biolm.models package

Submodules

biolm.models.examples module

Generate SDK usage examples for BioLM models.

class biolm.models.examples.ExampleGenerator(api_key: str | None = None, base_url: str | None = None)

Bases: object

Generate SDK usage examples for BioLM models.

async fetch_community_models() → List[Dict[str, Any]]

Fetch list of available models.

Uses biolm-hub OpenAPI when in hub mode, otherwise the platform community-api-models endpoint.

async fetch_model_details(model_slug: str, code_examples: bool = False, exclude_docs_html: bool = True) → Dict[str, Any] | None

Fetch detailed information for a specific model from community-api-models endpoint.

Args:

model_slug: Model slug (e.g., ‘esmfold’) code_examples: If True, include code examples in the response exclude_docs_html: If True, exclude HTML documentation

Returns:

Model details dictionary or None if not found

async generate_example(model_name: str, action: str | None = None, format: str = 'python', input_type: str | None = None) → str

Generate example for a model and action.

Args:

model_name: Name of the model. action: Action name (encode, predict, generate, lookup). If None, generates for all available actions. format: Output format (‘python’, ‘markdown’, ‘rst’, ‘json’). input_type: Optional input type override.

Returns:

Formatted example string.

async get_model_schema(model_name: str, action: str) → Dict[str, Any] | None

Get schema for a model and action.

Args:

model_name: Name of the model. action: Action name (encode, predict, generate, lookup).

Returns:

Schema dictionary or None if not found.

async shutdown()

Close HTTP client connections.

biolm.models.examples.ExampleGeneratorSync

alias of BlockingExampleGeneratorSync

biolm.models.examples.get_example(model_name: str, action: str | None = None, format: str = 'python', api_key: str | None = None, base_url: str | None = None) → str

Generate SDK usage example for a model (synchronous).

Args:

model_name: Name of the model. action: Action name (optional, will try to detect). format: Output format (‘python’, ‘markdown’, ‘rst’, ‘json’). api_key: Optional API key. base_url: Optional base URL.

Returns:

Formatted example string.

async biolm.models.examples.get_example_async(model_name: str, action: str | None = None, format: str = 'python', api_key: str | None = None, base_url: str | None = None) → str

Generate SDK usage example for a model (async).

Args:

model_name: Name of the model. action: Action name (optional, will try to detect). format: Output format (‘python’, ‘markdown’, ‘rst’, ‘json’). api_key: Optional API key. base_url: Optional base URL.

Returns:

Formatted example string.

biolm.models.examples.get_model_details(model_slug: str, code_examples: bool = False, exclude_docs_html: bool = True, api_key: str | None = None, base_url: str | None = None) → Dict[str, Any] | None

Fetch detailed information for a specific model (synchronous).

Args:

model_slug: Model slug (e.g., ‘esmfold’). code_examples: If True, include code examples in the response. exclude_docs_html: If True, exclude HTML documentation. api_key: Optional API key. base_url: Optional base URL.

Returns:

Model details dictionary or None if not found.

biolm.models.examples.list_models(api_key: str | None = None, base_url: str | None = None) → List[Dict[str, Any]]

List all available models from community-api-models endpoint (synchronous).

Args:

api_key: Optional API key. base_url: Optional base URL.

Returns:

List of model dictionaries.

async biolm.models.examples.list_models_async(api_key: str | None = None, base_url: str | None = None) → List[Dict[str, Any]]

List all available models from community-api-models endpoint (async).

Args:

api_key: Optional API key. base_url: Optional base URL.

Returns:

List of model dictionaries.

Module contents

High-level model interface for BioLM (Model, encode/predict/generate helpers).

exception biolm.models.BuildError

Bases: RuntimeError

BioLM definition build failed.

class biolm.models.BuiltPackage(path: Path, manifest: Dict[str, Any])

Bases: object

Result of a successful build_model.

manifest: Dict[str, Any]

path: Path

class biolm.models.Model(name: str, api_key: str | None = None, **kwargs)

Bases: object

User-friendly model interface for BioLM API.

Args:

name (str): The model name (e.g., ‘esm2-8m’, ‘esmfold’). api_key (Optional[str]): API key for authentication. **kwargs: Additional arguments passed to BioLMApi.

encode(items: Any | List[Any], type: str | None = None, params: dict | None = None, progress: bool = True, progress_callback: Callable[[int, int], None] | None = None, **kwargs)

Encode using the model.

Args:

items: Single item or list of items to encode. type: Type of item (e.g., ‘sequence’). Required if items are not dicts. params: Optional parameters for the encoding. progress: If True (default), show Rich progress bar (multiple items only). progress_callback: Optional (completed, total) callback; overrides progress=True if provided. **kwargs: Additional arguments (stop_on_error, output, file_path, etc.).

Returns:

Encoding results.

generate(items: Any | List[Any], type: str | None = None, params: dict | None = None, progress: bool = True, progress_callback: Callable[[int, int], None] | None = None, **kwargs)

Generate using the model.

Args:

items: Single item or list of items to generate from. type: Type of item (e.g., ‘context’, ‘pdb’). Required if items are not dicts. params: Optional parameters for the generation. progress: If True (default), show Rich progress bar (multiple items only). progress_callback: Optional (completed, total) callback; overrides progress=True if provided. **kwargs: Additional arguments (stop_on_error, output, file_path, etc.).

Returns:

Generation results.

get_example(action: str | None = None, format: str = 'python', **kwargs) → str

Get SDK usage example for this model.

Args:

action: Action name (encode, predict, generate, lookup). If None, generates for first available action. format: Output format (‘python’, ‘markdown’, ‘rst’, ‘json’). **kwargs: Additional arguments passed to ExampleGenerator (base_url).

Returns:

Formatted example string.

get_examples(format: str = 'python', **kwargs) → str

Get SDK usage examples for all supported actions of this model.

Args:

format: Output format (‘python’, ‘markdown’, ‘rst’, ‘json’). **kwargs: Additional arguments passed to ExampleGenerator (base_url).

Returns:

Formatted examples string with all actions.

lookup(query: dict | List[dict], **kwargs)

Lookup using the model.

Args:

query: Query dict or list of query dicts. **kwargs: Additional arguments (raw, output, file_path).

Returns:

Lookup results.

predict(items: Any | List[Any], type: str | None = None, params: dict | None = None, progress: bool = True, progress_callback: Callable[[int, int], None] | None = None, **kwargs)

Predict using the model.

Args:

items: Single item or list of items to predict. type: Type of item (e.g., ‘sequence’, ‘pdb’). Required if items are not dicts. params: Optional parameters for the prediction. progress: If True (default), show Rich progress bar (multiple items only). progress_callback: Optional (completed, total) callback; overrides progress=True if provided. **kwargs: Additional arguments (stop_on_error, output, file_path, etc.).

Returns:

Prediction results.

exception biolm.models.RecipeError

Bases: ValueError

Invalid or unreadable BioLM definition recipe.

biolm.models.build_model(recipe_path: str | Path, *, tag: str = 'latest', name: str | None = None, api_key: str | None = None, poll_interval: float = 15.0, timeout: float | None = None, bundle: bool = False, artifact: str | None = None) → BuiltPackage

Compile a recipe into a locked BioLM package under ~/.biolm/models.

Does not modify the recipe file. Overwrites an existing package dir for the same name/tag.

When bundle=True, requires a resolvable head artifact URI (from the finetune result or artifact= override), downloads into artifacts/, and sets artifact.path with load: preload.

biolm.models.encode(model_name: str, items: Any | List[Any], type: str | None = None, params: dict | None = None, **kwargs)

Quick encoding using a model.

biolm.models.generate(model_name: str, items: Any | List[Any], type: str | None = None, params: dict | None = None, **kwargs)

Quick generation using a model.

biolm.models.load_recipe(path: str | Path) → Dict[str, Any]

Load and validate a BioLM definition recipe YAML.

Returns a normalized dict. The single layer includes data_path as an absolute Path to the training CSV.

biolm.models.predict(model_name: str, items: Any | List[Any], type: str | None = None, params: dict | None = None, **kwargs)

Quick prediction using a model.