Rseng Code Quality

Readable code and project structure

Use this skill when writing or reviewing research code for readability, or when laying out a project's directories. Both goals serve the same end: code is read far more often than it is written (a commonly cited read/write ratio is 7:1), so anything that helps a future reader - including the original author months later - directly improves reusability, the "R" in the FAIR research software principles. Favour conventions others already recognise over clever, project-specific inventions.

Make code readable

Apply these rules when authoring or reviewing code:

• Use descriptive names for variables, functions, classes, and modules that explain their purpose. Avoid single-letter names outside tight loops or well-known math notation.
• Format consistently: consistent indentation and spacing throughout. Consistency within a project or module matters more than any global ideal - when joining existing code, adopt the conventions already in place rather than imposing your own.
• Separate code into sections with blank lines (between classes, functions, logical blocks) so structure is visible at a glance.
• Keep lines short. Prefer many short lines over few long ones - blocks that are horizontally short and vertically long are easier to scan.
• Use indentation to show hierarchy and mark the beginning and end of control structures.
• Add type annotations (type hints) for untyped or dynamically typed languages such as Python or JavaScript, and validate them with a type checker (e.g. mypy for Python). Type checking catches faulty assumptions as well as faulty annotations.
• Write informative comments and docstrings that convey intent and context - what the code is for and why - not a restatement of the syntax. Comment where logic is not self-evident.

Follow a style guide

• Adopt the community-standard style guide for the language rather than inventing one: PEP 8 for Python, the Google R style guide for R; Google's style guides cover Python, Java, R, C++, and Shell.
• A style guide is a shared set of conventions so everyone's contributions look similar. Consistency across the project is the point.
• When contributing to an existing project, match its existing style even if it differs from your preference.

Automate style and quality checks

Do not enforce style by hand - let tools do it:

• Run an auto-formatter to apply style mechanically (e.g. Black for Python). This removes formatting from code review entirely.
• Run a linter - static analysis that flags inconsistencies, stylistic errors, suspicious constructs, and some real bugs (e.g. Pylint for Python).
• Lean on editor/IDE support: VS Code, PyCharm, RStudio, and Eclipse can check conformance as you type, warn on deviations, and often autocorrect.
• Wire formatters and linters into pre-commit hooks and CI so every change is checked automatically, not just when someone remembers.

Pre-commit: the guardrail framework

The pre-commit framework runs the checks automatically at commit time, from one versioned config - the difference between "we have a linter" and "nothing unlinted lands":

• Anatomy: a .pre-commit-config.yaml at the repo root lists hook repositories PINNED to revisions; start from the basics (trailing whitespace, end-of-file, merge-conflict markers, large-file guard), add the ecosystem's linter/formatter (ruff for Python), a secret scanner (rseng-security), and project-specific local hooks where a custom check earns automation.
• Adoption on an existing repo: install the hooks, then run pre-commit run --all-files ONCE in its own commit - a dedicated formatting commit keeps blame readable (the same reasoning as avoiding repo-wide reformats in rseng-legacy-code).
• Keep hooks fast: commit-time checks have a seconds budget - slow checks (test suites, type-checking large trees) belong in CI, not in the hook, or people bypass hooks entirely and the guardrail is gone.
• Update deliberately: pre-commit autoupdate bumps pinned hook revisions - treat it like any dependency update, on a cadence with green tests (rseng-dependency-management).
• SKIP honestly: skipping a hook (SKIP=) is legitimate when the hook itself is broken or inapplicable to the change - record why in the commit; skipping to silence a real finding just moves the failure to CI or review.
• Mirror in CI: run the same hooks in the pipeline (pre-commit run --all-files as a CI step or pre-commit.ci) so a locally bypassed hook (--no-verify) cannot land unchecked (rseng-ci-cd) - local hooks are convenience; CI is enforcement.

Write modular, reusable code

• Split code into small functions that each achieve a single, clear purpose - easier to read, test, and reuse.
• Group related functions into reusable libraries and packages.
• Reach for established design patterns for common, well-defined problems instead of reinventing a solution; this saves time and raises quality.
• Prefer existing, well-tested libraries for common tasks (e.g. reading and writing standard data formats) over bespoke, error-prone code.

Structure the project directory

A clear, conventional layout lets people (and you) locate things fast, keep code, config, and data separate, isolate issues quickly, and reproduce results - especially valuable for long-term or collaborative work. There is no single official standard, but the following is widely understood.

Put everything for the project in a single, meaningfully named directory.

Keep auxiliary information and metadata at the top level so others can tell what the project does and how to reuse it:

• README - what the project is, how to install and run it, how to reproduce results.
• LICENSE - the reuse terms.
• CITATION.cff - how to cite the project (Citation File Format).
• codemeta.json or a similar metadata standard - machine-readable software metadata.

Organise the rest into sub-directories labelled by content type:

• src/ (or code, scripts) - source code.
• data/ - data, with raw kept separate and never modified: e.g. data/raw, data/clean, data/processed. This prevents overwriting or losing the original.
• results/ - analysis outputs, tables, summary statistics.
• figures/ (or fig) - generated plots and figures (or fold these into results/).
• doc/ - documentation and guides.
• papers/, presentations/, or references/ - literature; consider keeping these in a separate project so papers do not mix with a reusable software package.
• Add a nested README or LICENSE inside a sub-directory when its terms differ (for example, code and data licensed differently).

Name files and directories consistently

• Use standard, self-explanatory directory names (as above).
• Avoid spaces and special characters - they break tools; use underscores or hyphens and stay consistent.
• Name files to reflect their contents; let version control track versions rather than encoding _v2, _final in filenames.

Version-control the project

• Put the whole project under version control in its own repository; at minimum version-control code and data sub-directories, plus anything written by hand (docs, manuscripts) rather than generated.
• Untrack files too large or too sensitive to expose (use .gitignore in Git); never version-control passwords or secrets.
• Use tags/releases to mark specific versions (a journal submission, a dissertation version) instead of proliferating dated filenames.

Scaffold new projects with tooling

• For Python, a src-layout with src/your_package/, tests/, pyproject.toml, README, and .gitignore is the common modern shape.
• Poetry manages dependencies, virtual environments, versioning, and publishing from a single pyproject.toml, and scaffolds a new project directory; it works well with the recommended src layout.
• Project templates/skeletons enforce a standardised layout and modern tooling, cutting setup time and keeping teams consistent.

A concrete reference stack (as encoded by the NLeSC python-template; see rseng-project-scaffolding): ruff as the single linter, formatter and import sorter; EditorConfig for cross-editor consistency; SonarCloud for hosted static analysis; and first-class type checking with Pyright (or Mypy) - treat type checks as part of linting, not an optional extra.

Working with this skill

The generated references.md beside this file lists the source material and pointers:

• references.md - verified Learn more pointers

Learn more (verified):

• https://peps.python.org/pep-0008/ - PEP 8 style guide for Python code
• https://google.github.io/styleguide/ - Google style guides for many languages
• https://docs.astral.sh/ruff/ - Ruff Python linter and formatter
• https://pre-commit.com - pre-commit hook framework
• https://editorconfig.org - consistent editor settings across tools

Related skills

Check whether any of these applies before moving on:

• rseng-documentation - docstrings and README quality
• rseng-fair-software - readability serves reusability
• rseng-language-guides - per-language style and tool choice
• rseng-legacy-code - repo-wide reformat cautions
• rseng-project-scaffolding - templates encode this tooling baseline
• rseng-software-metrics - quantifying complexity and duplication