xenium-devkit

Repo Structure

This repo is for the Latch Agent to work specifically with the 10x Genomics Xenium platform.

Each Devkit has the following components:

• main.md
• steps/
• lib/
• wf/
• requirements.txt

main.md

The agent reads from the following fields in main.md:

• <pre_analysis_questions> any questions to ask before analysis if they are not obvious from context
• <pre_analysis_step> step to run before starting the plan to set up the environment
• <plan> the names of the steps and where to find step docs
• <data_structure> the organization of data in the customer's workspace
• <self_eval_criteria> specific, often numerical, pass/fail sanity checks after the agent has completed the entire plan

steps/

Each step in the <plan> has its own document that is loaded before executing the step.

• <goal> describes the scientific goal of the step
• <method> contains a description of the procedure to accomplish the goal
• <workflows> contains the names of any Latch workflows the agent should invoke
• <library> contains the names of any technology-specific library the agent should use
• <self_eval_criteria> contains specific, often numerical, sanity checks to run through before determining the step is complete

lib/

Contains Python library code with technology-specific helper functions the agent can import and use.

wf/

Contains documentation for Latch workflows the agent can invoke. Each workflow document includes:

• <goal> describes what the workflow accomplishes
• <parameters> describes the workflow parameters and their expected values
• <outputs> describes what the workflow returns
• <example> provides example code for invoking the workflow

requirements.txt

Optional file listing additional pip packages to install at pod startup. New packages can be added, but versions of packages already in the base image requirements cannot be changed due to version constraints.

How to Test

If your changes are on the main branch of your devkit, they will be pulled in automatically for new pods. However, if you want to test changes before merging to main, follow these steps:

1. Create a branch in your devkit with your proposed changes
2. SSH into your pod
3. Navigate to your tech docs directory and checkout your branch:

   cd /opt/latch/plots-faas/runtime/mount/agent_config/context/technology_docs/xenium
   git fetch origin
   git checkout <your_branch_name>

4. Test your changes

Note: The branch will be reset to main on pod restart. Testing changes to requirements.txt on branches is not currently supported.