Shell script run_retrieve.sh for non-LLM

gneration queries (returns only chunks), track
development notes and README.

README.md

@@ -33,7 +33,7 @@ ssearch/
 ├── archived/                   # Superseded script versions
 ├── saved_output/               # Saved query results and model comparisons
 ├── requirements.txt            # Python dependencies
-├── devlog.txt                  # Development log and experimental findings
+├── devlog.md                   # Development log and experimental findings
 └── *.ipynb                     # Jupyter notebooks (HyDE, metrics, sandbox)
 ```
 
@@ -198,4 +198,4 @@ Three Jupyter notebooks document exploration and analysis:
 - **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.txt` for detailed development notes and experimental findings.
+See `devlog.md` for detailed development notes and experimental findings.

deploy_public.sh

@@ -3,9 +3,11 @@
 #
 # Usage: ./deploy_public.sh ["optional commit message"]
 #
-# Checks out an orphan public branch, copies the public files from main,
+# Checks out the public branch, updates it with public files from main,
-# generates a public README (stripping private sections), commits, and
+# generates a public README (stripping private sections), commits if
-# force-pushes to origin. Then switches back to main.
+# 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
 
@@ -50,12 +52,14 @@ MAIN_HEAD=$(git rev-parse --short HEAD)
 
 echo "Deploying main ($MAIN_HEAD) -> $BRANCH..."
 
-# Delete local public branch if it exists
+# Check out public branch, or create orphan if it doesn't exist yet
-git branch -D "$BRANCH" 2>/dev/null || true
+if git show-ref --verify --quiet "refs/heads/$BRANCH"; then
-
+    git checkout "$BRANCH"
-# Create fresh orphan
+else
-git checkout --orphan "$BRANCH"
+    echo "No local $BRANCH branch — creating orphan..."
-git rm -rf . >/dev/null 2>&1 || true
+    git checkout --orphan "$BRANCH"
+    git rm -rf . >/dev/null 2>&1 || true
+fi
 
 # Copy public files from main
 for f in "${PUBLIC_FILES[@]}"; do
@@ -74,22 +78,23 @@ awk '
 skip                    { next }
 /archived\//            { next }
 /saved_output\//        { next }
-/devlog\.txt/           { 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 "${PUBLIC_FILES[@]}" README.md
-git commit -m "$COMMIT_MSG
 
-Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>"
+# Commit only if there are changes
-
+if git diff --cached --quiet; then
-# Push
+    echo "No changes to deploy."
-git push --force "$REMOTE" "$BRANCH"
+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
-
-echo ""
-echo "Done. Deployed main ($MAIN_HEAD) -> $REMOTE/$BRANCH"

run_retrieve.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+# This shell script will handle I/O for the python query engine
+# It will take a query and return the formatted results
+
+# E.M.F. August 2025
+
+# Usage: ./run_query.sh 
+
+QUERY_SCRIPT="retrieve.py"
+
+echo -e "$QUERY_SCRIPT -- retrieve vector store chunks based on similaity + BM25 with reranking.\n"
+
+# Loop until input is "exit"
+while true; do
+    read -p "Enter your query (or type 'exit' to quit): " query
+    if [ "$query" == "exit" ] || [ "$query" == "quit" ] || [ "$query" == "" ] ; then
+        echo "Exiting..."
+        break
+    fi
+    time_start=$(date +%s)
+
+    # Call the python script with the query and format the output
+    python3 $QUERY_SCRIPT --query "$query" | \
+        expand | sed -E 's|(.* )(.*/data)|\1./data|' | fold -s -w 131
+    
+    time_end=$(date +%s)
+    elapsed=$((time_end - time_start))
+    echo -e "Query processed in $elapsed seconds.\n"
+done