refactor: reorganize FHIR bundle structure and update configuration files

Author: Ardenexal

README.md

@@ -1,119 +1,161 @@
 # PHP FHIR Tools
 
-This project generates PHP model classes and enums from FHIR Structure Definitions using Symfony Console and Nette PhpGenerator. It also provides a comprehensive FHIR serialization system for converting between FHIR objects and JSON/XML formats.
+A PHP library monorepo for working with [FHIR](https://www.hl7.org/fhir/) (Fast Healthcare Interoperability Resources). This monorepo contains multiple standalone packages that can be used independently or together:
 
-## Requirements
-- PHP >= 8.2
-- Composer
+- **FHIR Code Generation**: Generate PHP model classes from FHIR Structure Definitions
+- **FHIR Serialization**: JSON/XML serialization and deserialization
+- **FHIRPath**: Expression evaluator for FHIRPath 2.0
+- **FHIR Models**: Pre-generated FHIR model classes (R4, R4B, R5)
+- **FHIR Bundle**: Symfony integration bundle
 
 ## Installation
-Clone the repository and install dependencies:
+
+### As a Library (Recommended)
+
+Install individual components in your project:
+
 ```bash
-composer install
+# For Symfony applications - includes console commands
+composer require ardenexal/fhir-bundle
+
+# For code generation
+composer require ardenexal/fhir-code-generation
+
+# For serialization
+composer require ardenexal/fhir-serialization
+
+# For FHIRPath evaluation
+composer require ardenexal/fhir-path
+
+# For pre-generated models
+composer require ardenexal/fhir-models
 ```
 
-## Usage
-Run the Symfony Console application:
+### For Development
+
+Clone and develop on this monorepo:
+
 ```bash
-php bin/console
+git clone https://github.com/Ardenexal/php-fhir-tools.git
+cd php-fhir-tools
+composer install
 ```
 
-### Available Commands
+## Quick Start
 
-#### `fhir:generate`
-Generates FHIR model classes from FHIR definitions.
+### Using FHIR Bundle in Symfony
 
-**Arguments:**
-- `version` (required): Select FHIR version to generate model classes for.
-  - Suggested values: `R4`, `R4B`, `R5`
+If you've installed `ardenexal/fhir-bundle` in your Symfony application:
 
-**Example:**
 ```bash
-php bin/console fhir:generate R4B
-```
+# Generate FHIR models
+php bin/console fhir:generate --package=hl7.fhir.r4.core -vvv
 
-## FHIR Serialization
+# Evaluate FHIRPath expressions
+php bin/console fhir:path:evaluate "5 + 3"
 
-This project includes a comprehensive FHIR serialization system that provides:
+# Against a JSON file
+php bin/console fhir:path:evaluate "Patient.name.given" patient.json
 
-- **JSON and XML serialization** following official FHIR specifications
-- **Configurable validation modes** (strict/lenient)
-- **Flexible unknown element handling** (ignore/error/preserve)
-- **Performance optimization options**
-- **Debug information support**
-- **Extension handling** with proper FHIR formatting
+# Output as JSON
+php bin/console fhir:path:evaluate "name" patient.json --format=json --pretty
+```
 
-### Quick Example
+### Serialize FHIR Resources
 
 ```php
-use Symfony\Component\Serializer\Serializer;
-use Ardenexal\FHIRTools\Serialization\FHIRResourceNormalizer;
-use Ardenexal\FHIRTools\Serialization\FHIRSerializationContext;
+use Ardenexal\FHIRTools\Component\Serialization\FHIRSerializationService;
 
-// Set up FHIR-aware serializer
-$normalizers = [new FHIRResourceNormalizer($metadataExtractor, $typeResolver)];
-$serializer = new Serializer($normalizers);
+// Serialize to JSON
+$json = $service->serializeToJson($patient);
 
-// Configure serialization context
-$context = FHIRSerializationContext::forJson()
-    ->withValidationMode(FHIRSerializationContext::VALIDATION_STRICT);
+// Deserialize from JSON
+$patient = $service->deserializeFromJson($json, FHIRPatient::class);
 
-// Serialize FHIR resource
-$json = $serializer->serialize($patient, 'json', $context->toSymfonyContext());
+// Auto-detect format (JSON or XML)
+$resource = $service->deserialize($data);
+```
+
+## Project Structure
 
-// Deserialize back to FHIR object
-$patient = $serializer->deserialize($json, FHIRPatient::class, 'json', $context->toSymfonyContext());
+```
+src/
+├── Bundle/FHIRBundle/              # Symfony Bundle integration and console commands
+├── Component/
+│   ├── CodeGeneration/src/         # FHIR model class generation from Structure Definitions
+│   ├── Serialization/src/          # FHIR JSON/XML serialization and deserialization
+│   ├── Models/src/                 # Generated FHIR model classes (R4, R4B, R5)
+│   └── FHIRPath/src/               # FHIRPath 2.0 expression evaluator
 ```
 
-For comprehensive documentation on the serialization system, see: **[FHIR Serialization Guide](docs/FHIR-Serialization-Guide.md)**
-
-## Documentation
-
-- **[FHIR Serialization Guide](docs/FHIR-Serialization-Guide.md)** - Comprehensive guide for using the FHIR serialization system
-
-## Composer Scripts
-- Run static analysis:
-  ```bash
-  composer phpstan
-  ```
-- Run code style linter:
-  ```bash
-  composer lint
-  ```
-- Run tests:
-  ```bash
-  composer test
-  ```
-- Generate FHIR models:
-  ```bash
-  composer run generate-models-all
-  ```
-
-## GitHub Actions
-
-### Regenerate FHIR Models
-This repository includes a GitHub Actions workflow that allows you to manually regenerate FHIR models and commit them to the main branch.
-
-**To trigger the workflow:**
-1. Go to the "Actions" tab in the GitHub repository
-2. Select "Regenerate FHIR Models" from the workflows list
-3. Click "Run workflow"
-4. Optionally customize the commit message (default: "chore: regenerate FHIR models")
-5. Click the green "Run workflow" button
-
-The workflow will:
-- Set up PHP 8.3 environment with required extensions
-- Install Composer dependencies
-- Run `composer run generate-models-all` to generate models for R4, R4B, and R5
-- Automatically commit and push changes to main if models were updated
-- Provide a summary of the operation
+Each component has its own README with detailed documentation:
 
-## Project Structure
-- `src/` - Source code
-- `bin/console` - Symfony Console entry point
-- `resources/definitions/` - FHIR definition files
+- [FHIRBundle](src/Bundle/FHIRBundle/README.md) — Symfony integration and console commands
+- [CodeGeneration](src/Component/CodeGeneration/README.md) — Model generation from FHIR packages
+- [Serialization](src/Component/Serialization/README.md) — JSON/XML serialization
+- [FHIRPath](src/Component/FHIRPath/README.md) — FHIRPath expression evaluation
+- [Models](src/Component/Models/README.md) — Generated FHIR model classes
 
-## License
+## Monorepo Structure
+
+This is a library monorepo. Each component can be installed and used independently:
+
+| Package | Description | Composer Install |
+|---------|-------------|------------------|
+| `ardenexal/fhir-bundle` | Symfony Bundle with console commands | `composer require ardenexal/fhir-bundle` |
+| `ardenexal/fhir-code-generation` | Generate PHP from FHIR definitions | `composer require ardenexal/fhir-code-generation` |
+| `ardenexal/fhir-serialization` | JSON/XML serialization | `composer require ardenexal/fhir-serialization` |
+| `ardenexal/fhir-path` | FHIRPath expression evaluator | `composer require ardenexal/fhir-path` |
+| `ardenexal/fhir-models` | Pre-generated FHIR models | `composer require ardenexal/fhir-models` |
 
-This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+## Development
+
+### Code Quality
+
+```bash
+# Fix code style (PSR-12 via Laravel Pint)
+composer lint
+
+# Static analysis (PHPStan level 8)
+composer phpstan
+
+# Run all tests
+composer test
+
+# Run specific test suites
+composer test-unit
+composer test-integration
+composer test-fhir
+
+# Full quality check (lint + phpstan + test)
+composer quality:all
+```
+
+### Component-Specific Quality Checks
+
+```bash
+composer quality:bundle
+composer quality:codegen
+composer quality:serialization
+composer quality:fhir-path
+```
+
+## Console Commands (via FHIR Bundle)
+
+When you install `ardenexal/fhir-bundle` in your Symfony application, you get these console commands:
+
+| Command | Description |
+|---------|-------------|
+| `fhir:generate` | Generate PHP model classes from FHIR packages |
+| `fhir:path:evaluate` | Evaluate a FHIRPath expression against FHIR data |
+| `fhir:path:validate` | Validate FHIRPath expression syntax |
+
+**Note**: These commands are only available when using the FHIR Bundle in a Symfony application. This monorepo is a library, not an application.
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for development setup, coding standards, and contribution guidelines.
+
+## License
 
+This project is licensed under the MIT License — see the [LICENSE](LICENSE) file for details.

composer.json

@@ -1,7 +1,7 @@
 {
     "name": "ardenexal/fhir-tools",
-    "description": "PHP CLI tool for generating FHIR types, resources, and profiles from FHIR StructureDefinitions",
-    "type": "project",
+    "description": "PHP monorepo library for FHIR tools - code generation, serialization, FHIRPath, and models",
+    "type": "library",
     "license": "MIT",
     "minimum-stability": "stable",
     "prefer-stable": true,
@@ -14,16 +14,12 @@
         "composer/semver": "^3.4.4",
         "nette/php-generator": "^4.2.1",
         "symfony/console": "^6.4|^7.4",
-        "symfony/dotenv": "^6.4|^7.4",
         "symfony/filesystem": "^6.4|^7.4",
-        "symfony/flex": "^2.10",
-        "symfony/framework-bundle": "^6.4|^7.4",
         "symfony/http-client": "^6.4|^7.4",
         "symfony/intl": "^6.4|^7.4",
         "symfony/polyfill-php84": "^v1.33.0",
         "symfony/polyfill-php85": "^v1.33.0",
         "symfony/property-access": "^6.4|^7.4",
-        "symfony/runtime": "^6.4|^7.4",
         "symfony/serializer": "^6.4|^7.4",
         "symfony/string": "^6.4|^7.4",
         "symfony/validator": "^6.4|^7.4",
@@ -38,14 +34,11 @@
         "symfony/browser-kit": "^6.4|^7.4",
         "symfony/css-selector": "^6.4|^7.4",
         "symfony/dom-crawler": "^6.4|^7.4",
-        "symfony/maker-bundle": "^1.66.0",
         "symfony/phpunit-bridge": "^6.4|^7.4"
     },
     "config": {
         "allow-plugins": {
-            "php-http/discovery": true,
-            "symfony/flex": true,
-            "symfony/runtime": true
+            "php-http/discovery": true
         },
         "bump-after-update": true,
         "sort-packages": true
@@ -76,16 +69,6 @@
         "symfony/polyfill-php82": "*"
     },
     "scripts": {
-        "auto-scripts": {
-            "cache:clear": "symfony-cmd",
-            "assets:install %PUBLIC_DIR%": "symfony-cmd"
-        },
-        "post-install-cmd": [
-            "@auto-scripts"
-        ],
-        "post-update-cmd": [
-            "@auto-scripts"
-        ],
         "phpstan": "php ./vendor/bin/phpstan.phar analyse --configuration=phpstan.neon --memory-limit=-1 -v",
         "phpstan:bundle": "php ./vendor/bin/phpstan.phar analyse src/Bundle/ --configuration=phpstan.neon --memory-limit=-1 -v",
         "phpstan:codegen": "php ./vendor/bin/phpstan.phar analyse src/Component/CodeGeneration/ --configuration=phpstan.neon --memory-limit=-1 -v",
@@ -154,14 +137,5 @@
         "validate-recipe": "php scripts/validate-recipe.php",
         "test-recipe": "php ./vendor/phpunit/phpunit/phpunit tests/Integration/FlexRecipeTest.php",
         "test-package-installation": "php scripts/test-package-installation.php"
-    },
-    "conflict": {
-        "symfony/symfony": "*"
-    },
-    "extra": {
-        "symfony": {
-            "allow-contrib": false,
-            "require": "^6.4|^7.4"
-        }
     }
 }