coverage-expansion

name	coverage-expansion
description	Mycelia-specific test coverage expansion workflow

Mycelia Test Coverage Expansion

Systematically expand test coverage for the Mycelia Julia package.

Prerequisites

1. Check for existing coverage files:

   find . -name "*.cov" -mtime -1 2>/dev/null
   

   If recent .cov files exist, use them to identify gaps without re-running.

2. Environment flags - ALWAYS enable these for accurate coverage:

   export MYCELIA_RUN_ALL=true
   export MYCELIA_RUN_EXTERNAL=true
   

   Coverage needs non-precompiled code for accurate line hits. Use --compiled-modules=no (matches ci/hpc/run_hpc_ci.sh).

Running Coverage Analysis

# Full coverage with all tests enabled (matches HPC CI flags)
MYCELIA_RUN_ALL=true MYCELIA_RUN_EXTERNAL=true \
  julia --project=. --compiled-modules=no \
  -e "import Pkg; Pkg.test(coverage=true)"

# Coverage files will be generated as src/*.jl.cov

Optional parity with HPC CI (skips Codecov upload):

ci/hpc/run_hpc_ci.sh --tests-only --no-codecov

Analyzing Coverage

Coverage files are generated alongside source files (e.g., src/utility-functions.jl.cov).

Format: Each line shows execution count, then source line:

    1  function foo(x)
    0      if x < 0      # uncovered branch
    -          return -x
    1      end
    1      return x
    -  end

• Number = times executed
• 0 = never executed (needs test)
• - = non-executable line

Test Placement

Match source file to test stage:

Source File	Test Stage
reference-databases.jl	test/1_data_acquisition/
fastx.jl, preprocessing.jl	test/2_preprocessing_qc/
kmer-analysis.jl	test/3_feature_extraction_kmer/
src/rhizomorph/	test/4_assembly/
quality-control-and-benchmarking.jl	test/5_validation/
annotation.jl, genome-features.jl	test/6_annotation/
taxonomy-and-trees.jl, pangenome.jl	test/7_comparative_pangenomics/
bioconda.jl, sentencepiece.jl	test/8_tool_integration/

Test Template

import Test
import StableRNGs
import Mycelia

Test.@testset "FunctionName - description" begin
    rng = StableRNGs.StableRNG(42)

    Test.@testset "normal case" begin
        result = Mycelia.function_name(input)
        Test.@test result == expected
    end

    Test.@testset "edge case - empty input" begin
        result = Mycelia.function_name([])
        Test.@test isempty(result)
    end

    Test.@testset "error case" begin
        Test.@test_throws ArgumentError Mycelia.function_name(invalid)
    end
end

Priority Order

1. Core utilities - utility-functions.jl (used everywhere)
2. Data I/O - fastx.jl, reference-databases.jl
3. Assembly core - src/rhizomorph/ modules
4. Analysis - kmer-analysis.jl, taxonomy-and-trees.jl
5. External tools - bioconda.jl, sentencepiece.jl (require MYCELIA_RUN_EXTERNAL)

Rules

• NEVER disable tests because functionality is broken - fix the implementation
• Use Test.@test_skip ONLY for explicitly planned but unimplemented features
• Always use fully qualified names: Mycelia.function_name(), not imported functions
• Use StableRNGs.StableRNG(seed) for any randomness
• Use small synthetic data, not large external files
• Commit after each file's tests pass

Commit Format

add: tests for utility-functions.jl coverage

- Add tests for memory_estimate() normal and edge cases
- Add tests for safe_mkdir() error handling
- Coverage: 45% -> 72% for utility-functions.jl

Verifying Progress

After adding tests, re-run coverage and compare:

# Quick check of specific file coverage
MYCELIA_RUN_ALL=true MYCELIA_RUN_EXTERNAL=true \
  julia --project=. --compiled-modules=no -e '
    import Pkg; Pkg.test()
' && grep -c "^    0" src/utility-functions.jl.cov