Mycelia Test Coverage Expansion

Systematically expand test coverage for the Mycelia Julia package.

Prerequisites

1. Check for existing coverage files:

   bash
   1find . -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:

   bash
   1export MYCELIA_RUN_ALL=true
   2export 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

bash
1# Full coverage with all tests enabled (matches HPC CI flags)
2MYCELIA_RUN_ALL=true MYCELIA_RUN_EXTERNAL=true \
3  julia --project=. --compiled-modules=no \
4  -e "import Pkg; Pkg.test(coverage=true)"
5
6# Coverage files will be generated as src/*.jl.cov

Optional parity with HPC CI (skips Codecov upload):

bash
1ci/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:

Test Template

julia
1import Test
2import StableRNGs
3import Mycelia
4
5Test.@testset "FunctionName - description" begin
6    rng = StableRNGs.StableRNG(42)
7
8    Test.@testset "normal case" begin
9        result = Mycelia.function_name(input)
10        Test.@test result == expected
11    end
12
13    Test.@testset "edge case - empty input" begin
14        result = Mycelia.function_name([])
15        Test.@test isempty(result)
16    end
17
18    Test.@testset "error case" begin
19        Test.@test_throws ArgumentError Mycelia.function_name(invalid)
20    end
21end

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:

bash
1# Quick check of specific file coverage
2MYCELIA_RUN_ALL=true MYCELIA_RUN_EXTERNAL=true \
3  julia --project=. --compiled-modules=no -e '
4    import Pkg; Pkg.test()
5' && grep -c "^    0" src/utility-functions.jl.cov