Tag: github

Applied Gitflow

Posted in Git


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

How We Apply Gitflow

In some prior blog posts, we've covered a few patterns that we use for software development, including:

Tags:    git    github    programming    gitflow    hubflow    patterns   

centillion: a document search engine

Posted in Centillion


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 …

Tags:    python    centillion    search    search engine    google drive    github    flask   

First Post of the Fall, Part 2: Flaskadillo

Posted in Python


Flask + ILLO = Flaskadillo

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 …

Tags:    Github    Software    Python    Flask   

First Post of the Fall, Part 1: Data Commons

Posted in Centillion


Background: a bit about the Data Commons

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 …

Tags:    DCPPC    Data Commons    Github    Community    Science    Centillion   

Current Projects

Posted in General


A list of various ongoing projects:

The Git College of Surgery:

Python + APIs:

  • building an API that calls APIs so you can API while you API (a webhook that calls a hook - see captain hook)
  • testing APIs with Python + requests (currently top secret, coming soon.)

Python + Command line:

  • command line utilities with python …

Tags:    Git    Github    Software    Python