Mycelia Julia Coding Style

When working in the Mycelia repository, follow these strict coding rules.

Import Rules (STRICT)

• •NEVER use using - always use import
• •Fully qualify all names - use Mycelia.Rhizomorph, DataFrames.DataFrame(), etc.
• •No shorthand aliases - avoid R = Mycelia.Rhizomorph; use full qualified names
• •Dependencies are imported at top-level in src/Mycelia.jl and available in all source files

Example:

# WRONG
using DataFrames
df = DataFrame()

# WRONG
import DataFrames: DataFrame
df = DataFrame()

# CORRECT
import DataFrames
df = DataFrames.DataFrame()

Naming Conventions

• •Modules: CamelCase (e.g., Rhizomorph, KmerAnalysis)
• •Functions/Variables: snake_case (e.g., process_sequences, kmer_count)
• •Constants: SCREAMING_SNAKE_CASE (e.g., MAX_KMER_SIZE)
• •No emojis in code or comments

Sequence Types (BioSequences)

Always use proper BioSequences types:

• •BioSequences.LongDNA{4} for DNA
• •BioSequences.LongRNA{4} for RNA
• •BioSequences.LongAA for amino acids

Extract from FASTQ:

FASTX.sequence(BioSequences.LongDNA{4}, record)

Avoid string conversions in k-mer graphs, qualmer graphs, and assembly algorithms. Use string() only for external tool interfaces or final output.

Formatting

• •4-space indentation
• •Clear docstrings: """signature..."""
• •Prefer pure functions and explicit keyword arguments
• •Use joinpath for file paths (portability)
• •Avoid type piracy

Default formatter: JuliaFormatter.jl with SciMLStyle or BlueStyle, unless repo indicates Runic.jl.

Architecture Notes

• •Main module uses dynamic file inclusion
• •All .jl files in src/ are auto-included via Mycelia.jl
• •Rhizomorph and Mycelia do NOT export symbols by design
• •Tests and callers MUST use fully qualified names