From 94928fba0e050f71ed2def60bdbe134f87f060b5 Mon Sep 17 00:00:00 2001
From: Divik Chotani <divikchotani@g.ucla.edu>
Date: Sun, 23 Feb 2025 17:43:06 -0800
Subject: [PATCH 1/5] Improve local annotations setup and dependency handling

- Modified `pa.sh` for compatibility with local annotations
- Added `local-annotations-library-documentation.md` with setup instructions
- Introduced `local-or-pypi.sh` to configure package installation mode for local annotations

Signed-off-by: Divik Chotani divikchotani@g.ucla.edu
Signed-off-by: Divik Chotani <divikchotani@g.ucla.edu>
---
 .gitignore                                 |  3 +
 local-annotations-library-documentation.md | 83 ++++++++++++++++++++++
 local-or-pypi.sh                           | 58 +++++++++++++++
 pa.sh                                      |  4 ++
 requirements.txt                           |  2 +-
 5 files changed, 149 insertions(+), 1 deletion(-)
 create mode 100644 local-annotations-library-documentation.md
 create mode 100755 local-or-pypi.sh

diff --git a/.gitignore b/.gitignore
index e3c9c8857..cee5eab49 100644
--- a/.gitignore
+++ b/.gitignore
@@ -56,3 +56,6 @@ runtime/dgsh-tee
 .vscode/*
 .idea/*
 .vs/*
+
+#venv
+venv/*
diff --git a/local-annotations-library-documentation.md b/local-annotations-library-documentation.md
new file mode 100644
index 000000000..477c2afd8
--- /dev/null
+++ b/local-annotations-library-documentation.md
@@ -0,0 +1,83 @@
+# PaSh Setup and Execution Guide
+
+This guide walks you through **setting up and running PaSh** in an isolated environment, including:
+- Installing dependencies
+- Setting up the virtual environment (`venv`)
+- Running `setup-pash.sh` to install required tools
+- Exporting `PASH_TOP`
+- Running the custom `local-or-pypi.sh` script to configure package installation
+
+---
+
+## **🔹 Step 1: Clone PaSh Repository (If Not Already Cloned)**
+If you haven't already cloned PaSh, do so with:
+
+```sh
+git clone https://github.com/binpash/pash.git ~/pash
+cd ~/pash
+```
+
+## **🔹 Step 2: Set Up the Virtual Environment (venv)**
+PaSh requires Python dependencies that should be installed inside a virtual environment.
+
+Create and activate a virtual environment:
+
+```sh
+python3 -m venv venv
+source venv/bin/activate
+```
+
+
+## **🔹 Step 3: Run setup-pash.sh to Install Dependencies and Build Runtime Tools**
+PaSh includes a setup script that installs necessary dependencies and compiles missing runtime binaries.
+
+Run:
+
+```sh
+./scripts/setup-pash.sh
+```
+
+
+
+Do not forget to export before using pash: `export PASH_TOP=/home/your-username/pash`
+To make this persistent across terminal sessions, add it to your shell configuration file:
+
+```sh
+echo 'export PASH_TOP=/home/your-username/pash >> ~/.bashrc
+source ~/.bashrc
+```
+
+## **🔹 Step 5: Run local-or-pypi.sh to Configure Package Installation**
+PaSh provides a script to configure whether dependencies should be installed locally (using a cloned repository) or from PyPI.
+
+To use local dependencies:
+
+```sh
+./local-or-pypi.sh local
+```
+
+This will:
+- Check if `~/annotations` exists.
+- If not, clone it from GitHub.
+- Update `requirements.txt` to use the local `annotations` repo.
+
+To use PyPI dependencies:
+
+```sh
+./local-or-pypi.sh pypi
+```
+
+
+## **🔹 Step 6: Run PaSh**
+Once everything is set up, test PaSh with:
+
+```sh
+cd ~/pash/evaluation/intro
+time $PASH_TOP/pa.sh $PASH_TOP/evaluation/intro/hello-world.sh
+```
+
+### **Expected Output:**
+
+```sh
+3712
+
diff --git a/local-or-pypi.sh b/local-or-pypi.sh
new file mode 100755
index 000000000..7cc865cc2
--- /dev/null
+++ b/local-or-pypi.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+# Define the requirements file path
+REQ_FILE="requirements.txt"
+ANNOTATIONS_DIR="$HOME/annotations"
+
+# Check if an argument is provided
+if [ $# -ne 1 ]; then
+    echo "Usage: $0 <local|pypi>"
+    exit 1
+fi
+
+# If using local mode, ensure ~/annotations exists
+if [ "$1" == "local" ]; then
+    if [ ! -d "$ANNOTATIONS_DIR" ]; then
+        echo "🔍 ~/annotations not found. Cloning annotations repository..."
+        git clone https://github.com/binpash/annotations.git "$ANNOTATIONS_DIR"
+
+        # Check if cloning was successful
+        if [ $? -ne 0 ]; then
+            echo "❌ Failed to clone annotations repository."
+            exit 1
+        fi
+    else
+        echo "✅ ~/annotations already exists. Skipping clone."
+    fi
+
+    # Get the absolute path
+    ANNOTATIONS_PATH=$(realpath "$ANNOTATIONS_DIR")
+fi
+
+# Write the correct `requirements.txt`
+if [ "$1" == "pypi" ]; then
+    echo "📦 Writing PyPI requirements to $REQ_FILE..."
+    cat <<EOF > "$REQ_FILE"
+graphviz
+libdash
+pash-annotations==0.2.2
+shasta==0.1.0
+sh-expand>=0.1.6
+EOF
+elif [ "$1" == "local" ]; then
+    echo "💻 Writing local development requirements to $REQ_FILE..."
+    cat <<EOF > "$REQ_FILE"
+graphviz
+libdash
+shasta==0.1.0
+sh-expand>=0.1.6
+-e $ANNOTATIONS_PATH
+EOF
+else
+    echo "❌ Invalid argument: $1"
+    echo "Usage: $0 <local|pypi>"
+    exit 1
+fi
+
+echo "✅ Requirements file updated successfully."
+
diff --git a/pa.sh b/pa.sh
index 609dad786..e873a8cab 100755
--- a/pa.sh
+++ b/pa.sh
@@ -3,7 +3,10 @@
 export PASH_TOP=${PASH_TOP:-${BASH_SOURCE%/*}}
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib/"
 # point to the local downloaded folders
+export PYTHONPATH=$PASH_TOP/venv/lib/python3.12/site-packages:$PYTHONPATH
 export PYTHONPATH="${PASH_TOP}/python_pkgs/:${PYTHONPATH}"
+export PYTHONPATH=~/annotations:$PYTHONPATH
+
 ## Register the signal handlers, we can add more signals here
 trap kill_all SIGTERM SIGINT
 
@@ -74,3 +77,4 @@ if [ "$PASH_DEBUG_LEVEL" -eq 0 ]; then
 fi
 
 (exit "$pash_exit_code")
+
diff --git a/requirements.txt b/requirements.txt
index 4fee3bebe..af7cdfc8d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 graphviz
 libdash
-pash-annotations==0.2.2
 shasta==0.1.0
 sh-expand>=0.1.6
+-e /home/divikchotani.linux/annotations

From cccca4e2ecfa1f9a1fc9bad9c8c1ff0614037219 Mon Sep 17 00:00:00 2001
From: Divik Chotani <divik.chotani@gmail.com>
Date: Fri, 28 Feb 2025 00:47:25 -0800
Subject: [PATCH 2/5] Improve local annotations setup and dependency handling

- Modified `pa.sh` for compatibility with local annotations
- Added `local-annotations-library-documentation.md` with setup instructions
- Introduced `setup-local.sh` to configure package installation mode for local annotations

Signed-off-by: Divik Chotani <divik.chotani@gmail.com>
---
 README.md                                     |   4 +
 ...local-annotations-library-documentation.md |  79 +++++++++++++
 local-annotations-library-documentation.md    |  83 --------------
 local-annotations-path.txt                    |   1 +
 local-or-pypi.sh                              |  58 ----------
 pa.sh                                         |  49 +++++++-
 requirements.txt                              |   3 +-
 setup-local.sh                                | 106 ++++++++++++++++++
 8 files changed, 235 insertions(+), 148 deletions(-)
 create mode 100644 docs/local-annotations-library-documentation.md
 delete mode 100644 local-annotations-library-documentation.md
 create mode 100644 local-annotations-path.txt
 delete mode 100755 local-or-pypi.sh
 create mode 100755 setup-local.sh

diff --git a/README.md b/README.md
index 1f0a84478..0553249d5 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,10 @@ export PASH_TOP="$PWD/pash/"
 
 For more details, manual installation, or other platforms see [installation instructions](./docs/install).
 
+## Running with a local annotations library
+
+To run with a local version of the library, please refer to the documentation [local annotations setup and usage](docs/local-annotations-library-documentation.md) 
+
 ## Repo Structure
 
 This repo hosts the core `pash` development. The structure is as follows:
diff --git a/docs/local-annotations-library-documentation.md b/docs/local-annotations-library-documentation.md
new file mode 100644
index 000000000..0b5b0655f
--- /dev/null
+++ b/docs/local-annotations-library-documentation.md
@@ -0,0 +1,79 @@
+# PaSh Setup and Execution Guide
+
+This guide walks you through **setting up and running PaSh**, including:
+- Installing dependencies
+- Running `setup-pash.sh` to install required tools
+- Exporting `PASH_TOP`
+- Running the `setup-annotations.sh` script to configure package installation with an optional `--local-annotations` flag
+
+---
+
+## **🔹 Step 1: Clone PaSh Repository (If Not Already Cloned)**
+If you haven't already cloned PaSh, do so with:
+
+```sh
+git clone https://github.com/binpash/pash.git
+cd pash
+```
+
+## **🔹 Step 2: Run setup-pash.sh to Install Dependencies and Build Runtime Tools**
+PaSh includes a setup script that installs necessary dependencies and compiles missing runtime binaries.
+
+Run:
+
+```sh
+./scripts/setup-pash.sh
+```
+
+Before using PaSh, set the `PASH_TOP` environment variable to the directory where PaSh is stored:
+
+```sh
+export PASH_TOP=/path/to/pash
+```
+
+To make this persistent across terminal sessions, add it to your shell configuration file:
+
+```sh
+echo 'export PASH_TOP=/path/to/pash' >> ~/.bashrc
+source ~/.bashrc
+```
+
+## **🔹 Step 3: Run setup-annotations.sh to Configure Package Installation**
+PaSh provides a script to configure dependencies, including an option to install local annotations.
+
+To install dependencies normally:
+
+```sh
+./setup-annotations.sh
+```
+
+To install local annotations:
+```sh
+./setup-local.sh
+```
+
+To install local annotations:
+```sh
+./pash.sh --local-annotations
+```
+
+This will:
+- Clone the `annotations` repository as a **sibling** to `pash` (i.e., in the same parent directory), or in a specified path if provided.
+- Update `requirements.txt` to add the local `annotations` repo.
+
+## **🔹 Step 4: Run PaSh**
+Once everything is set up, test PaSh with:
+
+```sh
+cd pash/evaluation/intro
+time $PASH_TOP/pa.sh $PASH_TOP/evaluation/intro/hello-world.sh
+```
+
+You can also run the full PaSh test suite:
+```sh
+$PASH_TOP/evaluation/tests/test_evaluation_scripts.sh
+```
+For more details, check the test script here:  
+[PaSh Evaluation Tests](https://github.com/binpash/pash/blob/main/evaluation/tests/test_evaluation_scripts.sh)
+
+
diff --git a/local-annotations-library-documentation.md b/local-annotations-library-documentation.md
deleted file mode 100644
index 477c2afd8..000000000
--- a/local-annotations-library-documentation.md
+++ /dev/null
@@ -1,83 +0,0 @@
-# PaSh Setup and Execution Guide
-
-This guide walks you through **setting up and running PaSh** in an isolated environment, including:
-- Installing dependencies
-- Setting up the virtual environment (`venv`)
-- Running `setup-pash.sh` to install required tools
-- Exporting `PASH_TOP`
-- Running the custom `local-or-pypi.sh` script to configure package installation
-
----
-
-## **🔹 Step 1: Clone PaSh Repository (If Not Already Cloned)**
-If you haven't already cloned PaSh, do so with:
-
-```sh
-git clone https://github.com/binpash/pash.git ~/pash
-cd ~/pash
-```
-
-## **🔹 Step 2: Set Up the Virtual Environment (venv)**
-PaSh requires Python dependencies that should be installed inside a virtual environment.
-
-Create and activate a virtual environment:
-
-```sh
-python3 -m venv venv
-source venv/bin/activate
-```
-
-
-## **🔹 Step 3: Run setup-pash.sh to Install Dependencies and Build Runtime Tools**
-PaSh includes a setup script that installs necessary dependencies and compiles missing runtime binaries.
-
-Run:
-
-```sh
-./scripts/setup-pash.sh
-```
-
-
-
-Do not forget to export before using pash: `export PASH_TOP=/home/your-username/pash`
-To make this persistent across terminal sessions, add it to your shell configuration file:
-
-```sh
-echo 'export PASH_TOP=/home/your-username/pash >> ~/.bashrc
-source ~/.bashrc
-```
-
-## **🔹 Step 5: Run local-or-pypi.sh to Configure Package Installation**
-PaSh provides a script to configure whether dependencies should be installed locally (using a cloned repository) or from PyPI.
-
-To use local dependencies:
-
-```sh
-./local-or-pypi.sh local
-```
-
-This will:
-- Check if `~/annotations` exists.
-- If not, clone it from GitHub.
-- Update `requirements.txt` to use the local `annotations` repo.
-
-To use PyPI dependencies:
-
-```sh
-./local-or-pypi.sh pypi
-```
-
-
-## **🔹 Step 6: Run PaSh**
-Once everything is set up, test PaSh with:
-
-```sh
-cd ~/pash/evaluation/intro
-time $PASH_TOP/pa.sh $PASH_TOP/evaluation/intro/hello-world.sh
-```
-
-### **Expected Output:**
-
-```sh
-3712
-
diff --git a/local-annotations-path.txt b/local-annotations-path.txt
new file mode 100644
index 000000000..cd2fd8737
--- /dev/null
+++ b/local-annotations-path.txt
@@ -0,0 +1 @@
+/home/divikchotani.linux/annotations
diff --git a/local-or-pypi.sh b/local-or-pypi.sh
deleted file mode 100755
index 7cc865cc2..000000000
--- a/local-or-pypi.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/bash
-
-# Define the requirements file path
-REQ_FILE="requirements.txt"
-ANNOTATIONS_DIR="$HOME/annotations"
-
-# Check if an argument is provided
-if [ $# -ne 1 ]; then
-    echo "Usage: $0 <local|pypi>"
-    exit 1
-fi
-
-# If using local mode, ensure ~/annotations exists
-if [ "$1" == "local" ]; then
-    if [ ! -d "$ANNOTATIONS_DIR" ]; then
-        echo "🔍 ~/annotations not found. Cloning annotations repository..."
-        git clone https://github.com/binpash/annotations.git "$ANNOTATIONS_DIR"
-
-        # Check if cloning was successful
-        if [ $? -ne 0 ]; then
-            echo "❌ Failed to clone annotations repository."
-            exit 1
-        fi
-    else
-        echo "✅ ~/annotations already exists. Skipping clone."
-    fi
-
-    # Get the absolute path
-    ANNOTATIONS_PATH=$(realpath "$ANNOTATIONS_DIR")
-fi
-
-# Write the correct `requirements.txt`
-if [ "$1" == "pypi" ]; then
-    echo "📦 Writing PyPI requirements to $REQ_FILE..."
-    cat <<EOF > "$REQ_FILE"
-graphviz
-libdash
-pash-annotations==0.2.2
-shasta==0.1.0
-sh-expand>=0.1.6
-EOF
-elif [ "$1" == "local" ]; then
-    echo "💻 Writing local development requirements to $REQ_FILE..."
-    cat <<EOF > "$REQ_FILE"
-graphviz
-libdash
-shasta==0.1.0
-sh-expand>=0.1.6
--e $ANNOTATIONS_PATH
-EOF
-else
-    echo "❌ Invalid argument: $1"
-    echo "Usage: $0 <local|pypi>"
-    exit 1
-fi
-
-echo "✅ Requirements file updated successfully."
-
diff --git a/pa.sh b/pa.sh
index e873a8cab..755e73f4a 100755
--- a/pa.sh
+++ b/pa.sh
@@ -3,9 +3,24 @@
 export PASH_TOP=${PASH_TOP:-${BASH_SOURCE%/*}}
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib/"
 # point to the local downloaded folders
-export PYTHONPATH=$PASH_TOP/venv/lib/python3.12/site-packages:$PYTHONPATH
 export PYTHONPATH="${PASH_TOP}/python_pkgs/:${PYTHONPATH}"
-export PYTHONPATH=~/annotations:$PYTHONPATH
+export ANNOTATIONS_PATH=$([ -f "$PASH_TOP/local-annotations-path.txt" ] && tr -d '[:space:]' < "$PASH_TOP/local-annotations-path.txt")
+#export PYTHONPATH="$ANNOTATIONS_PATH:$PYTHONPATH"
+trap cleanup EXIT
+
+## Function to restore `requirements.txt` on script exit
+cleanup() {
+    if [ -f "$PASH_TOP/requirements_backup.txt" ]; then
+        mv "$PASH_TOP/requirements_backup.txt" "$PASH_TOP/requirements.txt"
+    fi
+
+    if [ "$PASH_DEBUG_LEVEL" -eq 0 ]; then
+        rm -rf "${PASH_TMP_PREFIX}"
+    fi
+}
+
+## Backup `requirements.txt`
+cp "$PASH_TOP/requirements.txt" "$PASH_TOP/requirements_backup.txt"
 
 ## Register the signal handlers, we can add more signals here
 trap kill_all SIGTERM SIGINT
@@ -27,7 +42,25 @@ if [ "$#" -eq 1 ] && [ "$1" = "--init" ]; then
   "$PASH_TOP"/compiler/superoptimize.sh
   exit
 fi
-
+parsed_args=()
+skip_flag=0
+
+
+##This will check if use-local was passed in as a flag, and appropriately use the correct annotations library
+for arg in "$@"; do
+    if [ "$arg" == "--local-annotations" ]; then
+        sed -i 's/^pash-annotations.*/#&/' $PASH_TOP/requirements.txt
+        skip_flag=1
+	export PYTHONPATH="$ANNOTATIONS_PATH:$PYTHONPATH"
+	continue
+    fi
+    parsed_args+=("$arg")
+done
+
+if [ "$skip_flag" -eq 0 ]; then
+    sed -i "s|-e $ANNOTATIONS_PATH|#-e $ANNOTATIONS_PATH|" $PASH_TOP/requirements.txt
+fi
+cat $PASH_TOP/requirements.txt
 if ! command -v python3 &> /dev/null
 then
     echo "Python >=3 could not be found"
@@ -55,17 +88,17 @@ export DAEMON_SOCKET="${PASH_TMP_PREFIX}/daemon_socket"
 export DSPASH_SOCKET="${PASH_TMP_PREFIX}/dspash_socket"
 
 ## Initialize all things necessary for pash to execute (logging/functions/etc)
-source "$PASH_TOP/compiler/orchestrator_runtime/pash_init_setup.sh" "$@"
+source "$PASH_TOP/compiler/orchestrator_runtime/pash_init_setup.sh" "${parsed_args[@]}"
 
 ## This starts a different server depending on the configuration
 if [ "$show_version" -eq 0 ]; then
   ## Exports $daemon_pid
-  start_server "$@"
+  start_server "${parsed_args[@]}"
 fi
 
 ## Restore the umask before executing
 umask "$old_umask"
-PASH_FROM_SH="pa.sh" python3 -S "$PASH_TOP/compiler/pash.py" "$@"
+PASH_FROM_SH="pa.sh" python3 -S "$PASH_TOP/compiler/pash.py" "${parsed_args[@]}"
 pash_exit_code=$?
 if [ "$show_version" -eq 0 ]; then
   cleanup_server "${daemon_pid}"
@@ -76,5 +109,9 @@ if [ "$PASH_DEBUG_LEVEL" -eq 0 ]; then
   rm -rf "${PASH_TMP_PREFIX}"
 fi
 
+sed -i 's/^#\(pash-annotations.*\)$/\1/' "$PASH_TOP/requirements.txt"
+sed -i "s|^#-e $ANNOTATIONS_PATH|-e $ANNOTATIONS_PATH|" "$PASH_TOP/requirements.txt"
+
 (exit "$pash_exit_code")
 
+
diff --git a/requirements.txt b/requirements.txt
index af7cdfc8d..31197a9f9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,6 @@
 graphviz
 libdash
+pash-annotations==0.2.2
 shasta==0.1.0
 sh-expand>=0.1.6
--e /home/divikchotani.linux/annotations
+
diff --git a/setup-local.sh b/setup-local.sh
new file mode 100755
index 000000000..21a660a9f
--- /dev/null
+++ b/setup-local.sh
@@ -0,0 +1,106 @@
+# #!/bin/bash
+
+# # Define the requirements file path
+# REQ_FILE="requirements.txt"
+
+# # Determine PaSh top directory
+# PASH_TOP=$(dirname "$(realpath "$0")")
+
+# # Default annotations directory (sibling of PASH_TOP)
+# DEFAULT_ANNOTATIONS_DIR="$(dirname "$PASH_TOP")/annotations"
+
+# # Use user-provided path if given, otherwise use default
+# if [ -n "$2" ]; then
+#     ANNOTATIONS_DIR="$2"
+#     ANNOTATIONS_DIR=$(realpath "$ANNOTATIONS_DIR")
+# else
+#     ANNOTATIONS_DIR="$DEFAULT_ANNOTATIONS_DIR"
+# fi
+
+# echo "📂 Annotations directory set to: $ANNOTATIONS_DIR"
+
+# # Check if at least one argument is provided
+# if [ $# -lt 1 ]; then
+#     echo "Usage: $0 <local|pypi> [annotations_dir]"
+#     exit 1
+# fi
+
+# # Store the current version of pash-annotations only if using pypi mode or if it is for the first time
+# if [ "$1" == "pypi" ] && [ ! -s pash-annotations.version ]; then
+#     grep 'pash-annotations' requirements.txt > pash-annotations.version
+# fi
+
+
+# # Ensure the annotations directory exists for local mode
+# if [ "$1" == "local" ]; then
+#     if [ ! -d "$ANNOTATIONS_DIR" ]; then
+#         echo "🔍 $ANNOTATIONS_DIR not found. Cloning annotations repository..."
+#         git clone https://github.com/binpash/annotations.git "$ANNOTATIONS_DIR"
+
+#         if [ $? -ne 0 ]; then
+#             echo "❌ Failed to clone annotations repository."
+#             exit 1
+#         fi
+#     else
+#         echo "✅ $ANNOTATIONS_DIR already exists. Skipping clone."
+#     fi
+
+#     # Get the absolute path
+#     ANNOTATIONS_PATH=$(realpath "$ANNOTATIONS_DIR")
+# fi
+
+# # Generate `requirements.txt` dynamically
+# echo "🔄 Generating $REQ_FILE..."
+
+# # Copy base requirements
+# cp requirements.base.txt $REQ_FILE
+
+# # If local mode is selected, add the editable annotation repo
+# if [ "$1" == "local" ]; then
+#     echo "-e $ANNOTATIONS_PATH" >> $REQ_FILE
+#     echo "✅ Local annotations added to $REQ_FILE"
+# else
+#     # Ensure `pash-annotations` is only added once
+#     if ! grep -q 'pash-annotations' $REQ_FILE; then
+#         cat pash-annotations.version >> $REQ_FILE
+#     fi
+#     echo "✅ Using PyPI annotations: $(cat pash-annotations.version)"
+# fi
+
+#!/bin/bash
+
+# Define the requirements file path
+REQ_FILE="requirements.txt"
+
+# Determine PaSh top directory
+PASH_TOP=$(dirname "$(realpath "$0")")
+
+# Default annotations directory (sibling of PASH_TOP)
+DEFAULT_ANNOTATIONS_DIR="$(dirname "$PASH_TOP")/annotations"
+
+# Use user-provided path if given, otherwise use default
+if [ -n "$1" ]; then
+    ANNOTATIONS_DIR="$1"
+    ANNOTATIONS_DIR=$(realpath "$ANNOTATIONS_DIR")
+else
+    ANNOTATIONS_DIR="$DEFAULT_ANNOTATIONS_DIR"
+fi
+
+echo "📂 Annotations directory set to: $ANNOTATIONS_DIR"
+
+# Always clone the repository to the specified or default location
+echo "🔄 Downloading annotations repository..."
+rm -rf "$ANNOTATIONS_DIR"
+git clone https://github.com/binpash/annotations.git "$ANNOTATIONS_DIR"
+
+if [ $? -ne 0 ]; then
+    echo "❌ Failed to clone annotations repository."
+    exit 1
+fi
+
+# Get the absolute path
+ANNOTATIONS_PATH=$(realpath "$ANNOTATIONS_DIR")
+echo $ANNOTATIONS_PATH > local-annotations-path.txt
+echo "✅ Annotations repository cloned to: $ANNOTATIONS_PATH"
+grep -qxF "$ANNOTATIONS_PATH" requirements.txt || echo -e "\n-e $ANNOTATIONS_PATH" >> requirements.txt
+

From a606d7b070cc3ebc608103489ad0bf3948cb6eb0 Mon Sep 17 00:00:00 2001
From: Divik Chotani <108592052+DivikChotani@users.noreply.github.com>
Date: Fri, 28 Feb 2025 02:44:01 -0800
Subject: [PATCH 3/5] Update local-annotations-library-documentation.md

minor change to readme
---
 docs/local-annotations-library-documentation.md | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/docs/local-annotations-library-documentation.md b/docs/local-annotations-library-documentation.md
index 0b5b0655f..4262a74bf 100644
--- a/docs/local-annotations-library-documentation.md
+++ b/docs/local-annotations-library-documentation.md
@@ -43,20 +43,11 @@ PaSh provides a script to configure dependencies, including an option to install
 
 To install dependencies normally:
 
-```sh
-./setup-annotations.sh
-```
-
 To install local annotations:
 ```sh
 ./setup-local.sh
 ```
 
-To install local annotations:
-```sh
-./pash.sh --local-annotations
-```
-
 This will:
 - Clone the `annotations` repository as a **sibling** to `pash` (i.e., in the same parent directory), or in a specified path if provided.
 - Update `requirements.txt` to add the local `annotations` repo.
@@ -69,6 +60,12 @@ cd pash/evaluation/intro
 time $PASH_TOP/pa.sh $PASH_TOP/evaluation/intro/hello-world.sh
 ```
 
+To run it with local annotation:
+```sh
+cd pash/evaluation/intro
+time $PASH_TOP/pa.sh $PASH_TOP/evaluation/intro/hello-world.sh --local-annotations
+```
+
 You can also run the full PaSh test suite:
 ```sh
 $PASH_TOP/evaluation/tests/test_evaluation_scripts.sh

From a5623cf4cae1241304bdce65bd42dc1698708f3f Mon Sep 17 00:00:00 2001
From: Divik Chotani <divik.chotani@gmail.com>
Date: Fri, 28 Feb 2025 12:30:40 -0800
Subject: [PATCH 4/5] add --local-annotations-dir support for dynamic
 annotation loading

- Implemented `--local-annotations-dir` to allow dynamic switching of annotation.
- Updated `pash_init_setup.sh` to adjust `PYTHONPATH` based on user input.
- Allowed `cli.py` to recognize and prioritize local annotations when provided.
- Ensured clean handling of `requirements.txt`, avoiding unnecessary modifications.

Signed-off-by: Divik Chotani divikchotani@g.ucla.edu
Signed-off-by: Divik Chotani <divik.chotani@gmail.com>
---
 .gitignore                                    |  3 +
 compiler/cli.py                               |  8 +++
 .../orchestrator_runtime/pash_init_setup.sh   | 22 ++++++
 pa.sh                                         | 14 ++--
 setup-local.sh                                | 71 +------------------
 5 files changed, 43 insertions(+), 75 deletions(-)

diff --git a/.gitignore b/.gitignore
index cee5eab49..0d22043b4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -59,3 +59,6 @@ runtime/dgsh-tee
 
 #venv
 venv/*
+
+# Ignore local annotations path
+local-annotations-path.txt
\ No newline at end of file
diff --git a/compiler/cli.py b/compiler/cli.py
index bfab6c988..ed596494d 100644
--- a/compiler/cli.py
+++ b/compiler/cli.py
@@ -215,6 +215,14 @@ def __init__(self, *args, **kwargs):
             help=" output the preprocessed script",
             action="store_true",
         )
+        self.add_argument(
+            "--local-annotations-dir",
+            help="Specify a local annotations directory instead of using the default one",
+            nargs="?",  # <-- Makes it optional (accepts zero or one argument)
+            const="",  # <-- Allows flag usage without an argument
+            type=str,
+            default=None,
+        )
         self.add_argument(
             "--interactive",
             help="Executes the script using an interactive internal shell session (experimental)",
diff --git a/compiler/orchestrator_runtime/pash_init_setup.sh b/compiler/orchestrator_runtime/pash_init_setup.sh
index 966474a5c..6b61c6e6a 100644
--- a/compiler/orchestrator_runtime/pash_init_setup.sh
+++ b/compiler/orchestrator_runtime/pash_init_setup.sh
@@ -23,6 +23,7 @@ export pash_daemon_communicates_through_unix_pipes_flag=0
 export pash_speculative_flag=0
 export show_version=0
 export distributed_exec=0
+export local_annotations=0
 
 for item in "$@"
 do
@@ -87,11 +88,27 @@ do
     if [ "--distributed_exec" == "$item" ]; then
         export distributed_exec=1
     fi
+
+    if [ "--local-annotations-dir" == "$item" ]; then
+        shift
+        export ANNOTATIONS_PATH=$(realpath "$2")
+        export local_annotations=1
+        export PYTHONPATH="$ANNOTATIONS_PATH:$PYTHONPATH"
+        #echo "✅ Using local annotations directory: $ANNOTATIONS_PATH"
+    fi
 done
 
 ## `pash_redir_output` and `pash_redir_all_output` are strictly for logging.
 ##
 ## They do not execute their arguments if there is no debugging.
+if [ "$local_annotations" -eq 1 ]; then
+    # Comment out the PyPI-installed `pash-annotations`
+    sed -i 's/^pash-annotations.*/#&/' "$PASH_TOP/requirements.txt"
+
+    # Add the local annotations path only if not already in `requirements.txt`
+    grep -qxF "-e $ANNOTATIONS_PATH" "$PASH_TOP/requirements.txt" || echo "-e $ANNOTATIONS_PATH" >> "$PASH_TOP/requirements.txt"
+fi
+
 if [ "$PASH_DEBUG_LEVEL" -eq 0 ]; then
     pash_redir_output()
     {
@@ -221,6 +238,11 @@ else
     {
         local daemon_pid=$1
         ## Only wait for daemon if it lives (it might be dead, rip)
+
+        ##bring back the pypi annotations and remove the local annotations library
+        sed -i 's/^#\(pash-annotations.*\)$/\1/' "$PASH_TOP/requirements.txt"
+        sed -i "\|^-e $ANNOTATIONS_PATH|d" "$PASH_TOP/requirements.txt"
+
         if ps -p "$daemon_pid" > /dev/null
         then
             ## Send and receive from daemon
diff --git a/pa.sh b/pa.sh
index 755e73f4a..280681884 100755
--- a/pa.sh
+++ b/pa.sh
@@ -42,8 +42,6 @@ if [ "$#" -eq 1 ] && [ "$1" = "--init" ]; then
   "$PASH_TOP"/compiler/superoptimize.sh
   exit
 fi
-parsed_args=()
-skip_flag=0
 
 
 ##This will check if use-local was passed in as a flag, and appropriately use the correct annotations library
@@ -88,17 +86,23 @@ export DAEMON_SOCKET="${PASH_TMP_PREFIX}/daemon_socket"
 export DSPASH_SOCKET="${PASH_TMP_PREFIX}/dspash_socket"
 
 ## Initialize all things necessary for pash to execute (logging/functions/etc)
-source "$PASH_TOP/compiler/orchestrator_runtime/pash_init_setup.sh" "${parsed_args[@]}"
+source "$PASH_TOP/compiler/orchestrator_runtime/pash_init_setup.sh" "$@"
+
+# Read annotations path if set
+
+#echo $PYTHONPATH
+
+# Ensure the local annotations directory is in `PYTHONPATH`
 
 ## This starts a different server depending on the configuration
 if [ "$show_version" -eq 0 ]; then
   ## Exports $daemon_pid
-  start_server "${parsed_args[@]}"
+  start_server "$@"
 fi
 
 ## Restore the umask before executing
 umask "$old_umask"
-PASH_FROM_SH="pa.sh" python3 -S "$PASH_TOP/compiler/pash.py" "${parsed_args[@]}"
+PASH_FROM_SH="pa.sh" python3 -S "$PASH_TOP/compiler/pash.py" "$@"
 pash_exit_code=$?
 if [ "$show_version" -eq 0 ]; then
   cleanup_server "${daemon_pid}"
diff --git a/setup-local.sh b/setup-local.sh
index 21a660a9f..9ee37916b 100755
--- a/setup-local.sh
+++ b/setup-local.sh
@@ -1,72 +1,3 @@
-# #!/bin/bash
-
-# # Define the requirements file path
-# REQ_FILE="requirements.txt"
-
-# # Determine PaSh top directory
-# PASH_TOP=$(dirname "$(realpath "$0")")
-
-# # Default annotations directory (sibling of PASH_TOP)
-# DEFAULT_ANNOTATIONS_DIR="$(dirname "$PASH_TOP")/annotations"
-
-# # Use user-provided path if given, otherwise use default
-# if [ -n "$2" ]; then
-#     ANNOTATIONS_DIR="$2"
-#     ANNOTATIONS_DIR=$(realpath "$ANNOTATIONS_DIR")
-# else
-#     ANNOTATIONS_DIR="$DEFAULT_ANNOTATIONS_DIR"
-# fi
-
-# echo "📂 Annotations directory set to: $ANNOTATIONS_DIR"
-
-# # Check if at least one argument is provided
-# if [ $# -lt 1 ]; then
-#     echo "Usage: $0 <local|pypi> [annotations_dir]"
-#     exit 1
-# fi
-
-# # Store the current version of pash-annotations only if using pypi mode or if it is for the first time
-# if [ "$1" == "pypi" ] && [ ! -s pash-annotations.version ]; then
-#     grep 'pash-annotations' requirements.txt > pash-annotations.version
-# fi
-
-
-# # Ensure the annotations directory exists for local mode
-# if [ "$1" == "local" ]; then
-#     if [ ! -d "$ANNOTATIONS_DIR" ]; then
-#         echo "🔍 $ANNOTATIONS_DIR not found. Cloning annotations repository..."
-#         git clone https://github.com/binpash/annotations.git "$ANNOTATIONS_DIR"
-
-#         if [ $? -ne 0 ]; then
-#             echo "❌ Failed to clone annotations repository."
-#             exit 1
-#         fi
-#     else
-#         echo "✅ $ANNOTATIONS_DIR already exists. Skipping clone."
-#     fi
-
-#     # Get the absolute path
-#     ANNOTATIONS_PATH=$(realpath "$ANNOTATIONS_DIR")
-# fi
-
-# # Generate `requirements.txt` dynamically
-# echo "🔄 Generating $REQ_FILE..."
-
-# # Copy base requirements
-# cp requirements.base.txt $REQ_FILE
-
-# # If local mode is selected, add the editable annotation repo
-# if [ "$1" == "local" ]; then
-#     echo "-e $ANNOTATIONS_PATH" >> $REQ_FILE
-#     echo "✅ Local annotations added to $REQ_FILE"
-# else
-#     # Ensure `pash-annotations` is only added once
-#     if ! grep -q 'pash-annotations' $REQ_FILE; then
-#         cat pash-annotations.version >> $REQ_FILE
-#     fi
-#     echo "✅ Using PyPI annotations: $(cat pash-annotations.version)"
-# fi
-
 #!/bin/bash
 
 # Define the requirements file path
@@ -91,7 +22,7 @@ echo "📂 Annotations directory set to: $ANNOTATIONS_DIR"
 # Always clone the repository to the specified or default location
 echo "🔄 Downloading annotations repository..."
 rm -rf "$ANNOTATIONS_DIR"
-git clone https://github.com/binpash/annotations.git "$ANNOTATIONS_DIR"
+git clone https://github.com/binpash/annotations.git "$ANNOTATIONS_DIR" 
 
 if [ $? -ne 0 ]; then
     echo "❌ Failed to clone annotations repository."

From a73ffa9a208b0045324e2cf9fd5002f0b18eddbe Mon Sep 17 00:00:00 2001
From: Divik Chotani <divik.chotani@gmail.com>
Date: Fri, 28 Feb 2025 12:45:46 -0800
Subject: [PATCH 5/5] feat: add --local-annotations-dir support for dynamic
 annotation loading

- Resolved merge conflicts between remote and local

Signed-off-by: Divik Chotani divikchotani@g.ucla.edu
Signed-off-by: Divik Chotani <divik.chotani@gmail.com>
---
 evaluation/intro/hello-world.sh |  2 +-
 pa.sh                           | 15 ---------------
 2 files changed, 1 insertion(+), 16 deletions(-)

diff --git a/evaluation/intro/hello-world.sh b/evaluation/intro/hello-world.sh
index 21498d3b2..b63e665fc 100755
--- a/evaluation/intro/hello-world.sh
+++ b/evaluation/intro/hello-world.sh
@@ -1,7 +1,7 @@
 [ $(uname) = 'Darwin' ] && a=/usr/share/dict/web2 || a=/usr/share/dict/words
 
 if [ -f $a ]; then
-  cat $a $a $a $a $a $a $a $a | grep '\(.\).*\1\(.\).*\2\(.\).*\3\(.\).*\4' | wc -l
+  cat-wrapper $a $a $a $a $a $a $a $a | grep '\(.\).*\1\(.\).*\2\(.\).*\3\(.\).*\4' | wc -l
 else
   echo "Dictionary file $a not found.."
 fi
diff --git a/pa.sh b/pa.sh
index 280681884..ac40b5fca 100755
--- a/pa.sh
+++ b/pa.sh
@@ -44,21 +44,6 @@ if [ "$#" -eq 1 ] && [ "$1" = "--init" ]; then
 fi
 
 
-##This will check if use-local was passed in as a flag, and appropriately use the correct annotations library
-for arg in "$@"; do
-    if [ "$arg" == "--local-annotations" ]; then
-        sed -i 's/^pash-annotations.*/#&/' $PASH_TOP/requirements.txt
-        skip_flag=1
-	export PYTHONPATH="$ANNOTATIONS_PATH:$PYTHONPATH"
-	continue
-    fi
-    parsed_args+=("$arg")
-done
-
-if [ "$skip_flag" -eq 0 ]; then
-    sed -i "s|-e $ANNOTATIONS_PATH|#-e $ANNOTATIONS_PATH|" $PASH_TOP/requirements.txt
-fi
-cat $PASH_TOP/requirements.txt
 if ! command -v python3 &> /dev/null
 then
     echo "Python >=3 could not be found"