The structure is inspired by the gin-tonic project and the file naming conventions of The Turing Way.
If you are starting the project for the first time, run the 00_setup/python_setup.sh or 00_setup/r_setup.sh scripts as necessary to initiate project-level package management. If you're checking out an existing project, us python_join.sh or r_join.sh as necessary.
00_setup # Scripts to run the first time you start, join, or clone a project
| *<.def,.dockerfile> # Compute environments defining system dependencies needed for packages
│ py_setup.sh # Setup project-level python package management through UV
| py_install_common_deps.sh # Quick startup for adding common Python packages to UV project
│ r_setup.sh # Setup project-level R package manamenet with Renv
│ r_join.sh # Use existing project library or public cache
| r_install_common_deps.r # Quick startup script for adding common R packages to Renv project
|
01_documentation
│ project-notebook.txt # Running account of efforts
│ project-details.txt
02_data # Data generated as *inputs* to analysis
└─── 01_raw-data # Symlinks, copies, or directions for retrieving raw data
└─── 02_data-processing # Code or receipts from data processing
└─── 03_processed-data # processed data (include instructions for retrieval)
03_analysis
└─── 01_config # Project level definitions that affect multiple scripts.
└─── 02_src # Source files for helper code/functions
└─── 03_notebooks # Data exploration and manipulation experiments
│ └─── 01_primary-analyses # Main workflow notebooks
│ │ 01_first-script.rmd/ipynb/etc
│ │ 02...
│ └─── 02_secondary-analyses # Separate lines of inquiry that may not continue
│ │ 02.1_spinoff.rmd/ipynb/etc
└─── 04_checkpoints # Saved objects reflecting a checkpoint after computationally expensive portions of an analysis
│
04_results # Tables, models, etc that represent outputs of an analysis for dissemination
└─── tables
└─── figures
│ qc_pics.svg
│ └─── figure-scripts # Isolated script to iterate on figures for publication
│ │ qc_pics.R
│ └─── figure-data # Tables of values to accomapny generated figures, for reference & publication
│ │ qc_pics.txt
05_disseminations # More comprehensive outputs. Reports, slides, tweets, manuscripts, etc.