Writing the Code

Coding style

• While there is no strict coding style, it's important to maintain consistency → Instead look at and follow the structure of the existing code to keep it consistent.
• Whitespace Management: Please remove trailing whitespaces as they can lead to unnecessary changes in version control and can affect readability.

Naming Conventions and Intent

• Descriptive Naming: Choose names that clearly describe the purpose of the variable, function, or class. Avoid cryptic names that can end up unclear to other team members.
• Function Names: Make function names descriptive and action-oriented. Examples include:
  • get_gene_name() — Indicates retrieval of a name.
  • find_downstream_feature() — Suggests searching for a feature.
  • is_circular() — Checks for a circular condition.
  • has_multiple_flurbs() — Tests the existence of multiple flurbs.
• Loop Variables: Use simple names like i, j, and k for short-lived loop counters.
• Broad Scope Variables: Use more informative names for variables with a broader scope to enhance understanding and maintainability, such as filename_map, common_prefix, current_gene, feature_length.

Leaving Comments on the Code

• Purpose of Comments: Focus on 'why' something is done, rather than 'what' is done. The code should be self-explanatory; comments should explain rationale, context, or intent.
• Clarifying Complex Code: Whenever a piece of code is not "self-explanatory" or contains complex logic, go ahead and add a comment explaining its purpose and how it works.
• Documentation for Onboarding: Commenting are also for the new developers, since they can provide a guidance and understanding to understand the codebase more effectively.

Legibility of the Code

• Consistent Indentation: Maintain consistent indentation levels across all code files to ensure that the code is organized and easy to read, or simply lint the code.
• Clarity Over Efficiency: Prefer clear, understandable code over compact, complex code. If a less optimal approach is clearer, document any efficiency trade-offs.
• Line Length: Keep lines to a maximum of 75-80 characters if you can. This makes it more readable and helps make side-by-side views in code reviews easier to do.

Refactoring Guidelines

• Regular Refactoring: If it's possible, do a refactoring sessions to improve code design.
• Refactoring Techniques:
  • Extract method
  • Rename for clarity
  • Reduce parameters

Best programming practices

• Adherence to Standards: Follow established coding standards and practices.
• Google has a good set of best practices for bunch of different programming languages.