About

Author

Neil Shephard

Hi, I’m Neil and work as a Research Software Engineer at the University of Sheffield. My education started with BSc in Zoology and Genetics followed by a MSc in Genetic Epidemiology. My academic career started with just over a decade as a Genetics Statistician where I learnt GNU/Linux system administration and reproducible research practices before shifting to Medical Statistics and working on Clinical Trials for a similar amount of time and taught myself R before a stint as a Data Scientist in industry company where I not only learnt Python but about good software development practices.

Here you’ll find posts about Research Software Engineering, Git/GitHub/GitLab, GNU/Linux (Gentoo, Arch, OpenWRT), Python, Bash, R, Emacs, Org-mode, Statistics, Genetics, Evolution and more.

When not working I enjoy climbing, running, cycling, cooking, hiking, photography, gardening and spending time with my family.

Quarto Custom domain on GitHub Pages

This blog is published using the excellent Quarto framework to GitHub Pages which offers free website hosting. However, astute readers familiar with this sort of setup will…

Pytest Matplotlib

Pytest is an excellent framework for writing tests in Python. Sometimes the code you want to test will generate images using Matplotlib or related libraries based around it…

Pennine Way 2024

This summer I decided to hike the iconic Pennine Way a 431 kilometre (261 miles) national trail stretching between Kirk Yetholm in the North and Edale in the South.…

virtualenvwrapper hooks

I’ve written previously about virtualenvwrapper which I use to manage my Python Virtual Environments and mentioned the possibility of using hooks but didn’t go into detail.

Pytest Fail and Skip

Pytest is an excellent framework for writing tests in Python. Sometimes tests don’t pass though and you might want to mark them as failing or skip them.

Git - Worktrees

A common task in Git workflow is the need to switch/checkout branches and check work that has been done on another branch, running tests, perhaps contributing to code that…

Git - Making Amends and Fixing things up

Git is the world’s most popular version control software out there at the moment and if you write code and version control it the chances are you are using it. It’s a…

Git Remotes Revisited

I’ve written before about Git Remotes but in my on-going effort to improve my understanding of the tools I use daily I’ve discovered that it is possible to have a single remo…

Pytest Parameterisation

Pytest is an excellent framework for writing tests in Python. One of the neat features it includes is the ability to parameterise your tests which means you can write one…

virtualenvwrapper

If you use Python heavily you will likely be familiar with Virtual Environments. These provide isolated installs of specific packages that take precedence over any packages…

Repository Review with Scientific Python

I’ve written before about Python Packaging and pre-commit which I’m a big fan of. Today I discovered a really useful tool for checking your packaging configuration and…

R Resources

R is a statistical programming languages and one of the most popular languages for data analysis, statistics and plotting in academia and industry. Learning a new language…

Git Remotes

Git and various forges such as GitHub GitLab are useful collaborative tools for version controlling, sharing and working collaboratively. Normally a repository resides on…

GitLab CI - Automatic Publishing to PyPI

I’ve written previously on Python Packaging and in that article included details of how to automate publishing to PyPI from GitHub. This article details how to automatically…

Pre-commit and R Packaging

This post is aimed at getting you up and running with the R precommit Package. This shouldn’t be confused with the Python pre-commit Package although as you might suspect…

Pre-Commit : Useful Hooks

I’m a big fan of pre-commit and have written about it before (see posts on pre-commit, pre-commit CI and pre-commit updating). This post discusses some of the hooks that I…

Sphinx Documentation

How to generate documentation websites for your Python package using Sphinx, including generating API documentation automatically, build multiple versions across releases…

Python Packaging

This post describes steps in creating a Python package. If you are looking for information on installing packages this is done using Python PIP.

Browser Extensions

Most people use web-browsers a fair bit. There are a number of extensions available which make their use more stream-lined and efficient. This post covers those that I use.…

Pre-Commit.ci : Integrating Pre-Commit into CI/CD

NB If you’ve not read it already I would recommend reading my previous post on using pre-commit as the contents described herein assume that you are already using pre-commit …

Running in 2022

I started running 🏃 in 2019. It never used to appeal but I wanted to get more regular exercise easily from my doorstep as despite commuting by bike for most of my life and…

Who’s to Blame

Git blame shows who made changes to which line of code for a given point in its history.

Pre-Commit : Customising and Updating

Pre-commit is a tool for running hooks prior to making commits to your Git history. If you’re not familiar with it then you may want to read the earlier post Pre-Commit …

Linux Command Line Alternatives

The command line is my second home when sat at a computer (Emacs is my first ;-) and the UNIX Philosophy is the key to the huge amount of highly productive tools that are…

Git : Custom SSH credentials for git repositories

How to configure individual Git repositories to use specific SSH keys. This is useful if you have more than one account on a forge, for example a personal and work account.

Pre-Commit : Protecting your future self

Pre-commit is a powerful tool for executing a range of hooks prior to making commits to your Git history. This is useful because it means you can automatically run a range…

Linting - What is all the fluff about?

NB This article originally appeared on RSE University of Sheffield but is updated here.

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