.gitignore
.readthedocs.yaml
AGENTS.md
LICENSE
MANIFEST.in
README.md
README_ZH.md
pyproject.toml
setup.py
.github/workflows/publish.yml
.github/workflows/test.yml
OperonDBS.egg-info/PKG-INFO
OperonDBS.egg-info/SOURCES.txt
OperonDBS.egg-info/dependency_links.txt
OperonDBS.egg-info/entry_points.txt
OperonDBS.egg-info/requires.txt
OperonDBS.egg-info/top_level.txt
benchmarks/qc_representative_entities.tsv
docs/conf.py
docs/index.md
docs/requirements.txt
docs/_static/language-switcher.js
docs/_static/operon.css
docs/_templates/layout.html
docs/en/index.md
docs/en/overview.md
docs/en/architecture/extensibility.md
docs/en/architecture/external-analysis.md
docs/en/architecture/files-and-storage.md
docs/en/architecture/index.md
docs/en/architecture/metadata-and-data-model.md
docs/en/architecture/overview.md
docs/en/architecture/qc-and-rules.md
docs/en/architecture/release-lifecycle.md
docs/en/architecture/taxonomy-coverage.md
docs/en/contributor/development-testing.md
docs/en/contributor/documentation-deployment.md
docs/en/contributor/index.md
docs/en/contributor/pypi-release.md
docs/en/contributor/repository-guide.md
docs/en/getting-started/daily-workflow.md
docs/en/getting-started/first-project.md
docs/en/getting-started/index.md
docs/en/getting-started/installation.md
docs/en/getting-started/quickstart.md
docs/en/guides/backup-migration.md
docs/en/guides/curation-lifecycle.md
docs/en/guides/external-analysis.md
docs/en/guides/file-archiving.md
docs/en/guides/index.md
docs/en/guides/metadata-import.md
docs/en/guides/ncbi-datasets.md
docs/en/guides/phylogenetics-workflow.md
docs/en/guides/qc-profiles.md
docs/en/guides/remote-execution.md
docs/en/guides/remote-first.md
docs/en/guides/remote-storage.md
docs/en/guides/taxonomy-coverage.md
docs/en/guides/troubleshooting.md
docs/en/operations/database-compatibility.md
docs/en/operations/index.md
docs/en/operations/ncbi-recovery-migration.md
docs/en/operations/qc-performance.md
docs/en/reference/behaviors-and-limitations.md
docs/en/reference/cli-analysis.md
docs/en/reference/cli-decisions-reports.md
docs/en/reference/cli-files-qc.md
docs/en/reference/cli-project-metadata.md
docs/en/reference/cli-remote.md
docs/en/reference/cli-taxonomy-lifecycle-admin.md
docs/en/reference/cli-tui.md
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docs/en/reference/index.md
docs/en/reference/recipe-fields.md
docs/en/reference/recipe-overview.md
docs/en/reference/recipe-parsers-examples.md
docs/zh/index.md
docs/zh/overview.md
docs/zh/architecture/extensibility.md
docs/zh/architecture/external-analysis.md
docs/zh/architecture/files-and-storage.md
docs/zh/architecture/index.md
docs/zh/architecture/metadata-and-data-model.md
docs/zh/architecture/overview.md
docs/zh/architecture/qc-and-rules.md
docs/zh/architecture/release-lifecycle.md
docs/zh/architecture/taxonomy-coverage.md
docs/zh/contributor/development-testing.md
docs/zh/contributor/documentation-deployment.md
docs/zh/contributor/index.md
docs/zh/contributor/pypi-release.md
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docs/zh/getting-started/daily-workflow.md
docs/zh/getting-started/first-project.md
docs/zh/getting-started/index.md
docs/zh/getting-started/installation.md
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docs/zh/guides/backup-migration.md
docs/zh/guides/curation-lifecycle.md
docs/zh/guides/external-analysis.md
docs/zh/guides/file-archiving.md
docs/zh/guides/index.md
docs/zh/guides/metadata-import.md
docs/zh/guides/ncbi-datasets.md
docs/zh/guides/phylogenetics-workflow.md
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docs/zh/reference/cli-decisions-reports.md
docs/zh/reference/cli-files-qc.md
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operon/__init__.py
operon/__main__.py
operon/backup.py
operon/classify.py
operon/cli.py
operon/config.py
operon/coverage.py
operon/database.py
operon/demo.py
operon/entity_view.py
operon/environment.py
operon/environment_capture.py
operon/errors.py
operon/execution.py
operon/export.py
operon/fanout.py
operon/files.py
operon/import_wizard.py
operon/lifecycle.py
operon/lineage.py
operon/metadata_files.py
operon/ncbi_reconcile.py
operon/profiles.py
operon/release.py
operon/remotes.py
operon/reports.py
operon/rules.py
operon/schema.py
operon/sequence_tools.py
operon/shutdown.py
operon/table_import.py
operon/taxonomy.py
operon/timetree.py
operon/tools.py
operon/utils.py
operon/workflow.py
operon/adapters/__init__.py
operon/adapters/ncbi_datasets.py
operon/adapters/timetree.py
operon/qc/__init__.py
operon/qc/_alignment.pyx
operon/qc/_parsers.pyx
operon/qc/alignment.py
operon/qc/measure.py
operon/qc/parsers.py
operon/tui/__init__.py
operon/tui/actions.py
operon/tui/app.py
operon/tui/app.tcss
operon/tui/data.py
operon/tui/splash.py
operon/tui/splash_terminal.py
operon/tui/assets/splash.png
operon/tui/assets/splash.rgb.z
operon/tui/screens/__init__.py
operon/tui/screens/common.py
operon/tui/screens/config.py
operon/tui/screens/coverage.py
operon/tui/screens/decisions.py
operon/tui/screens/entities.py
operon/tui/screens/files.py
operon/tui/screens/files_ops.py
operon/tui/screens/home.py
operon/tui/screens/import_wizard.py
operon/tui/screens/publish.py
operon/tui/screens/runs.py
tests/__init__.py
tests/helpers.py
tests/compatibility/__init__.py
tests/compatibility/test_python_support.py
tests/integration/__init__.py
tests/integration/test_analysis_resume.py
tests/integration/test_analysis_shutdown.py
tests/integration/test_analysis_tools.py
tests/integration/test_classify_sequences.py
tests/integration/test_execution_backends.py
tests/integration/test_fanout_analyze.py
tests/integration/test_lineage_cascade.py
tests/integration/test_ncbi_datasets_adapter.py
tests/integration/test_pipeline_and_release.py
tests/integration/test_python_packaging.py
tests/integration/test_qc_remote_measure.py
tests/integration/test_taxonomy_coverage.py
tests/regression/__init__.py
tests/regression/test_correctness.py
tests/regression/test_cython_alignment_parity.py
tests/regression/test_cython_parser_parity.py
tests/regression/test_parser_semantics.py
tests/unit/__init__.py
tests/unit/test_alignment_qc.py
tests/unit/test_classify.py
tests/unit/test_cli_edges.py
tests/unit/test_config_workflow_edges.py
tests/unit/test_core_coverage_more.py
tests/unit/test_coverage_edges.py
tests/unit/test_database_edges_more.py
tests/unit/test_docs_versions.py
tests/unit/test_environment.py
tests/unit/test_environment_capture.py
tests/unit/test_execution.py
tests/unit/test_execution_edges.py
tests/unit/test_export.py
tests/unit/test_fanout.py
tests/unit/test_files_edges.py
tests/unit/test_follow.py
tests/unit/test_import_backup_show.py
tests/unit/test_import_wizard_edges.py
tests/unit/test_lifecycle.py
tests/unit/test_lineage.py
tests/unit/test_misc_coverage_more.py
tests/unit/test_ncbi_coverage_gaps.py
tests/unit/test_ncbi_edge_cases.py
tests/unit/test_ncbi_reconcile_edges.py
tests/unit/test_parser_edge_paths.py
tests/unit/test_qc_and_rules.py
tests/unit/test_qc_edges_more.py
tests/unit/test_qc_measure.py
tests/unit/test_qc_remote_only.py
tests/unit/test_recipe_history.py
tests/unit/test_remote_taxonomy_more.py
tests/unit/test_remote_transport_edges.py
tests/unit/test_remotes.py
tests/unit/test_remotes_edges.py
tests/unit/test_rules_schema_edges.py
tests/unit/test_schema_2_10.py
tests/unit/test_schema_2_11.py
tests/unit/test_schema_2_9.py
tests/unit/test_schema_and_metadata.py
tests/unit/test_sequence_tools.py
tests/unit/test_sequences.py
tests/unit/test_shutdown.py
tests/unit/test_support_edges.py
tests/unit/test_table_import_edges.py
tests/unit/test_taxonomy_edges.py
tests/unit/test_timetree.py
tests/unit/test_timetree_snapshots.py
tests/unit/test_tools_edges.py
tests/unit/test_tools_execution_more.py
tests/unit/test_tui.py
tests/unit/test_tui_config.py
tests/unit/test_tui_flows_more.py
tests/unit/test_tui_publish.py
tests/unit/test_tui_screens_more.py
tests/unit/test_tui_splash_terminal.py
tests/unit/test_tui_writes.py
tests/unit/test_views_release_reports_edges.py
tests/unit/test_workflow_cli.py