fix: Fix json response parsing error

[hyper-param]

REQUIRED: Add a summary of your PR here, typically including why the change is needed and what was changed. Include any design alternatives for discussion purposes.

Response parsing fix

REQUIRED: Fill out the below checklists or remove if irrelevant

2. If you are opening a PR for Community Notebooks under the notebooks/community folder:

• This notebook has been added to the CODEOWNERS file under the Community Notebooks section, pointing to the author or the author's team.
• Passes all the required formatting and linting checks. You can locally test with these instructions.

[gemini-code-assist]

Summary of Changes

Hello @hyper-param, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses a JSON response parsing error by updating a key dependency and refining the client initialization within a Vertex AI quickstart notebook. The changes ensure the notebook utilizes the latest compatible alphagenome library version and correctly configures the HTTP DNA client, which is expected to resolve the reported parsing issues and improve notebook execution clarity.

Highlights

• Dependency Update: The alphagenome Python wheel version has been updated from 0.4.2.3 to 0.4.2.5 in the quickstart notebook.
• Notebook Output Cleanup: The clear_output() function call, previously commented out, has been enabled to ensure cleaner output during notebook execution.
• Client Initialization Refinement: The model_version parameter has been removed from the dna_client_http.create_http_client function call, simplifying the client initialization process.

Using Gemini Code Assist

The full guide for Gemini Code Assist can be found on our documentation page, here are some quick tips.

Invoking Gemini

You can request assistance from Gemini at any point by creating a comment using either /gemini <command> or @gemini-code-assist <command>. Below is a summary of the supported commands on the current page.

Feature	Command	Description
Code Review	/gemini review	Performs a code review for the current pull request in its current state.
Pull Request Summary	/gemini summary	Provides a summary of the current pull request in its current state.
Comment	@gemini-code-assist	Responds in comments when explicitly tagged, both in pull request comments and review comments.
Help	/gemini help	Displays a list of available commands.

Customization

To customize Gemini Code Assist for GitHub experience, repository maintainers can create a configuration file and/or provide a custom code review style guide (such as PEP-8 for Python) by creating and adding files to a .gemini/ folder in the base of the repository. Detailed instructions can be found here.

Limitations & Feedback

Gemini Code Assist may make mistakes. Please leave feedback on any instances where its feedback is incorrect or counter productive. You can react with 👍 and 👎 on @gemini-code-assist comments. If you're interested in giving your feedback about your experience with Gemini Code Assist for Github and other Google products, sign up here.

You can also get AI-powered code generation, chat, as well as code reviews directly in the IDE at no cost with the Gemini Code Assist IDE Extension.

Footnotes

1. Review the Privacy Notices, Generative AI Prohibited Use Policy, Terms of Service, and learn how to configure Gemini Code Assist in GitHub here. Gemini can make mistakes, so double check it and use code with caution. ↩

[gemini-code-assist]

Code Review

This pull request addresses a JSON response parsing error in the AlphaGenome quickstart notebook. The fix involves updating the alphagenome package to version 0.4.2.5 and removing the model_version parameter from the create_http_client call, which was likely causing the issue. Additionally, a clear_output() call has been uncommented to improve the notebook's user experience. The changes are logical and seem to correctly address the reported issue. The code quality is good.