Welcome to the virion wiki!

This wiki will be used for in-depth documentation of the repo.

Specifically it will cover:

• Accessing Versioned Data
• Development processes
• Github Actions
• Reproducing Virion on your machine

Early in the process of updating Virion after it's initial creation that started in fall 2023, we set up some tracking components using GitHub Projects / milestones. At the time, Virion ran entirely on GitHub Actions pipeline, and was limited by the memory limits of free GitHub Actions. The largest memory component of the Virion pipeline is the Genbank component of the pipeline. The goal was to address this in three ways, first by moving the workflow over to a targets framework, to clean up the code (which was mostly completed), and then also to let the GitHub Actions pipeline run on a Docker container so that it would be a bit more stable and hopefully reduce some of the challenges with the memory access. Code cleanup (Fall 2023) moved the pipeline into one somewhat-consistent flow of code organization and style, and some progress was made on the Docker container.

The Docker container (not updated since 2023) does exist on Docker Hub, and a version of the pipeline could successfully run on that image until at least summer 2024 without known issues related to the pipeline. Some of these solutions worked (and are documented in the merges of the relevant project on GitHub), but only a partial solution was implemented at the time, due to the fact that cleaning up the code base and working on some efficiency updates allowed the GA-based pipeline to continue working well enough for the time, since no resources existed beyond one grad student to continue to make progress. It was also put on the backburner due to the fact that other issues with virion (e.g. inclusion of GLOBi records) represented larger challenges that needed to be solved before development was worth continuing.

In the spring and summer of 2025, staff refactored the pipeline to use the targets package and refactored the github actions to be more memory efficient.