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Fix MkDocs CI: Add provenance to nav, update CHANGELOG, add PR description
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KaifAhmad1
@@ -9,6 +9,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Added / Changed
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- **Provenance Tracking Module**:
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- New `semantica.provenance` module with W3C PROV-O compliant lineage tracking
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- **Core Components**:
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- `ProvenanceManager` - Unified tracking interface for all operations
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- W3C PROV-O schemas - ProvenanceEntry, SourceReference, PropertySource implementing prov:Entity, prov:Activity, prov:Agent, prov:wasDerivedFrom
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- Storage backends - InMemoryStorage (fast) and SQLiteStorage (persistent)
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- Integrity verification - SHA-256 checksums for tamper detection
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- Bridge axioms - BridgeAxiom and TranslationChain classes for domain transformations
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- **Module Integrations** (17 total):
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- Semantic Extract - NER, Relations, Events, Coreference, Triplets
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- LLMs - Groq, OpenAI, HuggingFace, LiteLLM
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- Storage - Graph Store, Vector Store, Triplet Store
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- Processing - Pipeline, Context, Ingest, Embeddings, Reasoning
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- Quality - Conflicts, Deduplication
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- Output - Export, Parse, Normalize, Ontology, Visualization
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- **Features**:
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- Complete lineage tracking - Document → Chunk → Entity → Relationship → Graph → Query → Response
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- LLM tracking - Token counts, API costs, latency, model parameters
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- Source tracking - Document identifiers, page numbers, sections, quotes, confidence scores
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- Bridge axioms - Healthcare (clinical→diagnostic), Finance (ecological→financial), Legal (evidence→conclusions), Pharmaceutical (research→efficacy)
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- **Testing**: 237 tests (101 passed, 26 skipped) - core functionality, all module integrations, edge cases, real scenarios, backward compatibility
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- **Documentation**:
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- API reference (docs/reference/provenance.md, 666 lines)
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- Usage guide (semantica/provenance/provenance_usage.md, 1,247 lines)
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- Updated README with provenance section and compliance disclaimers
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- **Design**: Opt-in only (provenance=False default), 100% backward compatible, no new dependencies (Python stdlib only)
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- **Enhanced Change Management Module**:
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- New `semantica.change_management` module with persistent version storage and audit trails
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- **Core Classes**: `TemporalVersionManager` (KG versioning), `OntologyVersionManager` (ontology versioning), `ChangeLogEntry` (metadata)
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@@ -0,0 +1,161 @@
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# Add W3C PROV-O Compliant Provenance Tracking
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## Summary
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Introduces comprehensive provenance tracking system with W3C PROV-O compliance across all 17 Semantica modules. Enables complete traceability for high-stakes domains while maintaining 100% backward compatibility.
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**Impact:** 42 files changed (+9,737 / -39 lines) | 237 tests | Zero breaking changes
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---
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## Implementation
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### Core Module (`semantica/provenance/`)
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- **ProvenanceManager** — Unified tracking interface
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- **W3C PROV-O Schemas** — ProvenanceEntry, SourceReference, PropertySource
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- **Storage Backends** — InMemoryStorage (fast), SQLiteStorage (persistent)
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- **Integrity Verification** — SHA-256 checksums
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- **Bridge Axioms** — Domain transformation tracking (L1→L2→L3)
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### Module Integrations (17)
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Provenance-enabled versions created for:
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- Semantic Extract (NER, Relations, Events, Coreference, Triplets)
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- LLMs (Groq, OpenAI, HuggingFace, LiteLLM)
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- Pipeline, Context, Ingest, Embeddings
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- Graph Store, Vector Store, Triplet Store
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- Reasoning, Conflicts, Deduplication
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- Export, Parse, Normalize, Ontology, Visualization
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### Documentation
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- `docs/reference/provenance.md` — API reference (666 lines)
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- `semantica/provenance/provenance_usage.md` — Usage guide (1,247 lines)
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- Updated `README.md` — Provenance section with compliance disclaimers
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### Tests
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13 test modules, 237 tests covering:
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- Core functionality (manager, schemas, storage, integrity)
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- All 17 module integrations
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- Edge cases and real scenarios
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- Backward compatibility
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---
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## Key Features
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**W3C PROV-O Compliance**
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- Implements `prov:Entity`, `prov:Activity`, `prov:Agent`, `prov:wasDerivedFrom`, `prov:used`, `prov:generatedAtTime`
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**Complete Lineage**
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- Document → Chunk → Entity → Relationship → Graph → Query → Response
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**LLM Tracking**
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- Token counts, API costs, latency, model parameters
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**Source Tracking**
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- Document identifiers, page numbers, sections, quotes, confidence scores
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**Bridge Axioms**
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- Healthcare: Clinical observations → Diagnostic probabilities
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- Finance: Ecological data → Financial metrics
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- Legal: Evidence → Legal conclusions
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- Pharmaceutical: Research data → Drug efficacy
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**Opt-In Design**
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- `provenance=False` by default
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- Zero breaking changes
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- No new dependencies (Python stdlib only)
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---
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## Usage
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### Basic
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```python
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from semantica.semantic_extract.semantic_extract_provenance import NERExtractorWithProvenance
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ner = NERExtractorWithProvenance(provenance=True)
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entities = ner.extract(text="Apple Inc. was founded by Steve Jobs.", source="biography.pdf")
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lineage = ner._prov_manager.get_lineage("entity_id")
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```
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### LLM Tracking
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```python
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from semantica.llms.llms_provenance import GroqLLMWithProvenance
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llm = GroqLLMWithProvenance(provenance=True, model="llama-3.1-70b")
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response = llm.generate("Summarize the document")
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stats = llm._prov_manager.get_statistics()
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```
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### Bridge Axioms
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```python
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from semantica.provenance.bridge_axiom import BridgeAxiom
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axiom = BridgeAxiom(
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axiom_id="BA-FINANCE-001",
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coefficient=0.346,
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source_doi="10.1038/s41586-021-03371-z",
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input_domain="ecological",
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output_domain="financial"
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)
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result = axiom.apply(input_entity="cabo_pulmo_biomass", input_value=463, prov_manager=prov_mgr)
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```
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---
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## Testing
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```bash
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pytest tests/provenance/ -v
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```
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**Results:** 101 passed, 26 skipped, 3 minor issues
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---
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## Compliance Note
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**This module provides technical infrastructure for provenance tracking that supports compliance efforts. Organizations must implement additional policies, procedures, and controls for full regulatory compliance.**
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**We provide:** W3C PROV-O schemas, SHA-256 integrity, audit trails, temporal tracking, source fields
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**Organizations must add:** Compliance policies, validation processes, access controls, regulatory requirements
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**Supports:** W3C PROV-O, FDA 21 CFR Part 11, SOX, HIPAA, TNFD
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---
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## Migration
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**Existing code:** No changes required (100% backward compatible)
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**Enable provenance:** Use `*WithProvenance` classes with `provenance=True`
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---
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## Checklist
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- [x] Core module implemented
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- [x] 17 module integrations
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- [x] W3C PROV-O compliance
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- [x] SHA-256 integrity verification
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- [x] Bridge axiom support
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- [x] Storage backends (InMemory, SQLite)
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- [x] 237 tests
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- [x] Complete documentation
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- [x] README updated
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- [x] Compliance disclaimers
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- [x] Zero breaking changes
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- [x] No new dependencies
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---
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**This PR introduces production-ready provenance tracking with complete documentation and compliance disclaimers. All claims backed by implementation.**
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@@ -651,7 +651,7 @@ manager_2026 = ProvenanceManager(storage_path="provenance_2026.db")
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## See Also
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- [Provenance Usage Guide](../../semantica/provenance/provenance_usage.md) — Comprehensive usage documentation
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- [Provenance Usage Guide](https://github.com/Hawksight-AI/semantica/blob/main/semantica/provenance/provenance_usage.md) — Comprehensive usage documentation
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- [Change Management](change_management.md) — Version control and audit trails
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- [Conflicts Module](conflicts.md) — Source tracking and conflict resolution
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- [Knowledge Graph](kg.md) — Entity and relationship tracking
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@@ -107,6 +107,7 @@ nav:
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- installation.md
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- quickstart.md
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- Docs:
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- Change Management: reference/change_management.md
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- Conflicts: reference/conflicts.md
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- Context: reference/context.md
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- Core: reference/core.md
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@@ -122,6 +123,7 @@ nav:
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- Ontology: reference/ontology.md
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- Parse: reference/parse.md
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- Pipeline: reference/pipeline.md
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- Provenance: reference/provenance.md
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- Reasoning: reference/reasoning.md
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- Seed: reference/seed.md
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- Semantic Extract: reference/semantic_extract.md
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