Test Stages

Mycelia Test Stage Organization

The test suite is tiered by workflow stage.

Test Stage Directories

1. test/1_data_acquisition/ - Data loading and acquisition
2. test/2_preprocessing_qc/ - Quality control and preprocessing
3. test/3_feature_extraction_kmer/ - K-mer analysis and feature extraction
4. test/4_assembly/ - Assembly algorithms
5. test/5_validation/ - Validation and verification
6. test/6_annotation/ - Annotation workflows
7. test/7_comparative_pangenomics/ - Comparative and pangenomic analysis
8. test/8_tool_integration/ - External tool integration

Additional directories:

• test/in_development/ - Opt-in experimental tests
• test/deprecated/ - Legacy tests (do not use)

Adding New Tests

1. Place tests in the relevant stage directory
2. Name files after the feature (e.g., assembly_merging.jl)
3. Use Test.@testset with descriptive labels
4. Use small fixtures from assembly_test_data/
5. Use StableRNGs for deterministic seeds

Example:

import Test
import StableRNGs

Test.@testset "Assembly Merging" begin
    rng = StableRNGs.StableRNG(42)
    # Test code with deterministic randomness
end

Test Commands

# Core tests (Aqua + optional JET)
julia --project=. -e "import Pkg; Pkg.test()"

# Full pipeline tests
MYCELIA_RUN_ALL=true julia --project=. -e "import Pkg; Pkg.test()"

# External tool tests
MYCELIA_RUN_EXTERNAL=true julia --project=. -e "import Pkg; Pkg.test()"

# Coverage (disable precompilation for accurate line hits)
MYCELIA_RUN_ALL=true MYCELIA_RUN_EXTERNAL=true \
  julia --project=. --compiled-modules=no -e "import Pkg; Pkg.test(coverage=true)"

# Static analysis
julia --project=. test/jet.jl

Testing Rules

• NEVER disable tests because functionality is broken - fix the implementation first
• Use Test.@test_skip ONLY for explicitly planned but unimplemented features
• When debugging tests gated by environment flags (for example MYCELIA_RUN_EXTERNAL), enable them by default unless the user explicitly opts out
• External tool tests must run with MYCELIA_RUN_EXTERNAL=true without extra flags
• Use simulated inputs and default database paths where possible
• Extended tutorials/benchmarks are opt-in; note runtime or external-tool requirements

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