github
40 posts
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Video: best practices for AI-assisted coding with GitHub, tests and CI
A 52 minute video with five demos of coding with an AI agent under version control, tests and continuous integration, using OpenCode and free NRP models.
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A Marp theme that reproduces the official SDSC slide template
An open source Marp theme that reproduces the official SDSC slide template, extracted from the brand guide PowerPoint file, with a published HTML preview.
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Managing projects with GitHub and AI agents: the structure problem
In my previous post about managing projects with GitHub and AI agents I described how I organize events and workshops with a single GitHub repository as the source of truth, issues for every activity, and an agent per collaborator.
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healpy 1.20.1: last release with macOS 14 wheels
The healpy 1.20.1 release includes bug fixes and is the final release to provide macOS 14 arm64 wheels before the GitHub runner retirement.
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Managing projects with GitHub and AI agents
Organizing conferences and workshops can quickly become overwhelming when plans, decisions, contracts, and meeting notes are scattered across multiple platforms.
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Running AlphaFold3 and OpenFold3 protein-ligand structure prediction on SDSC Expanse
I built two self-contained, reproducible projects that run realistic (non-toy) protein structure prediction on a single SDSC Expanse GPU node: one with DeepMind AlphaFold3 (via nf-core/proteinfold) and one with the fully open OpenFold3 (MCL1 protein-ligand ensemble).
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Synchronizing Google Docs and GitHub with gdrivemd
Managing documentation often requires choosing between the collaborative ease of Google Docs and the version-controlled structure of GitHub.
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Terminal-based AI assistant with GitHub for Education
GitHub offers to all academic people a free GitHub Pro account which allows you to use GitHub Copilot Pro, which includes access to the latest and most powerful models from OpenAI, Anthropic, and Google.
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Cosmosage Unshelver
This post describes the Cosmosage Unshelver. You can find the project on GitHub: zonca/openstackunshelverwebapp. There is an active pull request for further development. You can find the branch I am working on here: cosmosageunshelver branch.
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Software Citation Station
This post introduces the "Software Citation Station" by Tom Wagg, a tool designed to help researchers generate accurate and comprehensive citations for software. It simplifies the process of giving credit to software used in academic work, ensuring proper attribution and reproducibility.
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Take control of your Kaiser Permanente blood test results (no coding knowledge required)
Want to make sense of your Kaiser Permanente blood test results without needing to be a coding expert? This guide will walk you through using readily available tools to analyze your health summary, specifically focusing on lipid panels, with a step-by-step approach.
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Going full agentic for scientific software development
The landscape of scientific software development is being transformed by AI coding agents. Over the past few weeks, I've been exploring GitHub Copilot's AI coding agent capabilities for maintaining healpy, and the experience has been remarkable.
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Auto-merge GitHub pull requests after GitHub Actions pass
Pull request auto-merge is a small feature that keeps teams from babysitting green builds. Once every required check is green, GitHub merges the PR for you—no extra clicks, no late-night merges. Here is how to get it running safely with GitHub Actions.
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How to use GitHub Copilot for scientific computing
GitHub Copilot is rapidly transforming the landscape of scientific computing by streamlining code development and accelerating research workflows. This guide outlines how computational scientists can leverage Copilot, with a focus on professional and research-oriented use cases.
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Authenticate to GitHub in the browser with the device flow
Authenticating to GitHub in the browser using the device flow is essential for applications that cannot directly handle OAuth redirects.