project_template

Directory structure

project_name/
├── data
│   ├── processed_data
│   └── raw_data
├── misc
├── reports
│   └── images
├── scripts
│   ├── matlab
│   ├── python
│   └── r
├── project_description.md
├── README.md
└── todo.md

Using this template

The .gitignore file has been configured to only track stuff in the scripts and reports directories (and any markdown files). Note that the images directory (inside the reports directory) will also not be tracked.

If you add a new directory and want it to be tracked by git (or if you want e.g. the misc directory to be tracked), you have to explicitly add an exception to the .gitignore file like so:

# start by ignoring all root files and all root directories
/*
/*/

# then explicitly un-ignore the things I want
!.gitignore
!/scripts
!/reports
/reports/images
!*.md
!*.placeholder

# I also want to have following directory to be tracked by git
!/my_new_dir

Git doesn't recognise empty directories, so I include a hidden file called .placeholder in all directories to make them show up here

Using other repositories in your project

Since this template will form a repository of some project, other repositories (e.g containing useful code) are most easily stored elsewhere (unless you like using git submodule). For instance, you can have a directory called code_base in which you keep repositories that might be useful to one or more of your projects (N.B. below, any directory that has a README.md file is supposed to be a repository):

.
├── code_base
│   ├── bash
│   │   └── summarise_all_projects
│   │       ├── overview_summary.sh
│   │       └── README.md
│   ├── python
│   └── r
│       ├── base_functions
│       │   ├── some_cool_functions.R
│       │   └── README.md
│       └── plotting_scripts
│           ├── make_my_favourite_plots.R
│           ├── set_theme.R
│           └── README.md
└── projects
    ├── project_name
    ├── different_project
    └── side_project

This will have the added benefit that your code in (for example) projects/project_name/scripts/my_analysis.R will use the same path to access the repositories in code_base as code sitting in any other project like different_project or in side_project (e.g. source '../../../code_base/r/base_functions/some_cool_functions.R'. Therefore whenever you write some code that could be used in other projects, consider putting it into a separate repository somewhere under the code_base directory.