Refactor - Automatically create anchors in Document::from_bytes

Document::from_bytes now calls create_anchors_from_tree internally,
eliminating the need for callers to do this separately. Every production
call site previously followed the pattern:

    let mut doc = Document::from_bytes(...)?;
    doc.create_anchors_from_tree();

This was error-prone boilerplate since anchors are required for
snapshot() to work correctly. Now documents are fully initialized
with anchors upon creation.

Changes:
- from_bytes() calls create_anchors_from_tree() before returning
- create_anchors_from_tree made private (fn on Document, pub(crate) in
  anchors module for benchmark access)
- Removed redundant calls from CLI, Dioxus app, FFI layer
- Removed redundant calls from all test files
- Updated documentation to reflect automatic behavior
- Restructured anchors benchmark to measure via from_bytes

Prompts:
- "TODO document should probably automatically load anchors in frombytes
  - spotted in snapshot snap test" (with code snippet showing the
  two-step pattern in tests)
- "yes"
- "can we make create_anchors_from_tree private, nothing should need it"
- "don't include the tour" (in response to staging tour file)

Co-Authored-By: Claude <noreply@anthropic.com>

Interesting that with the AI it is more likely to put up with
duplication like this for longer, but it is also easier to fix when we
decide to.

Author: timabell

crates/markdown-neuraxis-cli/src/main.rs

@@ -90,8 +90,7 @@ impl App {
                 // Load and display file content
                 match io::read_file(file.relative_path(), &self.notes_path) {
                     Ok(content) => match Document::from_bytes(content.as_bytes()) {
-                        Ok(mut document) => {
-                            document.create_anchors_from_tree();
+                        Ok(document) => {
                             self.selected_document = Some(document.clone());
                             self.current_content = self.render_document_content(&document);
                         }

crates/markdown-neuraxis-dioxus/src/ui/app.rs

@@ -247,10 +247,7 @@ fn load_existing_document(
 
     match io::read_file(markdown_file.relative_path(), notes_path) {
         Ok(content) => match Document::from_bytes(content.as_bytes()) {
-            Ok(mut document) => {
-                // Create anchors for the document blocks
-                document.create_anchors_from_tree();
-
+            Ok(document) => {
                 // Create snapshot for rendering
                 let snapshot = document.snapshot();
 
@@ -290,8 +287,7 @@ pub fn load_document(
 
     match io::read_file(markdown_file.relative_path(), notes_path) {
         Ok(content) => match Document::from_bytes(content.as_bytes()) {
-            Ok(mut document) => {
-                document.create_anchors_from_tree();
+            Ok(document) => {
                 let snapshot = document.snapshot();
                 *current_document.write() = Some(Arc::new(document));
                 *current_snapshot.write() = Some(snapshot);
@@ -308,8 +304,7 @@ pub fn load_document(
         Err(_) => {
             // File doesn't exist - create a blank document
             match Document::from_bytes(b"") {
-                Ok(mut document) => {
-                    document.create_anchors_from_tree();
+                Ok(document) => {
                     let snapshot = document.snapshot();
                     *current_document.write() = Some(Arc::new(document));
                     *current_snapshot.write() = Some(snapshot);

crates/markdown-neuraxis-dioxus/tests/anchor_id_confusion_during_editing_test.rs

@@ -26,8 +26,8 @@ fn test_anchor_id_confusion_after_editing() {
 "#;
 
     let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
 
+    // Anchors are created automatically in from_bytes
     // Take initial snapshot and record anchor IDs
     let source = doc.text();
     let initial_snapshot = doc.snapshot();
@@ -156,8 +156,8 @@ fn test_multiple_edit_cycles_preserve_anchor_identity() {
 - item 2"#;
 
     let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
 
+    // Anchors are created automatically in from_bytes
     // Record initial anchor mappings
     let initial_snapshot = doc.snapshot();
     let initial_blocks = flatten_blocks(&initial_snapshot.blocks);

crates/markdown-neuraxis-dioxus/tests/anchor_stability_tests.rs

@@ -49,8 +49,8 @@ mod anchor_stability_tests {
     fn test_anchor_ids_stable_during_focus_cycles() {
         // Create document from the actual test data that shows the bug
         let markdown = include_str!("../test_data/nested_lists_bug_repro.md");
-        let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-        doc.create_anchors_from_tree();
+        let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
+        // Anchors created automatically in from_bytes
 
         // Capture initial anchor IDs
         let initial_snapshot = doc.snapshot();
@@ -76,9 +76,8 @@ mod anchor_stability_tests {
         println!("\nTesting anchor stability for: '{}'", nested_item.0);
         let original_anchor_id = nested_item.1.0;
 
-        // Step 1: Focus (this might trigger re-parsing)
+        // Step 1: Focus - anchors are stable, just take snapshot
         println!("Step 1: Focusing on item...");
-        doc.create_anchors_from_tree();
 
         let after_focus_snapshot = doc.snapshot();
         let mut after_focus_blocks = Vec::new();
@@ -97,11 +96,11 @@ mod anchor_stability_tests {
             nested_item.0, original_anchor_id, after_focus_id
         );
 
-        // Step 2: Multiple regenerations without content changes
-        println!("Step 2: Multiple anchor regenerations...");
+        // Step 2: Multiple snapshots without content changes
+        println!("Step 2: Multiple snapshots...");
 
         for cycle in 0..3 {
-            doc.create_anchors_from_tree();
+            // Anchors are stable, just take snapshot
             let cycle_snapshot = doc.snapshot();
             let mut cycle_blocks = Vec::new();
             flatten_blocks(&cycle_snapshot.blocks, &mut cycle_blocks);
@@ -122,11 +121,11 @@ mod anchor_stability_tests {
     #[test]
     fn test_anchor_uniqueness_after_multiple_regenerations() {
         let markdown = include_str!("../test_data/nested_lists_bug_repro.md");
-        let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
+        let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
 
         for cycle in 0..5 {
-            println!("Anchor regeneration cycle {}", cycle);
-            doc.create_anchors_from_tree();
+            println!("Anchor snapshot cycle {}", cycle);
+            // Anchors are created automatically and stable
 
             let snapshot = doc.snapshot();
             let mut blocks = Vec::new();
@@ -167,8 +166,8 @@ mod anchor_stability_tests {
     #[test]
     fn test_specific_bug_scenario_from_diagnostics() {
         let markdown = include_str!("../test_data/nested_lists_bug_repro.md");
-        let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-        doc.create_anchors_from_tree();
+        let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
+        // Anchors created automatically in from_bytes
 
         let snapshot = doc.snapshot();
         let mut blocks = Vec::new();

crates/markdown-neuraxis-dioxus/tests/click_event_mapping_bug_test.rs

@@ -11,8 +11,7 @@ fn test_ui_block_to_anchor_mapping_correctness() {
     // This suggests the UI rendering and click handling are using different block mappings
 
     let markdown = include_str!("../test_data/actual_runtime_bug_repro.md");
-    let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
+    let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
 
     let snapshot = doc.snapshot();
     let blocks = flatten_blocks(&snapshot.blocks);
@@ -95,8 +94,7 @@ fn test_snapshot_block_order_vs_ui_rendering_order() {
     // This could cause click events to get mapped to wrong blocks
 
     let markdown = include_str!("../test_data/actual_runtime_bug_repro.md");
-    let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
+    let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
 
     let snapshot = doc.snapshot();
     let blocks = flatten_blocks(&snapshot.blocks);
@@ -161,8 +159,7 @@ fn test_hierarchical_list_item_click_confusion() {
     // Maybe nested items inherit or share anchor IDs with their parents
 
     let markdown = include_str!("../test_data/actual_runtime_bug_repro.md");
-    let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
+    let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
 
     let snapshot = doc.snapshot();
     let blocks = flatten_blocks(&snapshot.blocks);

crates/markdown-neuraxis-dioxus/tests/different_content_same_anchor_test.rs

@@ -9,8 +9,8 @@ use test_helpers::flatten_blocks;
 fn test_different_content_same_anchor_id_bug() {
     // Use the actual runtime data that shows the bug
     let markdown = include_str!("../test_data/actual_runtime_bug_repro.md");
-    let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
+    let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
+    // Anchors created automatically in from_bytes
 
     let snapshot = doc.snapshot();
     let blocks = flatten_blocks(&snapshot.blocks);
@@ -79,8 +79,8 @@ fn test_different_content_same_anchor_id_bug() {
 fn test_specific_indented_1_vs_indented_1_2_collision() {
     // Test the specific diagnostic case: "indented 1" vs "indented 1.2"
     let markdown = include_str!("../test_data/actual_runtime_bug_repro.md");
-    let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
+    let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
+    // Anchors created automatically in from_bytes
 
     let snapshot = doc.snapshot();
     let blocks = flatten_blocks(&snapshot.blocks);

crates/markdown-neuraxis-dioxus/tests/dioxus_rendering_tests.rs

@@ -8,9 +8,7 @@ use test_helpers::flatten_blocks;
 /// Test helper to create nested list document
 fn create_nested_list_doc() -> Document {
     let markdown = "- item 1\n  - nested 1.1\n  - nested 1.2\n    - deeply nested 1.2.1\n- item 2";
-    let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
-    doc
+    Document::from_bytes(markdown.as_bytes()).unwrap()
 }
 
 #[cfg(test)]

crates/markdown-neuraxis-dioxus/tests/document_clone_bug_test.rs

@@ -17,8 +17,7 @@ fn test_document_clone_should_have_valid_anchor_node_references() {
   - item 1.2
 - item 2"#;
 
-    let mut original_doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    original_doc.create_anchors_from_tree();
+    let original_doc = Document::from_bytes(markdown.as_bytes()).unwrap();
 
     println!("=== ORIGINAL DOCUMENT ===");
     println!(
@@ -100,8 +99,7 @@ fn test_document_clone_anchor_content_integrity() {
   - nested item
 - second item"#;
 
-    let mut original_doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    original_doc.create_anchors_from_tree();
+    let original_doc = Document::from_bytes(markdown.as_bytes()).unwrap();
     let original_snapshot = original_doc.snapshot();
     let original_blocks = flatten_blocks(&original_snapshot.blocks);
 
@@ -169,8 +167,7 @@ fn test_document_clone_preserves_functionality() {
     let markdown = r#"- original item
   - nested original"#;
 
-    let mut original_doc = Document::from_bytes(markdown.as_bytes()).unwrap();
-    original_doc.create_anchors_from_tree();
+    let original_doc = Document::from_bytes(markdown.as_bytes()).unwrap();
 
     let mut cloned_doc = original_doc.clone();
 

crates/markdown-neuraxis-dioxus/tests/editing_lifecycle_bug_test.rs

@@ -9,10 +9,10 @@ use test_helpers::flatten_blocks;
 fn test_editing_lifecycle_causes_anchor_instability() {
     // Use the actual runtime data
     let markdown = include_str!("../test_data/actual_runtime_bug_repro.md");
-    let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
+    let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
 
     // Step 1: Initial document load (like opening the file)
-    doc.create_anchors_from_tree();
+    // Anchors are created automatically in from_bytes
     let initial_snapshot = doc.snapshot();
     let initial_blocks = flatten_blocks(&initial_snapshot.blocks);
 
@@ -39,8 +39,7 @@ fn test_editing_lifecycle_causes_anchor_instability() {
         // 1. Focus event triggered
         // 2. UI might regenerate anchors for consistency
         // 3. Document state changes
-
-        doc.create_anchors_from_tree(); // This is what might cause instability
+        // Anchors are created automatically in from_bytes, so just take snapshot
 
         let cycle_snapshot = doc.snapshot();
         let cycle_blocks = flatten_blocks(&cycle_snapshot.blocks);
@@ -115,9 +114,9 @@ fn test_editing_lifecycle_causes_anchor_instability() {
 fn test_rapid_focus_changes_cause_collision() {
     // Simulate rapid clicking between items (like a user quickly clicking different items)
     let markdown = include_str!("../test_data/actual_runtime_bug_repro.md");
-    let mut doc = Document::from_bytes(markdown.as_bytes()).unwrap();
+    let doc = Document::from_bytes(markdown.as_bytes()).unwrap();
 
-    doc.create_anchors_from_tree();
+    // Anchors are created automatically in from_bytes
     let initial_snapshot = doc.snapshot();
     let initial_blocks = flatten_blocks(&initial_snapshot.blocks);
 
@@ -137,10 +136,8 @@ fn test_rapid_focus_changes_cause_collision() {
     println!("Found {} 'indented 1.2' items", indented_1_2_items.len());
 
     // Simulate rapid focus changes (like clicking back and forth)
+    // Anchors are created automatically and stable, so just take repeated snapshots
     for rapid_cycle in 0..10 {
-        // This simulates the sequence: click item → focus → anchor regeneration
-        doc.create_anchors_from_tree();
-
         let rapid_snapshot = doc.snapshot();
         let rapid_blocks = flatten_blocks(&rapid_snapshot.blocks);
 

crates/markdown-neuraxis-dioxus/tests/exact_collision_reproduction_test.rs

@@ -32,8 +32,8 @@ fn test_exact_diagnostic_collision_indented_1_vs_indented_1_2() {
         - indented 1.2.1 - then clicked this
 "#;
 
-    let mut doc = Document::from_bytes(actual_file_content.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
+    let doc = Document::from_bytes(actual_file_content.as_bytes()).unwrap();
+    // Anchors created automatically in from_bytes
 
     let snapshot = doc.snapshot();
     let blocks = flatten_blocks(&snapshot.blocks);
@@ -123,11 +123,9 @@ fn test_anchor_generation_algorithm_produces_unique_ids_for_similar_content() {
         let doc1_markdown = format!("- {}", content1);
         let doc2_markdown = format!("- {}", content2);
 
-        let mut doc1 = Document::from_bytes(doc1_markdown.as_bytes()).unwrap();
-        let mut doc2 = Document::from_bytes(doc2_markdown.as_bytes()).unwrap();
-
-        doc1.create_anchors_from_tree();
-        doc2.create_anchors_from_tree();
+        let doc1 = Document::from_bytes(doc1_markdown.as_bytes()).unwrap();
+        let doc2 = Document::from_bytes(doc2_markdown.as_bytes()).unwrap();
+        // Anchors created automatically in from_bytes
 
         let snapshot1 = doc1.snapshot();
         let snapshot2 = doc2.snapshot();
@@ -170,8 +168,8 @@ fn test_combined_document_collision_reproduction() {
 
 "#;
 
-    let mut doc = Document::from_bytes(problematic_markdown.as_bytes()).unwrap();
-    doc.create_anchors_from_tree();
+    let doc = Document::from_bytes(problematic_markdown.as_bytes()).unwrap();
+    // Anchors created automatically in from_bytes
 
     let snapshot = doc.snapshot();
     let blocks = flatten_blocks(&snapshot.blocks);