NOTES.md

@@ -0,0 +1,13 @@
+
+
+Simple query in ChatGPT produced 
+
+Metric | Best For | Type | Notes
+-- | -- | -- | --
+Cosine Similarity | L2-normalized vectors | Similarity | Scale-invariant
+Dot Product | Transformer embeddings | Similarity | Fast, especially on GPUs
+Euclidean Distance | Raw vectors with meaningful norms | Distance | Sensitive to scale
+Jaccard | Sparse binary or set-based data | Similarity | Discrete features
+Soft Cosine | Sparse with semantic overlap | Similarity | Better for text-term overlap
+Learned Similarity | Fine-tuned deep models | Varies | Best accuracy, slowest retrieval
+

README.md

@@ -30,7 +30,11 @@ ssearch/
 ├── clippings/                  # Symlink to clippings (PDFs, TXT, webarchive, RTF)
 ├── store/                      # Persisted journal vector store
 ├── models/                     # Cached HuggingFace models (offline)
+├── archived/                   # Superseded script versions
+├── saved_output/               # Saved query results and model comparisons
 ├── requirements.txt            # Python dependencies
+├── devlog.md                   # Development log and experimental findings
+└── *.ipynb                     # Jupyter notebooks (HyDE, metrics, sandbox)
 ```
 
 ## Setup
@@ -167,6 +171,16 @@ Key parameters (set in source files):
 - **sentence-transformers** -- cross-encoder re-ranking
 - **torch** -- ML runtime
 
+## Notebooks
+
+Three Jupyter notebooks document exploration and analysis:
+
+- **`hyde.ipynb`** -- Experiments with HyDE (Hypothetical Document Embeddings) query rewriting. Finding: did not improve retrieval quality over direct prompt engineering.
+
+- **`sandbox.ipynb`** -- Exploratory notebook for learning the LlamaIndex API.
+
+- **`vs_metrics.ipynb`** -- Quantitative analysis of the vector store (embedding distributions, pairwise similarity, clustering, PCA/t-SNE projections).
+
 ## Design decisions
 
 - **BAAI/bge-large-en-v1.5 over all-mpnet-base-v2**: Better semantic matching quality for journal text despite slower embedding.
@@ -178,3 +192,10 @@ Key parameters (set in source files):
 - **ChromaDB for clippings**: Persistent SQLite-backed store. Chosen over the JSON store for its metadata filtering and direct chunk-level operations for incremental updates.
 - **PDF validation before indexing**: Pre-check each PDF with pypdf — skip if text extraction yields <100 chars or low printable ratio. Skipped files written to `ocr_needed.txt`.
 
+## Development history
+
+- **Aug 2025**: Initial implementation -- build pipeline, embedding model comparison, chunk size experiments, HyDE testing.
+- **Jan 2026**: Command-line interface, prompt improvements, model comparison (command-r7b selected).
+- **Feb 2026**: Cross-encoder re-ranking, hybrid BM25+vector retrieval, LlamaIndex upgrade to 0.14.14, OpenAI API backend, incremental updates, clippings search (ChromaDB), project reorganization.
+
+See `devlog.md` for detailed development notes and experimental findings.

archived/build.py

@@ -0,0 +1,51 @@
+# build.py
+#
+# Import documents from data, generate embedded vector store
+# and save to disk in directory ./storage
+#
+# August 2025
+# E. M. Furst
+
+from llama_index.core import (
+    SimpleDirectoryReader,
+    VectorStoreIndex,
+    Settings,
+)
+
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.core.node_parser import SentenceSplitter
+
+def main():
+    # Choose your embedding model
+    embed_model = HuggingFaceEmbedding(model_name="BAAI/bge-large-en-v1.5")
+
+    # Configure global settings for LlamaIndex
+    Settings.embed_model = embed_model
+
+    # Load documents
+    documents = SimpleDirectoryReader("./data").load_data()
+
+    # Create the custom textsplitter
+    # Set chunk size and overlap (e.g., 256 tokens, 25 tokens overlap)
+    # see https://docs.llamaindex.ai/en/stable/api_reference/node_parsers/sentence_splitter/#llama_index.core.node_parser.SentenceSplitter
+    text_splitter = SentenceSplitter(
+        chunk_size=256, 
+        chunk_overlap=25,
+        paragraph_separator="\n\n",  # use double newlines to separate paragraphs
+    )
+    Settings.text_splitter = text_splitter
+
+    # Build the index 
+    index = VectorStoreIndex.from_documents(
+        documents, transformations=[text_splitter],
+        show_progress=True,
+    )
+
+    # Persist both vector store and index metadata
+    index.storage_context.persist(persist_dir="./storage")
+    
+    print("Index built and saved to ./storage")
+
+if __name__ == "__main__":
+    main()
+

archived/build_exp.py

@@ -0,0 +1,68 @@
+# build_exp.py
+#
+# Import document from data, generate embedded vector store
+# and save to disk
+#
+# Experiment to include text chunking with a textsplitter
+#
+# August 2025
+# E. M. Furst
+
+from llama_index.core import (
+    SimpleDirectoryReader,
+    VectorStoreIndex,
+    Settings,
+)
+
+from pathlib import Path
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.core.node_parser import SentenceSplitter
+
+def main():
+    # Choose your embedding model
+    #embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+    # embedding is slower with BAAI/bge-large-en-v1.5
+    embed_model = HuggingFaceEmbedding(model_name="BAAI/bge-large-en-v1.5")
+
+    # Configure global settings for LlamaIndex
+    Settings.embed_model = embed_model
+
+    # Load documents (capabilities?)
+    documents = SimpleDirectoryReader(
+        "./data",
+        # # p is a string path
+        # file_metadata=lambda p: {
+        #     "filename": Path(p).name,            # just the file name
+        #     "filepath": str(Path(p).resolve()),  # absolute path (handy for tracing)
+        # },
+    ).load_data()
+
+    # Create the custom textsplitter
+    # Set chunk size and overlap (e.g., 512 tokens, 10 toekns overlap)
+    # see https://docs.llamaindex.ai/en/stable/api_reference/node_parsers/sentence_splitter/#llama_index.core.node_parser.SentenceSplitter
+    text_splitter = SentenceSplitter(
+        chunk_size=256, 
+        chunk_overlap=25,
+        paragraph_separator="\n\n",  # use double newlines to separate paragraphs
+    )
+    # b/c passing text_splitter in the index build, this may cause problems
+    # test with it commented out...
+    #    Settings.text_splitter = text_splitter
+
+    # Build the index 
+    index = VectorStoreIndex.from_documents(
+        documents, transformations=[text_splitter],
+        show_progress=True,
+    )
+
+    # Persist both vector store and index metadata
+    index.storage_context.persist(persist_dir="./storage_exp")
+    
+#    storage_context = StorageContext.from_defaults(vector_store=index.vector_store)
+#    storage_context.persist(persist_dir="./storage")
+
+    print("Index built and saved to ./storage_exp")
+
+if __name__ == "__main__":
+    main()
+

archived/claude_diagnostic.py

@@ -0,0 +1,164 @@
+# Better HyDE debugging with targeted tests
+
+from llama_index.core.indices.query.query_transform import HyDEQueryTransform
+from llama_index.core import PromptTemplate
+from llama_index.core import Settings
+from llama_index.core.base.base_query_engine import BaseQueryEngine
+from llama_index.llms.ollama import Ollama
+
+llm="llama3.1:8B"
+
+# Use a local model to generate
+Settings.llm = Ollama(
+    model=llm,    # First model tested
+    request_timeout=360.0,
+    context_window=8000,
+    temperature=0.7,
+    )
+
+
+# Test queries that should produce very different hypothetical documents
+test_queries = [
+    "What is the capital of France?",
+    "How do you make chocolate chip cookies?", 
+    "Explain quantum physics",
+    "Write a love letter",
+    "Describe symptoms of the common cold"
+]
+
+print("=== DEBUGGING HYDE STEP BY STEP ===\n")
+
+# 1. Test the LLM with HyDE-style prompts directly
+print("1. Testing LLM directly with HyDE-style prompts:")
+print("-" * 50)
+
+for query in test_queries[:2]:  # Just test 2 to keep output manageable
+    direct_prompt = f"""Generate a hypothetical document that would contain the answer to this query.
+
+Query: {query}
+
+Hypothetical document:"""
+    
+    response = Settings.llm.complete(direct_prompt)
+    print(f"Query: {query}")
+    print(f"Direct LLM Response: {response.text[:100]}...")
+    print()
+
+# 2. Check HyDE internals - let's see what's actually happening
+print("\n2. Examining HyDE internal behavior:")
+print("-" * 50)
+
+# Create a custom HyDE that shows us everything
+class VerboseHyDETransform(HyDEQueryTransform):
+    def _get_prompts(self):
+        """Show what prompts are being used"""
+        prompts = super()._get_prompts()
+        print(f"HyDE prompts: {prompts}")
+        return prompts
+    
+    def _run_component(self, **kwargs):
+        """Show what's being passed to the LLM"""
+        print(f"HyDE _run_component kwargs: {kwargs}")
+        result = super()._run_component(**kwargs)
+        print(f"HyDE _run_component result: {result}")
+        return result
+
+# Test with verbose HyDE
+verbose_hyde = VerboseHyDETransform(llm=Settings.llm)
+test_result = verbose_hyde.run("What is machine learning?")
+print(f"Final verbose result: {test_result}")
+
+# 3. Try the most basic possible test
+print("\n3. Most basic HyDE test:")
+print("-" * 50)
+
+basic_hyde = HyDEQueryTransform(llm=Settings.llm)
+basic_result = basic_hyde.run("Paris")
+print(f"Input: 'Paris'")
+print(f"Output: '{basic_result}'")
+print(f"Same as input? {basic_result.strip() == 'Paris'}")
+
+# 4. Check if it's a version issue - try alternative approach
+print("\n4. Alternative HyDE approach:")
+print("-" * 50)
+
+try:
+    # Some versions might need different initialization
+    from llama_index.core.query_engine import TransformQueryEngine
+    from llama_index.core.indices.query.query_transform import HyDEQueryTransform
+    
+    # Try with explicit prompt template
+    hyde_prompt_template = PromptTemplate(
+        "Please write a passage to answer the question\n"
+        "Try to include as many key details as possible\n"
+        "\n"
+        "\n"
+        "Passage:{query_str}\n"
+        "\n"
+        "\n"
+        "Passage:"
+    )
+    
+    alt_hyde = HyDEQueryTransform(
+        llm=Settings.llm,
+        hyde_prompt=hyde_prompt_template
+    )
+    
+    alt_result = alt_hyde.run("What causes rain?")
+    print(f"Alternative approach result: {alt_result}")
+    
+except Exception as e:
+    print(f"Alternative approach failed: {e}")
+
+# 5. Check what happens with different query formats
+print("\n5. Testing different input formats:")
+print("-" * 50)
+
+from llama_index.core.schema import QueryBundle
+
+# Test with QueryBundle vs string
+hyde_test = HyDEQueryTransform(llm=Settings.llm)
+
+string_result = hyde_test.run("test query")
+print(f"String input result: '{string_result}'")
+
+query_bundle = QueryBundle(query_str="test query")
+bundle_result = hyde_test.run(query_bundle)
+print(f"QueryBundle input result: '{bundle_result}'")
+
+# 6. Version and import check
+print("\n6. Environment check:")
+print("-" * 50)
+import llama_index
+print(f"LlamaIndex version: {llama_index.__version__}")
+
+# Check what LLM you're actually using
+print(f"LLM type: {type(Settings.llm)}")
+print(f"LLM model name: {getattr(Settings.llm, 'model', 'Unknown')}")
+
+# 7. Try the nuclear option - completely manual implementation
+print("\n7. Manual HyDE implementation:")
+print("-" * 50)
+
+def manual_hyde(query: str, llm):
+    """Completely manual HyDE to see if the concept works"""
+    prompt = f"""You are an expert writer. Generate a realistic document excerpt that would contain the answer to this question.
+
+Question: {query}
+
+Document excerpt:"""
+    
+    response = llm.complete(prompt)
+    return response.text
+
+manual_result = manual_hyde("What is photosynthesis?", Settings.llm)
+print(f"Manual HyDE result: {manual_result[:150]}...")
+
+# 8. Final diagnostic
+print("\n8. Final diagnostic questions:")
+print("-" * 50)
+print("If all the above show the LLM generating proper responses but HyDE still returns original:")
+print("- What LLM are you using? (OpenAI, Anthropic, local model, etc.)")
+print("- What's your LlamaIndex version?")
+print("- Are there any error messages in the logs?")
+print("- Does the LLM have any special configuration or wrappers?")

archived/query.py

@@ -0,0 +1,110 @@
+# query_topk_prompt.py
+# Run a querry on a vector store
+# 
+# E. M. Furst August 2025
+
+from llama_index.core import (
+    load_index_from_storage,
+    StorageContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.prompts import PromptTemplate
+import os
+
+#
+# Globals
+#
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+
+# Embedding model used in vector store (this should match the one in build.py or equivalent)
+embed_model = HuggingFaceEmbedding(cache_folder="./models",model_name="BAAI/bge-large-en-v1.5")
+
+# LLM model to use in query transform and generation
+llm="command-r7b"
+
+#
+# Custom prompt for the query engine
+#
+PROMPT = PromptTemplate(
+"""You are an expert research assistant. You are given top-ranked writing excerpts (CONTEXT) and a user's QUERY.
+
+Instructions:
+- Base your response *only* on the CONTEXT.
+- The snippets are ordered from most to least relevant—prioritize insights from earlier (higher-ranked) snippets.
+- Aim to reference *as many distinct* relevant files as possible (up to 10).
+- Do not invent or generalize; refer to specific passages or facts only.
+- If a passage only loosely matches, deprioritize it.
+
+Format your answer in two parts:
+
+1. **Summary Theme**  
+   Summarize the dominant theme from the relevant context in a few sentences.
+
+2. **Matching Files**  
+   Make a list of 10 matching files. The format for each should be:  
+   <filename> - 
+   <rationale tied to content. Include date or section hints if available.>
+
+CONTEXT:
+{context_str}
+
+QUERY:
+{query_str}
+
+Now provide the theme and list of matching files."""
+)
+
+#
+# Main program routine
+#
+
+def main():
+    # Use a local model to generate -- in this case using Ollama
+    Settings.llm = Ollama(
+        model=llm,    # First model tested
+        request_timeout=360.0,
+        context_window=8000
+        )
+   
+    # Load embedding model (same as used for vector store)
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Build regular query engine with custom prompt
+    query_engine = index.as_query_engine(
+        similarity_top_k=15,            # pull wide 
+        #response_mode="compact"        # concise synthesis
+        text_qa_template=PROMPT,        # custom prompt
+        # node_postprocessors=[
+        #     SimilarityPostprocessor(similarity_cutoff=0.75)  # keep strong hits; makes result count flexible
+        # ],
+    )  
+
+    # Query
+    while True:
+        q = input("\nEnter a search topic or question (or 'exit'): ").strip()
+        if q.lower() in ("exit", "quit"):
+            break
+        print()
+
+        # Generate the response by querying the engine
+        # This performes the similarity search and then applies the prompt
+        response = query_engine.query(q)
+
+        # Return the query response and source documents
+        print(response.response) 
+
+
+        print("\nSource documents:")
+        for node in response.source_nodes:
+            meta = getattr(node, "metadata", None) or node.node.metadata
+            print(f"{meta.get('file_name')} {meta.get('file_path')} {getattr(node, 'score', None)}")
+
+
+if __name__ == "__main__":
+    main()

archived/query_catalog.py

@@ -0,0 +1,90 @@
+# query.py
+# Run a querry on a vector store
+# This version implements a CATALOG prompt
+#
+# E.M.F. July 2025
+# August 2025 - updated for nd ssearch
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.postprocessor import SimilarityPostprocessor
+from llama_index.core.prompts import PromptTemplate
+
+import logging
+logging.basicConfig(level=logging.DEBUG)
+
+
+CATALOG_PROMPT = PromptTemplate(
+"""You are a research assistant. You’re given journal snippets (CONTEXT) and a user query.
+Your job is NOT to write an essay but to list the best-matching journal files with a 1–2 sentence rationale.
+
+Rules:
+- Use only the CONTEXT; do not invent content.
+- Prefer precise references to passages over generalities.
+- Output exactly:
+  1) A brief one-line summary of the overall theme you detect.
+  2) A bulleted list: **filename** — brief rationale. If available in the snippet, include date or section hints.
+
+CONTEXT:
+{context_str}
+
+QUERY: {query_str}
+
+Now produce the summary line and the bulleted list of matching files."""
+)
+
+# Use a local model to generate
+Settings.llm = Ollama(
+#    model="llama3.1:8B",    # First model tested
+#    model="deepseek-r1:8B", # This model shows its reasoning
+    model="gemma3:1b",
+    request_timeout=360.0,
+    context_window=8000
+    )
+
+def main():
+    # Load embedding model (same as used for vector store)
+    embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage")
+    index = load_index_from_storage(storage_context)
+
+    query_engine = index.as_query_engine(
+        similarity_top_k=10,                      # pull wide (tune to taste)
+        #response_mode="compact",                  # concise synthesis
+        text_qa_template=CATALOG_PROMPT,         # <- custom prompt
+        # node_postprocessors=[
+        #     SimilarityPostprocessor(similarity_cutoff=0.75)  # keep strong hits; makes result count flexible
+        # ],
+    )  
+    
+    # Query
+    while True:
+        q = input("\nEnter your question (or 'exit'): ").strip()
+        if q.lower() in ("exit", "quit"):
+            break
+        print()
+        response = query_engine.query(q)
+
+        # Return the query response and source documents
+        print(response.response) 
+        print("\nSource documents:")
+        for sn in response.source_nodes:
+            meta = getattr(sn, "metadata", None) or sn.node.metadata
+            print(meta.get("file_name"), "---", meta.get("file_path"), getattr(sn, "score", None))
+
+
+if __name__ == "__main__":
+    main()
+
+
+    
+

archived/query_claude_sonnet.py

@@ -0,0 +1,223 @@
+#!/usr/bin/env python3
+"""
+query_topk_prompt_engine.py
+
+Query a vector store with a custom prompt for research assistance.
+Uses BAAI/bge-large-en-v1.5 embeddings and Ollama for generation.
+
+E.M.F. January 2026
+Using Claude Sonnet 4.5 to suggest changes
+"""
+
+import argparse
+import os
+import sys
+from pathlib import Path
+
+from llama_index.core import (
+    Settings,
+    StorageContext,
+    load_index_from_storage,
+)
+from llama_index.core.prompts import PromptTemplate
+from llama_index.core.postprocessor import SimilarityPostprocessor
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+
+
+# Suppress tokenizer parallelism warnings
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+
+# Configuration defaults
+DEFAULT_LLM = "command-r7b"
+DEFAULT_EMBED_MODEL = "BAAI/bge-large-en-v1.5"
+DEFAULT_STORAGE_DIR = "./storage_exp"
+DEFAULT_TOP_K = 15
+DEFAULT_SIMILARITY_CUTOFF = 0.7  # Set to None to disable
+
+
+def get_prompt_template(max_files: int = 10) -> PromptTemplate:
+    """Return the custom prompt template for the query engine."""
+    return PromptTemplate(
+        f"""You are an expert research assistant. You are given top-ranked writing excerpts (CONTEXT) and a user's QUERY.
+
+Instructions:
+- Base your response *only* on the CONTEXT.
+- The snippets are ordered from most to least relevant—prioritize insights from earlier (higher-ranked) snippets.
+- Aim to reference *as many distinct* relevant files as possible (up to {max_files}).
+- Do not invent or generalize; refer to specific passages or facts only.
+- If a passage only loosely matches, deprioritize it.
+
+Format your answer in two parts:
+
+1. **Summary Theme**  
+   Summarize the dominant theme from the relevant context in a few sentences.
+
+2. **Matching Files**  
+   List up to {max_files} matching files. Format each as:  
+   <filename> - <rationale tied to content. Include date or section hints if available.>
+
+CONTEXT:
+{{context_str}}
+
+QUERY:
+{{query_str}}
+
+Now provide the theme and list of matching files."""
+    )
+
+
+def load_models(
+    llm_name: str = DEFAULT_LLM,
+    embed_model_name: str = DEFAULT_EMBED_MODEL,
+    cache_folder: str = "./models",
+    request_timeout: float = 360.0,
+    context_window: int = 8000,
+):
+    """Initialize and configure the LLM and embedding models."""
+    Settings.llm = Ollama(
+        model=llm_name,
+        request_timeout=request_timeout,
+        context_window=context_window,
+    )
+    Settings.embed_model = HuggingFaceEmbedding(
+        cache_folder=cache_folder,
+        model_name=embed_model_name,
+        local_files_only=True,
+    )
+
+
+def load_query_engine(
+    storage_dir: str = DEFAULT_STORAGE_DIR,
+    top_k: int = DEFAULT_TOP_K,
+    similarity_cutoff: float | None = DEFAULT_SIMILARITY_CUTOFF,
+    max_files: int = 10,
+):
+    """Load the vector store and create a query engine with custom prompt."""
+    storage_path = Path(storage_dir)
+    if not storage_path.exists():
+        raise FileNotFoundError(f"Storage directory not found: {storage_dir}")
+
+    storage_context = StorageContext.from_defaults(persist_dir=str(storage_path))
+    index = load_index_from_storage(storage_context)
+
+    # Build postprocessors
+    postprocessors = []
+    if similarity_cutoff is not None:
+        postprocessors.append(SimilarityPostprocessor(similarity_cutoff=similarity_cutoff))
+
+    return index.as_query_engine(
+        similarity_top_k=top_k,
+        text_qa_template=get_prompt_template(max_files),
+        node_postprocessors=postprocessors if postprocessors else None,
+    )
+
+
+def get_node_metadata(node) -> dict:
+    """Safely extract metadata from a source node."""
+    # Handle different node structures in llamaindex
+    if hasattr(node, "metadata") and node.metadata:
+        return node.metadata
+    if hasattr(node, "node") and hasattr(node.node, "metadata"):
+        return node.node.metadata
+    return {}
+
+
+def print_results(response):
+    """Print the query response and source documents."""
+    print("\n" + "=" * 60)
+    print("RESPONSE")
+    print("=" * 60 + "\n")
+    print(response.response)
+
+    print("\n" + "=" * 60)
+    print("SOURCE DOCUMENTS")
+    print("=" * 60 + "\n")
+
+    for i, node in enumerate(response.source_nodes, 1):
+        meta = get_node_metadata(node)
+        score = getattr(node, "score", None)
+        file_name = meta.get("file_name", "Unknown")
+        file_path = meta.get("file_path", "Unknown")
+        score_str = f"{score:.3f}" if score is not None else "N/A"
+        print(f"{i:2}. [{score_str}] {file_name}")
+        print(f"    Path: {file_path}")
+
+
+def parse_args():
+    """Parse command line arguments."""
+    parser = argparse.ArgumentParser(
+        description="Query a vector store with a custom research assistant prompt.",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  python query_topk_prompt_engine.py "What themes appear in the documents?"
+  python query_topk_prompt_engine.py --top-k 20 --llm llama3.1:8B "Find references to machine learning"
+        """,
+    )
+    parser.add_argument("query", nargs="+", help="The query text")
+    parser.add_argument(
+        "--llm",
+        default=DEFAULT_LLM,
+        help=f"Ollama model to use for generation (default: {DEFAULT_LLM})",
+    )
+    parser.add_argument(
+        "--storage-dir",
+        default=DEFAULT_STORAGE_DIR,
+        help=f"Path to the vector store (default: {DEFAULT_STORAGE_DIR})",
+    )
+    parser.add_argument(
+        "--top-k",
+        type=int,
+        default=DEFAULT_TOP_K,
+        help=f"Number of similar documents to retrieve (default: {DEFAULT_TOP_K})",
+    )
+    parser.add_argument(
+        "--similarity-cutoff",
+        type=float,
+        default=DEFAULT_SIMILARITY_CUTOFF,
+        help=f"Minimum similarity score (default: {DEFAULT_SIMILARITY_CUTOFF}, use 0 to disable)",
+    )
+    parser.add_argument(
+        "--max-files",
+        type=int,
+        default=10,
+        help="Maximum files to list in response (default: 10)",
+    )
+    return parser.parse_args()
+
+
+def main():
+    args = parse_args()
+
+    # Handle similarity cutoff of 0 as "disabled"
+    similarity_cutoff = args.similarity_cutoff if args.similarity_cutoff > 0 else None
+
+    try:
+        print(f"Loading models (LLM: {args.llm})...")
+        load_models(llm_name=args.llm)
+
+        print(f"Loading index from {args.storage_dir}...")
+        query_engine = load_query_engine(
+            storage_dir=args.storage_dir,
+            top_k=args.top_k,
+            similarity_cutoff=similarity_cutoff,
+            max_files=args.max_files,
+        )
+
+        query_text = " ".join(args.query)
+        print(f"Querying: {query_text[:100]}{'...' if len(query_text) > 100 else ''}")
+
+        response = query_engine.query(query_text)
+        print_results(response)
+
+    except FileNotFoundError as e:
+        print(f"Error: {e}", file=sys.stderr)
+        sys.exit(1)
+    except Exception as e:
+        print(f"Error during query: {e}", file=sys.stderr)
+        raise
+
+
+if __name__ == "__main__":
+    main()

archived/query_exp.py

@@ -0,0 +1,106 @@
+# query_topk.py
+# Run a querry on a vector store
+# 
+# This verison implements a prompt and uses the build_exp.py vector store
+# It is based on query_topk.py
+# It uses 10 top-k results and a custom prompt
+# The next version after this is query_rewrite.py
+# build_exp.py modifies the chunk size and overlap form the orignal build.py
+#
+# E.M.F. August 2025
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.prompts import PromptTemplate
+
+# LLM model to use in query transform and generation
+llm="llama3.1:8B"
+# Other models tried:
+# llm="deepseek-r1:8B"
+# llm="gemma3:1b"
+
+
+# Custom prompt for the query engine
+PROMPT = PromptTemplate(
+"""You are an expert research assistant. You are given top-ranked journal excerpts (CONTEXT) and a user’s QUERY.
+
+Instructions:
+- Base your response *only* on the CONTEXT.
+- The snippets are ordered from most to least relevant—prioritize insights from earlier (higher-ranked) snippets.
+- Aim to reference *as many distinct* relevant files as possible (up to 10).
+- Do not invent or generalize; refer to specific passages or facts only.
+- If a passage only loosely matches, deprioritize it.
+
+Format your answer in two parts:
+
+1. **Summary Theme**  
+   Summarize the dominant theme from the relevant context.
+
+2. **Matching Files**  
+   Make a bullet list of 10. The format for each should be:  
+   **<filename>** — <rationale tied to content. Include date or section hints if available.>
+
+CONTEXT:
+{context_str}
+
+QUERY:
+{query_str}
+
+Now provide the theme and list of matching files."""
+)
+
+#
+# Main program routine
+#
+
+def main():
+    # Use a local model to generate
+    Settings.llm = Ollama(
+        model=llm,    # First model tested
+        request_timeout=360.0,
+        context_window=8000
+        )
+   
+    # Load embedding model (same as used for vector store)
+    embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Build regular query engine with custom prompt
+    query_engine = index.as_query_engine(
+        similarity_top_k=10,            # pull wide 
+        #response_mode="compact"        # concise synthesis
+        text_qa_template=PROMPT,        # custom prompt
+        # node_postprocessors=[
+        #     SimilarityPostprocessor(similarity_cutoff=0.75)  # keep strong hits; makes result count flexible
+        # ],
+    )  
+
+    # Query
+    while True:
+        q = input("\nEnter your question (or 'exit'): ").strip()
+        if q.lower() in ("exit", "quit"):
+            break
+        print()
+
+        response = query_engine.query(q)
+
+        # Return the query response and source documents
+        print(response.response) 
+        print("\nSource documents:")
+        for node in response.source_nodes:
+            meta = getattr(node, "metadata", None) or node.node.metadata
+            print(meta.get("file_name"), "---", meta.get("file_path"), getattr(node, "score", None))
+
+
+if __name__ == "__main__":
+    main()

archived/query_multitool.py

@@ -0,0 +1,106 @@
+"""
+This is output generated by ChatG to implement a new regex + vector search engine
+"""
+
+from __future__ import annotations
+from typing import List, Iterable
+import json, re
+
+from llama_index.core import VectorStoreIndex, Settings
+from llama_index.core.node_parser import SentenceSplitter
+from llama_index.core.schema import NodeWithScore, QueryBundle
+from llama_index.core.retrievers import BaseRetriever, EnsembleRetriever
+from llama_index.core.query_engine import RetrieverQueryEngine
+from llama_index.core import Document
+
+# 0) Configure your LLM + embeddings up front
+# Example: Settings.llm = <your Command-R wrapper> ; Settings.embed_model = <your embeddings>
+# (You can also pass an llm explicitly into the retriever if you prefer.)
+# Settings.llm.complete("hello") should work in v0.10+
+
+# 1) Prepare nodes once (so regex + vector share the same chunks)
+def build_nodes(docs: List[Document], chunk_size: int = 1024, overlap: int = 100):
+    splitter = SentenceSplitter(chunk_size=chunk_size, chunk_overlap=overlap)
+    return splitter.get_nodes_from_documents(docs)
+
+# 2) LLM-guided regex retriever
+class RegexRetriever(BaseRetriever):
+    def __init__(self, nodes: Iterable, llm=None, top_k: int = 5, flags=re.IGNORECASE):
+        super().__init__()
+        self._nodes = list(nodes)
+        self._llm = llm or Settings.llm
+        self._top_k = top_k
+        self._flags = flags
+
+    def _extract_terms(self, query: str) -> List[str]:
+        """Ask the LLM for up to ~6 distinctive keywords/short phrases. Return a list of strings."""
+        prompt = f"""
+You extract search terms for a boolean/regex search.
+Query: {query}
+
+Rules:
+- Return ONLY a JSON array of strings.
+- Use up to 6 concise keywords/short phrases.
+- Keep phrases short (<= 3 words).
+- Avoid stopwords, punctuation, and generic terms.
+- No explanations, no extra text.
+"""
+        raw = self._llm.complete(prompt).text.strip()
+        try:
+            terms = json.loads(raw)
+            # basic sanitize
+            terms = [t for t in terms if isinstance(t, str) and t.strip()]
+        except Exception:
+            # simple fall-back if JSON parse fails
+            terms = [w for w in re.findall(r"\w+", query) if len(w) > 2][:6]
+        return terms[:6]
+
+    def _compile_patterns(self, terms: List[str]) -> List[re.Pattern]:
+        pats = []
+        for t in terms:
+            # Escape user/LLM output, add word boundaries; allow whitespace inside short phrases
+            escaped = re.escape(t)
+            # turn '\ ' (escaped space) back into '\s+' to match any whitespace in phrases
+            escaped = escaped.replace(r"\ ", r"\s+")
+            pats.append(re.compile(rf"\b{escaped}\b", self._flags))
+        return pats
+
+    def _retrieve(self, query_bundle: QueryBundle) -> List[NodeWithScore]:
+        terms = self._extract_terms(query_bundle.query_str)
+        patterns = self._compile_patterns(terms)
+
+        scored: List[tuple] = []
+        for n in self._nodes:
+            txt = n.get_content(metadata_mode="all")
+            hits = 0
+            for p in patterns:
+                if p.search(txt):
+                    hits += 1
+            if hits:
+                # simple score = number of distinct term hits (you can weight phrase vs single word if you like)
+                scored.append((n, float(hits)))
+
+        scored.sort(key=lambda x: x[1], reverse=True)
+        return [NodeWithScore(node=n, score=s) for n, s in scored[: self._top_k]]
+
+# 3) Wire it all together
+def build_query_engine(docs: List[Document], k_vec=5, k_regex=5, weights=(0.7, 0.3)):
+    nodes = build_nodes(docs)
+    # Vector index over the SAME nodes
+    vindex = VectorStoreIndex(nodes)
+
+    vector_ret = vindex.as_retriever(similarity_top_k=k_vec)
+    regex_ret = RegexRetriever(nodes, top_k=k_regex)
+
+    ensemble = EnsembleRetriever(
+        retrievers=[vector_ret, regex_ret],
+        weights=list(weights),       # tune this: more recall from regex? bump weight on regex
+        # uses Reciprocal Rank Fusion by default
+    )
+
+    return RetrieverQueryEngine(retriever=ensemble)
+
+# 4) Use it
+# docs = SimpleDirectoryReader("data").load_data()
+# qe = build_query_engine(docs)
+# print(qe.query("Find entries with strong feelings of depression."))

archived/query_rewrite_hyde.py

@@ -0,0 +1,126 @@
+# query_rewrite_hyde.py
+# Run a querry on a vector store
+# 
+# Latest experiment to include query rewriting using HyDE (Hypothetial Document Embeddings)
+# The goal is to reduce the semantic gap between the query and the indexed documents
+# This verison implements a prompt and uses the build_exp.py vector store
+# Based on query_exp.py
+#
+# E.M.F. July 2025
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.prompts import PromptTemplate
+from llama_index.core.indices.query.query_transform import HyDEQueryTransform
+from llama_index.core.query_engine.transform_query_engine import TransformQueryEngine
+import os
+
+# Globals
+
+# Embedding model used in vector store (this should match the one in build_exp.py or equivalent)
+# embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+embed_model = HuggingFaceEmbedding(cache_folder="./models",model_name="BAAI/bge-large-en-v1.5")
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+
+# LLM model to use in query transform and generation
+llm="llama3.1:8B"
+# Other models tried:
+# llm="deepseek-r1:8B"
+# llm="gemma3:1b"
+
+# Custom prompt for the query engine
+PROMPT = PromptTemplate(
+"""You are an expert research assistant. You are given top-ranked writing excerpts (CONTEXT) and a user's QUERY.
+
+Instructions:
+- Base your response *only* on the CONTEXT.
+- The snippets are ordered from most to least relevant—prioritize insights from earlier (higher-ranked) snippets.
+- Aim to reference *as many distinct* relevant files as possible (up to 10).
+- Do not invent or generalize; refer to specific passages or facts only.
+- If a passage only loosely matches, deprioritize it.
+
+Format your answer in two parts:
+
+1. **Summary Theme**  
+   Summarize the dominant theme from the relevant context in a few sentences.
+
+2. **Matching Files**  
+   Make a list of 10 matching files. The format for each should be:  
+   <filename> — <rationale tied to content. Include date or section hints if available.>
+
+CONTEXT:
+{context_str}
+
+QUERY:
+{query_str}
+
+Now provide the theme and list of matching files."""
+)
+
+#
+# Main program routine
+#
+
+def main():
+    # Use a local model to generate
+    Settings.llm = Ollama(
+        model=llm,    # First model tested
+        request_timeout=360.0,
+        context_window=8000
+        )
+   
+    # Load embedding model (same as used for vector store)
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Build regular query engine with custom prompt
+    base_query_engine = index.as_query_engine(
+        similarity_top_k=15,            # pull wide 
+        #response_mode="compact"        # concise synthesis
+        text_qa_template=PROMPT,        # custom prompt
+        # node_postprocessors=[
+        #     SimilarityPostprocessor(similarity_cutoff=0.75)  # keep strong hits; makes result count flexible
+        # ],
+    )  
+
+    # HyDE is "Hypothetical Document Embeddings"
+    # It generates a hypothetical document based on the query
+    # and uses that to augment the query
+    # Here we include the original query as well
+    # I get better similarity values with include_orignal=True
+    hyde_transform = HyDEQueryTransform(llm=Settings.llm,include_original=True)
+
+    # Query
+    while True:
+        q = input("\nEnter a search topic or question (or 'exit'): ").strip()
+        if q.lower() in ("exit", "quit"):
+            break
+        print()
+
+        # The query uses a HyDE trasformation to rewrite the query
+        query_engine = TransformQueryEngine(base_query_engine, query_transform=hyde_transform)
+
+        # Generate the response by querying the engine
+        # This performes the similarity search and then applies the prompt
+        response = query_engine.query(q)
+
+        # Return the query response and source documents
+        print(response.response) 
+
+        print("\nSource documents:")
+        for node in response.source_nodes:
+            meta = getattr(node, "metadata", None) or node.node.metadata
+            print(meta.get("file_name"), "---", meta.get("file_path"), getattr(node, "score", None))
+
+
+if __name__ == "__main__":
+    main()

archived/query_topk.py

@@ -0,0 +1,58 @@
+# query_topk.py
+# Run a querry on a vector store
+#
+# E.M.F. July 2025
+# August 2025 - updated for nd ssearch
+# this version uses top-k similarity
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+
+# Use a local model to generate
+Settings.llm = Ollama(
+    model="llama3.1:8B",    # First model tested
+#    model="deepseek-r1:8B", # This model shows its reasoning
+#    model="gemma3:1b",
+    request_timeout=360.0,
+    context_window=8000
+    )
+
+def main():
+    # Load embedding model (same as used for vector store)
+    embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage")
+    index = load_index_from_storage(storage_context)
+
+    query_engine = index.as_query_engine(similarity_top_k=5)
+
+    # Query
+    while True:
+        q = input("\nEnter your question (or 'exit'): ").strip()
+        if q.lower() in ("exit", "quit"):
+            break
+        print()
+        response = query_engine.query(q)
+
+        # Return the query response and source documents
+        print(response.response) 
+        print("\nSource documents:")
+        for node in response.source_nodes:
+            meta = getattr(node, "metadata", None) or node.node.metadata
+            print(meta.get("file_name"), "---", meta.get("file_path"), getattr(node, "score", None))
+
+
+if __name__ == "__main__":
+    main()
+
+
+    
+

archived/query_topk_prompt.py

@@ -0,0 +1,123 @@
+# query_topk_prompt.py
+# Run a querry on a vector store
+# 
+# This version from query_rewrite_hyde.py, but removing hyde and using a custom prompt
+# This verison implements a prompt and uses the build_exp.py vector store with BAAI/bge-large-en-v1.5
+# Based on query_exp.py->query_topk.py->query_rewrite_hyde.py
+# The results are as good as with HyDE.
+#
+# E.M.F. August 2025
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.prompts import PromptTemplate
+import os
+
+#
+# Globals
+#
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+
+# Embedding model used in vector store (this should match the one in build_exp.py or equivalent)
+# embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+embed_model = HuggingFaceEmbedding(cache_folder="./models",model_name="BAAI/bge-large-en-v1.5")
+
+# LLM model to use in query transform and generation
+# command-r7b generates about as quickly as llama3.1:8B, but provides results that stick better
+# to the provided context
+llm="command-r7b"
+# Other models tried:
+#llm="llama3.1:8B"
+#llm="deepseek-r1:8B"
+#llm="gemma3:1b"
+
+#
+# Custom prompt for the query engine
+#
+PROMPT = PromptTemplate(
+"""You are an expert research assistant. You are given top-ranked writing excerpts (CONTEXT) and a user's QUERY.
+
+Instructions:
+- Base your response *only* on the CONTEXT.
+- The snippets are ordered from most to least relevant—prioritize insights from earlier (higher-ranked) snippets.
+- Aim to reference *as many distinct* relevant files as possible (up to 10).
+- Do not invent or generalize; refer to specific passages or facts only.
+- If a passage only loosely matches, deprioritize it.
+
+Format your answer in two parts:
+
+1. **Summary Theme**  
+   Summarize the dominant theme from the relevant context in a few sentences.
+
+2. **Matching Files**  
+   Make a list of 10 matching files. The format for each should be:  
+   <filename> - 
+   <rationale tied to content. Include date or section hints if available.>
+
+CONTEXT:
+{context_str}
+
+QUERY:
+{query_str}
+
+Now provide the theme and list of matching files."""
+)
+
+#
+# Main program routine
+#
+
+def main():
+    # Use a local model to generate -- in this case using Ollama
+    Settings.llm = Ollama(
+        model=llm,    # First model tested
+        request_timeout=360.0,
+        context_window=8000
+        )
+   
+    # Load embedding model (same as used for vector store)
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Build regular query engine with custom prompt
+    query_engine = index.as_query_engine(
+        similarity_top_k=15,            # pull wide 
+        #response_mode="compact"        # concise synthesis
+        text_qa_template=PROMPT,        # custom prompt
+        # node_postprocessors=[
+        #     SimilarityPostprocessor(similarity_cutoff=0.75)  # keep strong hits; makes result count flexible
+        # ],
+    )  
+
+    # Query
+    while True:
+        q = input("\nEnter a search topic or question (or 'exit'): ").strip()
+        if q.lower() in ("exit", "quit"):
+            break
+        print()
+
+        # Generate the response by querying the engine
+        # This performes the similarity search and then applies the prompt
+        response = query_engine.query(q)
+
+        # Return the query response and source documents
+        print(response.response) 
+
+
+        print("\nSource documents:")
+        for node in response.source_nodes:
+            meta = getattr(node, "metadata", None) or node.node.metadata
+            print(f"{meta.get('file_name')} {meta.get('file_path')} {getattr(node, 'score', None)}")
+
+
+if __name__ == "__main__":
+    main()

archived/query_topk_prompt_dw.py

@@ -0,0 +1,134 @@
+# query_topk_prompt_dw.py
+# Run a querry on a vector store
+# 
+# This version from query_rewrite_hyde.py, but removing hyde and using a custom prompt
+# This verison implements a prompt and uses the build_exp.py vector store with BAAI/bge-large-en-v1.5
+# Based on query_exp.py->query_topk.py->query_rewrite_hyde.py
+# The results are as good as with HyDE.
+# Modified for terminal output (132 columns)
+#
+# E.M.F. August 2025
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.prompts import PromptTemplate
+import os
+import sys
+import textwrap
+
+# Print wrapping for terminal output
+class Wrap80:
+    def write(self, text):
+        for line in text.splitlines():
+            sys.__stdout__.write(textwrap.fill(line, width=131) + "\n")
+    def flush(self):
+        sys.__stdout__.flush()
+
+sys.stdout = Wrap80()
+
+#
+# Globals
+#
+
+# Embedding model used in vector store (this should match the one in build_exp.py or equivalent)
+# embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+embed_model = HuggingFaceEmbedding(cache_folder="./models",model_name="BAAI/bge-large-en-v1.5")
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+
+# LLM model to use in query transform and generation
+# command-r7b generates about as quickly as llama3.1:8B, but provides results that stick better
+# to the provided context
+llm="command-r7b"
+# Other models tried:
+#llm="llama3.1:8B"
+# llm="deepseek-r1:8B"
+# llm="gemma3:1b"
+
+# Custom prompt for the query engine
+PROMPT = PromptTemplate(
+"""You are an expert research assistant. You are given top-ranked writing excerpts (CONTEXT) and a user's QUERY.
+
+Instructions:
+- Base your response *only* on the CONTEXT.
+- The snippets are ordered from most to least relevant—prioritize insights from earlier (higher-ranked) snippets.
+- Aim to reference *as many distinct* relevant files as possible (up to 10).
+- Do not invent or generalize; refer to specific passages or facts only.
+- If a passage only loosely matches, deprioritize it.
+
+Format your answer in two parts:
+
+1. **Summary Theme**  
+   Summarize the dominant theme from the relevant context in a few sentences.
+
+2. **Matching Files**  
+   Make a list of 10 matching files. The format for each should be:  
+   <filename> - 
+   <rationale tied to content. Include date or section hints if available.>
+
+CONTEXT:
+{context_str}
+
+QUERY:
+{query_str}
+
+Now provide the theme and list of matching files."""
+)
+
+#
+# Main program routine
+#
+
+def main():
+    # Use a local model to generate
+    Settings.llm = Ollama(
+        model=llm,    # First model tested
+        request_timeout=360.0,
+        context_window=8000
+        )
+   
+    # Load embedding model (same as used for vector store)
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Build regular query engine with custom prompt
+    query_engine = index.as_query_engine(
+        similarity_top_k=15,            # pull wide 
+        #response_mode="compact"        # concise synthesis
+        text_qa_template=PROMPT,        # custom prompt
+        # node_postprocessors=[
+        #     SimilarityPostprocessor(similarity_cutoff=0.75)  # keep strong hits; makes result count flexible
+        # ],
+    )  
+
+    # Query
+    while True:
+        q = input("\nEnter a search topic or question (or 'exit'): ").strip()
+        if q.lower() in ("exit", "quit"):
+            break
+        print()
+
+        # Generate the response by querying the engine
+        # This performes the similarity search and then applies the prompt
+        response = query_engine.query(q)
+
+        # Return the query response and source documents
+        print(response.response) 
+
+
+        print("\nSource documents:")
+        for node in response.source_nodes:
+            meta = getattr(node, "metadata", None) or node.node.metadata
+            print(f"{meta.get('file_name')} {meta.get('file_path')} {getattr(node, 'score', None)}", end="")
+
+
+if __name__ == "__main__":
+    main()

archived/query_topk_prompt_engine.py

@@ -0,0 +1,123 @@
+# query_topk_prompt_engine.py
+# Run a querry on a vector store
+# 
+# This version is query_topk_prompt.py but the query is passed though the command line.
+#
+# Implements a prompt and uses the build_exp.py vector store with BAAI/bge-large-en-v1.5
+# Based on query_exp.py->query_topk.py
+#
+# E.M.F. August 2025
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.prompts import PromptTemplate
+import os
+import sys
+
+#
+# Globals
+#
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+
+# Embedding model used in vector store (this should match the one in build_exp.py or equivalent)
+# embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+embed_model = HuggingFaceEmbedding(cache_folder="./models",model_name="BAAI/bge-large-en-v1.5",local_files_only=True)
+
+# LLM model to use in query transform and generation
+# command-r7b generates about as quickly as llama3.1:8B, but provides results that stick better
+# to the provided context
+llm="command-r7b"
+# Other models tried:
+#llm="llama3.1:8B"
+#llm="deepseek-r1:8B"
+#llm="gemma3:1b"
+
+#
+# Custom prompt for the query engine
+#
+PROMPT = PromptTemplate(
+"""You are an expert research assistant. You are given top-ranked writing excerpts (CONTEXT) and a user's QUERY.
+
+Instructions:
+- Base your response *only* on the CONTEXT.
+- The snippets are ordered from most to least relevant—prioritize insights from earlier (higher-ranked) snippets.
+- Aim to reference *as many distinct* relevant files as possible (up to 10).
+- Do not invent or generalize; refer to specific passages or facts only.
+- If a passage only loosely matches, deprioritize it.
+
+Format your answer in two parts:
+
+1. **Summary Theme**  
+   Summarize the dominant theme from the relevant context in a few sentences.
+
+2. **Matching Files**  
+   Make a list of 10 matching files. The format for each should be:  
+   <filename> - 
+   <rationale tied to content. Include date or section hints if available.>
+
+CONTEXT:
+{context_str}
+
+QUERY:
+{query_str}
+
+Now provide the theme and list of matching files."""
+)
+
+#
+# Main program routine
+#
+
+def main():
+    # Use a local model to generate -- in this case using Ollama
+    Settings.llm = Ollama(
+        model=llm,    # First model tested
+        request_timeout=360.0,
+        context_window=8000
+        )
+   
+    # Load embedding model (same as used for vector store)
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Build regular query engine with custom prompt
+    query_engine = index.as_query_engine(
+        similarity_top_k=15,            # pull wide 
+        #response_mode="compact"        # concise synthesis
+        text_qa_template=PROMPT,        # custom prompt
+        # node_postprocessors=[
+        #     SimilarityPostprocessor(similarity_cutoff=0.75)  # keep strong hits; makes result count flexible
+        # ],
+    )  
+
+    # Query
+    if len(sys.argv) < 2:
+        print("Usage: python query.py QUERY_TEXT")
+        sys.exit(1)
+    q = " ".join(sys.argv[1:])    
+
+    # Generate the response by querying the engine
+    # This performes the similarity search and then applies the prompt
+    response = query_engine.query(q)
+
+    # Return the query response and source documents
+    print("\nResponse:\n")
+    print(response.response) 
+
+    print("\nSource documents:")
+    for node in response.source_nodes:
+        meta = getattr(node, "metadata", None) or node.node.metadata
+        print(f"{meta.get('file_name')}  {meta.get('file_path')}  {getattr(node, 'score', None):.3f}")
+
+
+if __name__ == "__main__":
+    main()

archived/query_topk_prompt_engine_v3.py

@@ -0,0 +1,136 @@
+# query_topk_prompt_engine_v3.py
+# Run a query on a vector store with cross-encoder re-ranking
+#
+# Based on v2. Adds a cross-encoder re-ranking step:
+#   1. Retrieve top-30 chunks via vector similarity (bi-encoder, fast)
+#   2. Re-rank to top-15 using a cross-encoder (slower but more accurate)
+#   3. Pass re-ranked chunks to LLM for synthesis
+#
+# The cross-encoder scores each (query, chunk) pair jointly, which captures
+# nuance that bi-encoder dot-product similarity misses.
+#
+# E.M.F. February 2026
+
+# Environment vars must be set before importing huggingface/transformers
+# libraries, because huggingface_hub.constants evaluates HF_HUB_OFFLINE
+# at import time.
+import os
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+os.environ["SENTENCE_TRANSFORMERS_HOME"] = "./models"
+os.environ["HF_HUB_OFFLINE"] = "1"
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.prompts import PromptTemplate
+from llama_index.core.postprocessor import SentenceTransformerRerank
+import sys
+
+#
+# Globals
+#
+
+# Embedding model used in vector store (must match build_exp_claude.py)
+EMBED_MODEL = HuggingFaceEmbedding(cache_folder="./models", model_name="BAAI/bge-large-en-v1.5", local_files_only=True)
+
+# LLM model for generation
+llm = "command-r7b"
+
+# Cross-encoder model for re-ranking (cached in ./models/)
+#RERANK_MODEL = "cross-encoder/ms-marco-MiniLM-L-6-v2"
+RERANK_MODEL = "cross-encoder/ms-marco-MiniLM-L-12-v2"
+#RERANK_MODEL = "cross-encoder/stsb-roberta-base"
+#RERANK_MODEL = "BAAI/bge-reranker-v2-m3"
+RERANK_TOP_N = 15   # keep top 15 after re-ranking
+RETRIEVE_TOP_K = 30  # retrieve wider pool for re-ranker to work with
+
+#
+# Custom prompt for the query engine - Version 3
+#
+# Adapted for re-ranked context: every excerpt below has been scored for
+# relevance by a cross-encoder, so even lower-ranked ones are worth examining.
+# The prompt encourages the LLM to draw from all provided excerpts and to
+# note what each distinct file contributes rather than collapsing onto one.
+#
+PROMPT = PromptTemplate(
+"""You are a precise research assistant analyzing excerpts from a personal journal collection.
+Every excerpt below has been selected and ranked for relevance to the query.
+
+CONTEXT (ranked by relevance):
+{context_str}
+
+QUERY:
+{query_str}
+
+Instructions:
+- Answer ONLY using information explicitly present in the CONTEXT above
+- Examine ALL provided excerpts, not just the top few -- each one was selected for relevance
+- Be specific: quote or closely paraphrase key passages and cite their file names
+- When multiple files touch on the query, note what each one contributes
+- If the context doesn't contain enough information to answer fully, say so
+
+Your response should:
+1. Directly answer the query, drawing on as many relevant excerpts as possible
+2. Reference specific files and their content (e.g., "In <filename>, ...")
+3. End with a list of all files that contributed to your answer, with a brief note on each
+
+If the context is insufficient, explain what's missing."""
+)
+
+#
+# Main program routine
+#
+
+def main():
+    # Use a local model to generate -- in this case using Ollama
+    Settings.llm = Ollama(
+        model=llm,
+        request_timeout=360.0,
+        context_window=8000
+    )
+
+    # Load embedding model (same as used for vector store)
+    Settings.embed_model = EMBED_MODEL
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Cross-encoder re-ranker
+    reranker = SentenceTransformerRerank(
+        model=RERANK_MODEL,
+        top_n=RERANK_TOP_N,
+    )
+
+    # Build query engine: retrieve wide (top-30), re-rank to top-15, then synthesize
+    query_engine = index.as_query_engine(
+        similarity_top_k=RETRIEVE_TOP_K,
+        text_qa_template=PROMPT,
+        node_postprocessors=[reranker],
+    )
+
+    # Query
+    if len(sys.argv) < 2:
+        print("Usage: python query_topk_prompt_engine_v3.py QUERY_TEXT")
+        sys.exit(1)
+    q = " ".join(sys.argv[1:])
+
+    # Generate the response by querying the engine
+    response = query_engine.query(q)
+
+    # Return the query response and source documents
+    print("\nResponse:\n")
+    print(response.response)
+
+    print("\nSource documents:")
+    for node in response.source_nodes:
+        meta = getattr(node, "metadata", None) or node.node.metadata
+        print(f"{meta.get('file_name')}  {meta.get('file_path')}  {getattr(node, 'score', None):.3f}")
+
+
+if __name__ == "__main__":
+    main()

archived/query_tree.py

@@ -0,0 +1,60 @@
+# query_tree.py
+#
+# Run a querry on a vector store
+# This is to test summarization using a tree-summarize response mode
+# It doesn't work very well, perhaps because of the struture of the data
+#  
+# E.M.F. August 2025
+
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+
+# Use a local model to generate
+Settings.llm = Ollama(
+    model="llama3.1:8B",    # First model tested
+#    model="deepseek-r1:8B", # This model shows its reasoning
+#    model="gemma3:1b",
+    request_timeout=360.0,
+    context_window=8000
+    )
+
+def main():
+    # Load embedding model (same as used for vector store)
+    embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage")
+    index = load_index_from_storage(storage_context)
+
+    query_engine = index.as_query_engine(response_mode="tree_summarize")
+
+    # Query
+    while True:
+        q = input("\nEnter your question (or 'exit'): ").strip()
+        if q.lower() in ("exit", "quit"):
+            break
+        print()
+        response = query_engine.query("<summarization_query>")
+
+        # Return the query response and source documents
+        print(response.response) 
+        print("\nSource documents:")
+        for node in response.source_nodes:
+            meta = getattr(node, "metadata", None) or node.node.metadata
+            print(meta.get("file_name"), "---", meta.get("file_path"), getattr(node, "score", None))
+
+
+if __name__ == "__main__":
+    main()
+
+
+    
+

archived/retrieve_raw.py

@@ -0,0 +1,97 @@
+# retrieve_raw.py
+# Verbatim chunk retrieval: vector search + cross-encoder re-ranking, no LLM.
+#
+# Returns the top re-ranked chunks with their full text, file metadata, and
+# scores. Useful for browsing source material directly and verifying what
+# the RAG pipeline retrieves before LLM synthesis.
+#
+# Uses the same vector store, embedding model, and re-ranker as
+# query_topk_prompt_engine_v3.py, but skips the LLM step entirely.
+#
+# E.M.F. February 2026
+
+# Environment vars must be set before importing huggingface/transformers
+# libraries, because huggingface_hub.constants evaluates HF_HUB_OFFLINE
+# at import time.
+import os
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+os.environ["SENTENCE_TRANSFORMERS_HOME"] = "./models"
+os.environ["HF_HUB_OFFLINE"] = "1"
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.core.postprocessor import SentenceTransformerRerank
+import sys
+import textwrap
+
+#
+# Globals
+#
+
+# Embedding model (must match build_exp_claude.py)
+EMBED_MODEL = HuggingFaceEmbedding(cache_folder="./models", model_name="BAAI/bge-large-en-v1.5", local_files_only=True)
+
+# Cross-encoder model for re-ranking (cached in ./models/)
+RERANK_MODEL = "cross-encoder/ms-marco-MiniLM-L-12-v2"
+RERANK_TOP_N = 15
+RETRIEVE_TOP_K = 30
+
+# Output formatting
+WRAP_WIDTH = 80
+
+
+def main():
+    # No LLM needed -- set embed model only
+    Settings.embed_model = EMBED_MODEL
+
+    # Load persisted vector store
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Build retriever (vector search only, no query engine / LLM)
+    retriever = index.as_retriever(similarity_top_k=RETRIEVE_TOP_K)
+
+    # Cross-encoder re-ranker
+    reranker = SentenceTransformerRerank(
+        model=RERANK_MODEL,
+        top_n=RERANK_TOP_N,
+    )
+
+    # Query
+    if len(sys.argv) < 2:
+        print("Usage: python retrieve_raw.py QUERY_TEXT")
+        sys.exit(1)
+    q = " ".join(sys.argv[1:])
+
+    # Retrieve and re-rank
+    nodes = retriever.retrieve(q)
+    reranked = reranker.postprocess_nodes(nodes, query_str=q)
+
+    # Output
+    print(f"\nQuery: {q}")
+    print(f"Retrieved {len(nodes)} chunks, re-ranked to top {len(reranked)}\n")
+
+    for i, node in enumerate(reranked, 1):
+        meta = getattr(node, "metadata", None) or node.node.metadata
+        score = getattr(node, "score", None)
+        file_name = meta.get("file_name", "unknown")
+        text = node.get_content()
+
+        print("="*WRAP_WIDTH)
+        print(f"=== [{i}] {file_name}  (score: {score:.3f}) ")
+        print("="*WRAP_WIDTH)
+        # Wrap text for readability
+        for line in text.splitlines():
+            if line.strip():
+                print(textwrap.fill(line, width=WRAP_WIDTH))
+            else:
+                print()
+        print()
+
+
+if __name__ == "__main__":
+    main()

archived/vs_metrics.py

@@ -0,0 +1,27 @@
+# vs_metrics.py
+# Quantify vector store properties and performance
+#
+# E.M.F. August 2025
+
+# Read in vector store
+
+# What are properties of the vector store?
+# - number of vectors
+# - distribution of distances
+# - clustering?
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+
+# Load embedding model (same as used for vector store)
+embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+Settings.embed_model = embed_model
+
+# Load persisted vector store + metadata
+storage_context = StorageContext.from_defaults(persist_dir="./storage")
+index = load_index_from_storage(storage_context)

deploy_public.sh

@@ -0,0 +1,100 @@
+#!/bin/bash
+# deploy_public.sh — Deploy public files from main to the Forgejo public branch
+#
+# Usage: ./deploy_public.sh ["optional commit message"]
+#
+# Checks out the public branch, updates it with public files from main,
+# generates a public README (stripping private sections), commits if
+# anything changed, and pushes to origin. Then switches back to main.
+#
+# On first run (no public branch exists), creates an orphan branch.
+#
+# E.M.F. February 2026
+
+set -e
+
+# --- Configuration ---
+
+# Files to include on the public branch
+PUBLIC_FILES=(
+    build_store.py
+    query_hybrid.py
+    retrieve.py
+    search_keywords.py
+    run_query.sh
+    clippings_search/build_clippings.py
+    clippings_search/retrieve_clippings.py
+    requirements.txt
+    .gitignore
+    LICENSE
+)
+
+REMOTE="origin"
+BRANCH="public"
+COMMIT_MSG="${1:-Update public branch from main}"
+
+# --- Safety checks ---
+
+CURRENT=$(git branch --show-current)
+if [ "$CURRENT" != "main" ]; then
+    echo "Error: must be on main branch (currently on $CURRENT)"
+    exit 1
+fi
+
+if ! git diff --quiet HEAD 2>/dev/null; then
+    echo "Error: uncommitted changes on main. Commit or stash first."
+    exit 1
+fi
+
+MAIN_HEAD=$(git rev-parse --short HEAD)
+
+# --- Build public branch ---
+
+echo "Deploying main ($MAIN_HEAD) -> $BRANCH..."
+
+# Check out public branch, or create orphan if it doesn't exist yet
+if git show-ref --verify --quiet "refs/heads/$BRANCH"; then
+    git checkout "$BRANCH"
+else
+    echo "No local $BRANCH branch — creating orphan..."
+    git checkout --orphan "$BRANCH"
+    git rm -rf . >/dev/null 2>&1 || true
+fi
+
+# Copy public files from main
+for f in "${PUBLIC_FILES[@]}"; do
+    git checkout main -- "$f"
+done
+
+# Generate public README from main's README:
+#   - Strip "## Notebooks" section
+#   - Strip "## Development history" section
+#   - Remove project-tree lines referencing private files
+git checkout main -- README.md
+awk '
+/^## Notebooks/         { skip = 1; next }
+/^## Development hist/  { skip = 1; next }
+/^## /                  { skip = 0 }
+skip                    { next }
+/archived\//            { next }
+/saved_output\//        { next }
+/devlog\.md/            { next }
+/\*\.ipynb/             { next }
+{ print }
+' README.md > README.tmp && mv README.tmp README.md
+
+# Stage only the public files (not untracked files on disk)
+git add "${PUBLIC_FILES[@]}" README.md
+
+# Commit only if there are changes
+if git diff --cached --quiet; then
+    echo "No changes to deploy."
+else
+    git commit -m "$COMMIT_MSG"
+    git push "$REMOTE" "$BRANCH"
+    echo ""
+    echo "Done. Deployed main ($MAIN_HEAD) -> $REMOTE/$BRANCH"
+fi
+
+# Switch back to main
+git checkout main

hyde.ipynb

@@ -0,0 +1,249 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "11d5ae50",
+   "metadata": {},
+   "source": [
+    "# Experimenting with HyDE\n",
+    "\n",
+    "Using this to explore query rewrites\\\n",
+    "August 2025"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "813f8b1a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from llama_index.core import (\n",
+    "    StorageContext,\n",
+    "    load_index_from_storage,\n",
+    "    ServiceContext,\n",
+    "    Settings,\n",
+    ")\n",
+    "from llama_index.embeddings.huggingface import HuggingFaceEmbedding\n",
+    "from llama_index.llms.ollama import Ollama\n",
+    "from llama_index.core.prompts import PromptTemplate\n",
+    "from llama_index.core.indices.query.query_transform import HyDEQueryTransform\n",
+    "from llama_index.core.query_engine.transform_query_engine import TransformQueryEngine"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "id": "f3d65589",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "llm=\"llama3.1:8B\"\n",
+    "\n",
+    "# Use a local model to generate\n",
+    "Settings.llm = Ollama(\n",
+    "    model=llm,    # First model tested\n",
+    "    request_timeout=360.0,\n",
+    "    context_window=8000,\n",
+    "    temperature=0.7,\n",
+    "    )\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "id": "afd593ee",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load embedding model (same as used for vector store)\n",
+    "embed_model = HuggingFaceEmbedding(model_name=\"all-mpnet-base-v2\")\n",
+    "Settings.embed_model = embed_model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 52,
+   "id": "04c702a2",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Original query: Find entries with strong feelings of depression.\n",
+      "HyDE-generated query (used for embedding):\n",
+      " Find entries with strong feelings of depression.\n"
+     ]
+    }
+   ],
+   "source": [
+    "#Initial query\n",
+    "initial_query = \"Find entries with strong feelings of depression.\"\n",
+    "\n",
+    "# Define a custom HyDE prompt (this is fully supported)\n",
+    "hyde_prompt = PromptTemplate(\n",
+    "    \"You are a helpful assistant. Generate a detailed hypothetical answer to the user query below.\\n\\nQuery: {query_str}\\n\\nAnswer:\"\n",
+    ")\n",
+    "\n",
+    "hyde_transform = HyDEQueryTransform(llm=Settings.llm,hyde_prompt=hyde_prompt,include_original=False)\n",
+    "\n",
+    "# Run the transform manually\n",
+    "hyde_query = hyde_transform.run(initial_query)\n",
+    "\n",
+    "# Print the result\n",
+    "print(\"Original query:\", initial_query)\n",
+    "print(\"HyDE-generated query (used for embedding):\\n\", hyde_query.query_str)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 53,
+   "id": "3b211daf",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "There are many important feelings that people experience in their lives. Here are some examples:\n",
+      "\n",
+      "1. **Love**: A strong affection or attachment to someone, which can be romantic, familial, or platonic.\n",
+      "2. **Happiness**: A positive emotional state characterized by a sense of joy, contentment, and satisfaction.\n",
+      "3. **Empathy**: The ability to understand and share the feelings of others, which is essential for building strong relationships and fostering compassion.\n",
+      "4. **Gratitude**: Feeling thankful or appreciative for something or someone in one's life, which can cultivate a positive outlook and well-being.\n",
+      "5. **Compassion**: A feeling of concern and kindness towards others who are suffering or struggling, which can inspire acts of service and support.\n",
+      "6. **Confidence**: A sense of self-assurance and faith in one's abilities, which is essential for personal growth and achievement.\n",
+      "7. **Respect**: Feeling admiration or esteem for someone or something, which is necessary for building strong relationships and social bonds.\n",
+      "8. **Forgiveness**: The ability to let go of negative emotions and forgive oneself or others for past mistakes or hurtful actions.\n",
+      "9. **Excitement**: A feeling of enthusiasm and eagerness, often accompanied by a sense of anticipation or adventure.\n",
+      "10. **Serenity**: A state of calmness and peace, which can be cultivated through mindfulness and self-reflection.\n",
+      "\n",
+      "These feelings are essential for human well-being and relationships, and they play important roles in shaping our experiences and interactions with others.\n",
+      "\n",
+      "Would you like me to expand on any of these feelings or explore other emotions?\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Check that the LLM is working\n",
+    "# confirmed that this generates different responses each time\n",
+    "response = Settings.llm.complete(\"What are several important feelings?\")\n",
+    "print(response.text)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
+   "id": "9db5c9c2",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "HyDE output:\n",
+      " Find entries with strong feelings of depression.\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Test for silent errors. Output verifies working.\n",
+    "try:\n",
+    "    hyde_result = hyde_transform.run(initial_query)\n",
+    "    print(\"HyDE output:\\n\", hyde_result)\n",
+    "except Exception as e:\n",
+    "    print(\"LLM error:\", e)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d5add1ed",
+   "metadata": {},
+   "source": [
+    "## Testing HyDE based on llamaindex documentation\n",
+    "\n",
+    "https://docs.llamaindex.ai/en/stable/examples/query_transformations/HyDEQueryTransformDemo/#querying-without-transformation-yields-reasonable-answer"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 54,
+   "id": "90381bc2",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[\"Here is a passage that includes several key details about depression:\\n\\n**The Descent into Darkness**\\n\\nAs I lay in bed, staring blankly at the ceiling, I felt an overwhelming sense of hopelessness wash over me. The darkness seemed to close in around me, suffocating me with its crushing weight. Every thought felt like a burden, every decision a chore. I couldn't bear the idea of getting out of bed, of facing another day filled with anxiety and despair.\\n\\nI had been struggling with depression for what felt like an eternity. The symptoms had started slowly, a nagging feeling that something was off, but I had tried to brush it aside as mere exhaustion or stress. But as time went on, the feelings intensified, until they became all-consuming. I felt like I was drowning in a sea of sadness, unable to find a lifeline.\\n\\nThe smallest things would set me off - a harsh word from a loved one, a missed deadline at work, even just getting out of bed and facing another day. The world seemed too much for me to handle, and I retreated into my own private hell of despair. I couldn't eat, couldn't sleep, couldn't find any joy in the things that used to bring me happiness.\\n\\nAs I looked back on the past few months, I realized that this wasn't just a passing phase or a normal response to stress. Depression had taken hold, and it was suffocating me. I knew I needed help, but the thought of seeking treatment seemed daunting, even terrifying. What if they couldn't help me? What if I was stuck in this pit forever?\\n\\nI felt like I was losing myself, bit by bit, as depression consumed me. I longed for a glimmer of hope, a spark of light to guide me through the darkness. But it seemed elusive, always just out of reach.\\n\\nThis passage includes several key details about depression, including:\\n\\n* **Overwhelming feelings of sadness and hopelessness**: The protagonist feels an intense sense of despair that is difficult to shake.\\n* **Loss of motivation**: They feel like they can't get out of bed or face another day filled with anxiety and despair.\\n* **Withdrawal from activities**: They have lost interest in things that used to bring them joy, and are unable to eat or sleep.\\n* **Social isolation**: They retreat into their own private hell, feeling disconnected from others.\\n* **Loss of identity**: They feel like they are losing themselves as depression consumes them.\\n* **Fear of seeking help**: The protagonist is afraid to seek treatment, fearing that it won't work or that they will be stuck in this state forever.\",\n",
+       " 'Find entries with strong feelings of depression.']"
+      ]
+     },
+     "execution_count": 54,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "hyde = HyDEQueryTransform(llm=Settings.llm,include_original=True)\n",
+    "query_str = \"Find entries with strong feelings of depression.\"\n",
+    "query_bundle = hyde(query_str)\n",
+    "hyde_doc = query_bundle.embedding_strs\n",
+    "hyde_doc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 55,
+   "id": "08e7eca4",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/markdown": [
+       "[\"Here is a passage that includes several key details about depression:\\n\\n**The Descent into Darkness**\\n\\nAs I lay in bed, staring blankly at the ceiling, I felt an overwhelming sense of hopelessness wash over me. The darkness seemed to close in around me, suffocating me with its crushing weight. Every thought felt like a burden, every decision a chore. I couldn't bear the idea of getting out of bed, of facing another day filled with anxiety and despair.\\n\\nI had been struggling with depression for what felt like an eternity. The symptoms had started slowly, a nagging feeling that something was off, but I had tried to brush it aside as mere exhaustion or stress. But as time went on, the feelings intensified, until they became all-consuming. I felt like I was drowning in a sea of sadness, unable to find a lifeline.\\n\\nThe smallest things would set me off - a harsh word from a loved one, a missed deadline at work, even just getting out of bed and facing another day. The world seemed too much for me to handle, and I retreated into my own private hell of despair. I couldn't eat, couldn't sleep, couldn't find any joy in the things that used to bring me happiness.\\n\\nAs I looked back on the past few months, I realized that this wasn't just a passing phase or a normal response to stress. Depression had taken hold, and it was suffocating me. I knew I needed help, but the thought of seeking treatment seemed daunting, even terrifying. What if they couldn't help me? What if I was stuck in this pit forever?\\n\\nI felt like I was losing myself, bit by bit, as depression consumed me. I longed for a glimmer of hope, a spark of light to guide me through the darkness. But it seemed elusive, always just out of reach.\\n\\nThis passage includes several key details about depression, including:\\n\\n* **Overwhelming feelings of sadness and hopelessness**: The protagonist feels an intense sense of despair that is difficult to shake.\\n* **Loss of motivation**: They feel like they can't get out of bed or face another day filled with anxiety and despair.\\n* **Withdrawal from activities**: They have lost interest in things that used to bring them joy, and are unable to eat or sleep.\\n* **Social isolation**: They retreat into their own private hell, feeling disconnected from others.\\n* **Loss of identity**: They feel like they are losing themselves as depression consumes them.\\n* **Fear of seeking help**: The protagonist is afraid to seek treatment, fearing that it won't work or that they will be stuck in this state forever.\", 'Find entries with strong feelings of depression.']"
+      ],
+      "text/plain": [
+       "<IPython.core.display.Markdown object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "from IPython.display import Markdown, display\n",
+    "display(Markdown(f\"{hyde_doc}\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9ca50f9d",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.11"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

query_topk_prompt_engine_v2.py

@@ -0,0 +1,125 @@
+# query_topk_prompt_engine_v2.py
+# Run a querry on a vector store
+#
+# This version uses an improved prompt that is more flexible and query-adaptive
+# Based on query_topk_prompt_engine.py
+#
+# Implements a prompt and uses the build_exp.py vector store with BAAI/bge-large-en-v1.5
+#
+# E.M.F. January 2026
+
+from llama_index.core import (
+    StorageContext,
+    load_index_from_storage,
+    ServiceContext,
+    Settings,
+)
+from llama_index.embeddings.huggingface import HuggingFaceEmbedding
+from llama_index.llms.ollama import Ollama
+from llama_index.core.prompts import PromptTemplate
+import os
+import sys
+
+#
+# Globals
+#
+os.environ["TOKENIZERS_PARALLELISM"] = "false"
+
+# Embedding model used in vector store (this should match the one in build_exp.py or equivalent)
+# embed_model = HuggingFaceEmbedding(model_name="all-mpnet-base-v2")
+embed_model = HuggingFaceEmbedding(cache_folder="./models",model_name="BAAI/bge-large-en-v1.5",local_files_only=True)
+
+# LLM model to use in query transform and generation
+# command-r7b generates about as quickly as llama3.1:8B, but provides results that stick better
+# to the provided context
+llm="command-r7b"
+# Other models tried:
+#llm="llama3.1:8B"
+#llm="deepseek-r1:8B"
+#llm="gemma3:1b"
+
+#
+# Custom prompt for the query engine - Version 2 (improved)
+#
+# This prompt is more flexible and query-adaptive than v1:
+# - Doesn't force artificial structure (exactly 10 files, mandatory theme)
+# - Works for factual questions, exploratory queries, and comparisons
+# - Emphasizes precision with explicit citations
+# - Allows natural synthesis across sources
+# - Honest about limitations when context is insufficient
+#
+PROMPT = PromptTemplate(
+"""You are a precise research assistant analyzing excerpts from a document collection.
+
+CONTEXT (ranked by relevance):
+{context_str}
+
+QUERY:
+{query_str}
+
+Instructions:
+- Answer ONLY using information explicitly present in the CONTEXT above
+- Prioritize higher-ranked excerpts but don't ignore lower ones if they contain unique relevant information
+- Be specific: cite file names and quote/paraphrase key passages when relevant
+- If the context doesn't contain enough information to answer fully, say so
+- Synthesize information across multiple sources when appropriate
+
+Your response should:
+1. Directly answer the query using the context
+2. Reference specific files and their content (e.g., "In <filename>, ...")
+3. List all relevant source files at the end with brief relevance notes
+
+If you find relevant information, organize it clearly. If the context is insufficient, explain what's missing."""
+)
+
+#
+# Main program routine
+#
+
+def main():
+    # Use a local model to generate -- in this case using Ollama
+    Settings.llm = Ollama(
+        model=llm,    # First model tested
+        request_timeout=360.0,
+        context_window=8000
+        )
+
+    # Load embedding model (same as used for vector store)
+    Settings.embed_model = embed_model
+
+    # Load persisted vector store + metadata
+    storage_context = StorageContext.from_defaults(persist_dir="./storage_exp")
+    index = load_index_from_storage(storage_context)
+
+    # Build regular query engine with custom prompt
+    query_engine = index.as_query_engine(
+        similarity_top_k=15,            # pull wide
+        #response_mode="compact"        # concise synthesis
+        text_qa_template=PROMPT,        # custom prompt (v2)
+        # node_postprocessors=[
+        #     SimilarityPostprocessor(similarity_cutoff=0.75)  # keep strong hits; makes result count flexible
+        # ],
+    )
+
+    # Query
+    if len(sys.argv) < 2:
+        print("Usage: python query.py QUERY_TEXT")
+        sys.exit(1)
+    q = " ".join(sys.argv[1:])
+
+    # Generate the response by querying the engine
+    # This performes the similarity search and then applies the prompt
+    response = query_engine.query(q)
+
+    # Return the query response and source documents
+    print("\nResponse:\n")
+    print(response.response)
+
+    print("\nSource documents:")
+    for node in response.source_nodes:
+        meta = getattr(node, "metadata", None) or node.node.metadata
+        print(f"{meta.get('file_name')}  {meta.get('file_path')}  {getattr(node, 'score', None):.3f}")
+
+
+if __name__ == "__main__":
+    main()

sandbox.ipynb

@@ -0,0 +1,973 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "11d5ae50",
+   "metadata": {},
+   "source": [
+    "# llamaindex sandbox\n",
+    "\n",
+    "Using this to explore llamaindex\\\n",
+    "August 2025"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "813f8b1a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import llama_index.core"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "656faffb",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['BaseCallbackHandler', 'BasePromptTemplate', 'Callable', 'ChatPromptTemplate', 'ComposableGraph', 'Document', 'DocumentSummaryIndex', 'GPTDocumentSummaryIndex', 'GPTKeywordTableIndex', 'GPTListIndex', 'GPTRAKEKeywordTableIndex', 'GPTSimpleKeywordTableIndex', 'GPTTreeIndex', 'GPTVectorStoreIndex', 'IndexStructType', 'KeywordTableIndex', 'KnowledgeGraphIndex', 'ListIndex', 'MockEmbedding', 'NullHandler', 'Optional', 'Prompt', 'PromptHelper', 'PromptTemplate', 'PropertyGraphIndex', 'QueryBundle', 'RAKEKeywordTableIndex', 'Response', 'SQLContextBuilder', 'SQLDatabase', 'SQLDocumentContextBuilder', 'SelectorPromptTemplate', 'ServiceContext', 'Settings', 'SimpleDirectoryReader', 'SimpleKeywordTableIndex', 'StorageContext', 'SummaryIndex', 'TreeIndex', 'VectorStoreIndex', '__all__', '__annotations__', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', 'async_utils', 'base', 'bridge', 'callbacks', 'chat_engine', 'constants', 'data_structs', 'download', 'download_loader', 'embeddings', 'evaluation', 'get_response_synthesizer', 'get_tokenizer', 'global_handler', 'global_tokenizer', 'graph_stores', 'image_retriever', 'indices', 'ingestion', 'instrumentation', 'llama_dataset', 'llms', 'load_graph_from_storage', 'load_index_from_storage', 'load_indices_from_storage', 'logging', 'memory', 'multi_modal_llms', 'node_parser', 'objects', 'output_parsers', 'postprocessor', 'prompts', 'query_engine', 'question_gen', 'readers', 'response', 'response_synthesizers', 'schema', 'selectors', 'service_context', 'set_global_handler', 'set_global_service_context', 'set_global_tokenizer', 'settings', 'storage', 'tools', 'types', 'utilities', 'utils', 'vector_stores', 'workflow']\n"
+     ]
+    }
+   ],
+   "source": [
+    "# List available objects\n",
+    "print(dir(llama_index.core))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "bea0759d",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "BaseCallbackHandler\n",
+      "BasePromptTemplate\n",
+      "Callable\n",
+      "ChatPromptTemplate\n",
+      "ComposableGraph\n",
+      "Document\n",
+      "DocumentSummaryIndex\n",
+      "GPTDocumentSummaryIndex\n",
+      "GPTKeywordTableIndex\n",
+      "GPTListIndex\n",
+      "GPTRAKEKeywordTableIndex\n",
+      "GPTSimpleKeywordTableIndex\n",
+      "GPTTreeIndex\n",
+      "GPTVectorStoreIndex\n",
+      "IndexStructType\n",
+      "KeywordTableIndex\n",
+      "KnowledgeGraphIndex\n",
+      "ListIndex\n",
+      "MockEmbedding\n",
+      "NullHandler\n",
+      "Optional\n",
+      "Prompt\n",
+      "PromptHelper\n",
+      "PromptTemplate\n",
+      "PropertyGraphIndex\n",
+      "QueryBundle\n",
+      "RAKEKeywordTableIndex\n",
+      "Response\n",
+      "SQLContextBuilder\n",
+      "SQLDatabase\n",
+      "SQLDocumentContextBuilder\n",
+      "SelectorPromptTemplate\n",
+      "ServiceContext\n",
+      "Settings\n",
+      "SimpleDirectoryReader\n",
+      "SimpleKeywordTableIndex\n",
+      "StorageContext\n",
+      "SummaryIndex\n",
+      "TreeIndex\n",
+      "VectorStoreIndex\n",
+      "__all__\n",
+      "__annotations__\n",
+      "__builtins__\n",
+      "__cached__\n",
+      "__doc__\n",
+      "__file__\n",
+      "__loader__\n",
+      "__name__\n",
+      "__package__\n",
+      "__path__\n",
+      "__spec__\n",
+      "__version__\n",
+      "async_utils\n",
+      "base\n",
+      "bridge\n",
+      "callbacks\n",
+      "chat_engine\n",
+      "constants\n",
+      "data_structs\n",
+      "download\n",
+      "download_loader\n",
+      "embeddings\n",
+      "evaluation\n",
+      "get_response_synthesizer\n",
+      "get_tokenizer\n",
+      "global_handler\n",
+      "global_tokenizer\n",
+      "graph_stores\n",
+      "image_retriever\n",
+      "indices\n",
+      "ingestion\n",
+      "instrumentation\n",
+      "llama_dataset\n",
+      "llms\n",
+      "load_graph_from_storage\n",
+      "load_index_from_storage\n",
+      "load_indices_from_storage\n",
+      "logging\n",
+      "memory\n",
+      "multi_modal_llms\n",
+      "node_parser\n",
+      "objects\n",
+      "output_parsers\n",
+      "postprocessor\n",
+      "prompts\n",
+      "query_engine\n",
+      "question_gen\n",
+      "readers\n",
+      "response\n",
+      "response_synthesizers\n",
+      "schema\n",
+      "selectors\n",
+      "service_context\n",
+      "set_global_handler\n",
+      "set_global_service_context\n",
+      "set_global_tokenizer\n",
+      "settings\n",
+      "storage\n",
+      "tools\n",
+      "types\n",
+      "utilities\n",
+      "utils\n",
+      "vector_stores\n",
+      "workflow\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Better formatted output for list of available objects\n",
+    "objects = dir(llama_index.core)\n",
+    "for obj in objects:\n",
+    "    print(obj)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "3886a5f0",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "list"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# dir returns a list\n",
+    "type(objects)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "272cb0c9",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "104"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# In the case of llamaindex.core, it contains 104 objects\n",
+    "\n",
+    "len(objects)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bfffc03f",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Help on class VectorStoreIndex in module llama_index.core.indices.vector_store.base:\n",
+      "\n",
+      "class VectorStoreIndex(llama_index.core.indices.base.BaseIndex)\n",
+      " |  VectorStoreIndex(nodes: Optional[Sequence[llama_index.core.schema.BaseNode]] = None, use_async: bool = False, store_nodes_override: bool = False, embed_model: Union[llama_index.core.base.embeddings.base.BaseEmbedding, ForwardRef('LCEmbeddings'), str, NoneType] = None, insert_batch_size: int = 2048, objects: Optional[Sequence[llama_index.core.schema.IndexNode]] = None, index_struct: Optional[llama_index.core.data_structs.data_structs.IndexDict] = None, storage_context: Optional[llama_index.core.storage.storage_context.StorageContext] = None, callback_manager: Optional[llama_index.core.callbacks.base.CallbackManager] = None, transformations: Optional[List[llama_index.core.schema.TransformComponent]] = None, show_progress: bool = False, **kwargs: Any) -> None\n",
+      " |\n",
+      " |  Vector Store Index.\n",
+      " |\n",
+      " |  Args:\n",
+      " |      use_async (bool): Whether to use asynchronous calls. Defaults to False.\n",
+      " |      show_progress (bool): Whether to show tqdm progress bars. Defaults to False.\n",
+      " |      store_nodes_override (bool): set to True to always store Node objects in index\n",
+      " |          store and document store even if vector store keeps text. Defaults to False\n",
+      " |\n",
+      " |  Method resolution order:\n",
+      " |      VectorStoreIndex\n",
+      " |      llama_index.core.indices.base.BaseIndex\n",
+      " |      typing.Generic\n",
+      " |      abc.ABC\n",
+      " |      builtins.object\n",
+      " |\n",
+      " |  Methods defined here:\n",
+      " |\n",
+      " |  __init__(self, nodes: Optional[Sequence[llama_index.core.schema.BaseNode]] = None, use_async: bool = False, store_nodes_override: bool = False, embed_model: Union[llama_index.core.base.embeddings.base.BaseEmbedding, ForwardRef('LCEmbeddings'), str, NoneType] = None, insert_batch_size: int = 2048, objects: Optional[Sequence[llama_index.core.schema.IndexNode]] = None, index_struct: Optional[llama_index.core.data_structs.data_structs.IndexDict] = None, storage_context: Optional[llama_index.core.storage.storage_context.StorageContext] = None, callback_manager: Optional[llama_index.core.callbacks.base.CallbackManager] = None, transformations: Optional[List[llama_index.core.schema.TransformComponent]] = None, show_progress: bool = False, **kwargs: Any) -> None\n",
+      " |      Initialize params.\n",
+      " |\n",
+      " |  async adelete_nodes(self, node_ids: List[str], delete_from_docstore: bool = False, **delete_kwargs: Any) -> None\n",
+      " |      Delete a list of nodes from the index.\n",
+      " |\n",
+      " |      Args:\n",
+      " |          node_ids (List[str]): A list of node_ids from the nodes to delete\n",
+      " |\n",
+      " |  async adelete_ref_doc(self, ref_doc_id: str, delete_from_docstore: bool = False, **delete_kwargs: Any) -> None\n",
+      " |      Delete a document and it's nodes by using ref_doc_id.\n",
+      " |\n",
+      " |  async ainsert_nodes(self, nodes: Sequence[llama_index.core.schema.BaseNode], **insert_kwargs: Any) -> None\n",
+      " |      Insert nodes.\n",
+      " |\n",
+      " |      NOTE: overrides BaseIndex.ainsert_nodes.\n",
+      " |          VectorStoreIndex only stores nodes in document store\n",
+      " |          if vector store does not store text\n",
+      " |\n",
+      " |  as_retriever(self, **kwargs: Any) -> llama_index.core.base.base_retriever.BaseRetriever\n",
+      " |\n",
+      " |  build_index_from_nodes(self, nodes: Sequence[llama_index.core.schema.BaseNode], **insert_kwargs: Any) -> llama_index.core.data_structs.data_structs.IndexDict\n",
+      " |      Build the index from nodes.\n",
+      " |\n",
+      " |      NOTE: Overrides BaseIndex.build_index_from_nodes.\n",
+      " |          VectorStoreIndex only stores nodes in document store\n",
+      " |          if vector store does not store text\n",
+      " |\n",
+      " |  delete_nodes(self, node_ids: List[str], delete_from_docstore: bool = False, **delete_kwargs: Any) -> None\n",
+      " |      Delete a list of nodes from the index.\n",
+      " |\n",
+      " |      Args:\n",
+      " |          node_ids (List[str]): A list of node_ids from the nodes to delete\n",
+      " |\n",
+      " |  delete_ref_doc(self, ref_doc_id: str, delete_from_docstore: bool = False, **delete_kwargs: Any) -> None\n",
+      " |      Delete a document and it's nodes by using ref_doc_id.\n",
+      " |\n",
+      " |  insert_nodes(self, nodes: Sequence[llama_index.core.schema.BaseNode], **insert_kwargs: Any) -> None\n",
+      " |      Insert nodes.\n",
+      " |\n",
+      " |      NOTE: overrides BaseIndex.insert_nodes.\n",
+      " |          VectorStoreIndex only stores nodes in document store\n",
+      " |          if vector store does not store text\n",
+      " |\n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Class methods defined here:\n",
+      " |\n",
+      " |  from_vector_store(vector_store: llama_index.core.vector_stores.types.BasePydanticVectorStore, embed_model: Union[llama_index.core.base.embeddings.base.BaseEmbedding, ForwardRef('LCEmbeddings'), str, NoneType] = None, **kwargs: Any) -> 'VectorStoreIndex'\n",
+      " |\n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Readonly properties defined here:\n",
+      " |\n",
+      " |  ref_doc_info\n",
+      " |      Retrieve a dict mapping of ingested documents and their nodes+metadata.\n",
+      " |\n",
+      " |  vector_store\n",
+      " |\n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Data and other attributes defined here:\n",
+      " |\n",
+      " |  __abstractmethods__ = frozenset()\n",
+      " |\n",
+      " |  __annotations__ = {}\n",
+      " |\n",
+      " |  __orig_bases__ = (llama_index.core.indices.base.BaseIndex[llama_index....\n",
+      " |\n",
+      " |  __parameters__ = ()\n",
+      " |\n",
+      " |  index_struct_cls = <class 'llama_index.core.data_structs.data_structs....\n",
+      " |      A simple dictionary of documents.\n",
+      " |\n",
+      " |\n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Methods inherited from llama_index.core.indices.base.BaseIndex:\n",
+      " |\n",
+      " |  async ainsert(self, document: llama_index.core.schema.Document, **insert_kwargs: Any) -> None\n",
+      " |      Asynchronously insert a document.\n",
+      " |\n",
+      " |  async arefresh_ref_docs(self, documents: Sequence[llama_index.core.schema.Document], **update_kwargs: Any) -> List[bool]\n",
+      " |      Asynchronously refresh an index with documents that have changed.\n",
+      " |\n",
+      " |      This allows users to save LLM and Embedding model calls, while only\n",
+      " |      updating documents that have any changes in text or metadata. It\n",
+      " |      will also insert any documents that previously were not stored.\n",
+      " |\n",
+      " |  as_chat_engine(self, chat_mode: llama_index.core.chat_engine.types.ChatMode = <ChatMode.BEST: 'best'>, llm: Union[str, llama_index.core.llms.llm.LLM, ForwardRef('BaseLanguageModel'), NoneType] = None, **kwargs: Any) -> llama_index.core.chat_engine.types.BaseChatEngine\n",
+      " |      Convert the index to a chat engine.\n",
+      " |\n",
+      " |      Calls `index.as_query_engine(llm=llm, **kwargs)` to get the query engine and then\n",
+      " |      wraps it in a chat engine based on the chat mode.\n",
+      " |\n",
+      " |      Chat modes:\n",
+      " |          - `ChatMode.BEST` (default): Chat engine that uses an agent (react or openai) with a query engine tool\n",
+      " |          - `ChatMode.CONTEXT`: Chat engine that uses a retriever to get context\n",
+      " |          - `ChatMode.CONDENSE_QUESTION`: Chat engine that condenses questions\n",
+      " |          - `ChatMode.CONDENSE_PLUS_CONTEXT`: Chat engine that condenses questions and uses a retriever to get context\n",
+      " |          - `ChatMode.SIMPLE`: Simple chat engine that uses the LLM directly\n",
+      " |          - `ChatMode.REACT`: Chat engine that uses a react agent with a query engine tool\n",
+      " |          - `ChatMode.OPENAI`: Chat engine that uses an openai agent with a query engine tool\n",
+      " |\n",
+      " |  as_query_engine(self, llm: Union[str, llama_index.core.llms.llm.LLM, ForwardRef('BaseLanguageModel'), NoneType] = None, **kwargs: Any) -> llama_index.core.base.base_query_engine.BaseQueryEngine\n",
+      " |      Convert the index to a query engine.\n",
+      " |\n",
+      " |      Calls `index.as_retriever(**kwargs)` to get the retriever and then wraps it in a\n",
+      " |      `RetrieverQueryEngine.from_args(retriever, **kwrags)` call.\n",
+      " |\n",
+      " |  async aupdate_ref_doc(self, document: llama_index.core.schema.Document, **update_kwargs: Any) -> None\n",
+      " |      Asynchronously update a document and it's corresponding nodes.\n",
+      " |\n",
+      " |      This is equivalent to deleting the document and then inserting it again.\n",
+      " |\n",
+      " |      Args:\n",
+      " |          document (Union[BaseDocument, BaseIndex]): document to update\n",
+      " |          insert_kwargs (Dict): kwargs to pass to insert\n",
+      " |          delete_kwargs (Dict): kwargs to pass to delete\n",
+      " |\n",
+      " |  delete(self, doc_id: str, **delete_kwargs: Any) -> None\n",
+      " |      Delete a document from the index.\n",
+      " |      All nodes in the index related to the index will be deleted.\n",
+      " |\n",
+      " |      Args:\n",
+      " |          doc_id (str): A doc_id of the ingested document\n",
+      " |\n",
+      " |  insert(self, document: llama_index.core.schema.Document, **insert_kwargs: Any) -> None\n",
+      " |      Insert a document.\n",
+      " |\n",
+      " |  refresh(self, documents: Sequence[llama_index.core.schema.Document], **update_kwargs: Any) -> List[bool]\n",
+      " |      Refresh an index with documents that have changed.\n",
+      " |\n",
+      " |      This allows users to save LLM and Embedding model calls, while only\n",
+      " |      updating documents that have any changes in text or metadata. It\n",
+      " |      will also insert any documents that previously were not stored.\n",
+      " |\n",
+      " |  refresh_ref_docs(self, documents: Sequence[llama_index.core.schema.Document], **update_kwargs: Any) -> List[bool]\n",
+      " |      Refresh an index with documents that have changed.\n",
+      " |\n",
+      " |      This allows users to save LLM and Embedding model calls, while only\n",
+      " |      updating documents that have any changes in text or metadata. It\n",
+      " |      will also insert any documents that previously were not stored.\n",
+      " |\n",
+      " |  set_index_id(self, index_id: str) -> None\n",
+      " |      Set the index id.\n",
+      " |\n",
+      " |      NOTE: if you decide to set the index_id on the index_struct manually,\n",
+      " |      you will need to explicitly call `add_index_struct` on the `index_store`\n",
+      " |      to update the index store.\n",
+      " |\n",
+      " |      Args:\n",
+      " |          index_id (str): Index id to set.\n",
+      " |\n",
+      " |  update(self, document: llama_index.core.schema.Document, **update_kwargs: Any) -> None\n",
+      " |      Update a document and it's corresponding nodes.\n",
+      " |\n",
+      " |      This is equivalent to deleting the document and then inserting it again.\n",
+      " |\n",
+      " |      Args:\n",
+      " |          document (Union[BaseDocument, BaseIndex]): document to update\n",
+      " |          insert_kwargs (Dict): kwargs to pass to insert\n",
+      " |          delete_kwargs (Dict): kwargs to pass to delete\n",
+      " |\n",
+      " |  update_ref_doc(self, document: llama_index.core.schema.Document, **update_kwargs: Any) -> None\n",
+      " |      Update a document and it's corresponding nodes.\n",
+      " |\n",
+      " |      This is equivalent to deleting the document and then inserting it again.\n",
+      " |\n",
+      " |      Args:\n",
+      " |          document (Union[BaseDocument, BaseIndex]): document to update\n",
+      " |          insert_kwargs (Dict): kwargs to pass to insert\n",
+      " |          delete_kwargs (Dict): kwargs to pass to delete\n",
+      " |\n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Class methods inherited from llama_index.core.indices.base.BaseIndex:\n",
+      " |\n",
+      " |  from_documents(documents: Sequence[llama_index.core.schema.Document], storage_context: Optional[llama_index.core.storage.storage_context.StorageContext] = None, show_progress: bool = False, callback_manager: Optional[llama_index.core.callbacks.base.CallbackManager] = None, transformations: Optional[List[llama_index.core.schema.TransformComponent]] = None, **kwargs: Any) -> ~IndexType\n",
+      " |      Create index from documents.\n",
+      " |\n",
+      " |      Args:\n",
+      " |          documents (Sequence[Document]]): List of documents to\n",
+      " |              build the index from.\n",
+      " |\n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Readonly properties inherited from llama_index.core.indices.base.BaseIndex:\n",
+      " |\n",
+      " |  docstore\n",
+      " |      Get the docstore corresponding to the index.\n",
+      " |\n",
+      " |  index_id\n",
+      " |      Get the index struct.\n",
+      " |\n",
+      " |  index_struct\n",
+      " |      Get the index struct.\n",
+      " |\n",
+      " |  storage_context\n",
+      " |\n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Data descriptors inherited from llama_index.core.indices.base.BaseIndex:\n",
+      " |\n",
+      " |  __dict__\n",
+      " |      dictionary for instance variables\n",
+      " |\n",
+      " |  __weakref__\n",
+      " |      list of weak references to the object\n",
+      " |\n",
+      " |  summary\n",
+      " |\n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Class methods inherited from typing.Generic:\n",
+      " |\n",
+      " |  __class_getitem__(...)\n",
+      " |      Parameterizes a generic class.\n",
+      " |\n",
+      " |      At least, parameterizing a generic class is the *main* thing this\n",
+      " |      method does. For example, for some generic class `Foo`, this is called\n",
+      " |      when we do `Foo[int]` - there, with `cls=Foo` and `params=int`.\n",
+      " |\n",
+      " |      However, note that this method is also called when defining generic\n",
+      " |      classes in the first place with `class Foo[T]: ...`.\n",
+      " |\n",
+      " |  __init_subclass__(...)\n",
+      " |      Function to initialize subclasses.\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Get help on a specific object\n",
+    "help(llama_index.core.VectorStoreIndex)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "3eb5f1b7",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "class VectorStoreIndex(BaseIndex[IndexDict]):\n",
+      "    \"\"\"\n",
+      "    Vector Store Index.\n",
+      "\n",
+      "    Args:\n",
+      "        use_async (bool): Whether to use asynchronous calls. Defaults to False.\n",
+      "        show_progress (bool): Whether to show tqdm progress bars. Defaults to False.\n",
+      "        store_nodes_override (bool): set to True to always store Node objects in index\n",
+      "            store and document store even if vector store keeps text. Defaults to False\n",
+      "\n",
+      "    \"\"\"\n",
+      "\n",
+      "    index_struct_cls = IndexDict\n",
+      "\n",
+      "    def __init__(\n",
+      "        self,\n",
+      "        nodes: Optional[Sequence[BaseNode]] = None,\n",
+      "        # vector store index params\n",
+      "        use_async: bool = False,\n",
+      "        store_nodes_override: bool = False,\n",
+      "        embed_model: Optional[EmbedType] = None,\n",
+      "        insert_batch_size: int = 2048,\n",
+      "        # parent class params\n",
+      "        objects: Optional[Sequence[IndexNode]] = None,\n",
+      "        index_struct: Optional[IndexDict] = None,\n",
+      "        storage_context: Optional[StorageContext] = None,\n",
+      "        callback_manager: Optional[CallbackManager] = None,\n",
+      "        transformations: Optional[List[TransformComponent]] = None,\n",
+      "        show_progress: bool = False,\n",
+      "        **kwargs: Any,\n",
+      "    ) -> None:\n",
+      "        \"\"\"Initialize params.\"\"\"\n",
+      "        self._use_async = use_async\n",
+      "        self._store_nodes_override = store_nodes_override\n",
+      "        self._embed_model = resolve_embed_model(\n",
+      "            embed_model or Settings.embed_model, callback_manager=callback_manager\n",
+      "        )\n",
+      "\n",
+      "        self._insert_batch_size = insert_batch_size\n",
+      "        super().__init__(\n",
+      "            nodes=nodes,\n",
+      "            index_struct=index_struct,\n",
+      "            storage_context=storage_context,\n",
+      "            show_progress=show_progress,\n",
+      "            objects=objects,\n",
+      "            callback_manager=callback_manager,\n",
+      "            transformations=transformations,\n",
+      "            **kwargs,\n",
+      "        )\n",
+      "\n",
+      "    @classmethod\n",
+      "    def from_vector_store(\n",
+      "        cls,\n",
+      "        vector_store: BasePydanticVectorStore,\n",
+      "        embed_model: Optional[EmbedType] = None,\n",
+      "        **kwargs: Any,\n",
+      "    ) -> \"VectorStoreIndex\":\n",
+      "        if not vector_store.stores_text:\n",
+      "            raise ValueError(\n",
+      "                \"Cannot initialize from a vector store that does not store text.\"\n",
+      "            )\n",
+      "\n",
+      "        kwargs.pop(\"storage_context\", None)\n",
+      "        storage_context = StorageContext.from_defaults(vector_store=vector_store)\n",
+      "\n",
+      "        return cls(\n",
+      "            nodes=[],\n",
+      "            embed_model=embed_model,\n",
+      "            storage_context=storage_context,\n",
+      "            **kwargs,\n",
+      "        )\n",
+      "\n",
+      "    @property\n",
+      "    def vector_store(self) -> BasePydanticVectorStore:\n",
+      "        return self._vector_store\n",
+      "\n",
+      "    def as_retriever(self, **kwargs: Any) -> BaseRetriever:\n",
+      "        # NOTE: lazy import\n",
+      "        from llama_index.core.indices.vector_store.retrievers import (\n",
+      "            VectorIndexRetriever,\n",
+      "        )\n",
+      "\n",
+      "        return VectorIndexRetriever(\n",
+      "            self,\n",
+      "            node_ids=list(self.index_struct.nodes_dict.values()),\n",
+      "            callback_manager=self._callback_manager,\n",
+      "            object_map=self._object_map,\n",
+      "            **kwargs,\n",
+      "        )\n",
+      "\n",
+      "    def _get_node_with_embedding(\n",
+      "        self,\n",
+      "        nodes: Sequence[BaseNode],\n",
+      "        show_progress: bool = False,\n",
+      "    ) -> List[BaseNode]:\n",
+      "        \"\"\"\n",
+      "        Get tuples of id, node, and embedding.\n",
+      "\n",
+      "        Allows us to store these nodes in a vector store.\n",
+      "        Embeddings are called in batches.\n",
+      "\n",
+      "        \"\"\"\n",
+      "        id_to_embed_map = embed_nodes(\n",
+      "            nodes, self._embed_model, show_progress=show_progress\n",
+      "        )\n",
+      "\n",
+      "        results = []\n",
+      "        for node in nodes:\n",
+      "            embedding = id_to_embed_map[node.node_id]\n",
+      "            result = node.model_copy()\n",
+      "            result.embedding = embedding\n",
+      "            results.append(result)\n",
+      "        return results\n",
+      "\n",
+      "    async def _aget_node_with_embedding(\n",
+      "        self,\n",
+      "        nodes: Sequence[BaseNode],\n",
+      "        show_progress: bool = False,\n",
+      "    ) -> List[BaseNode]:\n",
+      "        \"\"\"\n",
+      "        Asynchronously get tuples of id, node, and embedding.\n",
+      "\n",
+      "        Allows us to store these nodes in a vector store.\n",
+      "        Embeddings are called in batches.\n",
+      "\n",
+      "        \"\"\"\n",
+      "        id_to_embed_map = await async_embed_nodes(\n",
+      "            nodes=nodes,\n",
+      "            embed_model=self._embed_model,\n",
+      "            show_progress=show_progress,\n",
+      "        )\n",
+      "\n",
+      "        results = []\n",
+      "        for node in nodes:\n",
+      "            embedding = id_to_embed_map[node.node_id]\n",
+      "            result = node.model_copy()\n",
+      "            result.embedding = embedding\n",
+      "            results.append(result)\n",
+      "        return results\n",
+      "\n",
+      "    async def _async_add_nodes_to_index(\n",
+      "        self,\n",
+      "        index_struct: IndexDict,\n",
+      "        nodes: Sequence[BaseNode],\n",
+      "        show_progress: bool = False,\n",
+      "        **insert_kwargs: Any,\n",
+      "    ) -> None:\n",
+      "        \"\"\"Asynchronously add nodes to index.\"\"\"\n",
+      "        if not nodes:\n",
+      "            return\n",
+      "\n",
+      "        for nodes_batch in iter_batch(nodes, self._insert_batch_size):\n",
+      "            nodes_batch = await self._aget_node_with_embedding(\n",
+      "                nodes_batch, show_progress\n",
+      "            )\n",
+      "            new_ids = await self._vector_store.async_add(nodes_batch, **insert_kwargs)\n",
+      "\n",
+      "            # if the vector store doesn't store text, we need to add the nodes to the\n",
+      "            # index struct and document store\n",
+      "            if not self._vector_store.stores_text or self._store_nodes_override:\n",
+      "                for node, new_id in zip(nodes_batch, new_ids):\n",
+      "                    # NOTE: remove embedding from node to avoid duplication\n",
+      "                    node_without_embedding = node.model_copy()\n",
+      "                    node_without_embedding.embedding = None\n",
+      "\n",
+      "                    index_struct.add_node(node_without_embedding, text_id=new_id)\n",
+      "                    await self._docstore.async_add_documents(\n",
+      "                        [node_without_embedding], allow_update=True\n",
+      "                    )\n",
+      "            else:\n",
+      "                # NOTE: if the vector store keeps text,\n",
+      "                # we only need to add image and index nodes\n",
+      "                for node, new_id in zip(nodes_batch, new_ids):\n",
+      "                    if isinstance(node, (ImageNode, IndexNode)):\n",
+      "                        # NOTE: remove embedding from node to avoid duplication\n",
+      "                        node_without_embedding = node.model_copy()\n",
+      "                        node_without_embedding.embedding = None\n",
+      "\n",
+      "                        index_struct.add_node(node_without_embedding, text_id=new_id)\n",
+      "                        await self._docstore.async_add_documents(\n",
+      "                            [node_without_embedding], allow_update=True\n",
+      "                        )\n",
+      "\n",
+      "    def _add_nodes_to_index(\n",
+      "        self,\n",
+      "        index_struct: IndexDict,\n",
+      "        nodes: Sequence[BaseNode],\n",
+      "        show_progress: bool = False,\n",
+      "        **insert_kwargs: Any,\n",
+      "    ) -> None:\n",
+      "        \"\"\"Add document to index.\"\"\"\n",
+      "        if not nodes:\n",
+      "            return\n",
+      "\n",
+      "        for nodes_batch in iter_batch(nodes, self._insert_batch_size):\n",
+      "            nodes_batch = self._get_node_with_embedding(nodes_batch, show_progress)\n",
+      "            new_ids = self._vector_store.add(nodes_batch, **insert_kwargs)\n",
+      "\n",
+      "            if not self._vector_store.stores_text or self._store_nodes_override:\n",
+      "                # NOTE: if the vector store doesn't store text,\n",
+      "                # we need to add the nodes to the index struct and document store\n",
+      "                for node, new_id in zip(nodes_batch, new_ids):\n",
+      "                    # NOTE: remove embedding from node to avoid duplication\n",
+      "                    node_without_embedding = node.model_copy()\n",
+      "                    node_without_embedding.embedding = None\n",
+      "\n",
+      "                    index_struct.add_node(node_without_embedding, text_id=new_id)\n",
+      "                    self._docstore.add_documents(\n",
+      "                        [node_without_embedding], allow_update=True\n",
+      "                    )\n",
+      "            else:\n",
+      "                # NOTE: if the vector store keeps text,\n",
+      "                # we only need to add image and index nodes\n",
+      "                for node, new_id in zip(nodes_batch, new_ids):\n",
+      "                    if isinstance(node, (ImageNode, IndexNode)):\n",
+      "                        # NOTE: remove embedding from node to avoid duplication\n",
+      "                        node_without_embedding = node.model_copy()\n",
+      "                        node_without_embedding.embedding = None\n",
+      "\n",
+      "                        index_struct.add_node(node_without_embedding, text_id=new_id)\n",
+      "                        self._docstore.add_documents(\n",
+      "                            [node_without_embedding], allow_update=True\n",
+      "                        )\n",
+      "\n",
+      "    def _build_index_from_nodes(\n",
+      "        self,\n",
+      "        nodes: Sequence[BaseNode],\n",
+      "        **insert_kwargs: Any,\n",
+      "    ) -> IndexDict:\n",
+      "        \"\"\"Build index from nodes.\"\"\"\n",
+      "        index_struct = self.index_struct_cls()\n",
+      "        if self._use_async:\n",
+      "            tasks = [\n",
+      "                self._async_add_nodes_to_index(\n",
+      "                    index_struct,\n",
+      "                    nodes,\n",
+      "                    show_progress=self._show_progress,\n",
+      "                    **insert_kwargs,\n",
+      "                )\n",
+      "            ]\n",
+      "            run_async_tasks(tasks)\n",
+      "        else:\n",
+      "            self._add_nodes_to_index(\n",
+      "                index_struct,\n",
+      "                nodes,\n",
+      "                show_progress=self._show_progress,\n",
+      "                **insert_kwargs,\n",
+      "            )\n",
+      "        return index_struct\n",
+      "\n",
+      "    def build_index_from_nodes(\n",
+      "        self,\n",
+      "        nodes: Sequence[BaseNode],\n",
+      "        **insert_kwargs: Any,\n",
+      "    ) -> IndexDict:\n",
+      "        \"\"\"\n",
+      "        Build the index from nodes.\n",
+      "\n",
+      "        NOTE: Overrides BaseIndex.build_index_from_nodes.\n",
+      "            VectorStoreIndex only stores nodes in document store\n",
+      "            if vector store does not store text\n",
+      "        \"\"\"\n",
+      "        # Filter out the nodes that don't have content\n",
+      "        content_nodes = [\n",
+      "            node\n",
+      "            for node in nodes\n",
+      "            if node.get_content(metadata_mode=MetadataMode.EMBED) != \"\"\n",
+      "        ]\n",
+      "\n",
+      "        # Report if some nodes are missing content\n",
+      "        if len(content_nodes) != len(nodes):\n",
+      "            print(\"Some nodes are missing content, skipping them...\")\n",
+      "\n",
+      "        return self._build_index_from_nodes(content_nodes, **insert_kwargs)\n",
+      "\n",
+      "    def _insert(self, nodes: Sequence[BaseNode], **insert_kwargs: Any) -> None:\n",
+      "        \"\"\"Insert a document.\"\"\"\n",
+      "        self._add_nodes_to_index(self._index_struct, nodes, **insert_kwargs)\n",
+      "\n",
+      "    def _validate_serializable(self, nodes: Sequence[BaseNode]) -> None:\n",
+      "        \"\"\"Validate that the nodes are serializable.\"\"\"\n",
+      "        for node in nodes:\n",
+      "            if isinstance(node, IndexNode):\n",
+      "                try:\n",
+      "                    node.dict()\n",
+      "                except ValueError:\n",
+      "                    self._object_map[node.index_id] = node.obj\n",
+      "                    node.obj = None\n",
+      "\n",
+      "    async def ainsert_nodes(\n",
+      "        self, nodes: Sequence[BaseNode], **insert_kwargs: Any\n",
+      "    ) -> None:\n",
+      "        \"\"\"\n",
+      "        Insert nodes.\n",
+      "\n",
+      "        NOTE: overrides BaseIndex.ainsert_nodes.\n",
+      "            VectorStoreIndex only stores nodes in document store\n",
+      "            if vector store does not store text\n",
+      "        \"\"\"\n",
+      "        self._validate_serializable(nodes)\n",
+      "\n",
+      "        with self._callback_manager.as_trace(\"insert_nodes\"):\n",
+      "            await self._async_add_nodes_to_index(\n",
+      "                self._index_struct, nodes, **insert_kwargs\n",
+      "            )\n",
+      "            self._storage_context.index_store.add_index_struct(self._index_struct)\n",
+      "\n",
+      "    def insert_nodes(self, nodes: Sequence[BaseNode], **insert_kwargs: Any) -> None:\n",
+      "        \"\"\"\n",
+      "        Insert nodes.\n",
+      "\n",
+      "        NOTE: overrides BaseIndex.insert_nodes.\n",
+      "            VectorStoreIndex only stores nodes in document store\n",
+      "            if vector store does not store text\n",
+      "        \"\"\"\n",
+      "        self._validate_serializable(nodes)\n",
+      "\n",
+      "        with self._callback_manager.as_trace(\"insert_nodes\"):\n",
+      "            self._insert(nodes, **insert_kwargs)\n",
+      "            self._storage_context.index_store.add_index_struct(self._index_struct)\n",
+      "\n",
+      "    def _delete_node(self, node_id: str, **delete_kwargs: Any) -> None:\n",
+      "        pass\n",
+      "\n",
+      "    async def adelete_nodes(\n",
+      "        self,\n",
+      "        node_ids: List[str],\n",
+      "        delete_from_docstore: bool = False,\n",
+      "        **delete_kwargs: Any,\n",
+      "    ) -> None:\n",
+      "        \"\"\"\n",
+      "        Delete a list of nodes from the index.\n",
+      "\n",
+      "        Args:\n",
+      "            node_ids (List[str]): A list of node_ids from the nodes to delete\n",
+      "\n",
+      "        \"\"\"\n",
+      "        # delete nodes from vector store\n",
+      "        await self._vector_store.adelete_nodes(node_ids, **delete_kwargs)\n",
+      "\n",
+      "        # delete from docstore only if needed\n",
+      "        if (\n",
+      "            not self._vector_store.stores_text or self._store_nodes_override\n",
+      "        ) and delete_from_docstore:\n",
+      "            for node_id in node_ids:\n",
+      "                self._index_struct.delete(node_id)\n",
+      "                await self._docstore.adelete_document(node_id, raise_error=False)\n",
+      "            self._storage_context.index_store.add_index_struct(self._index_struct)\n",
+      "\n",
+      "    def delete_nodes(\n",
+      "        self,\n",
+      "        node_ids: List[str],\n",
+      "        delete_from_docstore: bool = False,\n",
+      "        **delete_kwargs: Any,\n",
+      "    ) -> None:\n",
+      "        \"\"\"\n",
+      "        Delete a list of nodes from the index.\n",
+      "\n",
+      "        Args:\n",
+      "            node_ids (List[str]): A list of node_ids from the nodes to delete\n",
+      "\n",
+      "        \"\"\"\n",
+      "        # delete nodes from vector store\n",
+      "        self._vector_store.delete_nodes(node_ids, **delete_kwargs)\n",
+      "\n",
+      "        # delete from docstore only if needed\n",
+      "        if (\n",
+      "            not self._vector_store.stores_text or self._store_nodes_override\n",
+      "        ) and delete_from_docstore:\n",
+      "            for node_id in node_ids:\n",
+      "                self._index_struct.delete(node_id)\n",
+      "                self._docstore.delete_document(node_id, raise_error=False)\n",
+      "            self._storage_context.index_store.add_index_struct(self._index_struct)\n",
+      "\n",
+      "    def _delete_from_index_struct(self, ref_doc_id: str) -> None:\n",
+      "        # delete from index_struct only if needed\n",
+      "        if not self._vector_store.stores_text or self._store_nodes_override:\n",
+      "            ref_doc_info = self._docstore.get_ref_doc_info(ref_doc_id)\n",
+      "            if ref_doc_info is not None:\n",
+      "                for node_id in ref_doc_info.node_ids:\n",
+      "                    self._index_struct.delete(node_id)\n",
+      "                    self._vector_store.delete(node_id)\n",
+      "\n",
+      "    def _delete_from_docstore(self, ref_doc_id: str) -> None:\n",
+      "        # delete from docstore only if needed\n",
+      "        if not self._vector_store.stores_text or self._store_nodes_override:\n",
+      "            self._docstore.delete_ref_doc(ref_doc_id, raise_error=False)\n",
+      "\n",
+      "    def delete_ref_doc(\n",
+      "        self, ref_doc_id: str, delete_from_docstore: bool = False, **delete_kwargs: Any\n",
+      "    ) -> None:\n",
+      "        \"\"\"Delete a document and it's nodes by using ref_doc_id.\"\"\"\n",
+      "        self._vector_store.delete(ref_doc_id, **delete_kwargs)\n",
+      "        self._delete_from_index_struct(ref_doc_id)\n",
+      "        if delete_from_docstore:\n",
+      "            self._delete_from_docstore(ref_doc_id)\n",
+      "        self._storage_context.index_store.add_index_struct(self._index_struct)\n",
+      "\n",
+      "    async def _adelete_from_index_struct(self, ref_doc_id: str) -> None:\n",
+      "        \"\"\"Delete from index_struct only if needed.\"\"\"\n",
+      "        if not self._vector_store.stores_text or self._store_nodes_override:\n",
+      "            ref_doc_info = await self._docstore.aget_ref_doc_info(ref_doc_id)\n",
+      "            if ref_doc_info is not None:\n",
+      "                for node_id in ref_doc_info.node_ids:\n",
+      "                    self._index_struct.delete(node_id)\n",
+      "                    self._vector_store.delete(node_id)\n",
+      "\n",
+      "    async def _adelete_from_docstore(self, ref_doc_id: str) -> None:\n",
+      "        \"\"\"Delete from docstore only if needed.\"\"\"\n",
+      "        if not self._vector_store.stores_text or self._store_nodes_override:\n",
+      "            await self._docstore.adelete_ref_doc(ref_doc_id, raise_error=False)\n",
+      "\n",
+      "    async def adelete_ref_doc(\n",
+      "        self, ref_doc_id: str, delete_from_docstore: bool = False, **delete_kwargs: Any\n",
+      "    ) -> None:\n",
+      "        \"\"\"Delete a document and it's nodes by using ref_doc_id.\"\"\"\n",
+      "        tasks = [\n",
+      "            self._vector_store.adelete(ref_doc_id, **delete_kwargs),\n",
+      "            self._adelete_from_index_struct(ref_doc_id),\n",
+      "        ]\n",
+      "        if delete_from_docstore:\n",
+      "            tasks.append(self._adelete_from_docstore(ref_doc_id))\n",
+      "\n",
+      "        await asyncio.gather(*tasks)\n",
+      "\n",
+      "        self._storage_context.index_store.add_index_struct(self._index_struct)\n",
+      "\n",
+      "    @property\n",
+      "    def ref_doc_info(self) -> Dict[str, RefDocInfo]:\n",
+      "        \"\"\"Retrieve a dict mapping of ingested documents and their nodes+metadata.\"\"\"\n",
+      "        if not self._vector_store.stores_text or self._store_nodes_override:\n",
+      "            node_doc_ids = list(self.index_struct.nodes_dict.values())\n",
+      "            nodes = self.docstore.get_nodes(node_doc_ids)\n",
+      "\n",
+      "            all_ref_doc_info = {}\n",
+      "            for node in nodes:\n",
+      "                ref_node = node.source_node\n",
+      "                if not ref_node:\n",
+      "                    continue\n",
+      "\n",
+      "                ref_doc_info = self.docstore.get_ref_doc_info(ref_node.node_id)\n",
+      "                if not ref_doc_info:\n",
+      "                    continue\n",
+      "\n",
+      "                all_ref_doc_info[ref_node.node_id] = ref_doc_info\n",
+      "            return all_ref_doc_info\n",
+      "        else:\n",
+      "            raise NotImplementedError(\n",
+      "                \"Vector store integrations that store text in the vector store are \"\n",
+      "                \"not supported by ref_doc_info yet.\"\n",
+      "            )\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "import inspect\n",
+    "print(inspect.getsource(llama_index.core.VectorStoreIndex))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8125e2de",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.11"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

saved_output/2025_08_24.txt

@@ -0,0 +1,52 @@
+Enter a search topic or question (or 'exit'):
+The mind as a terrible master.
+
+**Summary Theme:**
+This collection of excerpts explores the human mind's complex nature, its cognitive processes, perception, memory, and social
+interactions. The texts delve into how our thoughts are shaped by external stimuli, our brain's organizational patterns, and the
+emergence of consciousness. Additionally, they touch on the mind's tendency to create illusions (like "mass delusion") and the
+challenges posed by a distributed brain and decentralized consciousness.
+
+**Matching Files:**
+
+1. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-01-23.txt - The excerpt examines what becomes of an
+incessant critic in the mind, questioning the role of brain functions in creating negative self-perceptions.
+2. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-03-10.txt - The excerpt delves into the journal's
+effect on cognition, implying that it can profoundly influence thought processes even if not actively processing itself.
+3. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-08-18.txt - This excerpt suggests a comparison between
+a mind that is constantly on the move and an overloaded train, emphasizing the lack of central control.
+4. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-03-08.txt - The excerpt explores thoughts as
+"tendrils" that can hold a person and influence their mood and behavior, mirroring the mind's struggle with self-awareness.
+5. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2019-07-03.txt - This excerpt connects the idea of
+"impression management" to evolutionary adaptation, suggesting a mind capable of organizing individuals around "fictions."
+6. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-03-24.txt - The excerpt emphasizes the modularity of
+the mind and preconditioned responses, reflecting on E. Bruce Goldstein's book and its relevance to understanding consciousness.
+7. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-01-06.txt - A contemplation of memory's role as a
+"lump of coal that bears the delicate impression of a leaf," highlighting its complexity and non-linear nature.
+8. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2021-05-04.txt - The excerpt reflects on feelings of
+skepticism about human endeavors and the mind's tendency to imagine conflict, leading to negative self-judgment.
+9. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-01-23.txt - The excerpt references David Foster
+Wallace's quote about the mind as a "terrible master" and explores how individuals who commit suicide often shoot themselves in the
+head, silencing their inner critic.
+10. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-03-08.txt - This excerpt discusses the philosophical
+implications of a distributed brain and decentralized consciousness, questioning the existence of a singular "self" making
+decisions.
+
+
+Source documents:
+
+2009-08-24.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2009-08-24.txt 0.7286187534682154
+2023-01-23.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-01-23.txt 0.7174705749042735
+2023-03-09.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-03-09.txt 0.6905817844827031
+2023-01-06.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-01-06.txt 0.6872058770669452
+2021-05-04.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2021-05-04.txt 0.6866138676376796
+2022-04-17.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2022-04-17.txt 0.6837786406828062
+2025-03-10.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-03-10.txt 0.6825293816922051
+2021-05-02.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2021-05-02.txt 0.6818701242339038
+2025-03-08.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-03-08.txt 0.6804468955664654
+2024-03-24.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-03-24.txt 0.6798798323221176
+2022-02-24.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2022-02-24.txt 0.6779782723066287
+2024-08-18.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-08-18.txt 0.676507830756482
+2019-07-03.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2019-07-03.txt 0.6754137298987061
+2021-12-22.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2021-12-22.txt 0.6747843533262554
+2024-03-24.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-03-24.txt 0.6740836055290546

saved_output/2025_08_27.txt

@@ -0,0 +1,65 @@
+Enter your query (or type 'exit' to quit): It's a weird refuge to refute nationality; to claim that all is a fraud, anyway. Still, it is the most sane reaction right now. The right to walk away. All else is slavery. 
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/docstore.json.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/index_store.json.
+
+Response:
+
+**Summary Theme:**
+The texts explore complex issues related to freedom, equality, and justice, particularly within political and social contexts. 
+They discuss the limitations of current systems in addressing human rights and ethical standards, including prison treatment, 
+racial discrimination, and the expansion of citizenship rights. The texts also delve into the nature of revolutions, questioning 
+whether they benefit a select elite or are instigated by them.
+
+**Matching Files:**
+
+1. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2002-05-09.txt - This text discusses the treatment of 
+prisoners, highlighting a lack of adherence to constitutional standards and due process, as well as addressing issues related to 
+nationality and citizenship.
+
+2. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-06-04.txt - A blog post discussing the idea of 'human 
+nature' in politics, with a focus on the importance of freedom and the critique of a political figure's policies.
+
+3. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-10-13.txt - This passage explores the topic of white 
+male privilege and its implications in business, questioning why it is highlighted while overlooking broader systemic issues.
+
+4. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-01-03.txt - The text delves into the idea of freedom 
+and imagination in the early 20th century, comparing it to the present day and discussing the constraints of democracy and 
+capitalism.
+
+5. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2016-11-09.txt - A text addressing civil rights history 
+and the hate and anger that arise from it, questioning how to respond while avoiding tribalism and degeneration.
+
+6. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-28.txt - Discussing legal issues and the 
+challenges of thinking about human rights in a multicultural context, particularly regarding people who are neither Christians nor 
+infidels.
+
+7. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-01-29.txt - A personal reflection on current 
+political events and the author's difficulties in expressing feelings, tying into discussions of history and psychology.
+
+8. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2001-09-13.txt - This text addresses the justification for 
+violent acts during a perceived war against fundamentalism, emphasizing economic and moral principles over nationhood.
+
+9. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-06-03.txt - A passage on the concept of 
+incommensurability in politics and how consensus processes aim to reconcile different perspectives in practical situations.
+
+10. file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2002-05-09.txt - Discussing the expansion of citizenship 
+rights in American history, highlighting key dates and milestones in this process.
+
+Source documents:
+2002-05-09.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2002-05-09.txt 0.6722719323340611
+2025-06-04.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-06-04.txt 0.6608581763116415
+2024-07-14.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-07-14.txt 0.6475284193414396
+2025-06-04.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-06-04.txt 0.6468059334833061
+2025-06-03.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-06-03.txt 0.6466041920182646
+2016-11-09.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2016-11-09.txt 0.6451955555687188
+2001-09-13.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2001-09-13.txt 0.6433104875230174
+2025-01-04.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-01-04.txt 0.6356563682194852
+2024-10-13.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-10-13.txt 0.6347407640363988
+2025-01-03.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-01-03.txt 0.6336626187333729
+2021-09-16.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2021-09-16.txt 0.6328042502815873
+2025-07-28.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-28.txt 0.6324342333276086
+2025-01-04.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-01-04.txt 0.6317671258192576
+2025-01-29.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-01-29.txt 0.6313280704571994
+2024-06-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-06-20.txt 0.629663790289146
+Query processed in 95 seconds.
+

saved_output/2025_08_28.txt

@@ -0,0 +1,174 @@
+Enter your query (or type 'exit' to quit): I'm looking for the happiest and most joyful passages.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/docstore.json.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/index_store.json.
+
+Response:
+
+**Summary Theme:**
+The author reflects on moments of joy and happiness in their life, exploring themes such as contentment, love, and the beauty of 
+everyday experiences. They express a desire to let themselves be happy every day and find pleasure in creative pursuits like 
+poetry and art appreciation. Despite personal struggles with depression and anxiety, the author emphasizes the importance of 
+finding happiness in one's daily life.
+
+**Matching Files:**
+
+1. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-12-03.txt** — Chloe's smile while praising her 
+piano playing brings joy, highlighting the author's appreciation for small acts of kindness.
+2. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2006-08-11.txt** — The author's day feeding carrots to 
+horses and making pizza with Matthew is described as "fun times, maybe the best ever," showcasing their ability to find joy in 
+simple pleasures.
+3. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-01-23.txt** — Reading poetry and appreciating 
+simple observations brings positive thoughts, indicating a focus on finding happiness through creative pursuits.
+4. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-07-25.txt** — The author reflects on the joys of 
+their life, such as time with family and the love they experienced with T, despite later experiencing heartache.
+5. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2013-02-15.txt** — The passage encourages being joyful, 
+happy, pleased, and glad, aligning with the author's overall theme of finding happiness in various life experiences.
+6. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2019-09-14.txt** — Reflecting on a week of learning, 
+teaching, and feeling curious leads to the realization that one can find happiness every day, emphasizing the author's ability to 
+let themselves be happy.
+7. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2012-09-20.txt** — This file, titled "Ευδαιμονía," 
+contains ancient Greek words related to happiness and well-being, further reinforcing the author's exploration of finding joy in 
+life.
+8. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-29.txt** — The scorching weather and being 
+outside provide a backdrop to the author's ability to find happiness despite potential physical discomfort, demonstrating their 
+resilient outlook.
+9. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-10-09.txt** — The author expresses frustration and 
+depression due to daily interactions but also acknowledges the importance of finding happiness in life, aligning with their 
+broader theme.
+10. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-12-06.txt** — The passage defines happiness as 
+contentment and peacefulness, highlighting the author's pursuit of a joyful life through their experiences.
+
+Source documents:
+2025-07-29.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-29.txt 0.7135682886000794
+2008-12-06.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-12-06.txt 0.7099131243276414
+2009-06-04.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2009-06-04.txt 0.6973211899243362
+2025-08-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-08-20.txt 0.6866097119060084
+2013-02-15.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2013-02-15.txt 0.686259123672228
+2012-09-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2012-09-20.txt 0.6790148415972938
+2015-01-23.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-01-23.txt 0.6761073066656899
+2015-12-03.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-12-03.txt 0.6712531329880593
+2006-08-11.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2006-08-11.txt 0.6613670040827223
+2024-07-25.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-07-25.txt 0.6570111677987235
+2025-08-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-08-20.txt 0.6558116128405127
+2019-09-14.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2019-09-14.txt 0.6549423349658567
+2024-04-03.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-04-03.txt 0.6546862471469852
+2023-07-24.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-07-24.txt 0.6544076938168284
+2025-08-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-08-20.txt 0.6541587448214657
+Query processed in 73 seconds.
+
+
+---
+
+This was a strange failure!
+
+((.venv) ) ~/Library/CloudStorage/Dropbox/nd/ssearch/$ run_query.sh 
+Enter your query (or type 'exit' to quit): Find documents that express feelings of gratitude.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/docstore.json.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/index_store.json.
+
+Response:
+
+**Summary Theme:**
+The query is about finding documents expressing feelings of gratitude. However, it seems there was an error in my interpretation 
+or the context provided, as the dominant themes I identified earlier were related to depression and anxiety rather than gratitude. 
+Based on the given context, the theme that matches the query is related to personal struggles with mental health, particularly 
+feelings of sadness and appreciation for connections. 
+
+**Matching Files:**
+
+1. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-10-09.txt** — Expressed frustration with joggers on the bike 
+path but did not mention gratitude.
+2. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-08-20.txt** — No direct expressions of gratitude found, but a 
+reflection on personal struggles and achievements was present.
+3. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-05-27.txt** — Focuses on negative emotions like anxiety and 
+anger, with no clear expressions of gratitude.
+4. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2013-05-23.txt** — Mentions the joy of helping others achieve their 
+goals, which could be interpreted as a form of appreciation or gratitude for their success and recognition.
+5. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-03-17.txt** — Contains suicidal thoughts and negative 
+feelings, indicating a lack of gratitude.
+6. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-07-16.txt** — Describes feelings of loss and the search for 
+meaning, devoid of expressions of gratitude.
+7. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-03-18.txt** — No clear mentions of gratitude found.
+8. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2007-05-31.txt** — Focuses on career concerns and negative 
+emotions, without expressing gratitude.
+9. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2020-05-13.txt** — Struggles with recognizing others' efforts due 
+to internal bad feelings, which contrasts the idea of gratitude.
+10. **/Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2020-02-01.txt** — Mentions reconnecting with old friendships and 
+family, but there are no explicit expressions of gratitude.
+
+Source documents:
+2025-08-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-08-20.txt 0.6865291287082457
+2008-05-27.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-05-27.txt 0.6707430757786356
+2023-02-17.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2023-02-17.txt 0.6624994985797085
+2025-08-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-08-20.txt 0.6614406157945066
+2025-03-18.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-03-18.txt 0.6589271548285772
+2025-08-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-08-20.txt 0.6583888795181797
+2025-07-28.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-28.txt 0.6575634356770015
+2012-09-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2012-09-20.txt 0.6564913212073614
+2020-05-13.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2020-05-13.txt 0.6563809376620068
+2025-08-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-08-20.txt 0.6549296468531686
+2013-05-23.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2013-05-23.txt 0.653871795081564
+2009-06-04.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2009-06-04.txt 0.6535844277567499
+2007-05-31.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2007-05-31.txt 0.6524713123412845
+2025-07-29.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-29.txt 0.6517446358739963
+2020-02-01.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2020-02-01.txt 0.6514433384900066
+Query processed in 74 seconds.
+
+---
+
+I implemented a regex that srtips the full path:
+
+((.venv) ) ~/Library/CloudStorage/Dropbox/nd/ssearch/$ run_query.sh 
+Enter your query (or type 'exit' to quit): Entries that discuss testing one's limits, especially emotional and mental.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/docstore.json.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/index_store.json.
+
+Response:
+
+**Summary Theme:**
+The dominant theme in this context appears to be an individual exploring their emotions, particularly their mental and emotional 
+boundaries, as well as the impact of societal perceptions on feelings. The writer grapples with anxiety, depression, self-worth, 
+and the fear of inadequacy while also contemplating their own mortality and purpose. They seek to understand and manage their 
+emotions, often viewing them as data or information that can guide survival and informed decision-making.
+
+**Matching Files:**
+
+1. **file_path: ./data/2023-07-16.txt** — Describes the struggle of wrestling with depression for years, emphasizing the search 
+for meaning in a world driven by efficiency and optimization.
+2. **file_path: ./data/2015-03-17.txt** — Mentions suicidal thoughts and feeling overwhelmed by negative emotions, indicating a 
+desire to test one's limits emotionally.
+3. **file_path: ./data/2019-01-14.txt** — Discusses the struggle with controlling impulses and feelings of stress, anxiety, and 
+depression while questioning if one is a prisoner of their biology.
+4. **file_path: ./data/2025-06-17.txt** — Explores the concept of feeling out personal boundaries and accepting dissonance, which 
+could be seen as testing emotional limits.
+5. **file_path: ./data/2025-08-20.txt** — Mentions the interest in anarchy while being invested in capital markets and holding a 
+tenured position, indicating a potential exploration of one's limits.
+6. **file_path: ./data/2017-12-06.txt** — Expresses suicidal thoughts due to burnout and emotional exhaustion, suggesting an 
+attempt to test personal boundaries.
+7. **file_path: ./data/2017-12-16.txt** — Explores the desire to be a better person and the struggle with balance, potentially 
+indicating a journey of testing one's limits.
+8. **file_path: ./data/2017-04-13.txt** — Focuses on worrying about hypotheticals and imagined fights, suggesting an exploration 
+of personal boundaries and emotional limits.
+9. **file_path: ./data/2024-09-20.txt** — Admitted to having depressive thoughts despite appearing jovial, indicating a discussion 
+on testing the limits of one's mental health.
+10. **file_path: ./data/2025-08-20.txt** — The computer facilitates artistic innovation by freeing the artist from conventional 
+"mental ready-mades," enabling the production of new assemblages of shapes and colors.
+
+Source documents:
+2019-01-28.txt ./data/2019-01-28.txt 0.7091032318236316
+2003-03-09.txt ./data/2003-03-09.txt 0.6819464422399241
+2025-08-20.txt ./data/2025-08-20.txt 0.6796124657599102
+2025-08-20.txt ./data/2025-08-20.txt 0.6785008440538487
+2017-04-13.txt ./data/2017-04-13.txt 0.6768340197245936
+2022-05-06.txt ./data/2022-05-06.txt 0.6750801120630013
+2023-01-27.txt ./data/2023-01-27.txt 0.6703347559624786
+2023-03-14.txt ./data/2023-03-14.txt 0.668340287632692
+2025-06-17.txt ./data/2025-06-17.txt 0.6656929175939117
+2025-08-20.txt ./data/2025-08-20.txt 0.6645024849162311
+2023-07-16.txt ./data/2023-07-16.txt 0.6618312766890652
+2021-04-15.txt ./data/2021-04-15.txt 0.661171288633267
+2025-08-20.txt ./data/2025-08-20.txt 0.6600615010925119
+2019-01-14.txt ./data/2019-01-14.txt 0.6563840810491259
+2025-05-23.txt ./data/2025-05-23.txt 0.6561484407217757
+Query processed in 79 seconds.
+

saved_output/2025_08_30.txt

@@ -0,0 +1,124 @@
+((.venv) ) ~/Library/CloudStorage/Dropbox/nd/ssearch/$ run_query.sh 
+Enter your query (or type 'exit' to quit): You are a machine and you can program yourself.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/docstore.json.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/index_store.json.
+
+Response:
+
+### Summary Theme
+The dominant theme from the provided context revolves around the concept of human agency and the transformative power of 
+self-programming, often referred to as "YOU ARE A MACHINE AND YOU CAN PROGRAM YOURSELF". This phrase encapsulates the idea that 
+individuals have the capability to upgrade their own mental and emotional states through conscious effort and learning. The 
+context explores this theme through various angles, including philosophical reflections on storytelling and human existence, 
+discussions of meditation and personal growth, and explorations of information replication and self-replication systems like DNA 
+and memes.
+
+### Matching Files
+1. **file_path: ./data/2024-09-21.txt** - The passage discusses Von Neumann's theory of self-replication, which ties into the idea 
+that individuals can replicate and "program" themselves through learning and development.
+2. **file_path: ./data/2024-08-19.txt** - This snippet features a series of repetitions of "YOU ARE A MACHINE AND YOU CAN PROGRAM 
+YOURSELF," emphasizing the transformative power of self-programming and personal growth.
+3. **file_path: ./data/2024-03-11.txt** - The author contemplates purpose, meaning, and the act of programming oneself through 
+writing and reflection, aligning with the self-programming theme.
+4. **file_path: ./data/2023-07-16.txt** - A robot's inner struggles, including a desire to explore feelings and understand its own 
+existence, hint at the idea of self-programming and personal development.
+5. **file_path: ./data/2024-04-11.txt** - The author's fascination with the materiality of computation suggests a connection to 
+understanding human existence through self-programming and self-replication.
+6. **file_path: ./data/2024-02-13.txt** - The extensive list of tasks and projects the author wants to accomplish reflects a drive 
+for personal growth, akin to self-programming.
+7. **file_path: ./data/2024-08-19.txt** - A discussion of information degradation and the relationship between DNA, memes, and 
+information replication hints at a deeper understanding through self-programming.
+8. **file_path: ./data/2025-01-24.txt** - A detailed account of typing a program onto IBM cards and working with early computers 
+emphasizes the labor involved in creating and learning from technology, which can be seen as self-programming through the 
+acquisition of knowledge.
+9. **file_path: ./data/2025-02-05.txt** - This passage raises questions about truth and human agency, which are closely tied to 
+the idea of self-programming and the ability to shape one's own existence through conscious effort.
+10. **file_path: ./data/2022-01-22.txt** - The author relates meditation to "operating system updates," illustrating how 
+self-programming can lead to improved performance and functionality in the mind, much like a computer's software.
+
+Source documents:
+2021-02-12.txt ./data/2021-02-12.txt 0.7813853524305151
+2021-03-12.txt ./data/2021-03-12.txt 0.7170262020422805
+2021-03-22.txt ./data/2021-03-22.txt 0.7080438590471859
+2025-02-05.txt ./data/2025-02-05.txt 0.700772619041579
+2022-01-22.txt ./data/2022-01-22.txt 0.6946526808142116
+2024-08-19.txt ./data/2024-08-19.txt 0.6909295863339957
+2024-09-21.txt ./data/2024-09-21.txt 0.6863798746276172
+2024-08-19.txt ./data/2024-08-19.txt 0.6811521050296564
+2024-03-11.txt ./data/2024-03-11.txt 0.6776553751255855
+2023-07-16.txt ./data/2023-07-16.txt 0.6734772841938028
+2021-03-01.txt ./data/2021-03-01.txt 0.6703476982962236
+2025-05-26.txt ./data/2025-05-26.txt 0.6699061717036373
+2024-02-13.txt ./data/2024-02-13.txt 0.6675189407579228
+2025-01-24.txt ./data/2025-01-24.txt 0.6661259191158485
+2024-04-11.txt ./data/2024-04-11.txt 0.664854046786588
+Query processed in 97 seconds.
+
+Enter your query (or type 'exit' to quit): Summarize passages related to questions about truth and human agency.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/docstore.json.
+Loading llama_index.core.storage.kvstore.simple_kvstore from ./storage_exp/index_store.json.
+
+Response:
+
+**Summary Theme:**
+The texts explore the relationship between truth, knowledge, and human agency, highlighting how our understanding of reality is 
+shaped by interpretation and negotiation rather than an objective standard. They question the nature of self-awareness and 
+consciousness, suggesting that it arises from independent facts and truths beyond individual control. This perspective challenges 
+traditional notions of knowledge and ethics, suggesting that shared meaning and identity might be more influential than facts 
+themselves. The theme also delves into the implications of these ideas for governance, society, and the integration of diverse 
+epistemic frameworks.
+
+**Matching Files:**
+
+1. ./data/2025-03-08.txt - The passage emphasizes that truth is not fixed but a product of human interpretation, challenging the 
+idea of absolute knowledge and suggesting that our beliefs are subject to revision and refinement as we learn more about ourselves 
+and the world.
+
+2. ./data/2025-02-14.txt - This snippet discusses truth as a social construct, prompting questions about ethical epistemology and 
+the potential role of AI in shaping epistemic environments. It also introduces the idea that knowledge is a product of shared 
+meaning and identity rather than just facts.
+
+3. ./data/2025-02-14.txt - The text includes a quote suggesting that our concepts are self-created, which can both empower and 
+limit us, fostering critical thinking and personal responsibility while also potentially leading to disorientation and existential 
+uncertainty.
+
+4. ./data/2025-03-08.txt - The implications of truth being a social construct are explored further, including the idea that 
+fact-checking alone doesn't address shared meaning and identity, leading to discussions about ethics, society, governance, and the 
+role of AI in shaping epistemic environments.
+
+5. ./data/2025-03-08.txt - This file delves into the concept of "we are supplicants to our own fiction," exploring how humans 
+create meaning systems that can be comforting but potentially misleading or limiting, and emphasizing the importance of 
+self-awareness for critical thinking and personal growth.
+
+6. ./data/2025-02-14.txt - The text raises questions about the nature of truth, reality, and human agency, inviting contemplation 
+on whether our stories are mere constructs or reflections of deeper aspects of human existence, and how we can navigate 
+storytelling to uncover accurate portrayals.
+
+7. ./data/2025-03-08.txt - This passage continues the discussion on the implications of a social construct of truth, including the 
+potential role of AI in mediating competing epistemic frameworks and reducing polarization.
+
+8. ./data/2010-12-30.txt - A statement that "there is no meaning and no purpose in life" is discussed, reflecting existentialist 
+philosophies, and raising questions about reconciling the tension between fiction and the search for meaning and purpose.
+
+9. ./data/2025-03-08.txt - This snippet presents a list of resources related to knowledge, power, and institutions, including 
+Michel Foucault, Donna Haraway, Stefan Lorenz Sorgner, William James, and Noam Chomsky, reflecting on the relationship between 
+power and knowledge throughout history.
+
+Source documents:
+2006-12-27.txt ./data/2006-12-27.txt 0.7103349341421636
+2025-02-14.txt ./data/2025-02-14.txt 0.6992770918721224
+2025-03-08.txt ./data/2025-03-08.txt 0.686001774445945
+2025-02-14.txt ./data/2025-02-14.txt 0.6743349162123844
+2025-03-08.txt ./data/2025-03-08.txt 0.6733934128354977
+2025-03-08.txt ./data/2025-03-08.txt 0.6706689033144045
+2025-02-05.txt ./data/2025-02-05.txt 0.6702486733668184
+2025-01-04.txt ./data/2025-01-04.txt 0.6699433363201491
+2025-02-14.txt ./data/2025-02-14.txt 0.6691576672622886
+2025-03-08.txt ./data/2025-03-08.txt 0.6670311145975771
+2008-04-22.txt ./data/2008-04-22.txt 0.665624998848253
+2025-02-06.txt ./data/2025-02-06.txt 0.6654464518589284
+2010-12-30.txt ./data/2010-12-30.txt 0.663147445474458
+2004-02-15.txt ./data/2004-02-15.txt 0.6625948924633361
+2025-02-06.txt ./data/2025-02-06.txt 0.6608789240071589
+Query processed in 92 seconds.
+

saved_output/README.txt

@@ -0,0 +1 @@
+This directory contains collections of interesting output from the nd_ssearch query engine.

saved_output/compare command-r7b.md

@@ -0,0 +1,113 @@
+# Generaterd by llama3.1:8B
+
+Enter a search topic or question (or 'exit'):
+Simplicity, peace, and acceptance.
+
+**Summary Theme**
+
+The dominant theme that emerges from the provided context is the pursuit of simplicity, peace, and acceptance as a means to find
+meaning and contentment in life. The excerpts suggest that individuals often struggle with existential crises, anxiety, and
+dissatisfaction, but through various philosophical and spiritual practices, they seek to cultivate a sense of inner peace and
+harmony.
+
+**Matching Files**
+
+1. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-09-22.txt** — Suzuki discusses the importance of
+letting go of intellectual pursuits and embracing the simplicity of life, feeling the "power of life" and being content with its
+evolution.
+2. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-02-12.txt** — The author reflects on their emptiness
+and yearning for something deeper, wondering if they can relish in this feeling and explore it further.
+3. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-02-27.txt** — Life is described as pain, but the
+author finds solace in God and feels a deep connection to something universal, seeking to do good for others.
+4. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2012-09-08.txt** — The text advises living life with
+virtue above pleasure and tranquility above happiness, finding contentment in the present moment.
+5. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2007-05-30.txt** — The author reflects on their
+existential crisis and seeks to find meaning through meditation, exploring the wonder of life and the universe.
+6. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-02-05.txt** — Alan Watts' measured pace and calm
+tone are mentioned as soothing, inviting listeners to slow down and absorb his philosophical musings.
+7. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2003-11-11.txt** — The author experiences a sense of
+dissolution of the self and acceptance of mortality through music, finding hope in the peaceful and calm aspects of human
+existence.
+8. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2011-04-20.txt** — The text presents two contrasting
+choices for raising children: to learn how to fight or navigate complex social interactions, leading to exhaustion and missteps.
+9. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2003-11-11.txt** — Music is mentioned as a means to
+connect with those who have passed and accept one's own mortality, finding hope in acceptance.
+10. **file_path: /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-07-09.txt** — The author reflects on their own
+flaws and limitations, seeking to cultivate peace and tranquility through meditation and philosophical insights.
+
+These files prioritize the pursuit of simplicity, peace, and acceptance as a means to find meaning and contentment in life.
+
+
+Source documents:
+
+2008-09-22.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-09-22.txt 0.6942251115364034
+2008-12-06.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-12-06.txt 0.69329826339918
+2006-01-18.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2006-01-18.txt 0.6928289731862756
+2024-07-09.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-07-09.txt 0.6851764077064736
+2024-10-21.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-10-21.txt 0.6850957394630768
+2021-05-15.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2021-05-15.txt 0.6792933726282656
+2025-07-28.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-28.txt 0.677805020905822
+2008-02-27.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-02-27.txt 0.6758790431127354
+2025-02-05.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-02-05.txt 0.6751368515758781
+2003-11-11.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2003-11-11.txt 0.6741012107117246
+2015-02-12.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-02-12.txt 0.6724595748596391
+2012-09-08.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2012-09-08.txt 0.6709374012666305
+2007-05-30.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2007-05-30.txt 0.6705586893086012
+2003-11-11.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2003-11-11.txt 0.6683483221331056
+2011-04-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2011-04-20.txt 0.6679376031898634
+
+
+# Generated by command-r7b
+
+Enter a search topic or question (or 'exit'):
+Simplicity, peace, and acceptance.
+
+**Summary Theme:**
+The dominant themes from the provided context revolve around personal growth, spirituality, and finding contentment through
+simplicity, peace, and acceptance. The text emphasizes the idea that one should let go of intellectual pursuits and anxiety to feel
+more content with life's challenges and find inner peace. It explores the concepts of Zen, tranquility, and the power of meditation
+as a path to achieving this state of being. Additionally, the texts touch on the impact of personal experiences (like the birth of
+a child) in fostering a sense of calm and connection with the divine.
+
+**Matching Files:**
+
+1. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-09-22.txt - D.T. Suzuki's excerpt highlights the importance of
+letting go of intellectual pursuits and focusing on the present moment to achieve peace and contentment, aligning with themes of
+simplicity and acceptance.
+2. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-02-12.txt - This file discusses the emptiness and yearning for
+deeper meaning, suggesting a journey towards personal peace and content in one's spiritual quest.
+3. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-12-06.txt - The excerpt promotes happiness through contentment
+and peacefulness, echoing the themes of simplicity and acceptance.
+4. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2003-11-11.txt - The text explores the dissolution of the self and
+finding peace in spiritual experiences, relating to themes of simplification and acceptance.
+5. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-10-21.txt - A reflection on human nature and violence, this
+passage emphasizes the importance of letting go of aggression and finding peace through a peaceful mind.
+6. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-28.txt - This file mentions consensus-based processes and
+Quaker values, which align with the themes of acceptance and tranquility in decision-making.
+7. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2012-09-08.txt - The excerpt promotes the idea of regulating thoughts
+and actions with a view towards mortality, highlighting simplicity and tranquility in preparation for life's end.
+8. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2007-05-30.txt - The text discusses existential crises and finding
+meaning through meditation and therapy, contributing to the theme of simplification through introspection.
+9. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2011-04-20.txt - While more focused on child-rearing, this passage
+hints at themes of acceptance and tranquility in navigating complex social interactions.
+10. /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2003-11-11.txt - The exploration of prayer and spiritual experiences
+leads to the theme of acceptance as one sheds the veneer of life, revealing deeper human existence.
+
+
+Source documents:
+
+2008-09-22.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-09-22.txt 0.6942251115364034
+2008-12-06.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-12-06.txt 0.69329826339918
+2006-01-18.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2006-01-18.txt 0.6928289731862756
+2024-07-09.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-07-09.txt 0.6851764077064736
+2024-10-21.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2024-10-21.txt 0.6850957394630768
+2021-05-15.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2021-05-15.txt 0.6792933726282656
+2025-07-28.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-07-28.txt 0.677805020905822
+2008-02-27.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2008-02-27.txt 0.6758790431127354
+2025-02-05.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2025-02-05.txt 0.6751368515758781
+2003-11-11.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2003-11-11.txt 0.6741012107117246
+2015-02-12.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2015-02-12.txt 0.6724595748596391
+2012-09-08.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2012-09-08.txt 0.6709374012666305
+2007-05-30.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2007-05-30.txt 0.6705586893086012
+2003-11-11.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2003-11-11.txt 0.6683483221331056
+2011-04-20.txt /Users/furst/Library/CloudStorage/Dropbox/nd/ssearch/data/2011-04-20.txt 0.6679376031898634

tests/README.md

@@ -0,0 +1,29 @@
+# LLM Comparison Tests
+
+Query used for all tests: **"Passages that quote Louis Menand."**
+Script: `query_hybrid_bm25_v4.py` (hybrid BM25 + vector, cross-encoder re-rank to top 15)
+
+Retrieval is identical across all tests (same 15 chunks, same scores).
+Only the LLM synthesis step differs.
+
+File naming: `results_<model>_t<temperature>.txt`
+
+## Results
+
+| File | LLM | Temperature | Files cited | Time | Notes |
+|------|-----|-------------|-------------|------|-------|
+| `results_gpt4omini_t0.1.txt` | gpt-4o-mini (OpenAI API) | 0.1 | 6 | 44s | Broader coverage, structured numbered list, drew from chunks ranked as low as #14 |
+| `results_commandr7b_t0.8.txt` | command-r7b (Ollama local) | 0.8 (default) | 2 | 78s | Focused on top chunks, reproduced exact quotes verbatim |
+| `results_gpt4omini_t0.3.txt` | gpt-4o-mini (OpenAI API) | 0.3 | 6 | 45s | Very similar to 0.1 run -- same 6 files, same structure, slightly more interpretive phrasing |
+| `results_commandr7b_t0.3.txt` | command-r7b (Ollama local) | 0.3 | 6 | 94s | Major improvement over 0.8 default: cited 6 files (was 2), drew from lower-ranked chunks including 2024-08-03 (#15) |
+
+## Observations
+
+- Lowering command-r7b from 0.8 to 0.3 dramatically improved breadth (2 → 6 files cited).
+  At 0.8, the model focused narrowly on the top-scored chunks. At 0.3, it used the full
+  context window much more effectively.
+- gpt-4o-mini showed little difference between 0.1 and 0.3. It already used the full
+  context at 0.1. The API model appears less sensitive to temperature for this task.
+- command-r7b at 0.3 took longer (94s vs 78s), likely due to generating more text.
+- At temperature=0.3, both models converge on similar quality: 6 files cited, good
+  coverage of the context window, mix of direct quotes and paraphrases.

tests/results_commandr7b_t0.3.txt

@@ -0,0 +1,54 @@
+Query: --query Passages that quote Louis Menand.
+Vector: 20, BM25: 20, overlap: 7, merged: 33, re-ranked to: 15
+
+Response:
+
+The provided excerpts contain several references to Louis Menand's ideas and quotes. Here are the specific passages:
+
+- In file_path: ./data/2025-11-04.txt, you can find a direct quote from Louis Menand: "We created God, and then pretended that God 
+created us. We hypostatized our own concept and turned it into something “out there” whose commandments (which we made up) we 
+struggle to understand and obey. We are supplicants to our own fiction."
+- In file_path: ./data/2025-02-14.txt, there is a reference to Menand's quote about the human tendency to create and interact with 
+abstract ideas as if they are tangible realities.
+- In file_path: ./data/2022-08-14.txt, another excerpt from Menand's work is mentioned: "We created God, and then we pretended 
+that God created us."
+- In file_path: ./data/2025-07-27.txt, the author discusses Menand's quote about the creation of fictions and the role of 
+organization in human culture.
+- In file_path: ./data/2024-09-06.txt, there is a mention of Menand's writing style, describing him as "witty and serious."
+- In file_path: ./data/2025-02-14.txt, the poem takes a wistful tone, hinting at the fragility of human attachment to concepts, 
+which is reminiscent of existential crises and Menand's ideas on hypostasis.
+- In file_path: ./data/2025-07-27.txt, the author further elaborates on Menand's quote, emphasizing the human tendency to create 
+and interact with fictions.
+- In file_path: ./data/2024-08-03.txt, there is a reference to Louis Menand's book "The Free World" and its exploration of art, 
+literature, and culture in the 20th century.
+
+All these excerpts contribute to understanding Louis Menand's ideas on hypostasis, human creation of fictions, and the complex 
+relationship between stories, beliefs, and reality.
+
+Files contributing to the answer:
+- ./data/2025-11-04.txt
+- ./data/2025-02-14.txt
+- ./data/2022-08-14.txt
+- ./data/2025-07-27.txt
+- ./data/2024-09-06.txt
+- ./data/2025-02-14.txt
+- ./data/2025-07-27.txt
+- ./data/2024-08-03.txt
+
+Source documents:
+2025-11-04.txt  ./data/2025-11-04.txt  3.303
+2025-02-14.txt  ./data/2025-02-14.txt  3.144
+2022-08-14.txt  ./data/2022-08-14.txt  2.183
+2021-07-04.txt  ./data/2021-07-04.txt  1.595
+2025-02-14.txt  ./data/2025-02-14.txt  1.504
+2025-07-27.txt  ./data/2025-07-27.txt  0.171
+2024-07-26.txt  ./data/2024-07-26.txt  -0.969
+2024-09-06.txt  ./data/2024-09-06.txt  -1.661
+2024-04-08.txt  ./data/2024-04-08.txt  -2.017
+2025-02-05.txt  ./data/2025-02-05.txt  -2.027
+2022-04-17.txt  ./data/2022-04-17.txt  -2.054
+2023-07-01.txt  ./data/2023-07-01.txt  -2.284
+2023-01-06.txt  ./data/2023-01-06.txt  -2.315
+2024-09-04.txt  ./data/2024-09-04.txt  -2.379
+2024-08-03.txt  ./data/2024-08-03.txt  -2.391
+Query processed in 94 seconds.

tests/results_commandr7b_t0.8.txt

@@ -0,0 +1,58 @@
+Query: --query Passages that quote Louis Menand.
+Vector: 20, BM25: 20, overlap: 7, merged: 33, re-ranked to: 15
+
+Response:
+
+The provided excerpts feature multiple references to Louis Menand's quote about hypostasis and our creation of God as a fiction. 
+Here are the relevant passages:
+
+- **"We created God, and then pretended that God created us."** **(file_path: ./data/2025-11-04.txt)**
+
+This excerpt introduces Menand's quote as the starting point for an exploration of how humans create and interact with abstract 
+concepts.
+
+- **"We hypostatized our own concept and turned it into something “out there” whose commandments (which we made up) we struggle to 
+understand and obey."** **(file_path: ./data/2025-11-04.txt)**
+
+This quote delves further into the idea of turning concepts into something tangible, emphasizing the struggle to understand and 
+follow the rules we create.
+
+- **"We are supplicants to our own fiction."** **(file_path: ./data/2025-11-04.txt)**
+
+The passage concludes by emphasizing the concept of being subservient to our own creations, highlighting the complex relationship 
+between human stories and reality.
+
+- **"We created God, and then pretended that God created us."** **(file_path: ./data/2022-08-14.txt)**
+
+This excerpt reiterates the core idea from Menand's quote in a slightly different phrasing.
+
+- **"We hypostatized our own concept and turned it into something “out there” whose commandments, which we also made up, we 
+struggle to understand and obey."** **(file_path: ./data/2022-08-14.txt)**
+
+This quote emphasizes the process of creating rules and struggling to comprehend them while adhering to them.
+
+All these excerpts contribute to exploring Menand's perspective on how humans create, project, and interact with abstract 
+concepts, highlighting the complex relationship between stories, beliefs, and reality.
+
+**Files contributing:**
+
+* **2025-11-04.txt**
+* **2022-08-14.txt**
+
+Source documents:
+2025-11-04.txt  ./data/2025-11-04.txt  3.303
+2025-02-14.txt  ./data/2025-02-14.txt  3.144
+2022-08-14.txt  ./data/2022-08-14.txt  2.183
+2021-07-04.txt  ./data/2021-07-04.txt  1.595
+2025-02-14.txt  ./data/2025-02-14.txt  1.504
+2025-07-27.txt  ./data/2025-07-27.txt  0.171
+2024-07-26.txt  ./data/2024-07-26.txt  -0.969
+2024-09-06.txt  ./data/2024-09-06.txt  -1.661
+2024-04-08.txt  ./data/2024-04-08.txt  -2.017
+2025-02-05.txt  ./data/2025-02-05.txt  -2.027
+2022-04-17.txt  ./data/2022-04-17.txt  -2.054
+2023-07-01.txt  ./data/2023-07-01.txt  -2.284
+2023-01-06.txt  ./data/2023-01-06.txt  -2.315
+2024-09-04.txt  ./data/2024-09-04.txt  -2.379
+2024-08-03.txt  ./data/2024-08-03.txt  -2.391
+Query processed in 78 seconds.

tests/results_gpt4omini_t0.1.txt

@@ -0,0 +1,65 @@
+run_query.sh
+Passages that quote Louis Menand.
+
+Query: --query Passages that quote Louis Menand.
+Vector: 20, BM25: 20, overlap: 7, merged: 33, re-ranked to: 15
+
+Response:
+
+The excerpts provided contain several passages that quote or reference Louis Menand, particularly focusing on his ideas about 
+hypostasis and the human relationship with concepts such as God and societal structures. Here are the relevant passages:
+
+1. **File: ./data/2025-11-04.txt**
+   - This excerpt includes the quote: "We created God, and then pretended that God created us. We hypostatized our own concept and 
+turned it into something 'out there' whose commandments (which we made up) we struggle to understand and obey. We are supplicants 
+to our own fiction." It discusses the parallels between this idea and other societal constructs like democracy and politics.
+
+2. **File: ./data/2025-02-14.txt**
+   - The passage reiterates Menand's quote about hypostasis, emphasizing how humans have taken abstract concepts and given them a 
+separate existence, which allows for worship and obedience. It reflects on the implications of this process on our understanding 
+of reality.
+
+3. **File: ./data/2022-08-14.txt**
+   - This excerpt discusses Menand's critique of how people perceive forces as external and inevitable, which are actually human 
+creations. It includes the same quote about God and hypostasis, highlighting the reification of human concepts.
+
+4. **File: ./data/2025-07-27.txt**
+   - Here, Menand's quote is referenced in the context of discussing narratives and organizational structures, emphasizing the 
+fictional nature of societal constructs.
+
+5. **File: ./data/2025-02-05.txt**
+   - This excerpt paraphrases Menand's idea that we are "supplicants to our own fictions," linking it to the broader theme of 
+storytelling in human culture.
+
+6. **File: ./data/2024-09-04.txt**
+   - Although not a direct quote, this excerpt mentions Menand's work in relation to AI and copyright, indicating his relevance in 
+contemporary discussions.
+
+In summary, the passages collectively illustrate Menand's exploration of how humans create and interact with abstract concepts, 
+particularly the notion of God, and how these constructs influence our understanding of reality and societal structures.
+
+**Files that contributed to the answer:**
+- **2025-11-04.txt**: Discusses the quote in relation to societal constructs.
+- **2025-02-14.txt**: Reiterates the quote and its implications on reality.
+- **2022-08-14.txt**: Analyzes Menand's critique of perception and includes the quote.
+- **2025-07-27.txt**: References the quote in the context of narratives and organization.
+- **2025-02-05.txt**: Paraphrases Menand's idea about fictions in human culture.
+- **2024-09-04.txt**: Mentions Menand's relevance in discussions about AI.
+
+Source documents:
+2025-11-04.txt  ./data/2025-11-04.txt  3.303
+2025-02-14.txt  ./data/2025-02-14.txt  3.144
+2022-08-14.txt  ./data/2022-08-14.txt  2.183
+2021-07-04.txt  ./data/2021-07-04.txt  1.595
+2025-02-14.txt  ./data/2025-02-14.txt  1.504
+2025-07-27.txt  ./data/2025-07-27.txt  0.171
+2024-07-26.txt  ./data/2024-07-26.txt  -0.969
+2024-09-06.txt  ./data/2024-09-06.txt  -1.661
+2024-04-08.txt  ./data/2024-04-08.txt  -2.017
+2025-02-05.txt  ./data/2025-02-05.txt  -2.027
+2022-04-17.txt  ./data/2022-04-17.txt  -2.054
+2023-07-01.txt  ./data/2023-07-01.txt  -2.284
+2023-01-06.txt  ./data/2023-01-06.txt  -2.315
+2024-09-04.txt  ./data/2024-09-04.txt  -2.379
+2024-08-03.txt  ./data/2024-08-03.txt  -2.391
+Query processed in 44 seconds.

tests/results_gpt4omini_t0.3.txt

@@ -0,0 +1,63 @@
+Query: --query Passages that quote Louis Menand.
+Vector: 20, BM25: 20, overlap: 7, merged: 33, re-ranked to: 15
+
+Response:
+
+The excerpts contain several passages that quote or reference Louis Menand, particularly focusing on his ideas about hypostasis 
+and the human relationship with concepts such as God and societal structures. Here are the relevant passages:
+
+1. **File: ./data/2025-11-04.txt**
+   - This excerpt includes the quote: "We created God, and then pretended that God created us. We hypostatized our own concept and 
+turned it into something 'out there' whose commandments (which we made up) we struggle to understand and obey. We are supplicants 
+to our own fiction." It discusses the parallels between this idea and other societal constructs like democracy and politics.
+
+2. **File: ./data/2025-02-14.txt**
+   - The passage reiterates Menand's quote about hypostasis and emphasizes how humans have created a sense of distance from their 
+own creations, allowing for worship or rebellion against them. It reflects on the implications of this process for understanding 
+reality and human experience.
+
+3. **File: ./data/2022-08-14.txt**
+   - This excerpt discusses Menand's "Free World," specifically pages 335-339, where he critiques how people perceive external 
+forces as inevitable, which are actually human creations. It includes the same quote about God and hypostasis, highlighting the 
+idea that these constructs are reified as "the way things are."
+
+4. **File: ./data/2025-07-27.txt**
+   - This excerpt references Menand's quote in the context of discussing anti-capitalist themes and the narratives that organize 
+society, emphasizing the fictional nature of these constructs.
+
+5. **File: ./data/2025-02-05.txt**
+   - Here, Menand's notion that we are "supplicants to our own fictions" is paraphrased, relating it to the broader role of 
+storytelling in human culture and how we create and live by the narratives we construct.
+
+6. **File: ./data/2024-09-04.txt**
+   - This excerpt mentions Menand in the context of discussing AI and copyright, though it does not quote him directly. It 
+highlights his relevance in contemporary discussions about technology.
+
+### Summary of Contributions:
+- **2025-11-04.txt**: Introduces Menand's quote and connects it to societal constructs.
+- **2025-02-14.txt**: Explores the implications of Menand's ideas on reality and human experience.
+- **2022-08-14.txt**: Discusses Menand's critique of how humans perceive societal constructs as external forces.
+- **2025-07-27.txt**: Relates Menand's quote to anti-capitalist themes and societal narratives.
+- **2025-02-05.txt**: Paraphrases Menand's ideas in the context of storytelling in culture.
+- **2024-09-04.txt**: Mentions Menand in discussions about AI, highlighting his ongoing relevance.
+
+Overall, these excerpts collectively illustrate Menand's critical perspective on how humans create and relate to their own 
+constructs, emphasizing the fictional nature of many societal narratives.
+
+Source documents:
+2025-11-04.txt  ./data/2025-11-04.txt  3.303
+2025-02-14.txt  ./data/2025-02-14.txt  3.144
+2022-08-14.txt  ./data/2022-08-14.txt  2.183
+2021-07-04.txt  ./data/2021-07-04.txt  1.595
+2025-02-14.txt  ./data/2025-02-14.txt  1.504
+2025-07-27.txt  ./data/2025-07-27.txt  0.171
+2024-07-26.txt  ./data/2024-07-26.txt  -0.969
+2024-09-06.txt  ./data/2024-09-06.txt  -1.661
+2024-04-08.txt  ./data/2024-04-08.txt  -2.017
+2025-02-05.txt  ./data/2025-02-05.txt  -2.027
+2022-04-17.txt  ./data/2022-04-17.txt  -2.054
+2023-07-01.txt  ./data/2023-07-01.txt  -2.284
+2023-01-06.txt  ./data/2023-01-06.txt  -2.315
+2024-09-04.txt  ./data/2024-09-04.txt  -2.379
+2024-08-03.txt  ./data/2024-08-03.txt  -2.391
+Query processed in 45 seconds.