Merge pull request #41 from FAIRChemistry/update-docs-add-jsonld

Enhance documentation, build workflow, and add OWL export

Author: JR-1991

.github/scripts/generate_types.sh

@@ -30,5 +30,5 @@ GEN_FILES=$(find types -name '*.toml')
 for file in $GEN_FILES; do
   # Generate the go file
   echo "Generating $file"
-  md-models pipeline -i $file
+  cargo run -- pipeline -i $file
 done

Cargo.lock

@@ -45,6 +45,7 @@ schemars = { version = "1.0.4" }
 json-patch = "4.0.0"
 thiserror = "2.0.12"
 variantly = "0.4.0"
+case = "1.0.0"
 
 [features]
 default = ["openai"]

Cargo.toml

@@ -12,7 +12,7 @@
   - [Full example](./syntax/full_example.md)
   - [Best practices](./syntax/best_practices.md)
 - [Command Line Interface](./cli/cli.md)
-  - [Generation](./cli/code_generation.md)
+  - [Generation](./cli/generation.md)
   - [Pipelines](./cli/pipelines.md)
   - [Validation](./cli/schema_validation.md)
   - [Large Language Models](./cli/llm.md)
@@ -21,8 +21,5 @@
   - [Schema languages](./exporters/schemas.md)
   - [API specifications](./exporters/apis.md)
   - [Documentation](./exporters/documentation.md)
-- [Examples](./examples/examples.md)
-  - [Hello MD-Models](./examples/hello_md_models.md)
-  - [Union types](./examples/union_types.md)
-  - [Database models](./examples/database_models.md)
 - [FAQ](./faq/faq.md)
+  - [My model is not validating](./faq/validation.md)

docs/src/SUMMARY.md

@@ -1,3 +1,196 @@
 # Command Line Interface
 
-*To be added*
+The MD-Models command-line interface (CLI) provides a comprehensive set of tools for working with markdown data models. It enables you to validate models, generate code in multiple formats, extract data using AI, and automate workflows through pipelines.
+
+## Installation
+
+Install the MD-Models CLI using Cargo:
+
+```bash
+cargo install mdmodels
+```
+
+Once installed, you can use the `md-models` command from anywhere in your terminal.
+
+## Available Commands
+
+The MD-Models CLI provides the following commands:
+
+### `validate`
+
+Validates markdown model files for structural integrity, naming conventions, and type consistency.
+
+**Quick start:**
+
+```bash
+md-models validate -i model.md
+```
+
+**Use cases:**
+- Check models before code generation
+- Validate models in CI/CD pipelines
+- Ensure models meet naming and structure requirements
+
+**Learn more:** [Schema Validation](schema_validation.md)
+
+---
+
+### `convert`
+
+Converts markdown models to various output formats including programming languages, schema definitions, API specifications, and documentation.
+
+**Quick start:**
+
+```bash
+# Generate Python Pydantic models
+md-models convert -i model.md -t python-pydantic -o models.py
+
+# Generate JSON Schema
+md-models convert -i model.md -t json-schema -r Document -o schema.json
+```
+
+**Use cases:**
+- Generate type-safe code for your application
+- Create API schemas and specifications
+- Produce documentation from models
+- Export to semantic web formats
+
+**Learn more:** [Code Generation](generation.md)
+
+**Available formats:** See [Exporters](../exporters/exporters.md) for a complete list of supported templates.
+
+---
+
+### `pipeline`
+
+Generates multiple output files from one or more models using a TOML configuration file. Ideal for automating code generation workflows.
+
+**Quick start:**
+
+```bash
+md-models pipeline -i pipeline.toml
+```
+
+**Use cases:**
+- Generate multiple formats in one command
+- Automate code generation for entire projects
+- Maintain consistency across generated outputs
+- Integrate with CI/CD workflows
+
+**Learn more:** [Pipelines](pipelines.md)
+
+---
+
+### `extract`
+
+Uses Large Language Models (LLMs) to extract structured data from unstructured text based on your data model.
+
+**Quick start:**
+
+```bash
+md-models extract -m model.md -i text.txt -o output.json
+```
+
+**Use cases:**
+- Extract structured data from documents
+- Parse unstructured text into typed objects
+- Convert legacy data formats to structured JSON
+- Automate data entry tasks
+
+**Learn more:** [Large Language Models](llm.md)
+
+---
+
+### `dataset validate`
+
+Validates JSON datasets against markdown models to ensure data conforms to the model structure.
+
+**Quick start:**
+
+```bash
+md-models dataset validate -i data.json -m model.md
+```
+
+**Use cases:**
+- Validate API request/response data
+- Check data quality in ETL pipelines
+- Ensure data consistency before processing
+- Validate user-submitted data
+
+---
+
+## Common Workflows
+
+### Development Workflow
+
+```bash
+# 1. Validate your model
+md-models validate -i model.md
+
+# 2. Generate code for your application
+md-models convert -i model.md -t python-pydantic -o models.py
+
+# 3. Generate API schemas
+md-models convert -i model.md -t json-schema -r Document -o schema.json
+md-models convert -i model.md -t graphql -o schema.graphql
+```
+
+### Automated Pipeline Workflow
+
+```bash
+# Use a pipeline configuration to generate everything at once
+md-models pipeline -i pipeline.toml
+```
+
+### Data Extraction Workflow
+
+```bash
+# Extract structured data from unstructured text
+md-models extract -m model.md -i document.txt -o extracted.json
+
+# Validate the extracted data
+md-models dataset validate -i extracted.json -m model.md
+```
+
+## Input Sources
+
+All commands that accept input files support:
+
+- **Local file paths**: `md-models validate -i model.md`
+- **Remote URLs**: `md-models validate -i https://example.com/model.md`
+
+MD-Models automatically detects whether the input is a URL (starts with `http`/`https`) or a local file path.
+
+## Getting Help
+
+Get help for any command using the `--help` flag:
+
+```bash
+# General help
+md-models --help
+
+# Command-specific help
+md-models convert --help
+md-models validate --help
+md-models pipeline --help
+```
+
+## Command Reference
+
+| Command | Purpose | Documentation |
+|---------|---------|---------------|
+| `validate` | Validate model structure and syntax | [Schema Validation](schema_validation.md) |
+| `convert` | Generate code and schemas | [Code Generation](generation.md) |
+| `pipeline` | Batch generation from config | [Pipelines](pipelines.md) |
+| `extract` | LLM-powered data extraction | [Large Language Models](llm.md) |
+| `dataset validate` | Validate data against models | See `md-models dataset validate --help` |
+
+## Next Steps
+
+- **New to MD-Models?** Start with the [Quickstart](../quickstart.md) guide
+- **Want to generate code?** Read [Code Generation](generation.md) for detailed usage
+- **Need to validate models?** See [Schema Validation](schema_validation.md) for validation rules
+- **Automating workflows?** Check out [Pipelines](pipelines.md) for batch processing
+- **Working with AI?** Explore [Large Language Models](llm.md) for data extraction
+
+For detailed information about available export formats and templates, see the [Exporters](../exporters/exporters.md) documentation.