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Author: nshkrdotcom

research_paper_improvement_gemini_pro_delayed.yaml.tmp

@@ -6,7 +6,7 @@ workflow:
     - name: "analyze_and_improve_research"
       type: "gemini"
       model: "gemini-2.5-pro"
-      output_to_file: "202507110833_improved_chiral_narrative_synthesis.md"
+      output_to_file: "202507110839_improved_chiral_narrative_synthesis.md"
       token_budget:
         temperature: 0.7
         max_output_tokens: 65536
@@ -17,7 +17,7 @@ workflow:
 
             ```` 
         - type: "file"
-          path: "./workspace/202507110830_continuing_from_large_file.md"
+          path: "./workspace/202507110831_chiral_narrative_synthesis_scientific_paper.md"
         - type: "static"
           content: |
             ````

research_paper_improvement_pipeline.yaml

@@ -47,9 +47,7 @@ workflow:
         # Enable comprehensive conversation logging for debugging
         pass_through_streaming: true
         verbose: true
-      output_to_file:
-        path: "./logs/claude_conversation_TIMESTAMP_PLACEHOLDER.jsonl"
-        format: "jsonl"
+      output_to_file: "./logs/claude_conversation_TIMESTAMP_PLACEHOLDER.jsonl"
       prompt:
         - type: "static"
           content: |

research_paper_improvement_pipeline.yaml.tmp

@@ -47,9 +47,7 @@ workflow:
         # Enable comprehensive conversation logging for debugging
         pass_through_streaming: true
         verbose: true
-      output_to_file:
-        path: "./logs/claude_conversation_202507110831.jsonl"
-        format: "jsonl"
+      output_to_file: "./logs/claude_conversation_202507110837.jsonl"
       prompt:
         - type: "static"
           content: |
@@ -90,7 +88,7 @@ workflow:
             - Make the research more technically sound and publishable
             - Ensure proper scientific formatting and structure
 
-            IMPORTANT: Use the Write tool to save as markdown file with format: 202507110831_{descriptive_filename}.md
+            IMPORTANT: Use the Write tool to save as markdown file with format: 202507110837_{descriptive_filename}.md
 
             Here are the improvements and analysis to incorporate:
         - type: "previous_response"

run_research_paper_improvement_loop.sh

@@ -0,0 +1,85 @@
+#!/bin/bash
+
+# Research Paper Improvement Pipeline Loop
+# Hardcoded to use research_paper_improvement_gemini_pro_delayed.yaml
+# Chains iterations by feeding outputs back as inputs
+
+PIPELINE_FILE="research_paper_improvement_gemini_pro_delayed.yaml"
+
+# Check if the pipeline file exists
+if [ ! -f "$PIPELINE_FILE" ]; then
+    echo "Error: Pipeline file '$PIPELINE_FILE' not found!"
+    exit 1
+fi
+
+echo "Starting research paper improvement pipeline loop"
+echo "Pipeline: $PIPELINE_FILE"
+echo "Press Ctrl+C to stop"
+echo ""
+
+counter=1
+while true; do
+    timestamp=$(date -u +"%Y%m%d%H%M")
+    echo "=== Research Paper Improvement Run #$counter $(date -u) ==="
+    
+    # Create temporary YAML with unique timestamp
+    cp "$PIPELINE_FILE" "${PIPELINE_FILE}.tmp"
+    
+    # Replace {{timestamp}} markers in output_to_file fields with current timestamp
+    sed -i "s|{{timestamp}}|$timestamp|g" "${PIPELINE_FILE}.tmp"
+    
+    # Find the most recent output file to use as input for next iteration
+    if [ $counter -gt 1 ]; then
+        # Look for latest file in outputs directory (where files are actually saved)
+        latest_file=$(ls -t ./outputs/202*_improved_chiral_narrative_synthesis.md 2>/dev/null | head -1)
+        if [ -n "$latest_file" ]; then
+            echo "🔄 Using previous output as input: $latest_file"
+            # Update the file path in the YAML to point to the latest output
+            sed -i 's|path: "\.\./research_papers/tex/ResearchProposal-ChiralNarrativeSynthesis_3\.tex"|path: "'"$latest_file"'"|g' "${PIPELINE_FILE}.tmp"
+            sed -i 's|path: \.\./research_papers/tex/ResearchProposal-ChiralNarrativeSynthesis_3\.tex|path: "'"$latest_file"'"|g' "${PIPELINE_FILE}.tmp"
+        else
+            echo "⚠️  No previous output found, using original research proposal"
+        fi
+    else
+        echo "🚀 First run - using original research proposal"
+    fi
+    
+    # Run the pipeline
+    echo "🧠 Executing Gemini research improvement..."
+    start_time=$(date +%s)
+    
+    if timeout 3600 mix pipeline.run.live "${PIPELINE_FILE}.tmp"; then
+        end_time=$(date +%s)
+        duration=$((end_time - start_time))
+        echo "✅ Pipeline completed successfully in ${duration}s"
+        
+        # Check if new output file was created
+        latest_after=$(ls -t ./outputs/202*_improved_chiral_narrative_synthesis.md 2>/dev/null | head -1)
+        if [ "$latest_after" != "$latest_file" ]; then
+            echo "📄 New improved paper created: $latest_after"
+            
+            # Show file size for progress tracking
+            if [ -f "$latest_after" ]; then
+                size=$(wc -l < "$latest_after" 2>/dev/null || echo "unknown")
+                echo "📊 Paper length: $size lines"
+            fi
+        else
+            echo "⚠️  WARNING: No new output file detected!"
+        fi
+    else
+        end_time=$(date +%s)
+        duration=$((end_time - start_time))
+        echo "❌ Pipeline failed or timed out after ${duration}s"
+        
+        # Show current outputs for debugging
+        echo "📁 Current outputs:"
+        ls -lt ./outputs/202*_improved_chiral_narrative_synthesis.md 2>/dev/null | head -3
+    fi
+    
+    # Clean up temp file
+    rm "${PIPELINE_FILE}.tmp"
+    
+    echo "=== Completed Research Paper Improvement Run #$counter, waiting 5 seconds... ==="
+    sleep 5
+    ((counter++))
+done