Overview

In this post we cover a strategy for managing configurations for programs using a Singleton pattern to create a static Config class.

This allows the user to create an instance of the Config class, pointing it to a specific config file, which it loads into memory.

The Config class provides several static methods for accessing configuration options from the config file. Here's an example of its usage:

Config('/path/to/config.json')

if Config.get_foo() == "bar":
    do …

Summary

In a prior post, we covered how to write a mock API server that stored a thread as a class attribute and used it to run the server in the background by starting a thread.

However, we neglected to cover how to actually use the mock API server. So here we include some examples of how you can use the mock API server to write better tests for components that require interacting with APIs.

The MockAPIServer Class

Let's start with a recap of the mock API …

Overview

In this post we discuss a way of mocking an API server during tests. This technique will let you create a fake API server that can respond to API calls however you want.

The technique is twofold:

• First, we create a mock API handler that extends BaseHTTPRequestHandler, which is the built-in HTTP server class in Python. We can extend the server class to control how it responds to requests - to …

Overview

In this short blog post, we talk about how and when you can take a method signature that defines input positional arguments by name, like this:

def foo(arg1, arg2, arg3):
    pass

and write code that will return a dictionary containing a keyword arguments-like structure:

>>> foo('red', 'blue', 'green')
{
    'arg1': 'red',
    'arg2': 'blue',
    'arg3': 'green'
}

We will cover an example of writing a decorator that utilizes input arguments from both the decorator and from the …

Confuse-A-Constructor

Today, we are going to confuse a constructor.

What is the constructor?

One of the first concepts encountered in object-oriented programming is that of the constructor, the method that …

Overview

This post is a summary of a useful Python programming pattern called the Registry pattern.

The Registry pattern is a way of keeping track of all subclasses of a given class.

More details about this pattern are available at https://github.com/faif/python-patterns.

What is the Registry Pattern …

Summary

In this post, we cover a pattern for automatically generating a requirements.txt file that has the latest compatible versions of required software, and that specifies the full and exact version of each package to make the Python environment reproducible.

This will turn a requirements input file (called requirements.txt.in for example) that looks like

numpy

into a requirements file that specifies the exact version of numpy and all dependencies, like

numpy==1.18 …

Overview

This post covers a technique for mocking AWS in unit tests so that you can test functionality that normally requires API calls and handling responses, by mocking those responses instead of making actual API calls.

A Simple Example: Mocking API Responses

The Genuine AWS Call

Let's start with an example of an AWS API call. Here's how our program will be structured: start with a driver lister.py that creates an AWS secrets manager client and defines a function to list …

Table of Contents

• What's your favorite PEP?
• PEP 0
• PEP 8
• PEP 20
• PEP 3099
  • Addendum: 2 to 3 Changes
• PEP 202
• All the PEPs on Github

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 …

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 referred to as a dag) representing its task graph. Snakemake prints the dot …

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 …