Merge pull request #95 from OoriData/feature/kb-kg

Onya Knowledgebase support. See `KBBackend`

Author: uogbuji

AICONTEXT.md AICONTEXT-PYLIB.mdAICONTEXT.md renamed to AICONTEXT-PYLIB.md

@@ -1,4 +1,4 @@
-Additional context on this repository for AI tools & coding agents
+Additional context on this project for AI tools & coding agents
 
 - Python 3.12+ code, unless otherwise specified
 - Python code uses single outer quotes, including triple single quotes for e.g. docstrings
@@ -10,12 +10,13 @@ Additional context on this repository for AI tools & coding agents
 - Try to stick to 120 characters per line
   - if one of those comments would break this guideline, just put that comment above the line instead, as is standard convention
 - If there is a pyproject.toml in place, use it as a reference for builds, installs, etc. The basic packaging and dev preference, including if you have to supply your own pyproject.toml, is as follows:
-  - Use pyproject.toml with hatchling, not e.g. setup.py
+  - Prefer hatchling build system over setuptools, poetry, etc. Avoid setuptools as much as possible. No setup.py.
   - Reusable Python code modules are developed in the `pylib` folder, and installed using e.g. `uv pip install -U .`, which includes proper mapping to Python library package namespace via `tool.hatch.build.sources`. The `__init__.py` and other modules in the top-level package go directly in `pylib`, though submodules can use subdirectories, e.g. `pylib/a/b` becomes `installed_library_name.a.b`. Ultimately this will mean the installed package is importable as `from installed_library_name.etc import …`
-  - Yes this means editable and "dev mode" environments are NOT desirable, nor are shenanigans adding pylib to `sys.path`. Layer-efficient dockerization is an option if that's needed.
-  - The ethos is to always develop keeping things properly installable. No dev mode shortcuts
-  - Prefer hatchling build system over setuptools, poetry, etc. Avoid setuptools as much as possible. Use `[tool.hatch.build.sources]` to map source directories to package namespaces (e.g., `"pylib" = "installed_library_name"`).
   - Use `[tool.hatch.build.targets.wheel]` with `only-include = ["pylib"]` to ensure the pylib directory structure gets included properly in the wheel, avoiding the duplication issue that can occur with sources mapping
+  - Yes this means editable and "dev mode" environments are NOT desirable, nor are shenanigans adding pylib to `sys.path`. Layer-efficient dockerization is an option if that's needed.
+  - The ethos is to always develop keeping things properly installable. No dev mode shortcuts. Substantive modification to libray code requires e.g. `uv pip install -U .` each time.
+  - Note: This avoidance of editable installs can be relaxed for non-library code, such as demos or main app launch scripts (e.g. webapp back ends)
+  - If it's a CLI provided as part of a library, though, it should still use proper installation via `[project.scripts]` entry points (e.g., `ooriscout = 'ooriscout.cli.scout:main'`), which creates console scripts that work correctly after `uv pip install -U .`. The CLI module lives in `pylib/cli/` and exposes a `main()` function that uses fire to handle command-line arguments. 
 - **Debugging package issues**: When modules aren't importing correctly after installation, check:
   - That you are in the correct virtualenv (you may have to ask the developer)
   - Package structure in site-packages (e.g., `ls -la /path/to/site-packages/package_name/`)

CHANGELOG.md

@@ -2,10 +2,30 @@
 
 Notable changes to  Format based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/). Project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-<!--
 ## [Unreleased]
 
--->
+### Added
+- **Onya Knowledge Graph Support**: New `OnyaKB` backend for loading and searching `.onya` files from directories
+  - File-based knowledge graph storage without database overhead
+  - Compatible with `KBBackend` protocol for unified KB system integration
+  - Text-based search across node properties
+  - Type-based filtering using `search_by_type()`
+  - Direct node retrieval by IRI with `get_node()`
+- **Graph Retrieval Strategies**: New retrieval strategies in `ogbujipt.retrieval.graph`
+  - `TypeSearch`: Filter nodes by type (e.g., all Person entities)
+  - `PropertySearch`: Match nodes by property values with multiple match types (contains, equals, startswith, endswith)
+- **Demo**: Complete demonstration in `demo/kgraph/simple_onya_demo.py` showing all Onya KG features
+- **Tests**: Comprehensive test suite for Onya KG functionality in `test/store/kgraph/` and `test/retrieval/test_graph.py`
+
+## [0.10.0] - 20251129
+
+Major reorientation (or "pivot" as the cool kids say) for the project. OgbujiPT is now a general-purpose knowledge bank system for LLM-based applications. It provides a unified API for storing, retrieving, and managing semantic knowledge across multiple backends, with support for dense vector search, sparse retrieval, hybrid search, and more.
+
+As always, we build with Pythonic simplicity and transparency in mind; avoiding the over-frameworks that plague the LLM ecosystem.
+
+Please see the discussion, as this is ongoing work: https://github.com/OoriData/OgbujiPT/discussions/92
+
+Not listing granular changes for this change set, as it is a foundational one; a full reset, just about.
 
 ## [0.9.4] - 20241119
 

demo/kgraph/README.md

@@ -0,0 +1,218 @@
+Onya Knowledge Graph Demos. [Onya](https://github.com/OoriData/Onya) is a knowledge graph format and implementation that uses human-readable `.onya` files to represent structured knowledge. The name comes from Igbo "ọ́nyà" meaning web/network.
+
+# OnyaKB Features
+
+OgbujiPT's `OnyaKB` backend provides:
+
+- **File-based knowledge graphs**: Load `.onya` files from a directory
+- **In-memory storage**: No database required for static knowledge bases
+- **Multiple search strategies**: Text search, type-based filtering, property matching
+- **KBBackend protocol**: Compatible with OgbujiPT's unified KB system
+- **Human-editable**: Edit `.onya` files directly and reload
+
+# Demos
+
+## 1. `simple_onya_demo.py`
+
+Basic demonstration covering:
+- Loading `.onya` files from a directory
+- Text-based search across node properties
+- Type-based filtering (e.g., find all Person nodes)
+- Property-based search (e.g., find nodes with specific values)
+- Individual node retrieval by IRI
+
+Run:
+```bash
+python demo/kgraph/simple_onya_demo.py
+```
+
+# Onya File Format
+
+Basic `.onya` format example:
+
+```onya
+# @docheader
+* @document: http://example.org/mydata
+* @nodebase: http://example.org/entities/
+* @schema: https://schema.org/
+* @language: en
+
+# Alice [Person]
+* name: Alice Smith
+* age: 30
+* bio: Software engineer who loves Python
+
+# Bob [Person]
+* name: Bob Jones
+* occupation: Data Scientist
+```
+
+There is a document header which declares namespaces and base IRIs (URIs). Node definitions are marked with `# NodeID [Type]`. Node IDs are resolved against `@nodebase`, while types and property labels are resolved against `@schema`.
+- **Properties**: Listed with `* property: value`
+- **Types**: Entities can have one or more types
+
+# Creating Your Own Knowledge Graph
+
+1. **Create `.onya` files** in a directory:
+   ```bash
+   mkdir my_knowledge
+   ```
+
+2. **Write your knowledge** in `.onya` format:
+   ```bash
+   cat > my_knowledge/people.onya << 'EOF'
+   # @docheader
+   * @document: http://example.org/mykg
+   * @nodebase: http://example.org/
+   * @schema: https://schema.org/
+   * @language: en
+
+   # Person1 [Person]
+   * name: Your Name
+   * jobTitle: Your Role
+   * knowsAbout: Your Expertise
+   EOF
+   ```
+
+3. **Load and search**:
+   ```python
+   from ogbujipt.store.kgraph import OnyaKB
+
+   kb = OnyaKB(folder_path='./my_knowledge')
+   await kb.setup()
+
+   # Search your knowledge
+   async for result in kb.search('expertise', limit=5):
+       print(result.content)
+   ```
+
+# Integration with Other OgbujiPT Features
+
+## Hybrid Search with Vectors
+
+Combine graph-based search with vector search:
+
+```python
+from ogbujipt.store.kgraph import OnyaKB
+from ogbujipt.store.ram import RAMDataDB
+from ogbujipt.retrieval import TypeSearch, DenseSearch, HybridSearch
+from sentence_transformers import SentenceTransformer
+
+# Load knowledge graph
+kg = OnyaKB(folder_path='./knowledge')
+await kg.setup()
+
+# Create vector store
+model = SentenceTransformer('all-MiniLM-L6-v2')
+vector_db = RAMDataDB(embedding_model=model, collection_name='docs')
+await vector_db.setup()
+
+# Add graph content to vector store for semantic search
+async for result in kg.search('', limit=0):  # Get all nodes
+    await vector_db.insert(result.content, result.metadata)
+
+# Hybrid search across both
+hybrid = HybridSearch(
+    strategies=[DenseSearch(), TypeSearch(type_iri='http://schema.org/Person')],
+)
+
+async for result in hybrid.execute('machine learning expert',
+                                   backends=[kg, vector_db],
+                                   limit=5):
+    print(result.content, result.score)
+```
+
+## GraphRAG Applications
+
+Use Onya KG as the knowledge layer in RAG applications:
+
+```python
+from ogbujipt.store.kgraph import OnyaKB
+from ogbujipt.llm_wrapper import openai_chat_api, prompt_to_chat
+
+# Load domain knowledge
+kb = OnyaKB(folder_path='./domain_knowledge')
+await kb.setup()
+
+# Retrieve relevant knowledge
+contexts = []
+async for result in kb.search(user_query, limit=3):
+    contexts.append(result.content)
+
+# Build RAG prompt
+context_text = '\n\n'.join(contexts)
+prompt = f"""Based on this knowledge:
+
+{context_text}
+
+Question: {user_query}"""
+
+# Get LLM response
+llm = openai_chat_api(base_url='http://localhost:8000')
+response = await llm(prompt_to_chat(prompt))
+print(response.first_choice_text)
+```
+
+# Use Cases
+
+## Static Knowledge Bases
+- **Ontologies**: Load domain ontologies (schema.org, FOAF, etc.)
+- **Taxonomies**: Product catalogs, classification systems
+- **Reference data**: Countries, currencies, standards
+- **Company knowledge**: Org charts, procedures, policies
+
+## Human-Curated Knowledge
+- **Expert knowledge**: Subject matter expertise in structured form
+- **Documentation**: Technical docs as knowledge graphs
+- **Metadata**: Structured descriptions of assets/resources
+
+## Embedded Applications
+- **No database required**: Bundle knowledge with your application
+- **Version controlled**: `.onya` files in git for change tracking
+- **Reviewable**: Human-readable format for peer review
+- **Composable**: Multiple `.onya` files for modular knowledge
+
+# Architecture Notes
+
+## Read-Only by Design
+
+`OnyaKB` is intentionally read-only:
+- `insert()` and `delete()` raise `NotImplementedError`
+- Edit `.onya` files directly using your text editor
+- Reload by calling `cleanup()` then `setup()` again
+- This design encourages human curation and version control
+
+## In-Memory Performance
+
+All nodes are loaded into memory:
+- **Fast**: No database queries, instant lookups
+- **Scalable**: Suitable for graphs with up to ~100K nodes
+- **Simple**: No external dependencies or setup
+- **Predictable**: Performance independent of query complexity
+
+## Search Strategies
+
+Three built-in strategies:
+1. **Text search** (`kb.search()`): Substring matching across properties
+2. **Type search** (`TypeSearch`): Filter by entity type
+3. **Property search** (`PropertySearch`): Match specific property values
+
+For semantic search, combine with vector stores using hybrid strategies.
+
+# Prerequisites
+
+```bash
+# Easiest to just use the "mega" package, with all demo requirements
+uv pip install -U ".[mega]"
+```
+
+# References
+
+- **Onya**: [https://github.com/OoriData/Onya](https://github.com/OoriData/Onya)
+- **OgbujiPT Documentation**: [https://github.com/OoriData/OgbujiPT](https://github.com/OoriData/OgbujiPT)
+- **Knowledge Graphs**: [https://en.wikipedia.org/wiki/Knowledge_graph](https://en.wikipedia.org/wiki/Knowledge_graph)
+- **GraphRAG**: [https://arxiv.org/abs/2404.16130](https://arxiv.org/abs/2404.16130)
+
+---
+
+**Need help?** Open an issue at [OgbujiPT GitHub](https://github.com/OoriData/OgbujiPT/issues)