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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
, andaudit
. - 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 usingmake
) - 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)
Versioned any sensitive data?
Before making a GitHub repository public, we recommend you check that you have not stored any sensitive information in it (such as any passwords). This tool has worked great for us: GitHub credentials scanner.
See Also
- This tutorial covers the fundemantal principles of project setup and workflows underlying this checklist.