Python

Show current Python class and method name or function name in Vim

Submitted by Jeet Sukumaran on

There are a number of Vim plugins to show the current Python class and method name or function name (e.g., this). However, they can be extremely "heavy" (the linked example requires Vim compiled with Python, and is pretty slow when indexing a large Python file) and moreover, all seem to be geared to showing the information dynamically in the status bar. While the latter might be desirable in some contexts, the required binding to a CursorHold trigger coupled with the slowness in indexing, make it clumsy to use when navigating large files. Sometimes, all that is wanted or needed is an "on-demand" brief display of the information. The following code takes care of this. When sourced into your Vim session, it echos the current Python class and method name or function name when invoked via "<Leader>?" or ":EchoPythonLocation".

Execute Selected Lines of (Optionally) Marked Up Python Code in a Vim Buffer

Submitted by Jeet Sukumaran on

There are a number of solutions for executing Python code in your active buffer in Vim. All of these expect the buffer lines to be well-formatted Python code, with correct indentation. Many times, however, I am working on program or other documentation (in, for example reStructuredTex or Markdown format), and the code fragments that I want to execute have extra indentation or line leaders.

Using DendroPy Interoperability Modules to Download and Align GenBank Sequences and Estimate a Maximum Likelihood Tree

Submitted by Jeet Sukumaran on

The following example shows how easy it can be to use the three interoperability modules provided by the DendroPy Phylogenetic Computing Library to download nucleotide sequences from GenBank, align them using MUSCLE, and estimate a maximum-likelihood tree using RAxML.

Pure-Python Implementation of Fisher's Exact Test for a 2x2 Contingency Table

Submitted by Jeet Sukumaran on

While Python comes with many "batteries included", many others are not. Luckily, thanks to generosity and hard work of various members of the Python community, there are a number of third-party implementations to fill in this gap. For example, Fisher's exact test is not part of the standard library.

A Story of a Heisenbug Hunt

Submitted by Jeet Sukumaran on

It is past 4 am, and the bug hunt is over. It was a weird one. One that I'll remember. It led me on a wild exhausting chase through dark nooks and crannies of a horribly-written nightmare of a code base. What made it weird was that, with the same random number seed, I got different behavior depending on whether there were some (debugging-related) print statements in some parts of code. Even if these statements were in parts of the code that were entirely separate from where the failure was happening.

An Idiosyncratic Analogical Overview of Some Programming Languages from an Evolutionary Biologist's Perspective

Submitted by Jeet Sukumaran on

This article was originally posted at geodendron.

R

R is like a microwave oven. It is capable of handling a wide range of pre-packaged tasks, but can be frustrating or inappropriate when trying to do even simple things that are outside of its (admittedly vast) library of functions.

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