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test-stages

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Aktualisiert27. Januar 2026 um 20:53

Staged test organization and testing guidelines for Mycelia

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cjprybol/Mycelia

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Softwarequalitätssicherungsanalysten und -testerInformatik- und Mathematikberufe·SOC 15-1253

SKILL.md

readonly

name	test-stages
description	Staged test organization and testing guidelines for Mycelia

Mycelia Test Stage Organization

The test suite is tiered by workflow stage.

Test Stage Directories

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

Place tests in the relevant stage directory
Name files after the feature (e.g., assembly_merging.jl)
Use Test.@testset with descriptive labels
Use small fixtures from assembly_test_data/
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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Mycelia Test Stage Organization

The test suite is tiered by workflow stage.

Test Stage Directories

test/1_data_acquisition/ - Data loading and acquisition

test/2_preprocessing_qc/ - Quality control and preprocessing

test/3_feature_extraction_kmer/ - K-mer analysis and feature extraction

test/4_assembly/ - Assembly algorithms

test/5_validation/ - Validation and verification

test/6_annotation/ - Annotation workflows

test/7_comparative_pangenomics/ - Comparative and pangenomic analysis

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

Place tests in the relevant stage directory

Name files after the feature (e.g., assembly_merging.jl)

Use Test.@testset with descriptive labels

Use small fixtures from assembly_test_data/

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