4 test coverage threshold logic for output table passfail #15
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… docstring - Add to verify FastP threshold logic (Q30, read length), duplication, N-content, adapter detection, and species coverage handling. - Add to verify coverage estimation, expected genome-size parsing, GC content PASS/WARNING/OUTSIDE behavior, and multi-species warning text. - Update docstring in to match implementation (explicit GC tolerance semantics and fields written). - Minor lint fixes in tests (remove unused imports).
Add bactscout preflight command to run preflight checks and download/validate databases/tools.
Add --write-json option to collect CLI; emit {sample_id}_summary.json alongside CSV.
Implement optional JSON summary writing in thread.py (write_summary_file).
Add scripts/build_paper.sh wrapper and build-paper-safe Pixi task to validate paper.md before invoking JOSS Docker image.
Replace problematic Unicode ≥ in JOSS paper sources (math/entity forms) to avoid LaTeX font glyph errors.
Update docs:
index.md: Docker quickstart and expanded Key Features.
configuration.md: sync with bactscout_config.yml and add guidance on alternative Sylph DBs.
Make QC threshold logic consistent: use warn/fail keys (e.g. coverage_warn_threshold/coverage_fail_threshold, contamination_warn_threshold/contamination_fail_threshold) with legacy fallbacks; fix related logic/indentation.
Add tests for resource monitor (test_resource_monitor.py) covering psutil present/missing cases.
Minor wording and compatibility fixes to preserve test expectations.
…tibility shim, round resource memory metrics - Apply breaking rename of coverage-related output fields: - coverage_estimate -> coverage_estimate_sylph - coverage_message -> coverage_estimate_sylph_message - coverage_alt_* -> coverage_estimate_qualibact_* (estimate/message/status) - Remove one-release backwards-compatibility shim; outputs now contain canonical keys only. - Round resource memory metrics before writing output: resource_memory_avg_mb and resource_memory_peak_mb are rounded to integers. - Update header ordering and blank defaults to include new canonical keys. - Update tests/docs referencing the renamed fields. Migration notes: This is a breaking change; downstream consumers must update legacy field names to the new ones.
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