Category: Python

centillion: a document search engine

Posted in Python


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   

A Few of My Favorite PEPs

Posted in Python


Table of Contents

What's your favorite PEP?

PEPs, or Python Enhancement Proposals, are documents in which features, additions, or general ideas are proposed as additions to the core Python language.

As a Python user, we believe it's important to ask questions like this.

Picking a "favorite PEP" is not just about having a ready and clever answer to a question you might expect in a technical interview; the PEP documents really are important, and really do …

Tags:    python    pep    computer science    programming   

Context Managers in Python

Posted in Python


Table of Contents

A Predicament

Recently we spent some time contributing to dib-lab/eelpond (renamed to elvers), an executable Snakemake workflow for running the eelpond mRNAseq workflow.

In the process of tracking down a confusing bug in the Snakemake workflow, we used Snakemake's ability to print a directed acyclic graph (hereafter …

Tags:    context managers    testing    python    programming   

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 or on …

Tags:    Github    Software    Python    Flask