releasing an App Panel Capsule
    • Executing an App Panel Capsule
  • MLflow Guide
    • Enable MLflow Tracking
    • MLflow UI
    • Creating Models
    • MLflow Permissions
  • Models Guide
    • Creating Models
    • Managing Models
  • Git Provider Integration Guide
    • Setting up the Integration
    • Using Git Provider Integration
  • Code Ocean API
    • Authentication
    • Errors
    • Capsule
    • Computation
    • Data Asset
    • Python SDK
  • More Support
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On this page
  • File and Folder Status in Git
  • Additional options from Cloud Workstation
  • .gitignore
  • Duplicate a Capsule
  • Switching Branches

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  1. Capsule Guide

Version Control

PreviousReproducible RunsNextImporting a Capsule from a Git Provider

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Code Ocean integrates Git for version control , allowing seamless management of file versions within a Capsule. Each Capsule is a Git repository, enabling you to perform Git operations through the Capsule IDE or any command-line interface (CLI) in a Cloud Workstation.

File and Folder Status in Git

Each file and folder in the Capsule is accompanied by a small status icon that reflects its Git status:

  • Yellow icons: Indicate files or folders with uncommitted changes.

  • Green icons: Appear after selecting Commit Changes, signaling that changes have been committed to Git.

Icon

Is tracked by Git?

Is committed?

Yes

Yes

Yes

No

No

No

Additional options from Cloud Workstation

The Capsule IDE supports basic Git features such as committing and viewing differences (diffing). For more advanced Git operations such as revert, log, or managing remotes, you can use the CLI in a Cloud Workstation.

You can also amend the git commit comment in the terminal from a Cloud Workstation.

.gitignore

The .gitignore file in the Capsule specifies files or folders to exclude from version control and Git will not keep track of changes in these files.

  • The files and folder in .gitignore are indicated with a gray icon

  • Code Ocean automatically adds/data/to the .gitignore to follow best practices of excluding data files from version control.

Duplicate a Capsule

When duplicating a Capsule, both the committed history and uncommitted changes are copied to the new Capsule.

To duplicate a Capsule:

  1. From the top menu, click Capsule and select Duplicate.

  2. You will be redirected to the duplicated Capsule.

  3. Click Show Prior History to view the commit history from the parent Capsule.

Switching Branches

You can switch between Git branches in your Capsule using the branch drop-down menu as shown below. By default, the primary branch is master unless otherwise defined in the remote Git repository.

  • Branch switching is disabled while there are uncommitted changes -- once you start editing the Capsule, the drop-down button for switching branches is disabled until all of the changes are committed.

  • Using the CLI in a Cloud Workstation, you can also execute native Git commands to create, delete, or manage branches. These changes sync to the Capsule and appear in the branch list and other relevant locations.

This feature is especially useful when the Capsule is linked to an external Git repository (e.g. GitHub, GitLab, etc.).