Vim Regular Expression Special Characters: To Escape or Not To Escape
Vim's regular expression dialect is distinct from many of the other more popular ones out there today (and actually predates them). One of the dialect differences that always leaves me fumbling has to...
View ArticleUsing DendroPy Interoperability Modules to Download, Align, and Estimate a...
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...
View ArticleSetting Up Git to Use Your Diff Viewer or Editor of Choice
Git offers two ways of viewing differences between commits, or between commits and your working tree: diff and difftool. The first of these, by default, dumps the results to the standard output. This...
View ArticleUseful diff Aliases
Add the following aliases to your '~/.bashrc' for some diff goodness: alias diff-side-by-side='diff --side-by-side -W"`tput cols`"' alias diff-side-by-side-changes='diff --side-by-side...
View ArticleSafe and const-correct std::map Access in C++ STL
The Standard Template Library std::map[] operator will create and return a new entry if passed a key that does not already exist in the map. This means that you cannot use this operator when you do not...
View ArticleSome Vim Movement Tips
Within-line character-based movement: `h` and `l` move you left and right one character, respectively. `fc` or `Fc` will take you forward to the next or back to the previous, respectively, occurrence...
View ArticleYonderGit: Simplified Git Remote Repository Management
One of the great strengths of Git is the multiple and flexible ways of handling remote repositories. Just like Subversion, they can be "served" out of a location, but more generally, if you can reach...
View Article‘xargs’– Handling Filenames With Spaces or Other Special Characters
xargs is a great little utility to perform batch operations on a large set of files. Typically, the results of a find operation are piped to the xargs command: find . -iname "*.pdf" | xargs -I{} mv {}...
View ArticleUsing Python’s “timeit” Module to Benchmark Functions Directly (Instead of...
All the basic examples for Python's timeit module show strings being executed. This lead to, in my opinion, somewhat convoluted code such as: #! /usr/bin/env python import timeit def f(): pass if...
View ArticleBuilding MacVim Natively on OS X 10.7 and Higher
You might want to do this if you want to install the latest snapshot and no pre-built release is available. OR you might want MacVim to use a custom Python installation instead of the default one on...
View ArticleSmart (`infercase`) Dictionary Completions in Vim While Preserving Your...
Dictionary completions in Vim can use a 'infer case' mode, where, e.g., "Probab" will correctly autocomplete to, e.g., "Probability", even though the entry in the dictionary might be in a different...
View ArticleSetting up the Text Editor in My Computing Ecosystem
Image from WikiMedia Commons Basic Setup of Shell to Support My Text Editor Preferences By "text editor", I mean Vim, of course. There are pseudo-operating systems that include rudimentary text-editing...
View ArticleDynamic On-Demand LaTeX Compilation
Most of the existing approaches to integrating LaTeX compilation into a LaTeX writing workflow centered around a text editor (as opposed to a fancy-schmancy IDE) are horrendously bloated creatures,...
View ArticleTaking it to a 11: Dramatically Speeding Up Keyboard/Typing Responsiveness in...
If you use a Mac/OSX, then enter the following commands in your shell and reboot: $ defaults write -g KeyRepeat -int 0 $ defaults write -g InitialKeyRepeat -int 15 If you live in a text editor or the...
View ArticleSetting up a Python Scientific Environment (NumPy, SciPy, pandas,...
It is better than a nightmare from which you cannot wake up ... Install Homebrew: $ ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)" Find problems and fix them (typically...
View ArticleNefertiti – Color Scheme for Vim with Dynamically-Controlled Brightness Levels
A queen of color schemes ....
View ArticleFrom Acolyte to Adept: The Next Step After NOP-ing Arrow Keys in Vim
We all know about no-op'ing arrow keys in Vim to get us to break the habit of relying on them for inefficient movement. But, as this post points out, it is not the location of the arrow keys that makes...
View ArticleVim: Insert Mode is Like the Passing Lane
Insert mode is not the mode for editing text. It is a mode for editing text, because both normal and insert modes are modes for editing text. Insert mode, however, is the mode for inserting new/raw...
View ArticleSolving the “Could not find all biber source files” Error
Biblatex is a fantastic bibliography/citation manager for LaTeX. It trumps the older bibtex for its much easier customizability and configuration. It does however, have one bug that can be very...
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