pytest.ini

[pytest]
pythonpath = .
addopts = --import-mode=importlib
testpaths =
    clawbio/common/tests
    clawbio/tests
    robotary/tests
    skills/affinity-proteomics/tests
    skills/archaic-introgression/tests
    skills/bgpt-mcp/tests
    skills/bigquery-public/tests
    skills/bio-orchestrator/tests
    skills/bioconductor-bridge/tests
    skills/cell-detection/tests
    skills/claw-ancestry-pca/tests
    skills/clinical-trial-finder/tests
    skills/clinical-variant-reporter/tests
    skills/clinpgx/tests
    skills/data-extractor/tests
    skills/diff-visualizer/tests
    skills/eqtl-catalogue-region-fetch/tests
    skills/equity-scorer/tests
    skills/fine-mapping/tests
    skills/flow-bio/tests
    skills/galaxy-bridge/tests
    skills/genome-compare/tests
    skills/gwas-lookup/tests
    skills/gwas-pipeline/tests
    skills/gwas-prs/tests
    skills/hla-typing/tests
    skills/illumina-bridge/tests
    skills/labstep/tests
    skills/lit-synthesizer/tests
    skills/mendelian-randomisation/tests
    skills/nfcore-scrnaseq-wrapper/tests
    skills/methylation-clock/tests
    skills/multiqc-reporter/tests
    skills/nutrigx-advisor/tests
    skills/omics-target-evidence-mapper/tests
    skills/pharmgx-reporter/tests
    skills/profile-report/tests
    skills/proteomics-clock/tests
    skills/proteomics-de/tests
    skills/protocols-io/tests
    skills/pubmed-summariser/tests
    skills/rnaseq-de/tests
    skills/scrna-embedding/tests
    skills/scrna-orchestrator/tests
    skills/seq-wrangler/tests
    skills/target-validation-scorer/tests
    skills/turingdb-graph/tests
    skills/ukb-navigator/tests
    skills/variant-annotation/tests
    skills/vcf-annotator/tests
    skills/wes-clinical-report-en/tests
    skills/wes-clinical-report-es/tests
    skills/wgs-prs/tests
    tests
python_files = test_*.py
python_functions = test_*
markers =
    integration: marks tests that require external tools or network access (deselect with '-m "not integration"')