initial commit

Author: linkmluser

.coverage

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+ehr
+assertIn
+nin

.github/codespell-ignore.txt

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+name: Codespell
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: codespell-project/actions-codespell@v2
+        with:
+          check_filenames: true
+          check_hidden: true
+          skip: ".git,*.pdf,*.svg,*.lock,uv.lock"
+          ignore_words_file: .github/codespell-ignore.txt

.github/workflows/codespell.yml

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+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Build with MkDocs
+        run: uv run mkdocs build
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./site
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/deploy_documentation.yml

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+name: Build and test
+
+on:
+  push:
+    branches: [ main ]
+
+  pull_request:
+      types:
+          - opened
+          - reopened
+          - synchronize
+          - ready_for_review
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Check code quality with ruff
+        run: uv run ruff check .
+
+      - name: Check formatting with ruff
+        run: uv run ruff format --check .
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.10', '3.11', '3.12', '3.13' ]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Run test suite
+        run: uv run pytest
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          fail_ci_if_error: false

.github/workflows/main.yaml

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+name: Publish Python Package
+
+on:
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Build source and wheel archives
+        run: uv build
+
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true

.github/workflows/pypi-publish.yaml

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+tests/output
+
+ .coverage
+coverage.xml
+tests/.coverage
+tests/coverage.xml
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual Environment
+venv/
+env/
+ENV/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# Logs
+*.log
+logs/
+
+# Local development
+.env
+.env.local
+
+**/.claude/settings.local.json

.gitignore

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+3.10

.python-version

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+OWL-Server is a Python server for managing OWL (Web Ontology Language) ontologies. It provides a simplified API for common operations like adding/removing axioms, finding axioms by pattern, and managing prefix mappings.
+
+The project uses:
+- py-horned-owl for OWL ontology manipulation
+- watchdog for file monitoring
+- click for command-line interface
+- FastMCP for Model-Context-Protocol integration
+
+## Architecture
+
+The codebase is organized into these main components:
+
+1. **SimpleOwlAPI** (`owl_api.py`): Core class that provides thread-safe ontology management:
+   - Handles file synchronization with disk
+   - Provides observer pattern for change notifications
+   - Manages prefix mappings
+   - Supports adding/removing/finding axioms
+   - Respects readonly settings from configuration
+
+2. **Axiom Parser** (`axiom_parser.py`): Handles conversion between string representations of OWL axioms and py-horned-owl objects.
+
+3. **Server CLI** (`server.py`): Command-line interface for starting the server and initializing ontology files.
+
+4. **MCP Tools** (`mcp_tools.py`): ModelContextProtocol wrapper around the core API:
+   - Provides MCP tools for OWL operations
+   - Handles API instance caching and management
+   - Exposes file-path based interfaces for OWL manipulation
+   - Includes configuration management tools
+
+5. **Configuration System** (`config.py`): Manages session-wide configuration:
+   - Stores ontology paths, metadata, and settings in `~/.owl-mcp/config.yaml`
+   - Provides named access to frequently used ontologies
+   - Supports readonly ontologies and metadata axioms
+   - Offers session-wide settings like default serialization format
+
+## Common Commands
+
+### Installation
+
+```bash
+# Install dependencies and set up development environment
+make install
+```
+
+### Running Tests
+
+```bash
+# Run all tests
+make test
+
+# Run a specific test
+uv run pytest tests/test_owl_api.py::test_add_axiom
+
+# Run tests with verbose output
+uv run pytest -v
+
+# Run only MCP tool tests
+uv run pytest tests/test_mcp_tools.py
+```
+
+### Development Workflow
+
+```bash
+# Clean up build artifacts
+make clean
+
+# Run example script
+make example
+```
+
+### Code Quality
+
+```bash
+# Format code with black
+uv run black src tests
+
+# Sort imports
+uv run isort src tests
+
+# Type checking with mypy
+uv run mypy src
+```
+
+### Running the MCP Server
+
+```bash
+# Run the MCP server with stdio transport
+python -m owl_server.mcp_tools
+```
+
+## Known Issues
+
+The project has compatibility issues with py-horned-owl API as documented in KNOWN_ISSUES.md:
+
+1. Methods like `add_default_prefix_names()` and `clazz()` are referenced in the code but may not be available in the installed version of py-horned-owl.
+2. Adaptations may be needed for axiom types (SubClassOf, etc.).