Bash dotfiles

.bashrc

At the top of .bashrc, the following files are sourced if they’re present. This keeps things a little more organized and modular:

for file in ~/.{path,exports,bash_prompt,functions,aliases,extra}; do
    [ -r "$file" ] && [ -f "$file" ] && source "$file";
done;
unset file;

These files are described in the sections below, but a quick summary:

• .path: all export PATH=... can go here.

• .aliases: store your aliases here.

• .functions: store your bash functions here.

• .bash_prompt: edit your bash prompt here.

• .exports: add your various env var exports here.

• .extra: any machine-specific config goes here.

The modular organization for bash configuration is inspired by this repo.

Other notable parts of the .bashrc:

• Update terminal size after commands

• Enables autocd if available. When enabled, just the name of a directory will be sufficient to cd to it.

• Enables globstar if available. When enabled, the pattern ** used in a filename expansion context will match all files and zero or more directories and subdirectories. If the pattern is followed by a ‘/’, only directories and subdirectories match.

• Enables bash completion and git completion

• Enables color support for ls

• If running under tmux, always deactivate environments when creating a new bash shell (see conda for more details on this)

.bash_profile

.bash_profile does only one thing: it sources .bashrc.

.path

This file ends up being lots of export PATH="$PATH:/some/other/path" lines. It is initially populated to put ~/opt/bin and ~/mambaforge/condabin on the path. As you install more software in other locations, this is a tidy place to put the various exports.

.aliases

This file keeps aliase separate for easier maintenance. See .aliases for the commands set for each alias.

alias	description
vim	always use neovim (this is added only if nvim is found on the path)
D	sometimes when using tmux the display is not set, causing GUI programs launched from the terminal to complain. This sets the display variable.
ll	useful ls arguments (long format, human-readable sizes, sorted by time (latest at bottom), use color). MacOS has different options, so this alias tries to handle that correctly.
la	same as above, but also show hidden files
v	Live, searchable, syntax-highlighted preview of files in a directory. Needs fzf and bat installed
..	faster way of moving up a directory
gsv	Opens vim and runs vim-fugitive. See vim-fugitive for details.
glv	Opens vim and runs diffview for browsing git history. See diffview.nvim for details.
s	Runs the start_agent function (see .functions below)
git-clean-branches-master	Deletes any git branches that have been merged into the master branch
git-clean-branches-main	Similar to above, but used for repos where main is the default branch instead of master.

.functions

Separate file for bash functions. This is also where fzf and autojump are set up. Some notable functions defined here:

function	description
start_agent	Use this to start the ssh agent so you don’t need to keep entering your ssh key during a session
tre	Nicer tree output, colored and piped to less
sa	Open fzf to search across all conda environments, and activates the selected one
prsetup	When run in a clone of a repo with a pull request from a fork, get set up to push changes back to the contributor’s branch
ca	Equivalent to conda activate, but done in such a way that you don’t always need to have conda activated. See conda for details.
conda_deactivate_all	Deactivate all conda environments. Useful when running under tmux; see conda for more details.
hostlist	Print out a nice table of hostnames and aliases from your .ssh/config file. Useful for when you’re trying to remember how to log in to an infrequently-accessed host.

.bash_prompt

This file changes the prompt color for Biowulf or Helix (NIH HPC), but here you can add any other hosts or colors. See https://misc.flogisoft.com/bash/tip_colors_and_formatting for color options.

.extra

Nothing is in here by default. This is a good place to store host-specific details.

.exports

Exported environment variables.

env var	value and description
EDITOR	set nvim as the default editor if it exists, otherwise use vim
LC_ALL	en_US.UTF-8, localization setting for US English. $LANG and $LANGUAGE should also be set (see below)
LC_LANG	en_US.UTF-8, localization setting for US English
LC_LANGUAGE	en_US.UTF-8, localization setting for US English
HISTSIZE	Set a large history size
HISTFILESIZE	Same for history file
LESS_TERMCAP_se, LESS_TERMCAP_so	In tmux, default is to italicize identified search terms. This highlights instead.
MANGPAGER	Uses less -X, which does not clear the screen after exiting.
SHELL	Exports shell as /bin/bash if on Mac. See Mac for details on newer Macs