Andrea Zonca

Software Citation Station

software

citation

github

This post introduces the “Software Citation Station” by Tom Wagg, a tool designed to help researchers generate accurate and comprehensive citations for software. It…

How to install codex and gemini cli

ai

When installing @google/gemini-cli or @openai/codex using npm, you might encounter permission errors with the default global installation command.

Container and Product EZID DOIs with Python

python

doi

This post refers to the ezid_api repository.

Disable Gemini CLI Loading Phrases

cli

gemini

How to disable the annoying loading phrases in Gemini CLI for a smoother experience.

Take control of your Kaiser Permanente blood test results (no coding knowledge required)

ai

github

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…

Auto-build JupyterHub images with GitHub Actions

jupyterhub

python

Overview: https://github.com/zonca/custom-jupyterhub-docker-image is a template that ships a JupyterHub-ready single-user image with common scientific Python tooling and…

Deploy the Dask Operator for JupyterHub on Kubernetes

kubernetes

jetstream2

jupyterhub

python

This post describes how to deploy the Dask Operator for Kubernetes alongside a Helm-based JupyterHub installation. The Operator provides a Kubernetes-native way to create…

Mixing Nextflow Executors for Hybrid Workflows

hpc

sdsc

nextflow

This post demonstrates how to combine different Nextflow executors within a single workflow, a powerful pattern for optimizing resource usage in scientific computing. By…

Implementing Conditional Logic in Nextflow Workflows

hpc

sdsc

nextflow

This post serves as a follow-up to my previous tutorial, “Running Nextflow on Expanse”, where I covered the foundational aspects of deploying Nextflow workflows on an HPC…

Hierarchical EZID DOIs with Python

python

doi

This post refers to the ezid_api repository.

Going Full Agentic for Scientific Software Development

github

ai

python

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…

Software Citation Station helper script

Proof-of-concept generate_citation.py in the software_citation repo pulls PyPI metadata plus repo CITATION files to produce the Markdown block that Software Citation Station …

Updated Tutorial on The Littlest JupyterHub on Jetstream

jupyterhub

jetstream2

I’m excited to share that I’ve contributed an updated tutorial on how to deploy “The Littlest JupyterHub” (TLJH) on a Jetstream instance!

Tampermonkey Script for Audible Filtering

This Tampermonkey script helps filter Audible search results by hiding items that do not meet certain criteria. Specifically, it hides audiobooks with a rating less than 4.0…

Running Nextflow on Expanse with Seqera

hpc

sdsc

nextflow

This tutorial will guide you through setting up Nextflow on Expanse using the Seqera platform. Nextflow is a powerful and flexible workflow management system that enables…

Auto-merge GitHub Pull Requests After GitHub Actions Pass

github

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…

Manage calendar of a scientific collaboration using Google Groups

openscience

Managing a calendar for a large scientific collaboration can be challenging. Over the years, I have tried different approaches to solve this problem.

Building Singularity Containers with Conda Environments from requirements.txt

singularity

python

This post introduces a method for building Singularity containers that include a Conda environment based on a requirements.txt file. This approach provides a reproducible…

EZID DOI Management with Python

python

doi

This project offers Python scripts for interacting with the EZID API to create and verify Digital Object Identifiers (DOIs).

Running Nextflow on Expanse

hpc

sdsc

nextflow

This tutorial will guide you through setting up Nextflow on Expanse. Nextflow is a powerful and flexible workflow management system that enables scalable and reproducible…

PySM 3.4.3 Released

openscience

pysm

python

PySM version 3.4.3 is now live. Install it from PyPI or upgrade existing environments with pip install --upgrade pysm3. Full details are available in the GitHub release notes.

Deploy a ChatGPT-like LLM on Jetstream with llama.cpp

jetstream

llm

This is a crosspost of the official Jetstream documentation: Deploy a ChatGPT-like LLM service on Jetstream. I built a brand new version of that tutorial that swaps in llama.…

PySM Methods Paper Published in ApJ

openscience

pysm

python

The Astrophysical Journal formally published our paper, Full-sky Models of Galactic Microwave Emission and Polarization at Sub-arcminute Scales for the Python Sky Model, on S…

Inspect SMTP sending through UCSD

Python

When configuring email sending through UCSD, it can be surprisingly unclear which SMTP server to use. The official documentation mentions three options: smtp.ucsd.edu, smtp.g…

OpenStack Unshelver Demo

openstack

jetstream

I recently vibe-coded a lightweight web application, using gpt-5-codex, that revives shelved OpenStack instances on demand. The stack is intentionally minimal: a FastHTML…