biblicus 0.6.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

biblicus/inference.py

@@ -0,0 +1,104 @@
+"""
+Inference backend abstraction for machine learning powered components.
+
+This module provides reusable configuration and credential resolution patterns for components
+that can execute locally or via API providers.
+"""
+
+from __future__ import annotations
+
+import os
+from enum import Enum
+from typing import Optional
+
+from pydantic import BaseModel, ConfigDict, Field, model_validator
+
+
+class InferenceBackendMode(str, Enum):
+    """Execution mode for inference backends."""
+
+    LOCAL = "local"
+    API = "api"
+
+
+class ApiProvider(str, Enum):
+    """Supported application programming interface providers for inference."""
+
+    HUGGINGFACE = "huggingface"
+    OPENAI = "openai"
+
+
+class InferenceBackendConfig(BaseModel):
+    """
+    Composable configuration for inference backends.
+
+    This config can be embedded in extractor or transformer configurations to provide
+    a uniform interface for local versus application programming interface execution.
+
+    :ivar mode: Execution mode, local or application programming interface.
+    :vartype mode: InferenceBackendMode
+    :ivar api_provider: Application programming interface provider when mode is application programming interface.
+    :vartype api_provider: ApiProvider or None
+    :ivar api_key: Optional per-config application programming interface key override.
+    :vartype api_key: str or None
+    :ivar model_id: Optional model identifier for application programming interface requests.
+    :vartype model_id: str or None
+    """
+
+    model_config = ConfigDict(extra="forbid")
+
+    mode: InferenceBackendMode = Field(default=InferenceBackendMode.LOCAL)
+    api_provider: Optional[ApiProvider] = Field(default=None)
+    api_key: Optional[str] = Field(default=None)
+    model_id: Optional[str] = Field(default=None)
+
+    @model_validator(mode="after")
+    def _validate_api_provider_required(self) -> "InferenceBackendConfig":
+        if self.mode == InferenceBackendMode.API and self.api_provider is None:
+            raise ValueError("api_provider is required when mode is 'api'")
+        return self
+
+
+def resolve_api_key(
+    provider: ApiProvider,
+    *,
+    config_override: Optional[str] = None,
+) -> Optional[str]:
+    """
+    Resolve an application programming interface key with precedence rules.
+
+    Precedence order (highest to lowest):
+    1. Explicit config override parameter
+    2. Environment variable for the provider
+    3. User configuration file
+
+    :param provider: Application programming interface provider to resolve key for.
+    :type provider: ApiProvider
+    :param config_override: Optional explicit key from configuration.
+    :type config_override: str or None
+    :return: Resolved application programming interface key or None if unavailable.
+    :rtype: str or None
+    """
+    if config_override is not None:
+        return config_override
+
+    from .user_config import load_user_config
+
+    if provider == ApiProvider.HUGGINGFACE:
+        env_key = os.environ.get("HUGGINGFACE_API_KEY")
+        if env_key:
+            return env_key
+        user_config = load_user_config()
+        if user_config.huggingface is not None:
+            return user_config.huggingface.api_key
+        return None
+    elif provider == ApiProvider.OPENAI:
+        env_key = os.environ.get("OPENAI_API_KEY")
+        if env_key:
+            return env_key
+        user_config = load_user_config()
+        if user_config.openai is not None:
+            return user_config.openai.api_key
+        return None
+    else:
+        return None

biblicus/models.py

@@ -399,6 +399,8 @@ class ExtractedText(BaseModel):
     :vartype producer_extractor_id: str
     :ivar source_step_index: Optional pipeline step index where this text originated.
     :vartype source_step_index: int or None
+    :ivar confidence: Optional confidence score from 0.0 to 1.0.
+    :vartype confidence: float or None
     """
 
     model_config = ConfigDict(extra="forbid")
@@ -406,6 +408,7 @@ class ExtractedText(BaseModel):
     text: str
     producer_extractor_id: str = Field(min_length=1)
     source_step_index: Optional[int] = Field(default=None, ge=1)
+    confidence: Optional[float] = Field(default=None, ge=0.0, le=1.0)
 
 
 class ExtractionStepOutput(BaseModel):
@@ -426,6 +429,8 @@ class ExtractionStepOutput(BaseModel):
     :vartype producer_extractor_id: str or None
     :ivar source_step_index: Optional step index that supplied the text for selection-style extractors.
     :vartype source_step_index: int or None
+    :ivar confidence: Optional confidence score from 0.0 to 1.0.
+    :vartype confidence: float or None
     :ivar error_type: Optional error type name for errored steps.
     :vartype error_type: str or None
     :ivar error_message: Optional error message for errored steps.
@@ -441,5 +446,6 @@ class ExtractionStepOutput(BaseModel):
     text_characters: int = Field(default=0, ge=0)
     producer_extractor_id: Optional[str] = None
     source_step_index: Optional[int] = Field(default=None, ge=1)
+    confidence: Optional[float] = Field(default=None, ge=0.0, le=1.0)
     error_type: Optional[str] = None
     error_message: Optional[str] = None

biblicus/user_config.py

@@ -29,17 +29,49 @@ class OpenAiUserConfig(BaseModel):
     api_key: str = Field(min_length=1)
 
 
+class HuggingFaceUserConfig(BaseModel):
+    """
+    Configuration for HuggingFace integrations.
+
+    :ivar api_key: HuggingFace API key used for authenticated requests.
+    :vartype api_key: str
+    """
+
+    model_config = ConfigDict(extra="forbid")
+
+    api_key: str = Field(min_length=1)
+
+
+class DeepgramUserConfig(BaseModel):
+    """
+    Configuration for Deepgram integrations.
+
+    :ivar api_key: Deepgram API key used for authenticated requests.
+    :vartype api_key: str
+    """
+
+    model_config = ConfigDict(extra="forbid")
+
+    api_key: str = Field(min_length=1)
+
+
 class BiblicusUserConfig(BaseModel):
     """
     Parsed user configuration for Biblicus.
 
     :ivar openai: Optional OpenAI configuration.
     :vartype openai: OpenAiUserConfig or None
+    :ivar huggingface: Optional HuggingFace configuration.
+    :vartype huggingface: HuggingFaceUserConfig or None
+    :ivar deepgram: Optional Deepgram configuration.
+    :vartype deepgram: DeepgramUserConfig or None
     """
 
     model_config = ConfigDict(extra="forbid")
 
     openai: Optional[OpenAiUserConfig] = None
+    huggingface: Optional[HuggingFaceUserConfig] = None
+    deepgram: Optional[DeepgramUserConfig] = None
 
 
 def default_user_config_paths(
@@ -136,3 +168,47 @@ def resolve_openai_api_key(*, config: Optional[BiblicusUserConfig] = None) -> Op
     if loaded.openai is None:
         return None
     return loaded.openai.api_key
+
+
+def resolve_huggingface_api_key(
+    *, config: Optional[BiblicusUserConfig] = None
+) -> Optional[str]:
+    """
+    Resolve a HuggingFace API key from environment or user configuration.
+
+    Environment takes precedence over configuration.
+
+    :param config: Optional pre-loaded user configuration.
+    :type config: BiblicusUserConfig or None
+    :return: API key string, or None when no key is available.
+    :rtype: str or None
+    """
+    env_key = os.environ.get("HUGGINGFACE_API_KEY")
+    if env_key:
+        return env_key
+    loaded = config or load_user_config()
+    if loaded.huggingface is None:
+        return None
+    return loaded.huggingface.api_key
+
+
+def resolve_deepgram_api_key(
+    *, config: Optional[BiblicusUserConfig] = None
+) -> Optional[str]:
+    """
+    Resolve a Deepgram API key from environment or user configuration.
+
+    Environment takes precedence over configuration.
+
+    :param config: Optional pre-loaded user configuration.
+    :type config: BiblicusUserConfig or None
+    :return: API key string, or None when no key is available.
+    :rtype: str or None
+    """
+    env_key = os.environ.get("DEEPGRAM_API_KEY")
+    if env_key:
+        return env_key
+    loaded = config or load_user_config()
+    if loaded.deepgram is None:
+        return None
+    return loaded.deepgram.api_key

{biblicus-0.6.0.dist-info → biblicus-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biblicus
-Version: 0.6.0
+Version: 0.8.0
 Summary: Command line interface and Python library for corpus ingestion, retrieval, and evaluation.
 License: MIT
 Requires-Python: >=3.9
@@ -25,6 +25,21 @@ Requires-Dist: unstructured>=0.12.0; extra == "unstructured"
 Requires-Dist: python-docx>=1.1.0; extra == "unstructured"
 Provides-Extra: ocr
 Requires-Dist: rapidocr-onnxruntime>=1.3.0; extra == "ocr"
+Provides-Extra: paddleocr
+Requires-Dist: paddleocr>=2.7.0; extra == "paddleocr"
+Requires-Dist: paddlepaddle>=2.5.0; extra == "paddleocr"
+Requires-Dist: huggingface_hub>=0.20.0; extra == "paddleocr"
+Requires-Dist: requests>=2.28.0; extra == "paddleocr"
+Provides-Extra: markitdown
+Requires-Dist: markitdown[all]>=0.1.0; python_version >= "3.10" and extra == "markitdown"
+Provides-Extra: deepgram
+Requires-Dist: deepgram-sdk>=3.0; extra == "deepgram"
+Provides-Extra: docling
+Requires-Dist: docling[vlm]>=2.0.0; extra == "docling"
+Provides-Extra: docling-mlx
+Requires-Dist: docling[mlx-vlm]>=2.0.0; extra == "docling-mlx"
+Provides-Extra: topic-modeling
+Requires-Dist: bertopic>=0.15.0; extra == "topic-modeling"
 Dynamic: license-file
 
 # Biblicus
@@ -67,7 +82,7 @@ If you want to run a real, executable version of this story, use `scripts/readme
 This simplified sequence diagram shows the same idea at a high level.
 
 ```mermaid
-%%{init: {"theme": "base", "themeVariables": {"primaryColor": "#f3e5f5", "primaryTextColor": "#111111", "primaryBorderColor": "#8e24aa", "lineColor": "#90a4ae", "secondaryColor": "#eceff1", "tertiaryColor": "#ffffff", "noteBkgColor": "#ffffff", "noteTextColor": "#111111", "actorBkg": "#f3e5f5", "actorBorder": "#8e24aa", "actorTextColor": "#111111"}}}%%
+%%{init: {"theme": "base", "themeVariables": {"background": "#ffffff", "primaryColor": "#f3e5f5", "primaryTextColor": "#111111", "primaryBorderColor": "#8e24aa", "lineColor": "#90a4ae", "secondaryColor": "#eceff1", "tertiaryColor": "#ffffff", "noteBkgColor": "#ffffff", "noteTextColor": "#111111", "actorBkg": "#f3e5f5", "actorBorder": "#8e24aa", "actorTextColor": "#111111"}}}%%
 sequenceDiagram
   participant App as Your assistant code
   participant KB as Knowledge base
@@ -106,7 +121,7 @@ In a coding assistant, retrieval is often triggered by what the user is doing ri
 This diagram shows two sequential Biblicus calls. They are shown separately to make the boundaries explicit: retrieval returns evidence, and context pack building consumes evidence.
 
 ```mermaid
-%%{init: {"theme": "base", "themeVariables": {"primaryColor": "#f3e5f5", "primaryTextColor": "#111111", "primaryBorderColor": "#8e24aa", "lineColor": "#90a4ae", "secondaryColor": "#eceff1", "tertiaryColor": "#ffffff", "noteBkgColor": "#ffffff", "noteTextColor": "#111111", "actorBkg": "#f3e5f5", "actorBorder": "#8e24aa", "actorTextColor": "#111111"}}}%%
+%%{init: {"theme": "base", "themeVariables": {"background": "#ffffff", "primaryColor": "#f3e5f5", "primaryTextColor": "#111111", "primaryBorderColor": "#8e24aa", "lineColor": "#90a4ae", "secondaryColor": "#eceff1", "tertiaryColor": "#ffffff", "noteBkgColor": "#ffffff", "noteTextColor": "#111111", "actorBkg": "#f3e5f5", "actorBorder": "#8e24aa", "actorTextColor": "#111111"}}}%%
 sequenceDiagram
   participant User
   participant App as Your assistant code
@@ -158,8 +173,14 @@ python3 -m pip install biblicus
 Some extractors are optional so the base install stays small.
 
 - Optical character recognition for images: `python3 -m pip install "biblicus[ocr]"`
-- Speech to text transcription: `python3 -m pip install "biblicus[openai]"` (requires an OpenAI API key in `~/.biblicus/config.yml` or `./.biblicus/config.yml`)
+- Advanced optical character recognition with PaddleOCR: `python3 -m pip install "biblicus[paddleocr]"`
+- Document understanding with Docling VLM: `python3 -m pip install "biblicus[docling]"`
+- Document understanding with Docling VLM and MLX acceleration: `python3 -m pip install "biblicus[docling-mlx]"`
+- Speech to text transcription with OpenAI: `python3 -m pip install "biblicus[openai]"` (requires an OpenAI API key in `~/.biblicus/config.yml` or `./.biblicus/config.yml`)
+- Speech to text transcription with Deepgram: `python3 -m pip install "biblicus[deepgram]"` (requires a Deepgram API key in `~/.biblicus/config.yml` or `./.biblicus/config.yml`)
 - Broad document parsing fallback: `python3 -m pip install "biblicus[unstructured]"`
+- MarkItDown document conversion (requires Python 3.10 or higher): `python3 -m pip install "biblicus[markitdown]"`
+- Topic modeling analysis with BERTopic: `python3 -m pip install "biblicus[topic-modeling]"`
 
 ## Quick start
 
@@ -417,6 +438,7 @@ The documents below follow the pipeline from raw items to model context:
 
 - [Corpus][corpus]
 - [Text extraction][text-extraction]
+- [Speech to text][speech-to-text]
 - [Knowledge base][knowledge-base]
 - [Backends][backends]
 - [Context packs][context-packs]
@@ -465,7 +487,97 @@ corpus/
 Two backends are included.
 
 - `scan` is a minimal baseline that scans raw items directly.
-- `sqlite-full-text-search` is a practical baseline that builds a full text search index in Sqlite.
+- `sqlite-full-text-search` is a practical baseline that builds a full text search index in SQLite.
+
+For detailed documentation including configuration options, performance characteristics, and usage examples, see the [Backend Reference][backend-reference].
+
+## Extraction backends
+
+These extractors are built in. Optional ones require extra dependencies. See [text extraction documentation][text-extraction] for details.
+
+### Text and document extraction
+
+- [`pass-through-text`](docs/extractors/text-document/pass-through.md) reads text items and strips Markdown front matter.
+- [`metadata-text`](docs/extractors/text-document/metadata.md) turns catalog metadata into a small text artifact.
+- [`pdf-text`](docs/extractors/text-document/pdf.md) extracts text from Portable Document Format items with `pypdf`.
+- [`unstructured`](docs/extractors/text-document/unstructured.md) provides broad document parsing (optional).
+- [`markitdown`](docs/extractors/text-document/markitdown.md) converts many formats into Markdown-like text (optional).
+
+### Optical character recognition
+
+- [`ocr-rapidocr`](docs/extractors/ocr/rapidocr.md) does optical character recognition on images (optional).
+- [`ocr-paddleocr-vl`](docs/extractors/ocr/paddleocr-vl.md) does advanced optical character recognition with PaddleOCR vision-language model (optional).
+
+### Vision-language models
+
+- [`docling-smol`](docs/extractors/vlm-document/docling-smol.md) uses the SmolDocling-256M vision-language model for fast document understanding (optional).
+- [`docling-granite`](docs/extractors/vlm-document/docling-granite.md) uses the Granite Docling-258M vision-language model for high-accuracy extraction (optional).
+
+### Speech to text
+
+- [`stt-openai`](docs/extractors/speech-to-text/openai.md) performs speech to text on audio using OpenAI (optional).
+- [`stt-deepgram`](docs/extractors/speech-to-text/deepgram.md) performs speech to text on audio using Deepgram (optional).
+
+### Pipeline utilities
+
+- [`select-text`](docs/extractors/pipeline-utilities/select-text.md) chooses one prior extraction result in a pipeline.
+- [`select-longest-text`](docs/extractors/pipeline-utilities/select-longest.md) chooses the longest prior extraction result.
+- [`select-override`](docs/extractors/pipeline-utilities/select-override.md) chooses the last extraction result for matching media types in a pipeline.
+- [`select-smart-override`](docs/extractors/pipeline-utilities/select-smart-override.md) intelligently chooses between extraction results based on confidence and content quality.
+
+For detailed documentation on all extractors, see the [Extractor Reference][extractor-reference].
+
+## Topic modeling analysis
+
+Biblicus can run analysis pipelines on extracted text without changing the raw corpus. Topic modeling is the first
+analysis backend. It reads an extraction run, optionally applies an LLM-driven extraction pass, applies lexical
+processing, runs BERTopic, and optionally applies an LLM fine-tuning pass to label topics. The output is structured
+JavaScript Object Notation.
+
+Run a topic analysis using a recipe file:
+
+```
+biblicus analyze topics --corpus corpora/example --recipe recipes/topic-modeling.yml --extraction-run pipeline:<run_id>
+```
+
+If `--extraction-run` is omitted, Biblicus uses the most recent extraction run and emits a warning about
+reproducibility. The analysis output is stored under:
+
+```
+.biblicus/runs/analysis/topic-modeling/<run_id>/output.json
+```
+
+Minimal recipe example:
+
+```yaml
+schema_version: 1
+text_source:
+  sample_size: 200
+llm_extraction:
+  enabled: false
+lexical_processing:
+  enabled: true
+  lowercase: true
+  strip_punctuation: false
+  collapse_whitespace: true
+bertopic_analysis:
+  parameters:
+    min_topic_size: 8
+    nr_topics: 10
+llm_fine_tuning:
+  enabled: false
+```
+
+LLM extraction and fine-tuning require `biblicus[openai]` and a configured OpenAI API key.
+Recipe files are validated strictly against the topic modeling schema, so type mismatches or unknown fields are errors.
+
+For a repeatable, real-world integration run that downloads a Wikipedia corpus and executes topic modeling, use:
+
+```
+python3 scripts/topic_modeling_integration.py --corpus corpora/wiki_demo --force
+```
+
+See `docs/TOPIC_MODELING.md` for parameter examples and per-topic output behavior.
 
 ## Integration corpus and evaluation dataset
 
@@ -522,6 +634,9 @@ License terms are in `LICENSE`.
 [corpus]: docs/CORPUS.md
 [knowledge-base]: docs/KNOWLEDGE_BASE.md
 [text-extraction]: docs/EXTRACTION.md
+[extractor-reference]: docs/extractors/index.md
+[backend-reference]: docs/backends/index.md
+[speech-to-text]: docs/STT.md
 [user-configuration]: docs/USER_CONFIGURATION.md
 [backends]: docs/BACKENDS.md
 [context-packs]: docs/CONTEXT_PACK.md

{biblicus-0.6.0.dist-info → biblicus-0.8.0.dist-info}/RECORD

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