This is a retroactive blog post. This post was authored in February 2022, using material authored in July 2020.
The most up-to-date version of this content is here: https://charlesreid1.com/wiki/Applied_Gitflow
In some prior blog posts, we've covered a few patterns that we use for software development, including:
Automatically generating requirements.txt files with pinned versions for Python projects, which covered a Makefile rule …
We're excited to announce the public release of centillion, a document search engine.
centillion is a search tool that can be used by any individual or organization to index Github repositories (including the content of markdown files), Google Drive folders (including the content of .docx files), and Disqus comment threads.
centillion is tested using Travis CI.
centillion was originally written for the NIH Data Commons effort (which recently concluded). centillion was built to facilitate information-finding in a project with hundreds of people at dozens of institutions generating a sea of email threads, Google Drive folders, markdown files, websites, and Github …
On October 15, 2018, I had the opportunity to offer an in-lab learning opportunity (ILLO) at the Lab for Data Intensive Biology. The ILLO focused on Flask, a useful Python library for creating and running web servers. This library is useful because it has a very low learning curve, but also has the complexity to handle complicated, real-world projects.
As a part of this in-lab learning opportunity, I created repository with five simple Flask examples to highlight five useful capabilities of Flask.
The repository is called flaskadillo and it is available on git.charlesreid1.com or on …
It has been a productive but busy summer at the Lab for Data Intensive Biology.
As part of my job, I am supporting a lot of websites and infrastructure for the Data Commons Pilot Phase Consortium (DCPPC), which wrapped up Phase 1 this month.
The Data Commons is a large-scale effort to establish a community-driven set of standards for interoperability for biological data and computation, a massive effort and a broad mandate that has the potential to enable breakthrough research that is currently impossible because data and computations cannot inter-operate between the data …
A list of various ongoing projects:
The Git College of Surgery:
Python + APIs:
Python + Command line: