Scott Chamberlain

cowsay is a command line program written in Perl. The original version had a final release in 2016 (that’s the version of many installed cowsay programs) and there’s a number of forks of that release in Perl. There are also many many versions of cowsay in other programming languages, like the one I maintain written in R, unimaginatively called cowsay. I wrote about cowsay here back in 2014.

cowsay v1

Introduction   At work (Fred Hutch Cancer Center) we’ve been working on an R package (sixtyfour) over the last ~1.5 years. This post is a quick intro to the package with some learnings about working with AWS. sixtyfour is a science-focused, more humane R interface to AWS.

sixtyfour: writing robust code against AWS

webmockr v2 is here. You can find the source at https://github.com/ropensci/webmockr, and the docs at https://docs.ropensci.org/webmockr. There’s some big changes in this version; most importantly a breaking change, thus the major version change this time. Here’s a run down of the important items in this release.

webmockr v2: another day, another stub

While reviewing an R package at work I realized I wasn’t totally sure what advice to give about examples for internal functions in a package. That is, there’s an R package. The package has some exported functions, and some internal functions that are not exported.

Keeping internal function examples alive

Over the past few months at work we’ve been looking into web framework options for a project that currently uses R Shiny. Our needs have grown beyond what Shiny can provide. We decided to try Rails, SvelteKit, and HTMX/FastAPI to see which one would best suit our needs.

Picking a web framework

At work I’ve been using Quarto quite a bit for website and books for work projects.

Software rules and Quarto

I worked on a refactor of an R package at work the other day. Here’s some notes about that after doing the work. This IS NOT a best practices post - it’s just a collection of thoughts. For context, the package is an API client.

Refactoring notes

I recently opened an issue in a repository for a package I’m working on to think about potential footguns and how to avoid them. That word “footguns” got me thinking;

Avoiding the word footgun(s)

I’ve been working on an inherited Shiny app at work for the past few months. One of the many frustrating things about Shiny lately has been around buttons. Well, it wasn’t really about buttons, but that’s where it started. I noticed that a number of buttons - some having file inputs, some having text inputs - did not trigger every time, and I expected them to trigger every time no matter what.

Shiny button weirdness

notes to self for next job hunt (some of which may be generally useful): don’t apply to general tech companies anymore for many reasons. heard back from very very few but that may be b/c I don’t know many people at general tech companies never been able to get through interviews; they’re presumably looking for computer science grads (not me) most of their missions are probably not stuff I’d be happy about at the end of the day.

Job searching notes

It’s been interesting switching jobs with respect to programming languages. I used to write 95% R - now I write 95% Python.  I have been using Python for many years, but not seriously or getting paid either. I’ve learned alot in the first 6 months.  Some Python things learned: Functions and methods   I used to think functions and methods were the same thing. But during the last 6 months I learned that functions and methods are not the same.

Notes on Python

Notes on The Emperor of All Maladies

What is uv   I’ve recently started using uv to manage Python projects and packages: many projects at work and the one active package I have on pypi.org (habanero).  I don’t really know enough about all the various Python tools similar to uv to give an informed opinion. Rather, this is purely reflections on using uv.  uv’s tagline is:  uv docs and source code. Reflections  Fast   It’s super fast.

uv notes

Since most of my education has taken place above the organism level, and since my current job concerns sub-organism processes, I want to get more familiar with those sub-organism things. So I’m reading and taking notes on my blog about the stuff I’m reading.

Notes on A Biology Primer for Computer Scientists

I recently had a use case at work where I wanted to check that file paths given in a Python script actually existed. These paths were in various GitHub repositories, so all I had to do was pull out the paths and check if they exist on GitHub. There were a few catches though.

Python, ast, and redbaron

This blog is now using Hugo. Important - if you subscribe to the RSS for this blog you likely have to delete/remove the old one and add the new RSS link.

Moved to Hugo

For work I’m reading and taking notes on my blog about cancer biology texts. The following are notes on most chapters of The Emperor of All Maladies by Siddhartha Mukherjee. Some of these are not actual chapters (e.g., “Leukemia” is not a chapter).  I listened (during many episodes getting a kid to sleep in the middle of the night) to this book borrowed from my local library with the Libby app.

Soooo, my last job at Deck was amazing. I loved it. I was doing data engineer stuff there, mostly maintaining infrastructure for data pipelines. Everyone was great and the mission was amazing: helping Democrats win. Yet the company was shut down about a month ago, sending me on another job search, the 3rd since early/mid 2021.

Working at Fred Hutchinson Cancer Center

taxizedb arose from pain in using taxize when dealing with large amounts of data in a single request or doing a lot of requests of any data size. taxize works with remote data sources on the web, so there’s a number of issues that can slow the response down: internet speed, server response speed (was a response already cached or not; or do they even use caching), etc.

taxizedb: an update

TL;DR  In 6 months (end of November 2022) the CRAN Checks API https://cranchecks.info/ will be gone You can still get badges at https://badges.cranchecks.info You can use the new badges like: [![cran checks](https://badges.cranchecks.info/worst/dplyr.svg)](https://cran.r-project.org/web/checks/check_results_dplyr.html)  Find more details at https://github.com/sckott/cchecksbadges Sunsetting the CRAN Checks API   If you contribute an R package to

CRAN Checks API and Badges

In February this year I wroute about how many parameters functions should have, looking at some other languages, with a detailed look at R. On a related topic …  As I work on many R packages that are API clients for various web services, I began wondering: What is the best way to deal with API routes that have a lot of parameters?

API client design: how to deal with lots of parameters?

I was working on a work task last week, and needed to filter out one instance of a class from a list of class instances. No matter how you do this speed doesn’t matter too much if you’re doing this operation once or a few times. However, I this operation needs to be done about 100K times each time the script runs - so speed definitely does matter in this case.

List comprehension vs. filter vs. key lookup

I wrote the other day about overcoming an issue with Shiny. Another issue I ran into concurrently was about file inputs. The issue was that file inputs (i.e., shiny::fileInput) was difficult to clear.

Shiny file inputs

\  Code is often arranged in packages for any given language. Packages are often cataloged in a package registry of some kind: NPM for node, crates.io for Rust, etc. For R, that registry is either CRAN or Bioconductor (for the most part).  CRAN has the concept of an archived package.

stories behind archived packages

You’ve experienced an HTTP redirect (or URL redirect, or URL forwarding) even if you haven’t noticed. We all use browsers (I assume, since you are reading this), either on a phone or laptop/desktop computer. Browsers don’t show all the HTTP requests going on in the background, some of which are redirects.

Mocking HTTP redirects

My parents just found this email they had printed out from me from May 19, 2006, when I was 26. I chatted about some family stuff, then had this rambling string of weird thoughts below. I thought others might appreciate a good cringe - or cringy laugh - at my expense. It’s especially funny because I’m most def an atheist. I don’t know, those Tucson sunsets really are transformative.

Recology