LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/cli.md
docs/design.md
docs/getting-started.md
docs/index.md
docs/providers.md
docs/python-api.md
docs/releasing.md
docs/third-party.md
docs/adr/001-provider-execution-boundary.md
docs/adr/002-dependency-and-database-policy.md
docs/adr/003-evidence-resolution-and-caching.md
examples/results/pBR322_J01749.1.standard.json
src/plasmid_oracle/__init__.py
src/plasmid_oracle/__main__.py
src/plasmid_oracle/_immutability.py
src/plasmid_oracle/api.py
src/plasmid_oracle/cli.py
src/plasmid_oracle/errors.py
src/plasmid_oracle/py.typed
src/plasmid_oracle/reporting.py
src/plasmid_oracle/resolution.py
src/plasmid_oracle.egg-info/PKG-INFO
src/plasmid_oracle.egg-info/SOURCES.txt
src/plasmid_oracle.egg-info/dependency_links.txt
src/plasmid_oracle.egg-info/entry_points.txt
src/plasmid_oracle.egg-info/requires.txt
src/plasmid_oracle.egg-info/top_level.txt
src/plasmid_oracle/databases/__init__.py
src/plasmid_oracle/databases/setup.py
src/plasmid_oracle/execution/__init__.py
src/plasmid_oracle/execution/process.py
src/plasmid_oracle/model/__init__.py
src/plasmid_oracle/model/annotation.py
src/plasmid_oracle/model/characterization.py
src/plasmid_oracle/model/location.py
src/plasmid_oracle/model/manifest.py
src/plasmid_oracle/model/plasmid.py
src/plasmid_oracle/model/resolution.py
src/plasmid_oracle/model/sequence.py
src/plasmid_oracle/pipeline/__init__.py
src/plasmid_oracle/pipeline/cache.py
src/plasmid_oracle/pipeline/diagnostics.py
src/plasmid_oracle/pipeline/provider.py
src/plasmid_oracle/pipeline/runner.py
src/plasmid_oracle/providers/__init__.py
src/plasmid_oracle/providers/_external.py
src/plasmid_oracle/providers/_parsing.py
src/plasmid_oracle/providers/amrfinder.py
src/plasmid_oracle/providers/builtin.py
src/plasmid_oracle/providers/mob_typer.py
src/plasmid_oracle/providers/plannotate.py
src/plasmid_oracle/providers/pyrodigal.py
src/plasmid_oracle/serialization/__init__.py
src/plasmid_oracle/serialization/json.py
tests/test_cache.py
tests/test_cli.py
tests/test_database_setup.py
tests/test_diagnostics.py
tests/test_location.py
tests/test_models.py
tests/test_package_metadata.py
tests/test_parallel_async.py
tests/test_pipeline.py
tests/test_reference_plasmids.py
tests/test_resolution.py
tests/test_sequence.py
tests/test_serialization.py
tests/test_user_interface.py
tests/execution/test_process.py
tests/fixtures/amrfinder.tsv
tests/fixtures/bla_tem.fasta
tests/fixtures/mob_typer.tsv
tests/fixtures/plasmids/manifest.json
tests/fixtures/plasmids/pACYC184_X06403.1.fasta
tests/fixtures/plasmids/pBR322_J01749.1.fasta
tests/fixtures/plasmids/pUC19_M77789.2.fasta
tests/integration/test_reference_bioinformatics.py
tests/providers/test_amrfinder.py
tests/providers/test_mob_typer.py
tests/providers/test_plannotate.py
tests/providers/test_pyrodigal.py