Greg Thomsen's Dotfiles

This collection of configuration files has been refined to support scientific computing (C/MATLAB/Fortran/Python) on Linux systems, usually without graphical interfaces. Development is centered around per-project screen sessions hosting an instance of Emacs that drives development, debugging, and testing for it.

Highlights

There are a couple of things worth mentioning in this collection of configuration files:

• An emphasis on driving everything from the keyboard. Graphical tools are used when they're better than text-based alternatives, though aren't the default approach.

• Having consistently setup, self-contained screen instances. Almost all project work starts with:

     $ screen code project-name

  An Emacs instance is started with a unique server name (project-name) and the environment is configured so all editing goes through it. This allows multiple projects to be worked on concurrently, without co-mingling files and buffers.

• XTerms are configured with 8-bit color when available. This provides a wider range of colors for Emacs to work with.

• Split shell configuration making intent clear by the fragment's name/contents. This is easy to adapt into existing shell configurations (sourcing the bootstrap piece) or dropping in wholesale.

• screen is configured with a prefix key of C-j instead of the normal C-a to spare my poor pinky when working in the shell and Emacs.

Installation

A simple installation script, install-as-symlinks.sh, is available which backs up existing configurations and creates symbolic links to the files in this repository. This enables easy updates as any changes made will visible to Git without additional effort.

Cloning the Repository

Since this repository includes other repositories as submodules, you'll need to either 1) recursively clone this repository or 2) fetch each of the submodules individually.

Recursive cloning is available for those who have setup SSH keys with their Github account via:

  $ git clone --recursive git@github.com:gthomsen/dotfiles.git

While fetching each submodule can be done like so:

  $ git clone https://github.com/gthomsen/dotfiles.git
  $ cd dotfiles
  $ git config -f .gitmodules submodule.".emacs.d/elisp/align-f90".url \
                  https://github.com/gthomsen/align-f90.git
  $ git config -f .gitmodules submodule.".emacs.d/elisp/align-matlab".url \
                  https://github.com/gthomsen/align-matlab.git
  $ for MODULE in align-f90 align-matlab matlab; do \
       git submodule update --init .emacs.d/elisp/${MODULE}; \
    done

Install Via Symbolic Links

Change into the repository's working directory and run install-as-symlinks.sh. Existing configurations will be moved into ${HOME}/.user-configuration-backups/ and new symbolic links will be made to the working copy's contents.

Install External Software

Several Emacs packages require external commands to function properly. Below are a list of external packages that should be installed for each Emacs package:

Markdown-mode

• Pandoc is needed to render Markdown files into HTML for previews. Optional if the mode is only used for syntax highlighting.

Post-Installation Setup

Some setup is required before development can be done with this user configuration. See below for details.

Git

The default user.name and user.email in the provided `.gitconfig are hardcoded for the repository owner's convenience. Please change them prior to making commits so changes are not attributed to them!

$ git config --global user.name "John Doe"
$ git config --global user.email "john.doe@domain.com"

Emacs

The following packages are optional and can be installed for additional functionality:

• dockerfile-mode Mode for editing Dockerfile files
• eglot Language Server Protocol (LSP) mode that interfaces with language-specific servers
• gptel Chat interface to large language models (LLMs)
• Magit Working with Git repositories
• markdown-mode Mode for editing Markdown files
• rmsbolt Local version of Compiler Explorer
• tramp Work with remote files (e.g. via SSH on remote servers, in containers, etc) as if they were local

To install all of the optional packages, launch Emacs and run the following Lisp (M-x : and then paste the following):

(progn
  (package-refresh-contents)
  (package-install 'dockerfile-mode)
  (package-install 'eglot)
  (package-install 'gptel)
  (package-install 'magit)
  (package-install 'markdown-mode)
  (package-install 'rmsbolt)
  (package-install 'tramp))

Language Server Installation

Eglot is a language-independent language server interface and requires external language-specific servers to perform the heavy lifting. This configuration file enables Eglot when editing Fortran and Python code, but only when the corresponding language servers are present so as to avoid spurious warnings like:

Warning (eglot): Searching for program: No such file or directory, fortls

Fortran

fortls is the preferred Fortran language server. This is forked from the original Fortran Language Server and provides active development and additional functionality and bug fixes.

If one has Python installation provided by Anaconda, fortls can be installed from Conda Forge like so:

$ conda install -c conda-forge fortls

Python

Many Python language servers are available and supported by Eglot though the Python LSP Server is preferred for the number of optional dependencies it supports (e.g. pycodestyle, Pyflakes, pylsp-mypy, etc).

Conveniently, it is included with a stock Anaconda Python distribution meaning that only dependencies are required to be installed. The following enables type checking support via MyPy as well as faster linting via Ruff.

$ conda install mypy pyslp-mypy ruff