Remove file and index getters and setters from project

src/phpDocumentor/Descriptor/ProjectDescriptor.php

@@ -13,7 +13,6 @@
 
 namespace phpDocumentor\Descriptor;
 
-use phpDocumentor\Descriptor\Interfaces\ElementInterface;
 use phpDocumentor\Descriptor\Interfaces\FileInterface;
 use phpDocumentor\Descriptor\ProjectDescriptor\Settings;
 use phpDocumentor\Descriptor\Traits\HasDescription;
@@ -66,18 +65,6 @@ public function __construct(string $name)
         $this->versions = Collection::fromClassString(VersionDescriptor::class);
     }
 
-    /**
-     * Sets all files on this project.
-     *
-     * @deprecated Please use {@see DocumentationSetDescriptor::getFiles()}
-     *
-     * @param Collection<FileInterface> $files
-     */
-    public function setFiles(Collection $files): void
-    {
-        $this->getApiDocumentationSet()->setFiles($files);
-    }
-
     /**
      * Returns all files with their sub-elements.
      *
@@ -90,18 +77,6 @@ public function getFiles(): Collection
         return $this->getApiDocumentationSet()->getFiles();
     }
 
-    /**
-     * Sets all indexes for this project.
-     *
-     * @deprecated Please use {@see DocumentationSetDescriptor::setIndexes()}
-     *
-     * @param Collection<Collection<ElementInterface>> $indexes
-     */
-    public function setIndexes(Collection $indexes): void
-    {
-        $this->getApiDocumentationSet()->setIndexes($indexes);
-    }
-
     /**
      * Returns all indexes in this project.
      *
@@ -153,14 +128,6 @@ public function getPartials(): Collection
         return $this->partials;
     }
 
-    /**
-     * @deprecated Please use {@see ApiSetDescriptor::findElement()}
-     */
-    public function findElement(Fqsen $fqsen): ?ElementInterface
-    {
-        return $this->getApiDocumentationSet()->findElement($fqsen);
-    }
-
     /**
      * @return Collection<VersionDescriptor>
      */

src/phpDocumentor/Pipeline/Stage/Transform.php

@@ -6,6 +6,7 @@
 
 use Exception;
 use League\Flysystem\FilesystemInterface;
+use phpDocumentor\Descriptor\ApiSetDescriptor;
 use phpDocumentor\Dsn;
 use phpDocumentor\Event\Dispatcher;
 use phpDocumentor\Parser\FlySystemFactory;
@@ -87,26 +88,32 @@ public function __invoke(Payload $payload): Payload
         $project = $payload->getBuilder()->getProjectDescriptor();
         $transformations = $templates->getTransformations();
 
-        /** @var PreTransformEvent $preTransformEvent */
-        $preTransformEvent = PreTransformEvent::createInstance($this);
-        $preTransformEvent->setProject($project);
-        $preTransformEvent->setTransformations($transformations);
-        Dispatcher::getInstance()->dispatch(
-            $preTransformEvent,
-            Transformer::EVENT_PRE_TRANSFORM
-        );
+        foreach ($project->getVersions() as $version) {
+            $apiSets = $version->getDocumentationSets()->filter(ApiSetDescriptor::class);
+            foreach ($apiSets as $apiSet) {
+                /** @var PreTransformEvent $preTransformEvent */
+                $preTransformEvent = PreTransformEvent::createInstance($this);
+                $preTransformEvent->setProject($project);
+                $preTransformEvent->setTransformations($transformations);
+                Dispatcher::getInstance()->dispatch(
+                    $preTransformEvent,
+                    Transformer::EVENT_PRE_TRANSFORM
+                );
 
-        $this->transformer->execute(
-            $project,
-            $transformations
-        );
+                $this->transformer->execute(
+                    $project,
+                    $apiSet,
+                    $transformations
+                );
 
-        /** @var PostTransformEvent $postTransformEvent */
-        $postTransformEvent = PostTransformEvent::createInstance($this);
-        $postTransformEvent->setProject($project);
-        $postTransformEvent->setTransformations($transformations);
+                /** @var PostTransformEvent $postTransformEvent */
+                $postTransformEvent = PostTransformEvent::createInstance($this);
+                $postTransformEvent->setProject($project);
+                $postTransformEvent->setTransformations($transformations);
 
-        Dispatcher::getInstance()->dispatch($postTransformEvent, Transformer::EVENT_POST_TRANSFORM);
+                Dispatcher::getInstance()->dispatch($postTransformEvent, Transformer::EVENT_POST_TRANSFORM);
+            }
+        }
 
         return $payload;
     }

src/phpDocumentor/Transformer/Transformer.php

@@ -14,6 +14,7 @@
 namespace phpDocumentor\Transformer;
 
 use League\Flysystem\FilesystemInterface;
+use phpDocumentor\Descriptor\DocumentationSetDescriptor;
 use phpDocumentor\Descriptor\ProjectDescriptor;
 use phpDocumentor\Dsn;
 use phpDocumentor\Event\Dispatcher;
@@ -127,9 +128,12 @@ public function destination(): FilesystemInterface
      *
      * @param Transformation[] $transformations
      */
-    public function execute(ProjectDescriptor $project, array $transformations): void
-    {
-        $this->initializeWriters($project, $transformations);
+    public function execute(
+        ProjectDescriptor $project,
+        DocumentationSetDescriptor $documentationSet,
+        array $transformations
+    ): void {
+        $this->initializeWriters($project, $documentationSet, $transformations);
         $this->transformProject($project, $transformations);
 
         $this->logger->log(LogLevel::NOTICE, 'Finished transformation process');
@@ -140,8 +144,11 @@ public function execute(ProjectDescriptor $project, array $transformations): voi
      *
      * @param Transformation[] $transformations
      */
-    private function initializeWriters(ProjectDescriptor $project, array $transformations): void
-    {
+    private function initializeWriters(
+        ProjectDescriptor $project,
+        DocumentationSetDescriptor $documentationSet,
+        array $transformations
+    ): void {
         $isInitialized = [];
         foreach ($transformations as $transformation) {
             $writerName = $transformation->getWriter();
@@ -152,7 +159,7 @@ private function initializeWriters(ProjectDescriptor $project, array $transforma
 
             $isInitialized[] = $writerName;
             $writer = $this->writers->get($writerName);
-            $this->initializeWriter($writer, $project, $transformation->template());
+            $this->initializeWriter($writer, $project, $documentationSet, $transformation->template());
         }
     }
 
@@ -172,15 +179,19 @@ private function initializeWriters(ProjectDescriptor $project, array $transforma
      *
      * @uses Dispatcher to emit the events surrounding an initialization.
      */
-    private function initializeWriter(WriterAbstract $writer, ProjectDescriptor $project, Template $template): void
-    {
+    private function initializeWriter(
+        WriterAbstract $writer,
+        ProjectDescriptor $project,
+        DocumentationSetDescriptor $documentationSet,
+        Template $template
+    ): void {
         /** @var WriterInitializationEvent $instance */
         $instance = WriterInitializationEvent::createInstance($this);
         $event = $instance->setWriter($writer);
         $this->eventDispatcher->dispatch($event, self::EVENT_PRE_INITIALIZATION);
 
         if ($writer instanceof Initializable) {
-            $writer->initialize($project, $template);
+            $writer->initialize($project, $documentationSet, $template);
         }
 
         $this->eventDispatcher->dispatch($event, self::EVENT_POST_INITIALIZATION);

src/phpDocumentor/Transformer/Writer/Initializable.php

@@ -13,10 +13,15 @@
 
 namespace phpDocumentor\Transformer\Writer;
 
+use phpDocumentor\Descriptor\DocumentationSetDescriptor;
 use phpDocumentor\Descriptor\ProjectDescriptor;
 use phpDocumentor\Transformer\Template;
 
 interface Initializable
 {
-    public function initialize(ProjectDescriptor $project, Template $template): void;
+    public function initialize(
+        ProjectDescriptor $project,
+        DocumentationSetDescriptor $documentationSet,
+        Template $template
+    ): void;
 }

src/phpDocumentor/Transformer/Writer/RenderGuide.php

@@ -87,11 +87,13 @@ public function transform(ProjectDescriptor $project, Transformation $transforma
                 //TODO Extract this, as this code is duplicated
                 $this->environmentBuilder->setEnvironmentFactory(
                     function () use ($transformation, $project, $documentationSet) {
-                        $twig = $this->environmentFactory->create($project, $transformation->template());
-                        $twig->addGlobal('project', $project);
+                        $twig = $this->environmentFactory->create(
+                            $project,
+                            $documentationSet,
+                            $transformation->template()
+                        );
                         $twig->addGlobal('usesNamespaces', count($project->getNamespace()->getChildren()) > 0);
                         $twig->addGlobal('usesPackages', count($project->getPackage()->getChildren()) > 0);
-                        $twig->addGlobal('documentationSet', $documentationSet);
                         $twig->addGlobal('destinationPath', null);
 
                         return $twig;

src/phpDocumentor/Transformer/Writer/Twig.php

@@ -15,6 +15,7 @@
 
 use phpDocumentor\Descriptor\Collection as DescriptorCollection;
 use phpDocumentor\Descriptor\Descriptor;
+use phpDocumentor\Descriptor\DocumentationSetDescriptor;
 use phpDocumentor\Descriptor\ProjectDescriptor;
 use phpDocumentor\Descriptor\Query\Engine;
 use phpDocumentor\Transformer\Template;
@@ -114,9 +115,12 @@ public function getName(): string
         return 'twig';
     }
 
-    public function initialize(ProjectDescriptor $project, Template $template): void
-    {
-        $this->environment = $this->environmentFactory->create($project, $template);
+    public function initialize(
+        ProjectDescriptor $project,
+        DocumentationSetDescriptor $documentationSet,
+        Template $template
+    ): void {
+        $this->environment = $this->environmentFactory->create($project, $documentationSet, $template);
     }
 
     /**
@@ -200,10 +204,8 @@ private function transformNode(
 
         $parameters = array_merge($transformation->getParameters(), $extraParameters);
 
-        $this->environment->addGlobal('project', $project);
         $this->environment->addGlobal('usesNamespaces', count($project->getNamespace()->getChildren()) > 0);
         $this->environment->addGlobal('usesPackages', count($project->getPackage()->getChildren()) > 0);
-        $this->environment->addGlobal('documentationSet', $project);
         $this->environment->addGlobal('node', $node);
         $this->environment->addGlobal('destinationPath', $path);
         $this->environment->addGlobal('parameter', $parameters);

src/phpDocumentor/Transformer/Writer/Twig/EnvironmentFactory.php

@@ -14,6 +14,7 @@
 namespace phpDocumentor\Transformer\Writer\Twig;
 
 use League\CommonMark\ConverterInterface;
+use phpDocumentor\Descriptor\DocumentationSetDescriptor;
 use phpDocumentor\Descriptor\ProjectDescriptor;
 use phpDocumentor\Guides\Graphs\Twig\UmlExtension;
 use phpDocumentor\Guides\Twig\AssetsExtension;
@@ -57,6 +58,7 @@ public function withTemplateOverridesAt(Path $path): void
 
     public function create(
         ProjectDescriptor $project,
+        DocumentationSetDescriptor $documentationSet,
         Template $template
     ): Environment {
         $mountManager = $template->files();
@@ -72,7 +74,7 @@ public function create(
 
         $env = new Environment(new ChainLoader($loaders));
 
-        $this->addPhpDocumentorExtension($project, $env);
+        $this->addPhpDocumentorExtension($project, $documentationSet, $env);
         $this->enableDebug($env);
 
         return $env;
@@ -83,10 +85,12 @@ public function create(
      */
     private function addPhpDocumentorExtension(
         ProjectDescriptor $project,
+        DocumentationSetDescriptor $documentationSet,
         Environment $twigEnvironment
     ): void {
         $extension = new Extension(
             $project,
+            $documentationSet,
             $this->markDownConverter,
             $this->renderer,
             $this->relativePathToRootConverter,

src/phpDocumentor/Transformer/Writer/Twig/Extension.php

@@ -21,6 +21,7 @@
 use phpDocumentor\Descriptor\Descriptor;
 use phpDocumentor\Descriptor\DescriptorAbstract;
 use phpDocumentor\Descriptor\DocBlock\DescriptionDescriptor;
+use phpDocumentor\Descriptor\DocumentationSetDescriptor;
 use phpDocumentor\Descriptor\EnumDescriptor;
 use phpDocumentor\Descriptor\Interfaces\ArgumentInterface;
 use phpDocumentor\Descriptor\Interfaces\ClassInterface;
@@ -92,6 +93,8 @@ final class Extension extends AbstractExtension implements ExtensionInterface, G
     private ConverterInterface $markdownConverter;
     private RelativePathToRootConverter $relativePathToRootConverter;
     private PathBuilder $pathBuilder;
+    private DocumentationSetDescriptor $documentationSet;
+    private ProjectDescriptor $project;
 
     /**
      * Registers the structure and transformation with this extension.
@@ -100,28 +103,40 @@ final class Extension extends AbstractExtension implements ExtensionInterface, G
      */
     public function __construct(
         ProjectDescriptor $project,
+        DocumentationSetDescriptor $documentationSet,
         ConverterInterface $markdownConverter,
         LinkRenderer $routeRenderer,
         RelativePathToRootConverter $relativePathToRootConverter,
         PathBuilder $pathBuilder
     ) {
+        $this->project = $project;
+        $this->documentationSet = $documentationSet;
         $this->markdownConverter = $markdownConverter;
         $this->routeRenderer = $routeRenderer;
-        $this->routeRenderer = $this->routeRenderer->withProject($project);
+        $this->routeRenderer = $this->routeRenderer->withProject($project)->forDocumentationSet($documentationSet);
         $this->relativePathToRootConverter = $relativePathToRootConverter;
         $this->pathBuilder = $pathBuilder;
     }
 
     /**
      * Initialize series of globals used by the writers to set the context
      *
-     * @return array<string, (true|string[]|null)>
+     * @return array{
+     *     project: ProjectDescriptor,
+     *     documentationSet: DocumentationSetDescriptor,
+     *     node: ?Descriptor,
+     *     usesNamespaces: bool,
+     *     usesPackages: bool,
+     *     destinationPath: ?string,
+     *     parameter: array<string, mixed>,
+     *     env: mixed
+     * }
      */
     public function getGlobals(): array
     {
         return [
-            'project' => null,
-            'documentationSet' => null,
+            'project' => $this->project,
+            'documentationSet' => $this->documentationSet,
             'node' => null,
             'usesNamespaces' => true,
             'usesPackages' => true,
@@ -447,7 +462,8 @@ private function contextRouteRenderer(array $context): LinkRenderer
     {
         return $this->routeRenderer
             ->withDestination(ltrim($context['destinationPath'] ?? $context['env']->getCurrentFileDestination(), '/\\'))
-            ->withProject($context['project']);
+            ->withProject($context['project'])
+            ->forDocumentationSet($context['documentationSet']);
     }
 
     /**