linkml-toolkit 0.1.0__tar.gz

linkml_toolkit-0.1.0/.coveragerc

@@ -0,0 +1,12 @@
+[run]
+source = linkml_toolkit
+omit = tests/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    if __name__ == .__main__.:
+
+[html]
+directory = coverage_html

linkml_toolkit-0.1.0/.gitignore

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+__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
+MANIFEST
+.tox/
+.coverage
+.coverage.*
+.cache
+coverage.xml
+*.cover
+*.py,cover
+.pytest_cache/
+.env
+.venv
+env/
+venv/
+ENV/
+docs/_build/
+.DS_Store

linkml_toolkit-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Antonio Fernandez-Guerra
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

linkml_toolkit-0.1.0/MANIFEST.in

@@ -0,0 +1,6 @@
+include LICENSE
+include README.md
+include pyproject.toml
+include requirements*.txt
+recursive-include docs *.md
+recursive-include tests *.py *.yaml

linkml_toolkit-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: linkml-toolkit
+Version: 0.1.0
+Summary: A simple toolkit for working with LinkML schemas
+Author: Antonio Fernandez-Guerra
+Author-email: antonio@metagenomics.eu
+License: MIT
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: linkml>=1.8.1
+Requires-Dist: click>=8.0.0
+Requires-Dist: rich>=10.0.0
+Requires-Dist: pyyaml>=5.4.0
+Requires-Dist: rdflib>=6.0.0
+Requires-Dist: jsonschema>=4.0.0
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-cov>=2.0; extra == "test"
+Requires-Dist: tox>=3.24; extra == "test"
+Requires-Dist: coverage>=5.0; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov>=2.0; extra == "dev"
+Requires-Dist: tox>=3.24; extra == "dev"
+Requires-Dist: coverage>=5.0; extra == "dev"
+Requires-Dist: black>=22.0; extra == "dev"
+Requires-Dist: isort>=5.0; extra == "dev"
+Requires-Dist: mypy>=0.910; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.2; extra == "docs"
+Requires-Dist: mkdocstrings>=0.18; extra == "docs"
+Requires-Dist: mkdocs-material>=8.0; extra == "docs"
+Dynamic: license-file
+
+# LinkML Toolkit (lmtk)
+
+[![Tests](https://github.com/genomewalker/linkml-toolkit/workflows/Tests/badge.svg)](https://github.com/genomewalker/linkml-toolkit/actions)
+[![PyPI version](https://badge.fury.io/py/linkml-toolkit.svg)](https://badge.fury.io/py/linkml-toolkit)
+[![Documentation Status](https://readthedocs.org/projects/linkml-toolkit/badge/?version=latest)](https://linkml-toolkit.readthedocs.io/en/latest/?badge=latest)
+
+A simple toolkit for working with LinkML schemas. This tool offers advanced schema analysis, validation, transformation, and visualization capabilities through a flexible command-line interface.
+
+## 🌟 Features
+
+- **Schema Analysis**
+  - Generate schema summaries.
+  - Detailed views of classes, slots, and types.
+  - Support for hierarchical and section-based analysis.
+
+- **Schema Validation**
+  - Rigorous validation checks with detailed error reporting.
+  - Optional metadata display for schemas.
+
+- **Schema Operations**
+  - Merge or concatenate multiple schemas.
+  - Subset schemas by specified classes.
+
+- **Format Conversion**
+  - Export schemas to JSON, RDF, GraphQL, CSV, TSV, and SQL formats.
+  - Customize RDF serialization formats (e.g., Turtle, XML).
+  - SQL export supporting PostgreSQL, MySQL, SQLite, and DuckDB dialects.
+
+- **Visualization**
+  - Generate interactive HTML visualizations of schemas.
+  - Options for inheritance, descriptions, and statistics display.
+
+## 🚀 Installation
+
+### Using pip
+
+```bash
+pip install linkml-toolkit
+```
+
+### Using conda
+
+```bash
+# Create environment from provided configuration
+conda env create -f environment-dev.yml
+conda activate linkml-toolkit-dev
+
+# For production environment only
+conda env create -f environment.yml
+conda activate linkml-toolkit
+```
+
+### Development Installation
+
+```bash
+# Clone the repository
+git clone https://github.com/genomewalker/linkml-toolkit.git
+cd linkml-toolkit
+
+# Create and activate conda environment
+conda env create -f environment-dev.yml
+conda activate linkml-toolkit-dev
+
+# Install in development mode
+pip install -e ".[dev,test,docs]"
+```
+
+## 📚 Usage
+
+### Core Commands
+
+#### Schema Summary
+```bash
+# Generate a summary of the schema
+lmtk summary --schema schema.yaml
+
+# Detailed view for specific sections
+lmtk summary --schema schema.yaml --section slots --detailed
+
+# Export summary to JSON
+lmtk summary --schema schema.yaml --output summary.json
+```
+
+#### Schema Validation
+```bash
+# Validate schema
+lmtk validate --schema schema.yaml
+
+# Validate with metadata display
+lmtk validate --schema schema.yaml --metadata
+```
+
+#### Schema Export
+```bash
+# Export to JSON Schema
+lmtk export --schema schema.yaml --format json --output schema.json
+
+# Export to RDF (Turtle format)
+lmtk export --schema schema.yaml --format rdf --rdf-format turtle --output schema.ttl
+
+# Export to SQL (PostgreSQL dialect)
+lmtk export --schema schema.yaml --format sql --sql-dialect postgresql --output schema.sql
+```
+
+#### Schema Subset
+```bash
+# Create a subset containing specific classes
+lmtk subset --schema schema.yaml --classes class1,class2 --output subset.yaml
+
+# Exclude inherited elements
+lmtk subset --schema schema.yaml --classes class1 --no-inherited --output subset.yaml
+```
+
+#### Schema Combination
+```bash
+# Merge schemas
+lmtk combine --schema base.yaml --additional-schemas schema1.yaml -a schema2.yaml --mode merge --output merged.yaml
+
+# Concatenate schemas
+lmtk combine --schema base.yaml --additional-schemas schema1.yaml -a schema2.yaml --mode concat --output concatenated.yaml
+```
+
+#### Schema Visualization
+```bash
+# Generate an interactive HTML visualization
+lmtk visualize --schema schema.yaml --output visualization.html
+
+# Generate full documentation bundle
+lmtk visualize --schema schema.yaml --output docs/ --full-docs
+```
+
+## 🛠️ Development
+
+### Environment Management
+
+```bash
+# Create development environment
+conda env create -f environment.yml
+
+# Update environment
+conda env update -f environment.yml
+
+# Create production environment
+conda env create -f environment.prod.yml
+```
+
+### Running Tests
+
+```bash
+# Run all tests
+pytest
+
+# Run with coverage
+pytest --cov=linkml_toolkit
+
+# Run specific test file
+pytest tests/test_core.py
+
+# Run tests with output
+pytest -v
+```
+
+### Building Documentation
+
+```bash
+# Build documentation
+cd docs
+mkdocs build
+
+# Serve documentation locally
+mkdocs serve
+```
+
+## 📖 Project Structure
+
+```
+linkml-toolkit/
+├── src/
+│   └── linkml_toolkit/      # Source code
+├── tests/                   # Test suite
+│   └── data/               # Test data
+├── docs/                    # Documentation
+├── environment.yml         # Development environment
+├── environment.prod.yml    # Production environment
+├── pyproject.toml         # Build configuration
+├── setup.cfg              # Package metadata
+└── tox.ini               # Test automation
+```
+
+## 🤝 Contributing
+
+We welcome contributions! Here's how you can help:
+
+1. **Fork the Repository**
+   ```bash
+   git clone https://github.com/genomewalker/linkml-toolkit.git
+   cd linkml-toolkit
+   ```
+
+2. **Set Up Development Environment**
+   ```bash
+   conda env create -f environment.yml
+   conda activate linkml-toolkit
+   pip install -e ".[dev,test,docs]"
+   ```
+
+3. **Create a Branch**
+   ```bash
+   git checkout -b feature/your-feature-name
+   ```
+
+4. **Make Changes**
+   - Write code
+   - Add tests
+   - Update documentation
+
+5. **Verify Changes**
+   ```bash
+   # Run tests
+   pytest
+   
+   # Run linting
+   tox -e lint
+   
+   # Build docs
+   cd docs && mkdocs build
+   ```
+
+6. **Submit Pull Request**
+   - Push changes to your fork
+   - Create pull request
+   - Wait for review
+
+## 📜 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## 🙏 Acknowledgments
+
+- LinkML community for the base LinkML implementation.
+- Contributors who have helped improve this toolkit.
+
+## 📫 Contact
+
+- Issue Tracker: [GitHub Issues](https://github.com/genomewalker/linkml-toolkit/issues)
+- Documentation: [ReadTheDocs](https://linkml-toolkit.readthedocs.io/)

linkml_toolkit-0.1.0/README.md

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+# LinkML Toolkit (lmtk)
+
+[![Tests](https://github.com/genomewalker/linkml-toolkit/workflows/Tests/badge.svg)](https://github.com/genomewalker/linkml-toolkit/actions)
+[![PyPI version](https://badge.fury.io/py/linkml-toolkit.svg)](https://badge.fury.io/py/linkml-toolkit)
+[![Documentation Status](https://readthedocs.org/projects/linkml-toolkit/badge/?version=latest)](https://linkml-toolkit.readthedocs.io/en/latest/?badge=latest)
+
+A simple toolkit for working with LinkML schemas. This tool offers advanced schema analysis, validation, transformation, and visualization capabilities through a flexible command-line interface.
+
+## 🌟 Features
+
+- **Schema Analysis**
+  - Generate schema summaries.
+  - Detailed views of classes, slots, and types.
+  - Support for hierarchical and section-based analysis.
+
+- **Schema Validation**
+  - Rigorous validation checks with detailed error reporting.
+  - Optional metadata display for schemas.
+
+- **Schema Operations**
+  - Merge or concatenate multiple schemas.
+  - Subset schemas by specified classes.
+
+- **Format Conversion**
+  - Export schemas to JSON, RDF, GraphQL, CSV, TSV, and SQL formats.
+  - Customize RDF serialization formats (e.g., Turtle, XML).
+  - SQL export supporting PostgreSQL, MySQL, SQLite, and DuckDB dialects.
+
+- **Visualization**
+  - Generate interactive HTML visualizations of schemas.
+  - Options for inheritance, descriptions, and statistics display.
+
+## 🚀 Installation
+
+### Using pip
+
+```bash
+pip install linkml-toolkit
+```
+
+### Using conda
+
+```bash
+# Create environment from provided configuration
+conda env create -f environment-dev.yml
+conda activate linkml-toolkit-dev
+
+# For production environment only
+conda env create -f environment.yml
+conda activate linkml-toolkit
+```
+
+### Development Installation
+
+```bash
+# Clone the repository
+git clone https://github.com/genomewalker/linkml-toolkit.git
+cd linkml-toolkit
+
+# Create and activate conda environment
+conda env create -f environment-dev.yml
+conda activate linkml-toolkit-dev
+
+# Install in development mode
+pip install -e ".[dev,test,docs]"
+```
+
+## 📚 Usage
+
+### Core Commands
+
+#### Schema Summary
+```bash
+# Generate a summary of the schema
+lmtk summary --schema schema.yaml
+
+# Detailed view for specific sections
+lmtk summary --schema schema.yaml --section slots --detailed
+
+# Export summary to JSON
+lmtk summary --schema schema.yaml --output summary.json
+```
+
+#### Schema Validation
+```bash
+# Validate schema
+lmtk validate --schema schema.yaml
+
+# Validate with metadata display
+lmtk validate --schema schema.yaml --metadata
+```
+
+#### Schema Export
+```bash
+# Export to JSON Schema
+lmtk export --schema schema.yaml --format json --output schema.json
+
+# Export to RDF (Turtle format)
+lmtk export --schema schema.yaml --format rdf --rdf-format turtle --output schema.ttl
+
+# Export to SQL (PostgreSQL dialect)
+lmtk export --schema schema.yaml --format sql --sql-dialect postgresql --output schema.sql
+```
+
+#### Schema Subset
+```bash
+# Create a subset containing specific classes
+lmtk subset --schema schema.yaml --classes class1,class2 --output subset.yaml
+
+# Exclude inherited elements
+lmtk subset --schema schema.yaml --classes class1 --no-inherited --output subset.yaml
+```
+
+#### Schema Combination
+```bash
+# Merge schemas
+lmtk combine --schema base.yaml --additional-schemas schema1.yaml -a schema2.yaml --mode merge --output merged.yaml
+
+# Concatenate schemas
+lmtk combine --schema base.yaml --additional-schemas schema1.yaml -a schema2.yaml --mode concat --output concatenated.yaml
+```
+
+#### Schema Visualization
+```bash
+# Generate an interactive HTML visualization
+lmtk visualize --schema schema.yaml --output visualization.html
+
+# Generate full documentation bundle
+lmtk visualize --schema schema.yaml --output docs/ --full-docs
+```
+
+## 🛠️ Development
+
+### Environment Management
+
+```bash
+# Create development environment
+conda env create -f environment.yml
+
+# Update environment
+conda env update -f environment.yml
+
+# Create production environment
+conda env create -f environment.prod.yml
+```
+
+### Running Tests
+
+```bash
+# Run all tests
+pytest
+
+# Run with coverage
+pytest --cov=linkml_toolkit
+
+# Run specific test file
+pytest tests/test_core.py
+
+# Run tests with output
+pytest -v
+```
+
+### Building Documentation
+
+```bash
+# Build documentation
+cd docs
+mkdocs build
+
+# Serve documentation locally
+mkdocs serve
+```
+
+## 📖 Project Structure
+
+```
+linkml-toolkit/
+├── src/
+│   └── linkml_toolkit/      # Source code
+├── tests/                   # Test suite
+│   └── data/               # Test data
+├── docs/                    # Documentation
+├── environment.yml         # Development environment
+├── environment.prod.yml    # Production environment
+├── pyproject.toml         # Build configuration
+├── setup.cfg              # Package metadata
+└── tox.ini               # Test automation
+```
+
+## 🤝 Contributing
+
+We welcome contributions! Here's how you can help:
+
+1. **Fork the Repository**
+   ```bash
+   git clone https://github.com/genomewalker/linkml-toolkit.git
+   cd linkml-toolkit
+   ```
+
+2. **Set Up Development Environment**
+   ```bash
+   conda env create -f environment.yml
+   conda activate linkml-toolkit
+   pip install -e ".[dev,test,docs]"
+   ```
+
+3. **Create a Branch**
+   ```bash
+   git checkout -b feature/your-feature-name
+   ```
+
+4. **Make Changes**
+   - Write code
+   - Add tests
+   - Update documentation
+
+5. **Verify Changes**
+   ```bash
+   # Run tests
+   pytest
+   
+   # Run linting
+   tox -e lint
+   
+   # Build docs
+   cd docs && mkdocs build
+   ```
+
+6. **Submit Pull Request**
+   - Push changes to your fork
+   - Create pull request
+   - Wait for review
+
+## 📜 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## 🙏 Acknowledgments
+
+- LinkML community for the base LinkML implementation.
+- Contributors who have helped improve this toolkit.
+
+## 📫 Contact
+
+- Issue Tracker: [GitHub Issues](https://github.com/genomewalker/linkml-toolkit/issues)
+- Documentation: [ReadTheDocs](https://linkml-toolkit.readthedocs.io/)

linkml_toolkit-0.1.0/docs/api/cli.md

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+# CLI Reference
+
+::: linkml_toolkit.cli
+    handler: python
+    selection:
+      members:
+        - main
+        - summary
+        - validate
+        - merge
+        - concat
+        - export

linkml_toolkit-0.1.0/docs/api/core.md

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+# Core API Reference
+
+::: linkml_toolkit.core.LinkMLProcessor
+    handler: python
+    selection:
+      members:
+        - __init__
+        - get_summary
+        - merge_multiple
+        - concat_multiple

linkml_toolkit-0.1.0/docs/api/export.md

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+# Export API Reference
+
+::: linkml_toolkit.export.SchemaExporter
+    handler: python
+    selection:
+      members:
+        - __init__
+        - to_json_schema
+        - to_rdf
+        - to_graphql

linkml_toolkit-0.1.0/docs/api/validation.md

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+# Validation API Reference
+
+::: linkml_toolkit.validation.SchemaValidator
+    handler: python
+    selection:
+      members:
+        - __init__
+        - validate_schema
+        - validate_multiple
+        - format_errors