CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
SECURITY.md
THIRD_PARTY_NOTICES.md
pyproject.toml
LICENSES/GPL-3.0-only.txt
LICENSES/LGPL-3.0-only.txt
docs/PHASE_1_SPEC.md
docs/ROADMAP.md
docs/SPRINT_1.md
docs/case-studies.md
docs/evidence-and-provenance.md
docs/gui-audit-workflow.md
docs/gui-distribution.md
docs/gui-framework-decision.md
docs/gui-workflow.md
docs/index.md
docs/limitations.md
docs/pep-and-acquisition.md
docs/privacy-and-security.md
docs/publication-evidence.md
docs/quickstart.md
docs/release-notes-1.0.0.md
docs/statistics.md
docs/runtime/SUPERVISOR.md
scripts/build_release_artifacts.py
scripts/validate_gui_distribution.py
scripts/validate_release_distribution.py
scripts/validate_release_guidance.py
src/geo_design_auditor/__init__.py
src/geo_design_auditor/__main__.py
src/geo_design_auditor/_pdf_worker.py
src/geo_design_auditor/_pep_yaml_worker.py
src/geo_design_auditor/_structured_worker.py
src/geo_design_auditor/_version.py
src/geo_design_auditor/accessions.py
src/geo_design_auditor/acquisition_cli.py
src/geo_design_auditor/acquisition_execute.py
src/geo_design_auditor/acquisition_plan.py
src/geo_design_auditor/audit.py
src/geo_design_auditor/biosample.py
src/geo_design_auditor/cli.py
src/geo_design_auditor/comparison_design_assessment.py
src/geo_design_auditor/comparison_design_assessment_report.py
src/geo_design_auditor/comparison_design_assessment_review_packet.py
src/geo_design_auditor/comparison_design_assessment_review_packet_report.py
src/geo_design_auditor/comparison_design_assessment_specification.py
src/geo_design_auditor/comparison_design_assessment_specification_draft.py
src/geo_design_auditor/comparison_design_assessment_specification_report.py
src/geo_design_auditor/comparison_design_assessment_transaction.py
src/geo_design_auditor/cross_db.py
src/geo_design_auditor/cross_db_report.py
src/geo_design_auditor/design_reconstruction_application.py
src/geo_design_auditor/design_reconstruction_application_report.py
src/geo_design_auditor/design_reconstruction_contract.py
src/geo_design_auditor/design_reconstruction_contract_builder.py
src/geo_design_auditor/design_reconstruction_contract_publication.py
src/geo_design_auditor/design_reconstruction_contract_publication_report.py
src/geo_design_auditor/design_reconstruction_contract_report.py
src/geo_design_auditor/design_reconstruction_contract_v1_1.py
src/geo_design_auditor/design_reconstruction_publication_evidence_attachment.py
src/geo_design_auditor/design_reconstruction_review_packet.py
src/geo_design_auditor/design_reconstruction_review_packet_report.py
src/geo_design_auditor/design_reconstruction_review_preflight.py
src/geo_design_auditor/design_reconstruction_review_preflight_report.py
src/geo_design_auditor/design_reconstruction_review_workspace.py
src/geo_design_auditor/design_reconstruction_review_workspace_report.py
src/geo_design_auditor/design_reconstruction_v1_1_review_report.py
src/geo_design_auditor/design_reconstruction_v1_1_review_workflow.py
src/geo_design_auditor/evidence_graph.py
src/geo_design_auditor/geo_relations.py
src/geo_design_auditor/gui.py
src/geo_design_auditor/gui_audit.py
src/geo_design_auditor/gui_service.py
src/geo_design_auditor/gui_workflow.py
src/geo_design_auditor/inventory.py
src/geo_design_auditor/meta_analysis.py
src/geo_design_auditor/models.py
src/geo_design_auditor/ncbi_client.py
src/geo_design_auditor/normalize.py
src/geo_design_auditor/pdf_intake.py
src/geo_design_auditor/pep_cli.py
src/geo_design_auditor/pep_export.py
src/geo_design_auditor/pep_import.py
src/geo_design_auditor/pep_import_report.py
src/geo_design_auditor/publication_authority.py
src/geo_design_auditor/publication_discovery.py
src/geo_design_auditor/publication_evidence.py
src/geo_design_auditor/publication_field_selection.py
src/geo_design_auditor/publication_reconciliation.py
src/geo_design_auditor/publication_reconciliation_review_packet.py
src/geo_design_auditor/publication_review_workspace.py
src/geo_design_auditor/relationship_builder.py
src/geo_design_auditor/relationship_consumption.py
src/geo_design_auditor/relationship_consumption_builder.py
src/geo_design_auditor/relationship_consumption_report.py
src/geo_design_auditor/relationship_evidence.py
src/geo_design_auditor/relationship_report.py
src/geo_design_auditor/relationship_review.py
src/geo_design_auditor/relationship_review_builder.py
src/geo_design_auditor/relationship_review_report.py
src/geo_design_auditor/relationship_rules.py
src/geo_design_auditor/relationship_sources.py
src/geo_design_auditor/release_dependency_inventory.json
src/geo_design_auditor/report.py
src/geo_design_auditor/representative_study_contract.py
src/geo_design_auditor/researcher_audit_console.py
src/geo_design_auditor/researcher_audit_outputs.py
src/geo_design_auditor/researcher_audit_pipeline.py
src/geo_design_auditor/researcher_audit_report.py
src/geo_design_auditor/researcher_audit_summary.py
src/geo_design_auditor/researcher_audit_summary_builder.py
src/geo_design_auditor/retrieval.py
src/geo_design_auditor/reviewed_key_mapping.py
src/geo_design_auditor/single_study_analysis.py
src/geo_design_auditor/soft_parser.py
src/geo_design_auditor/sra.py
src/geo_design_auditor/statistics_envelope.py
src/geo_design_auditor/structured_file_intake.py
src/geo_design_auditor/study_compatibility.py
src/geo_design_auditor/study_effect.py
src/geo_design_auditor/workflow.py
src/geo_design_auditor/workflow_cli.py
src/geo_design_auditor.egg-info/PKG-INFO
src/geo_design_auditor.egg-info/SOURCES.txt
src/geo_design_auditor.egg-info/dependency_links.txt
src/geo_design_auditor.egg-info/entry_points.txt
src/geo_design_auditor.egg-info/requires.txt
src/geo_design_auditor.egg-info/top_level.txt
tests/test_accessions.py
tests/test_acquisition_execute.py
tests/test_acquisition_plan.py
tests/test_benchmarks.py
tests/test_biosample.py
tests/test_biosample_benchmarks.py
tests/test_comparison_design_assessment.py
tests/test_comparison_design_assessment_linear_algebra.py
tests/test_comparison_design_assessment_review_packet.py
tests/test_comparison_design_assessment_specification.py
tests/test_comparison_design_assessment_specification_draft.py
tests/test_comparison_design_assessment_transaction.py
tests/test_cross_db_cli.py
tests/test_design_reconstruction_application.py
tests/test_design_reconstruction_contract.py
tests/test_design_reconstruction_contract_publication.py
tests/test_design_reconstruction_contract_v1_1.py
tests/test_design_reconstruction_publication_evidence_attachment.py
tests/test_design_reconstruction_review_packet.py
tests/test_design_reconstruction_review_preflight.py
tests/test_evidence_graph.py
tests/test_geo_relations.py
tests/test_geo_retrieval.py
tests/test_gse198683_design_reconstruction_review_preflight_v1_1.py
tests/test_gse198683_design_reconstruction_review_v1_1.py
tests/test_gse198683_design_reconstruction_review_workspace_v1_1.py
tests/test_gui.py
tests/test_gui_audit.py
tests/test_gui_distribution.py
tests/test_gui_service.py
tests/test_gui_workflow.py
tests/test_inventory.py
tests/test_meta_analysis.py
tests/test_ncbi_client.py
tests/test_parser_and_audit.py
tests/test_pdf_intake.py
tests/test_pep_export.py
tests/test_pep_import.py
tests/test_project_os_git_safety.py
tests/test_project_os_github.py
tests/test_project_os_runtime.py
tests/test_project_os_runtime_schemas.py
tests/test_publication_authority.py
tests/test_publication_discovery.py
tests/test_publication_evidence.py
tests/test_publication_field_selection.py
tests/test_publication_reconciliation.py
tests/test_publication_reconciliation_review_packet.py
tests/test_publication_review_workspace.py
tests/test_relationship_benchmarks.py
tests/test_relationship_consumption.py
tests/test_relationship_consumption_application.py
tests/test_relationship_consumption_policy.py
tests/test_relationship_evidence.py
tests/test_relationship_review.py
tests/test_relationship_review_package.py
tests/test_release_distribution.py
tests/test_release_guidance.py
tests/test_representative_study_contract.py
tests/test_researcher_audit_cli.py
tests/test_researcher_audit_console.py
tests/test_researcher_audit_outputs.py
tests/test_researcher_audit_report.py
tests/test_researcher_audit_summary.py
tests/test_reviewed_key_mapping.py
tests/test_single_study_analysis.py
tests/test_sra.py
tests/test_statistics_envelope.py
tests/test_structured_file_intake.py
tests/test_study_compatibility.py
tests/test_study_effect.py
tests/test_t0002_operational_proof.py
tests/test_t0035_gse184237_real_fit.py
tests/test_t0035_hosted_r_environment.py
tests/test_t0035_real_compatibility_refusal.py
tests/test_t0035_real_study_publication_evidence.py
tests/test_upstream_interoperation_decision.py
tests/test_workflow_cli.py