AUTHORS.rst
CONTRIBUTING.rst
LICENSE
MANIFEST.in
NOTICE
README.md
pyproject.toml
setup.cfg
setup.py
biolm/__init__.py
biolm/client.py
biolm/finetune.py
biolm/platform.py
biolm/progress.py
biolm/protocol_runs.py
biolm/protocols.py
biolm/volumes.py
biolm/workspaces.py
biolm/cli/__init__.py
biolm/cli/entry.py
biolm/cli/theme.py
biolm/core/__init__.py
biolm/core/asynch.py
biolm/core/auth.py
biolm/core/const.py
biolm/core/expression_evaluator.py
biolm/core/http.py
biolm/core/paths.py
biolm/core/payloads.py
biolm/core/seqflow_auth.py
biolm/core/utils.py
biolm/core/validate.py
biolm/core/legacy/__init__.py
biolm/core/legacy/api.py
biolm/core/legacy/cls.py
biolm/hub/__init__.py
biolm/hub/catalog.py
biolm/hub/config.py
biolm/hub/discovery.py
biolm/hub/data/__init__.py
biolm/hub/data/catalog.json
biolm/io/__init__.py
biolm/io/csv.py
biolm/io/fasta.py
biolm/io/json.py
biolm/io/pdb.py
biolm/models/__init__.py
biolm/models/examples.py
biolm/pipeline/__init__.py
biolm/pipeline/async_executor.py
biolm/pipeline/base.py
biolm/pipeline/clustering.py
biolm/pipeline/data.py
biolm/pipeline/datastore.py
biolm/pipeline/datastore_duckdb.py
biolm/pipeline/filters.py
biolm/pipeline/generative.py
biolm/pipeline/mlm_remasking.py
biolm/pipeline/pipeline_def.py
biolm/pipeline/utils.py
biolm/pipeline/visualization.py
biolm/plugins/__init__.py
biolm/plugins/mlflow/__init__.py
biolm/plugins/mlflow/datasets.py
biolm/plugins/mlflow/protocols.py
biolm_sdk.egg-info/PKG-INFO
biolm_sdk.egg-info/SOURCES.txt
biolm_sdk.egg-info/dependency_links.txt
biolm_sdk.egg-info/entry_points.txt
biolm_sdk.egg-info/not-zip-safe
biolm_sdk.egg-info/requires.txt
biolm_sdk.egg-info/top_level.txt
biolmai/__init__.py
biolmai/_shim.py
biolmai/finetune.py
biolmai/protocol_runs.py
docs/Makefile
docs/changelog.rst
docs/conf.py
docs/index.rst
docs/make.bat
docs/_static/api_reference_icon.png
docs/_static/biolm_docs_logo_dark.png
docs/_static/biolm_docs_logo_light.png
docs/_static/biolm_logomark_transparent.png
docs/_static/biolm_logomark_transparent_for_dark.png
docs/_static/chat_agents_icon.png
docs/_static/jupyter_notebooks_icon.png
docs/_static/model_docs_icon.png
docs/_static/python_sdk_icon.png
docs/_static/tutorials_icon.png
docs/api-reference/biolm.cli.rst
docs/api-reference/biolm.core.legacy.rst
docs/api-reference/biolm.core.rst
docs/api-reference/biolm.hub.data.rst
docs/api-reference/biolm.hub.rst
docs/api-reference/biolm.io.rst
docs/api-reference/biolm.models.rst
docs/api-reference/biolm.pipeline.rst
docs/api-reference/biolm.plugins.mlflow.rst
docs/api-reference/biolm.plugins.rst
docs/api-reference/biolm.rst
docs/api-reference/modules.rst
docs/cli/account.rst
docs/cli/dataset.rst
docs/cli/hub.rst
docs/cli/index.rst
docs/cli/login.rst
docs/cli/logout.rst
docs/cli/model.rst
docs/cli/protocol.rst
docs/cli/status.rst
docs/cli/whoami.rst
docs/cli/workspace.rst
docs/cli/usage/authenticating.rst
docs/cli/usage/datasets.rst
docs/cli/usage/models.rst
docs/cli/usage/protocols.rst
docs/cli/usage/workspaces.rst
docs/guide/account-management.rst
docs/guide/authentication.rst
docs/guide/batching.rst
docs/guide/biolm-hub.rst
docs/guide/choosing-models.rst
docs/guide/client-interfaces.rst
docs/guide/concepts.rst
docs/guide/concurrency.rst
docs/guide/error-handling.rst
docs/guide/faq.rst
docs/guide/finetuning-models.rst
docs/guide/how-biolms-work.rst
docs/guide/installation.rst
docs/guide/iterative-masking-dms.rst
docs/guide/managing-datasets.rst
docs/guide/overview.rst
docs/guide/pipeline-caching.rst
docs/guide/pipeline-workflows.rst
docs/guide/protocol-workflows.rst
docs/guide/quickstart.rst
docs/guide/rate-limiting.rst
docs/guide/running-inference.rst
docs/guide/saturation-mutagenesis.rst
docs/guide/sdk-overview.rst
docs/guide/sequence-and-structure-data.rst
docs/guide/structure-conditioned-generation.rst
docs/guide/what-are-biolms.rst
docs/guide/workflows-overview.rst
docs/notes/authoring-guide.rst
docs/notes/migration-1.0.rst
docs/notes/snippet-doctests.rst
docs/reference/cli.rst
docs/reference/rest-api.rst
docs/reference/sdk.rst
docs/sdk/core.rst
docs/sdk/finetune.rst
docs/sdk/hub.rst
docs/sdk/index.rst
docs/sdk/io.rst
docs/sdk/models.rst
docs/sdk/pipeline.rst
docs/sdk/protocols.rst
docs/sdk/volumes.rst
docs/sdk/workspaces.rst
docs/yaml/protocol-schema.rst
tests/__init__.py
tests/conftest.py
tests/test_abatch_calls.py
tests/test_aclient.py
tests/test_advanced_features.py
tests/test_auth_integration.py
tests/test_batch_error_retry.py
tests/test_batch_errors.py
tests/test_biolm_shim.py
tests/test_biolmai.py
tests/test_cli_help.py
tests/test_cli_hub.py
tests/test_cli_login.py
tests/test_cli_model_io.py
tests/test_cli_model_list.py
tests/test_cli_model_run.py
tests/test_cli_model_show.py
tests/test_cli_platform.py
tests/test_cli_protocol_runs.py
tests/test_cli_theme.py
tests/test_client.py
tests/test_clustering.py
tests/test_concurrent_batches.py
tests/test_const_env.py
tests/test_datasets_mlflow.py
tests/test_datastore.py
tests/test_design_primitives.py
tests/test_docs_manifest.py
tests/test_duckdb_datastore.py
tests/test_embedding_pipeline.py
tests/test_example_generation.py
tests/test_filters.py
tests/test_finetune.py
tests/test_generation_workingset.py
tests/test_hub_config.py
tests/test_hub_discovery.py
tests/test_init_extras_gate.py
tests/test_integration.py
tests/test_io.py
tests/test_iterables.py
tests/test_jupyter_context.py
tests/test_max_items.py
tests/test_mlm_remasking.py
tests/test_oauth_auth.py
tests/test_pipeline.py
tests/test_pipeline_complete.py
tests/test_platform_client.py
tests/test_progress.py
tests/test_protocol_client.py
tests/test_protocols.py
tests/test_protocols_mlflow.py
tests/test_ranking_filter.py
tests/test_rate_limit.py
tests/test_remasking_config.py
tests/test_schemas.py
tests/test_smoke.py
tests/test_specs.py
tests/test_user_paths.py
tests/test_utils.py
tests/test_volumes.py
tests/fixtures/generate_input.json
tests/fixtures/generate_input_antifold.json
tests/fixtures/generate_input_prompt.json
tests/fixtures/generate_input_sequence.json
tests/fixtures/generate_input_sequence_clean.json
tests/fixtures/multi_model.pdb
tests/fixtures/sample.csv
tests/fixtures/sample.fasta
tests/fixtures/sample.pdb