Dotfiles

This is a central repo for my dotfiles. It's designed to work on macOS Mojave and newer and on linux supercomputing clusters. It's a work in progress, use at your own risk.

Dependencies:

• bash >= 5.x
• nano >= 4.6
• git >= 2.24
• ack >= 3.x
• GNU coreutils >= 8.31
• GNU time

Summary

1. bash_profile.sh just sources ~/.bashrc which is symlinked to 'bashrc.sh'
2. bashrc.sh contains all the sourcing statements
3. bash_aliases.sh contains all the global aliases
4. bash_exports.sh contains all global variables and other export commands
5. bash_functions.sh contains all bash functions
6. <repo-root>/bin contains all global scripts
7. each host needs a directory with the hostname as the directory name and then must contain the local bash_aliases.sh, bash_exports.sh, and bash_functions.sh files and all the local scripts in <repo-root>/HOSTNAME/bin

• For long or unwieldy hostnames a remapping can be done in bashrc.sh. See the example for the h2p cluster

Setup Instructions

1. Make sure there is nothing in the original dotfiles that you want to keep. They will be backed up to ~/.old-dotfiles-backup but better safe than sorry
2. Check that ack, git, bash, and nano are all installed and of the appropriate version
   • If you are on macOS make sure to install GNU coreutils and GNU's implementation of time then add the following to your path and manpath in your bashrc_exports.sh file before running setup.sh
     • PATH="/usr/local/opt/coreutils/libexec/gnubin:$PATH"
     • MANPATH="/usr/local/opt/coreutils/libexec/gnuman:$MANPATH"
3. Clone this repo, it must be in the home directory. If you want to put it elsewhere you must change the setup script, the bashrc.sh file, and maybe others
4. Create a directory for the new machine that is name like <repo-root>/HOSTNAME. If the hostname is complex or there are multiple login nodes then you can remap them to a more human readable name in bashrc.sh; see the example there for the h2p cluster.
5. Update gitconfig with your info and preferences
6. Run setup.sh in <repo-root>/bin. This will add soft links to bash_profile.sh, bashrc.sh, nanorc, and gitconfig and will backup the old versions of those files to ~/.old-dotfiles-backup
7. (optional) Install iTerm2 Shell Integration by copying appropriate files from a machine that has up to date versions of them or by following iTerm2's installation instructions

Setup instructions/notes for other things

1. Setting up git
   • When setting up ssh you have to use the ~/.ssh/config file to tell ssh which key is for GitHub and which is for other things
2. Setting up GPG
   • If you want to set up commit signing see the instructions in <repo-root>/How-To-Guides/GPG setup.md

Features

Here you will find a list of various aliases, functions, scripts, etc that are in this repo along with brief usage instructions (more detailed documentation can be found in the comments of a specific tool). Most of the tools are minimal as this repo is intended to be skeleton for your dotfiles rather than a list of my dotfiles.

Miscellanous Features

• Always lists directory contents when you cd into a directory
• When starting a new shell it checks if your dotfiles are up to date. Note that this adds significantly to the startup time. See the section on the Repo-check-updates.sh script for details and how to disable it if you want
• Syntax coloring files for GNU Nano
• Bash should be case insensitive when autocompleting. This doesn't always work
• A pythonrc.py file that automatically imports a bunch of common libraries

Bash Aliases

• cp, mv, rm, ls, rsync, tree, du, and scp all of these common commands have been aliased to include data protection, verbosity, or just to increase general usefulness
• ldir list all direcotries
• la shows hidden files as well
• ack aliases the ack tool to ignore some directories (.git etc), ignore case, and ignore regex
• rmt moves files to ~/.Trash. A safer form of deleting
• .. = cd ../
• ... = cd ../../
• .X go back X directory levels where X = 3 to 6 inclusive
• dotfiles cd directly to your dotfiles directory
• root cd to the root of the current git repo
• time is dynamically aliased to the GNU implementation depending on OS
• cppDebug, cppPerf, gfort_debug, and gfort_perf various sets of compiler flags for C++ and Fortran to compile with debugging or performance oriented flags

Bash Functions

• message send a SMS or iMessage when on macOS
• remake runs make clean then make. Pipes the result to compile.log and outputs how long the compile took using GNU Time
• find-and-replace finds one string in all the directory files and replaces it with another

Bash Exports

• This is where you should be setting paths, environment variables, etc
• Sets the CLI prompt to be user@host:PWD$

Scripts

Note that scripts from any interpreted language (including python) can be run if they are in the <repo-root>/bin or <repo-root>/hostname/bin directories. Just make sure that the first line of the script is the appropriate shebang; #!/usr/bin/env bash for bash and #!/usr/bin/env python3 for python.

• Repo-check-updates.sh checks if the current github repos status compared to the upstream repo. It will tell you to pull or push or if the repo is up to date or has diverged. This script is mostly used indirectly through other scripts. It is run every time you start a new shell to check if the dotfiles repo is up to date. This add about 0.5 seconds to the startup time and can be disabled by commenting out the appropriate line in bashrc.sh -gitall.sh *command* run the same git command on a bunch of repos. Running gitall.sh check will run Repo-check-updates.sh on every git repo. The list of repos used is given in the gitall.sh script
• macos-update-script.sh updates homebrew, homebrew packages, and your conda environment. Make sure to edit it to include which homebrew packages you want updated.
• setup.sh used for initial setup of this dotfiles system

Git Config

• Make sure to set all the blank fields
• A git commit template is stored at <repo-root>/git-message-template.txt. Feel free to edit it to your own taste.
• Includes: this section is used for including GPG commit signing. See the instructions in <repo-root>/How-To-Guides/GPG setup.md for details

Git Aliases

• stick my preferred version of git log
• stat short for status
• com short for commit
• check runs Repo-check-updates.sh on the current git repo
• new shows all commits created by the last command
• edit opens all unstaged files for editing in VS Code. Easily edited to open unstaged files in any GUI editor that supports CLI invocation
• hub if you're on macOS it automatically opens the GitHub page for this repo. On other operating systems it prints out the URL for the GitHub page

How To Guides

This directory contains some basic guides on setting up GPG signing of git commits and bash performance profiling.

Templates

A collection of templates for common tasks. Most have self explanatory names.

• Host-directory-template A template directory for a machines local dotfiles
• git repo template A template for git repos
• Fortran module/program template.f90 Templates for Fortran code
• python template.py A template for python scripts
• slurm-template.slurm A template for a slurm submission script
• PerfTimer.h A C++ header only timing class for C++ code