Overview

As time goes on, projects tend to become messy which inhibits reproducibility. Hence, we recommend keeping an eye on this housekeeping checklist from time to time.

Checklist

Project level

• Implement a consistent directory structure: data/src/gen
• Include readme with project description and technical instruction how to run/build the project
• Store any authentication credentials outside of the repository (e.g., in a JSON file), NOT clear-text in source code
• Mirror your /data folder to a secure backup location; alternatively, store all raw data on a secure server and download relevant files to /data

Throughout the Pipeline

File/directory structure

• Create subdirectory for source code: /src/[pipeline-stage-name]/
• Create subdirectories for generated files in /gen/[pipeline-stage-name]/: temp, output, and audit.
• Make all file names relative, and not absolute (i.e., never refer to C:/mydata/myproject, but only use relative paths, e.g., ../output)
• Create directory structure from within your source code, or use .gitkeep
• Create subdirectories for generated files in /gen/[pipeline-stage-name]/: temp, output, and audit.
• Make all file names relative, and not absolute (i.e., never refer to C:/mydata/myproject, but only use relative paths, e.g., ../output)
• Create directory structure from within your source code, or use .gitkeep

Automation & documentation

• Have a makefile
• Alternatively, include a readme with running instructions
• Make dependencies between source code and files-to-be-built explicit, so that make automatically recognizes when a rule does not need to be run (properly define targets and source files)
• Include function to delete temp, output files, and audit files in makefile

Versioning

• Version all source code stored in /src (i.e., add to Git/GitHub)
• Do not version any files in /data and /gen (i.e., do NOT add them to Git/GitHub)
• Want to exclude additional files (e.g., files that (unintentionally) get written to /src? Use .gitignore for files/directories that need not to be versioned

Housekeeping

• Have short and accessible variable names
• Loop what can be looped
• Break down “long” source code in subprograms/functions, or split script in multiple smaller scripts
• Delete what can be deleted (including unnecessary comments, legacy calls to packages/libraries, variables)
• Use of asserts (i.e., make your program crash if it encounters an error which is not recognized as an error)

Testing for portability

• Tested on own computer (entirely wipe /gen, re-build the entire project using make)
• Tested on own computer (first clone to new directory, then re-build the entire project using make)
• Tested on different computer (Windows)
• Tested on different computer (Mac)
• Tested on different computer (Linux)

See Also

• This tutorial covers the fundemantal principles of project setup and workflows underlying this checklist.