Python

Closing my tabs (Sep 5 2025)

NIH budget, AI, R, Bluesky & Science, state of biotech, AI in higher ed, R packages Top 40, structural variation, statistical power, Python documentary…

Sep 5 •

uv, part 4: uv with Jupyter

Using uv with Jupyter: demo using polars and seaborn for analysis and visualization.

Jun 23 •

uv, part 3: Python in R with reticulate

Two demos using Python in R via reticulate+uv: (1) Hugging Face transformers for sentiment analysis, (2) pyBigWig to query a BigWig file and visualize…

May 6 •

uv, part 2: building and publishing packages

Using uv to create, manage, build, and publish a Python package to PyPI

Mar 24 •

uv, part 1: running scripts and tools

Over the past year I’ve heard a lot great things about uv, an extremely fast Python package and project manager, written in Rust.

Mar 3 •

Turn a GitHub repo into a single text file for LLM-friendly input

The open source repo2txt web app will take a GitHub repo URL, displays the directory structure, lets you choose which files to include, and provides a…

Dec 9, 2024 •

TIL: dplyr::mutate()'s .keep argument

Use the .keep argument in dplyr::mutate() to control which variables to retain after mutating to create new variables.

Dec 2, 2024 •

Tech I'm thankful for (2024)

Data science and bioinformatics tech I'm thankful for in 2024: tidyverse, RStudio, Positron, Bluesky, blogs, Quarto, bioRxiv, LLMs for code, Ollama…

Nov 25, 2024 •

Build a Python CLI with Click+Cookiecutter

Demonstration for how to build a Python command line utility with Click using a Cookiecutter project template, and how to publish to PyPI and Docker Hub

Nov 10, 2024 •

Python for R users

A Google search for “R vs Python” returns thousands of hits across sites like Reddit, IBM, Datacamp, Coursera, Kaggle, and many others.

Oct 21, 2024 •

AI code completion in Positron

Positron doesn't have GitHub Copilot, but Codeium and others are good alternatives.

Oct 1, 2024 •

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