Release Notes 3.8 (September 2025)

Activity Center

The new Activity Center, accessible from the main navigation bar, provides a centralized view of user-triggered long-running operations initiated via the UI or API such as Data Asset creation, imports, and downloads.

Users can view job states including In Progress, Completed, Cancelled, and Failed, and can cancel relevant jobs directly from the Activity Center.

Jobs that will appear in the Activity Center include:

• All Data Asset creation events (with the exception of local files)

• Importing a Code Ocean Apps Capsule

• Data Asset Transfer (via Public API)

• All download events (e.g. logs, support bundle, files)

Enhanced Secrets Management

Several updates have been introduced to enable broader integration with private resources, reduce manual setup, and generally make working with secrets more convenient and efficient.

Streamlined Actions Menu

Secrets Actions are now grouped under a three-dot menu to the right of the secret to provide a cleaner user interface.

Pipeline Settings Reorganization with Centralized Secrets Management

Pipeline Settings is now accessed via a side panel with tabs, including a Credentials tab for managing Pipeline Secrets. For Pipelines built with the UI, all secrets from constituent Capsules are now listed centrally in the Credentials tab for easier visibility and configuration.

Secrets Support in Custom Pipelines

You can now add and manage secrets in custom Pipelines to access private, non-AWS resources.

Updated Secrets Configuration in Capsule Environment

The GIT_ACCESS_TOKEN secret is now provided in the Capsule Dockerfile via a Docker secrets mount in the RUN commands of pip, pip3, and R GitHub as follows:

RUN --mount=type=secret,id=git-access-token,env=GIT_ACCESS_TOKEN \
    ...

All secrets are provided via a Docker secrets mount in the RUN /postInstall command as follows:

RUN --mount=type=secret,id=secrets . /run/secrets/secrets \
    && /postInstall

Existing Capsule environments will be automatically updated to the new configuration upon any modification or update of secrets in the Capsule.

Automatically generated secrets.json file in Capsules

Information regarding the secrets used in a Capsule, including their descriptions and associated environment variables, are now reflected in a new secrets.json file generated in the Capsule's .codeocean folder for enhanced reproducibility. Like other files in the .codeocean folder, the secrets.json file can't be manually edited.

Set Environment Variable Names

Easily set the names of environment variables associated with secrets in Capsules from the three-dot Secrets Actions menu. Any changes will be reflected in the aforementioned secrets.json file.

Pipelines - Automatic GPU Queue Routing

Custom and nf-core Pipeline processes labeled with process_gpu will now automatically run on the deployment's AWS Batch GPU Compute Environment, streamlining execution and eliminating the need for manual configuration to ensure GPU access.

UI Enhancements

• Copy & Pin parameter values directly from the run menu in the Timeline for easier comparison and reuse.

• Restore Pipeline Editor from the Pipelines action menu in custom Pipelines.

Git Branch Improvements

Git Branches now support:

• Slashes (e.g. feature/new-model)

• Uppercase characters (e.g. ReleaseCandidate)

Architecture - Local AMI Build Support & Packaged Install

You can now build Code Ocean AMIs locally without accessing private repos or Docker images. Installation is now encapsulated in an installable RPM package and Docker pulls are separated from the AMI build process.

Please reach out to [e-mail] if you'd like to implement this method of installing Code Ocean.

Architecture - Amazon Linux 2023 AMI Migration

Code Ocean AMIs are now based on Amazon Linux 2023 (previously Amazon Linux 2) for improved performance, security, and long-term support.