From 3168859268dfa125d79f35cabb9c1b86feaa363f Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Thu, 4 Jan 2024 22:00:43 -0500
Subject: [PATCH 01/20] updated install tool chain file to use verilator v5.016

---
 bin/wally-tool-chain-install.sh | 13 +++++++------
 tests/riscof/Makefile           |  5 +++--
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/bin/wally-tool-chain-install.sh b/bin/wally-tool-chain-install.sh
index ef2f9bcc7..5123836b0 100755
--- a/bin/wally-tool-chain-install.sh
+++ b/bin/wally-tool-chain-install.sh
@@ -39,7 +39,7 @@ set -e # break on error
 NUM_THREADS=8  # for >= 32GiB
 #NUM_THREADS=16  # for >= 64GiB
 
-sudo mkdir -p $RISCV
+#sudo mkdir -p $RISCV
 # *** need to update permissions to local user
 
 # Update and Upgrade tools (see https://itsfoss.com/apt-update-vs-upgrade/)
@@ -47,13 +47,13 @@ sudo apt update -y
 sudo apt upgrade -y
 sudo apt install -y git gawk make texinfo bison flex build-essential python3 libz-dev libexpat-dev autoconf device-tree-compiler ninja-build libpixman-1-dev ncurses-base ncurses-bin libncurses5-dev dialog curl wget ftp libgmp-dev libglib2.0-dev python3-pip pkg-config opam z3 zlib1g-dev automake autotools-dev libmpc-dev libmpfr-dev  gperf libtool patchutils bc 
 # Other python libraries used through the book.
-sudo pip3 install sphinx sphinx_rtd_theme matplotlib scipy scikit-learn adjustText lief
+# sudo pip3 install sphinx sphinx_rtd_theme matplotlib scipy scikit-learn adjustText lief
 
 # needed for Ubuntu 22.04, gcc cross compiler expects python not python2 or python3.
 if ! command -v python &> /dev/null
 then
     echo "WARNING: python3 was installed as python3 rather than python. Creating symlink."
-    sudo ln -sf /usr/bin/python3 /usr/bin/python
+    sudo ln -sf /bin/python3 /usr/bin/python
 fi
 
 # gcc cross-compiler (https://github.com/riscv-collab/riscv-gnu-toolchain)
@@ -71,8 +71,8 @@ cd riscv-gnu-toolchain
 # Temporarily use the following commands until gcc-13 is part of riscv-gnu-toolchain (issue #1249)
 #git clone https://github.com/gcc-mirror/gcc -b releases/gcc-13 gcc-13
 #./configure --prefix=/opt/riscv --with-multilib-generator="rv32e-ilp32e--;rv32i-ilp32--;rv32im-ilp32--;rv32iac-ilp32--;rv32imac-ilp32--;rv32imafc-ilp32f--;rv32imafdc-ilp32d--;rv64i-lp64--;rv64ic-lp64--;rv64iac-lp64--;rv64imac-lp64--;rv64imafdc-lp64d--;rv64im-lp64--;" --with-gcc-src=`pwd`/gcc-13
-./configure --prefix=${RISCV} --with-multilib-generator="rv32e-ilp32e--;rv32i-ilp32--;rv32im-ilp32--;rv32iac-ilp32--;rv32imac-ilp32--;rv32imafc-ilp32f--;rv32imafdc-ilp32d--;rv64i-lp64--;rv64ic-lp64--;rv64iac-lp64--;rv64imac-lp64--;rv64imafdc-lp64d--;rv64im-lp64--;"
-make -j ${NUM_THREADS}
+#./configure --prefix=${RISCV} --with-multilib-generator="rv32e-ilp32e--;rv32i-ilp32--;rv32im-ilp32--;rv32iac-ilp32--;rv32imac-ilp32--;rv32imafc-ilp32f--;rv32imafdc-ilp32d--;rv64i-lp64--;rv64ic-lp64--;rv64iac-lp64--;rv64imac-lp64--;rv64imafdc-lp64d--;rv64im-lp64--;"
+#make -j ${NUM_THREADS}
 
 # elf2hex (https://github.com/sifive/elf2hex)
 #The elf2hex utility to converts executable files into hexadecimal files for Verilog simulation. 
@@ -124,7 +124,8 @@ git clone https://github.com/verilator/verilator   # Only first time
 unset VERILATOR_ROOT     # For bash
 cd verilator
 git pull         # Make sure git repository is up-to-date
-git checkout master      # Use development branch (e.g. recent bug fixes)
+git checkout v5.016      # Use development branch (e.g. recent bug fixes)
+#git checkout master      # Use development branch (e.g. recent bug fixes)
 autoconf         # Create ./configure script
 ./configure      # Configure and create Makefile
 make -j ${NUM_THREADS}  # Build Verilator itself (if error, try just 'make')
diff --git a/tests/riscof/Makefile b/tests/riscof/Makefile
index a9855d41f..1a55f953f 100644
--- a/tests/riscof/Makefile
+++ b/tests/riscof/Makefile
@@ -8,8 +8,9 @@ wally_workdir = $(work)/wally-riscv-arch-test
 current_dir = $(shell pwd)
 #XLEN    ?= 64
 
-all: root arch32 wally32 arch32e arch64 wally64
-wally-riscv-arch-test: root wally32 wally64
+#all: root arch32 wally32 arch32e arch64 wally64
+#wally-riscv-arch-test: root wally32 wally64
+all: root wally32 wally64 
 
 root:
 	mkdir -p $(work_dir)

From 981c3ccf6b4775505c6356ff3e9bd60f7f0ba5f4 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Thu, 4 Jan 2024 22:01:52 -0500
Subject: [PATCH 02/20] updated gitignore file

---
 .gitignore | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.gitignore b/.gitignore
index 1664b939f..ae362d3ca 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,14 @@
 **/work*
 **/wally_*.log
 
+# files for my own repo
+setup_host.sh
+tests/riscof/Makefile
+bin/wally-tool-chain-install.sh
+sim/coverage_output.txt
+sim/regression_output.txt
+
+
 .nfs*
 
 __pycache__/

From 8d9f52061c5cee3f3e561e2479db442e185c67e3 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Wed, 31 Jan 2024 17:43:46 -0600
Subject: [PATCH 03/20] adding nightly tests

---
 bin/nightly_build/nightly_build_v13_beta.sh |  85 ++++++++++++++++
 bin/nightly_build/src/error_detector.py     |  37 +++++++
 bin/nightly_build/src/parse_coverage.py     |  95 ++++++++++++++++++
 bin/nightly_build/src/parse_regression.py   | 102 ++++++++++++++++++++
 bin/nightly_build/src/send_mail_html.sh     |  79 +++++++++++++++
 5 files changed, 398 insertions(+)
 create mode 100755 bin/nightly_build/nightly_build_v13_beta.sh
 create mode 100644 bin/nightly_build/src/error_detector.py
 create mode 100644 bin/nightly_build/src/parse_coverage.py
 create mode 100644 bin/nightly_build/src/parse_regression.py
 create mode 100755 bin/nightly_build/src/send_mail_html.sh

diff --git a/bin/nightly_build/nightly_build_v13_beta.sh b/bin/nightly_build/nightly_build_v13_beta.sh
new file mode 100755
index 000000000..2e0ca42d4
--- /dev/null
+++ b/bin/nightly_build/nightly_build_v13_beta.sh
@@ -0,0 +1,85 @@
+#!/bin/bash
+
+# set WALLY path
+WALLY=$(dirname ${BASH_SOURCE[0]:-$0})
+export WALLY=$(cd "$WALLY/../../" && pwd)
+echo "WALLY is set to: $WALLY"
+
+# Going to nightly runs
+cd $WALLY/../
+
+# check if directories exist
+if [ ! -d "build-results" ]; then
+    echo "Directory does not exist, creating it..."
+    mkdir -p "build-results"
+    if [ $? -eq 0 ]; then
+        echo "Directory created successfully."
+    else
+        echo "Failed to create directory."
+        exit 1
+    fi
+else
+    echo "Directory already exists."
+fi
+
+if [ ! -d "logs" ]; then
+    echo "Directory does not exist, creating it..."
+    mkdir -p "logs"
+    if [ $? -eq 0 ]; then
+        echo "Directory created successfully."
+    else
+        echo "Failed to create directory."
+        exit 1
+    fi
+else
+    echo "Directory already exists."
+fi
+
+# setup source okstate file
+echo "Sourcing setup files"
+source $WALLY/setup_host.sh
+source $WALLY/../setup-files/setup_tools.sh
+
+# Navigate to the gir repo
+cd $WALLY
+
+# pull the repository
+echo "Pulling submodules"
+#git pull --recurse-submodules origin main
+
+# build the regression tests
+echo "Building the regression tests"
+cd sim
+#if make wally-riscv-arch-test; then
+#if make all; then
+#	echo "Make successfull"
+#else
+#	echo "Make failed"
+#	cd $WALLY/..
+	# add the the regression result and the coverage result that there was an error in making the tests
+#	python $WALLY/bin/nightly_build/src/error_detector.py --tag make -o $WALLY/../build-results/regression_results.md
+#	python $WALLY/bin/nightly_build/src/error_detector.py --tag make -o $WALLY/../build-results/coverage_results.md
+
+	# exit the program
+	#exit 1
+#fi
+
+# execute the simulation / regression tests and save output to a file
+echo "running the regression test"
+#./regression-wally > $WALLY/../logs/regression_output.log 2>&1
+
+echo "running coverage tests"
+#./coverage > $WALLY/../logs/coverage_output.log 2>&1
+
+
+# run the Python script to parse the output and generate the log file
+echo "Parsing output data from the regression test"
+cd $WALLY/../
+
+python $WALLY/bin/nightly_build/src/parse_regression.py -i $WALLY/../logs/regression_output.log -o $WALLY/../build-results/regression_results.md
+
+python $WALLY/bin/nightly_build/src/parse_coverage.py -i $WALLY/../logs/coverage_output.log -o $WALLY/../build-results/coverage_results.md
+
+# email update
+cd $WALLY/bin/nightly_build/src/
+./send_mail_html.sh
diff --git a/bin/nightly_build/src/error_detector.py b/bin/nightly_build/src/error_detector.py
new file mode 100644
index 000000000..c239032e9
--- /dev/null
+++ b/bin/nightly_build/src/error_detector.py
@@ -0,0 +1,37 @@
+import argparse
+import datetime
+
+def add_failure_to_markdown(tag, output_file, input_file = None):
+    # Get the current date and time
+    current_datetime = datetime.datetime.now()
+    formatted_datetime = current_datetime.strftime("%Y-%m-%d %H:%M:%S")
+
+    # Create the failure message based on the provided tag and input content
+    if tag == "make":
+        failure_message = f"# {tag.capitalize()} riscof comilation failure - {formatted_datetime}\n\n"
+        failure_message += f"The error was due to a problem in compiling the the riscof tests:\n\n"
+        if input_file != None:
+            failure_message += f"The particular error: {input_file}\n\n"
+    else:
+        failure_message = f"# {tag.capitalize()} Failure - {formatted_datetime}\n\n"
+        failure_message += f":\n\n"
+
+    # Append the failure message to the specified output file
+    with open(output_file, "a") as file:
+        file.write(failure_message)
+
+    print(f"Failure information added to {output_file}.")
+
+if __name__ == "__main__":
+    # Set up argparse
+    parser = argparse.ArgumentParser(description="Add failure information to Markdown file.")
+    parser.add_argument("--tag", required=True, help="Specify the tag for the failure type (e.g., 'make', 'custom').")
+    parser.add_argument("-i", required=False, help="Specify the input file containing failure details.")
+    parser.add_argument("-o", required=True, help="Specify the output file to write the failure information.")
+
+    # Parse command-line arguments
+    args = parser.parse_args()
+
+    # Call the function with the specified tag, input file, and output file
+    add_failure_to_markdown(args.tag,  args.o)
+
diff --git a/bin/nightly_build/src/parse_coverage.py b/bin/nightly_build/src/parse_coverage.py
new file mode 100644
index 000000000..33811b0a1
--- /dev/null
+++ b/bin/nightly_build/src/parse_coverage.py
@@ -0,0 +1,95 @@
+import os
+import argparse
+from datetime import datetime
+import re
+from colorama import init, Fore, Style
+
+def parse_regression_output(output):
+    passed_configs = []
+    failed_configs = []
+
+    lines = output.split('\n')
+    index = 0
+
+    while index < len(lines):
+        # Remove ANSI escape codes
+        line = re.sub(r'\x1b\[[0-9;]*[mGK]', '', lines[index])  
+        if "Success" in line:
+            passed_configs.append(line.split(':')[0].strip())
+        elif "Failures detected in output" in line:
+            try:
+                config_name = line.split(':')[0].strip()
+                log_file = os.path.abspath(config_name+".log") 
+                failed_configs.append((config_name, log_file))
+            except:
+                failed_configs.append((config_name, "Log file not found"))
+
+        index += 1
+
+    # alphabetically sort the configurations
+    passed_configs.sort()
+    failed_configs.sort()
+    return passed_configs, failed_configs
+
+def write_to_markdown(passed_configs, failed_configs, output_file):
+    timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+
+    with open(output_file, 'a') as md_file:
+        md_file.write(f"\n\n# Coverage Test Results - {timestamp}\n\n")
+
+        md_file.write("\n## Failed Configurations\n")
+        for config, log_file in failed_configs:
+            md_file.write(f"- <span class=\"failure\" style=\"color: red;\">{config}</span> ({log_file})\n")
+            if len(failed_configs) == 0:
+                md_file.write(" - no failures\n")
+
+        md_file.write("\n## Passed Configurations\n")
+        for config in passed_configs:
+            md_file.write(f"- <span class=\"success\" style=\"color: green;\">{config}</span>\n")
+
+
+def write_new_markdown(passed_configs, failed_configs):
+    timestamp = datetime.now().strftime("%Y-%m-%d")
+    output_file = f"/home/thkidd/nightly_runs/build-results/builds/coverage/wally_coverage_{timestamp}.md"
+    
+    with open(output_file, 'w') as md_file:
+        # Title
+        md_file.write(f"\n\n# Coverage Test Results - {timestamp}\n\n")
+        
+        ## File path
+        md_file.write(f"\n**File:** {output_file}\n")
+
+        md_file.write("\n## Failed Configurations\n")
+        # add in if there were no failures
+        if len(failed_configs) == 0:
+            md_file.write(f"No Failures\n")
+        
+        for config, log_file in failed_configs:
+                md_file.write(f"- <span class=\"failure regression\" style=\"color: red;\">{config}</span> ({log_file})\n")
+
+        md_file.write("\n## Passed Configurations\n")
+        for config in passed_configs:
+            md_file.write(f"- <span class=\"success regression\" style=\"color: green;\">{config}</span>\n")
+
+
+
+
+if __name__ == "__main__":
+    init(autoreset=True)  # Initialize colorama
+    parser = argparse.ArgumentParser(description='Parse regression test output and append to a markdown file.')
+    parser.add_argument('-i', '--input', help='Input file containing regression test output', required=True)
+    parser.add_argument('-o', '--output', help='Output markdown file', default='regression_results.md')
+    args = parser.parse_args()
+
+    with open(args.input, 'r') as input_file:
+        regression_output = input_file.read()
+
+    passed_configs, failed_configs = parse_regression_output(regression_output)
+    write_to_markdown(passed_configs, failed_configs, args.output)
+
+    print(f"Markdown file updated: {args.output}")
+
+    write_new_markdown(passed_configs, failed_configs)
+
+    print("New markdown file created")
+
diff --git a/bin/nightly_build/src/parse_regression.py b/bin/nightly_build/src/parse_regression.py
new file mode 100644
index 000000000..0d8c9467d
--- /dev/null
+++ b/bin/nightly_build/src/parse_regression.py
@@ -0,0 +1,102 @@
+import argparse
+import os
+from datetime import datetime
+import re
+from colorama import init, Fore, Style
+
+def parse_regression_output(output):
+    passed_configs = []
+    failed_configs = []
+
+    lines = output.split('\n')
+    index = 0
+
+    while index < len(lines):
+        # Remove ANSI escape codes
+        line = re.sub(r'\x1b\[[0-9;]*[mGK]', '', lines[index])  
+        #print("The cleaned line: ", line)
+        if "Success" in line:
+            passed_configs.append(line.split(':')[0].strip())
+        elif "Failures detected in output" in line:
+            try:
+                config_name = line.split(':')[0].strip()
+                log_file = os.path.abspath(config_name+".log") 
+                failed_configs.append((config_name, log_file))
+            except:
+                failed_configs.append((config_name, "Log file not found"))
+        elif "Timeout" in line:
+            try:
+                config_name = line.split(':')[0].strip()
+                log_file = os.path.abspath(config_name+".log")
+                failed_configs.append((config_name, log_file))
+            except:
+                failed_configs.append((config_name, "Log file not found"))
+        index += 1
+    
+    # alphabetically sort the configurations
+    passed_configs.sort()
+    failed_configs.sort()
+    return passed_configs, failed_configs
+
+def write_to_markdown(passed_configs, failed_configs, output_file):
+    timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+    with open(output_file, 'a') as md_file:
+        md_file.write(f"\n\n<div class=\"regression\">\n# Regression Test Results - {timestamp}\n</div>\n\n")
+        #md_file.write(f"\n\n# Regression Test Results - {timestamp}\n\n")
+
+        if failed_configs:
+            md_file.write("## Failed Configurations\n")
+            for config, log_file in failed_configs:
+                md_file.write(f"- <span class=\"failure regression\" style=\"color: red;\">{config}</span> ({log_file})\n")
+            md_file.write("\n")
+        else:
+            md_file.write("## No Failed Configurations\n")
+
+        md_file.write("\n## Passed Configurations\n")
+        for config in passed_configs:
+            md_file.write(f"- <span class=\"success regression\" style=\"color: green;\">{config}</span>\n")
+
+def write_new_markdown(passed_configs, failed_configs):
+    timestamp = datetime.now().strftime("%Y-%m-%d")
+    output_file = f"/home/thkidd/nightly_runs/build-results/builds/regression/wally_regression_{timestamp}.md"
+    with open(output_file, 'w') as md_file:
+       
+        # Title
+        md_file.write(f"\n\n# Regression Test Results - {timestamp}\n\n")
+        #md_file.write(f"\n\n<div class=\"regression\">\n# Regression Test Results - {timestamp}\n</div>\n\n")
+
+        # File Path
+        md_file.write(f"\n**File:** {output_file}\n\n")
+
+        if failed_configs:
+            md_file.write("## Failed Configurations\n\n")
+            for config, log_file in failed_configs:
+                md_file.write(f"- <span class=\"failure regression\" style=\"color: red;\">{config}</span> ({log_file})\n")
+            md_file.write("\n")
+        else:
+            md_file.write("## Failed Configurations\n")
+            md_file.write(f"No Failures\n")
+        
+        md_file.write("\n## Passed Configurations\n")
+        for config in passed_configs:
+            md_file.write(f"- <span class=\"success regression\" style=\"color: green;\">{config}</span>\n")
+
+if __name__ == "__main__":
+    init(autoreset=True)  # Initialize colorama
+    parser = argparse.ArgumentParser(description='Parse regression test output and append to a markdown file.')
+    parser.add_argument('-i', '--input', help='Input file containing regression test output', required=True)
+    parser.add_argument('-o', '--output', help='Output markdown file containing formatted file', default='regression_results.md')
+    args = parser.parse_args()
+
+    with open(args.input, 'r') as input_file:
+        regression_output = input_file.read()
+
+    passed_configs, failed_configs = parse_regression_output(regression_output)
+    write_to_markdown(passed_configs, failed_configs, args.output)
+
+    print(f"Markdown file updated: {args.output}")
+
+    write_new_markdown(passed_configs, failed_configs)
+
+    print("New markdown file created")
+
diff --git a/bin/nightly_build/src/send_mail_html.sh b/bin/nightly_build/src/send_mail_html.sh
new file mode 100755
index 000000000..5c3735a3a
--- /dev/null
+++ b/bin/nightly_build/src/send_mail_html.sh
@@ -0,0 +1,79 @@
+current_date=$(date "+%Y-%m-%d")
+email_address="thomas.kidd@okstate.edu"
+#email_address="WALLY-REGRESSION@LISTSERV.OKSTATE.EDU"
+subject="WALLY regression and coverage test report"
+attachments=""
+html_body=""
+host_name=$(hostname) 
+os_info=$(lsb_release -a 2>/dev/null)
+script_location=$WALLY/bin/nightly_build/
+
+html_body="<div id='system-info'>
+    <h3>System Information</h3>
+    <p><strong>Server Name:</strong> $host_name@okstate.edu</p>  
+    <p><strong>Operating System:</strong> $os_info</p>
+    <p><strong>Script Origin:</strong> $script_location</p>
+</div>
+
+<p>Testing sending HTML content through mutt</p>"
+
+# Iterate through the files and concatenate their content to the body
+for file in $WALLY/../build-results/builds/*/wally_*_"$current_date"*.md; do
+    attachments+=" -a $file"
+
+    # Convert Markdown to HTML using pandoc
+    html_content=$(pandoc "$file")
+
+    # add the file full path
+    # html_body+="<p>File: $file</p>"
+    # Append the HTML content to the body
+    html_body+="$html_content"
+done
+echo "Sending email"
+
+# Get server hostname and OS information
+host_name=$(hostname)
+os_info=$(uname -a)
+
+# Define HTML body content
+
+# Use mutt to send the email with HTML body
+#mutt -e "my_hdr From:James Stine <james.stine@okstate.edu>" -s "$subject" $attachments \
+mutt -e "my_hdr From:Thomas Kidd <thomas.kidd@okstate.edu>" -s "$subject"  \
+    -e "set content_type=text/html" -- $email_address <<EOF
+<html>
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Nightly Build Results - $current_date</title>
+    <style>
+        body {
+            font-family: 'Helvetica Neue', Arial, sans-serif;
+            margin: 20px;
+            padding: 20px;
+            background-color: #f4f4f4;
+        }
+        h1, h3, p {
+            color: #333;
+        }
+        #system-info {
+            border: 1px solid #ddd;
+            padding: 15px;
+            margin-bottom: 20px;
+            background-color: #fff;
+            border-radius: 5px;
+            box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
+        }
+<!--	.success { color: green; } -->
+<!--    .failure { color: red; }   -->
+
+    </style>
+</head>
+<body>
+    <h1 id="test-results---$current_date">Test Results - $current_date</h1>
+    
+    $html_body
+</body>
+</html>
+EOF
+

From 942a2804c33a28cf31171f4a203144a91f50fb15 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Wed, 31 Jan 2024 17:48:03 -0600
Subject: [PATCH 04/20] reverted the verilator checkout to checkout master

---
 bin/wally-tool-chain-install.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/bin/wally-tool-chain-install.sh b/bin/wally-tool-chain-install.sh
index 473bc074b..79a556571 100755
--- a/bin/wally-tool-chain-install.sh
+++ b/bin/wally-tool-chain-install.sh
@@ -125,8 +125,7 @@ git clone https://github.com/verilator/verilator   # Only first time
 unset VERILATOR_ROOT     # For bash
 cd verilator
 git pull         # Make sure git repository is up-to-date
-git checkout v5.016      # Use development branch (e.g. recent bug fixes)
-#git checkout master      # Use development branch (e.g. recent bug fixes)
+git checkout master      # Use development branch (e.g. recent bug fixes)
 autoconf         # Create ./configure script
 ./configure      # Configure and create Makefile
 make -j ${NUM_THREADS}  # Build Verilator itself (if error, try just 'make')

From 85f214a02501b11aa5e69509b27e4684665b2e1d Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Thu, 1 Feb 2024 09:07:14 -0600
Subject: [PATCH 05/20] Revert "reverted the verilator checkout to checkout
 master"

This reverts commit 942a2804c33a28cf31171f4a203144a91f50fb15.
---
 bin/wally-tool-chain-install.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bin/wally-tool-chain-install.sh b/bin/wally-tool-chain-install.sh
index 79a556571..473bc074b 100755
--- a/bin/wally-tool-chain-install.sh
+++ b/bin/wally-tool-chain-install.sh
@@ -125,7 +125,8 @@ git clone https://github.com/verilator/verilator   # Only first time
 unset VERILATOR_ROOT     # For bash
 cd verilator
 git pull         # Make sure git repository is up-to-date
-git checkout master      # Use development branch (e.g. recent bug fixes)
+git checkout v5.016      # Use development branch (e.g. recent bug fixes)
+#git checkout master      # Use development branch (e.g. recent bug fixes)
 autoconf         # Create ./configure script
 ./configure      # Configure and create Makefile
 make -j ${NUM_THREADS}  # Build Verilator itself (if error, try just 'make')

From 590f53f5a55c97aba93bae9e649382ed005e68c4 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Thu, 1 Feb 2024 09:09:12 -0600
Subject: [PATCH 06/20] Revert "updated gitignore file"

This reverts commit 981c3ccf6b4775505c6356ff3e9bd60f7f0ba5f4.
---
 .gitignore | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index 66da1691c..a01f1c07d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,14 +1,6 @@
 **/work*
 **/wally_*.log
 
-# files for my own repo
-setup_host.sh
-tests/riscof/Makefile
-bin/wally-tool-chain-install.sh
-sim/coverage_output.txt
-sim/regression_output.txt
-
-
 .nfs*
 
 __pycache__/

From d2e606b41bd35d037cfa840ab271db0d6ce3f33e Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Thu, 1 Feb 2024 09:23:15 -0600
Subject: [PATCH 07/20] Revert "updated install tool chain file to use
 verilator v5.016"

This reverts commit 3168859268dfa125d79f35cabb9c1b86feaa363f.
---
 bin/wally-tool-chain-install.sh | 13 ++++++-------
 tests/riscof/Makefile           |  5 ++---
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/bin/wally-tool-chain-install.sh b/bin/wally-tool-chain-install.sh
index 473bc074b..ca8a28c05 100755
--- a/bin/wally-tool-chain-install.sh
+++ b/bin/wally-tool-chain-install.sh
@@ -40,7 +40,7 @@ set -e # break on error
 NUM_THREADS=8  # for >= 32GiB
 #NUM_THREADS=16  # for >= 64GiB
 
-#sudo mkdir -p $RISCV
+sudo mkdir -p $RISCV
 # *** need to update permissions to local user
 
 # Update and Upgrade tools (see https://itsfoss.com/apt-update-vs-upgrade/)
@@ -48,13 +48,13 @@ sudo apt update -y
 sudo apt upgrade -y
 sudo apt install -y git gawk make texinfo bison flex build-essential python3 libz-dev libexpat-dev autoconf device-tree-compiler ninja-build libpixman-1-dev ncurses-base ncurses-bin libncurses5-dev dialog curl wget ftp libgmp-dev libglib2.0-dev python3-pip pkg-config opam z3 zlib1g-dev automake autotools-dev libmpc-dev libmpfr-dev  gperf libtool patchutils bc 
 # Other python libraries used through the book.
-# sudo pip3 install sphinx sphinx_rtd_theme matplotlib scipy scikit-learn adjustText lief
+sudo pip3 install sphinx sphinx_rtd_theme matplotlib scipy scikit-learn adjustText lief
 
 # needed for Ubuntu 22.04, gcc cross compiler expects python not python2 or python3.
 if ! command -v python &> /dev/null
 then
     echo "WARNING: python3 was installed as python3 rather than python. Creating symlink."
-    sudo ln -sf /bin/python3 /usr/bin/python
+    sudo ln -sf /usr/bin/python3 /usr/bin/python
 fi
 
 # gcc cross-compiler (https://github.com/riscv-collab/riscv-gnu-toolchain)
@@ -72,8 +72,8 @@ cd riscv-gnu-toolchain
 # Temporarily use the following commands until gcc-13 is part of riscv-gnu-toolchain (issue #1249)
 #git clone https://github.com/gcc-mirror/gcc -b releases/gcc-13 gcc-13
 #./configure --prefix=/opt/riscv --with-multilib-generator="rv32e-ilp32e--;rv32i-ilp32--;rv32im-ilp32--;rv32iac-ilp32--;rv32imac-ilp32--;rv32imafc-ilp32f--;rv32imafdc-ilp32d--;rv64i-lp64--;rv64ic-lp64--;rv64iac-lp64--;rv64imac-lp64--;rv64imafdc-lp64d--;rv64im-lp64--;" --with-gcc-src=`pwd`/gcc-13
-#./configure --prefix=${RISCV} --with-multilib-generator="rv32e-ilp32e--;rv32i-ilp32--;rv32im-ilp32--;rv32iac-ilp32--;rv32imac-ilp32--;rv32imafc-ilp32f--;rv32imafdc-ilp32d--;rv64i-lp64--;rv64ic-lp64--;rv64iac-lp64--;rv64imac-lp64--;rv64imafdc-lp64d--;rv64im-lp64--;"
-#make -j ${NUM_THREADS}
+./configure --prefix=${RISCV} --with-multilib-generator="rv32e-ilp32e--;rv32i-ilp32--;rv32im-ilp32--;rv32iac-ilp32--;rv32imac-ilp32--;rv32imafc-ilp32f--;rv32imafdc-ilp32d--;rv64i-lp64--;rv64ic-lp64--;rv64iac-lp64--;rv64imac-lp64--;rv64imafdc-lp64d--;rv64im-lp64--;"
+make -j ${NUM_THREADS}
 
 # elf2hex (https://github.com/sifive/elf2hex)
 #The elf2hex utility to converts executable files into hexadecimal files for Verilog simulation. 
@@ -125,8 +125,7 @@ git clone https://github.com/verilator/verilator   # Only first time
 unset VERILATOR_ROOT     # For bash
 cd verilator
 git pull         # Make sure git repository is up-to-date
-git checkout v5.016      # Use development branch (e.g. recent bug fixes)
-#git checkout master      # Use development branch (e.g. recent bug fixes)
+git checkout master      # Use development branch (e.g. recent bug fixes)
 autoconf         # Create ./configure script
 ./configure      # Configure and create Makefile
 make -j ${NUM_THREADS}  # Build Verilator itself (if error, try just 'make')
diff --git a/tests/riscof/Makefile b/tests/riscof/Makefile
index 1a55f953f..a9855d41f 100644
--- a/tests/riscof/Makefile
+++ b/tests/riscof/Makefile
@@ -8,9 +8,8 @@ wally_workdir = $(work)/wally-riscv-arch-test
 current_dir = $(shell pwd)
 #XLEN    ?= 64
 
-#all: root arch32 wally32 arch32e arch64 wally64
-#wally-riscv-arch-test: root wally32 wally64
-all: root wally32 wally64 
+all: root arch32 wally32 arch32e arch64 wally64
+wally-riscv-arch-test: root wally32 wally64
 
 root:
 	mkdir -p $(work_dir)

From 78db8c584a334cad9b84f862f436d3867c1e7b68 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Thu, 1 Feb 2024 09:31:41 -0600
Subject: [PATCH 08/20] Revert "updated gitignore file"

This reverts commit 981c3ccf6b4775505c6356ff3e9bd60f7f0ba5f4.
---
 bin/wally-tool-chain-install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/wally-tool-chain-install.sh b/bin/wally-tool-chain-install.sh
index ca8a28c05..6e7e4c8e9 100755
--- a/bin/wally-tool-chain-install.sh
+++ b/bin/wally-tool-chain-install.sh
@@ -125,7 +125,7 @@ git clone https://github.com/verilator/verilator   # Only first time
 unset VERILATOR_ROOT     # For bash
 cd verilator
 git pull         # Make sure git repository is up-to-date
-git checkout master      # Use development branch (e.g. recent bug fixes)
+git checkout master      
 autoconf         # Create ./configure script
 ./configure      # Configure and create Makefile
 make -j ${NUM_THREADS}  # Build Verilator itself (if error, try just 'make')

From 190ef91751e3e2e9aa2eb2db2675c2ed9321b217 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Mon, 12 Feb 2024 18:21:04 -0600
Subject: [PATCH 09/20] Replacing nightly_build folder with nightly_build.py
 and bash wrapper script

---
 bin/nightly_build.py                        | 693 ++++++++++++++++++++
 bin/nightly_build/nightly_build_v13_beta.sh |  85 ---
 bin/nightly_build/src/error_detector.py     |  37 --
 bin/nightly_build/src/parse_coverage.py     |  95 ---
 bin/nightly_build/src/parse_regression.py   | 102 ---
 bin/nightly_build/src/send_mail_html.sh     |  79 ---
 bin/wrapper_nightly_runs.sh                 |  28 +
 7 files changed, 721 insertions(+), 398 deletions(-)
 create mode 100755 bin/nightly_build.py
 delete mode 100755 bin/nightly_build/nightly_build_v13_beta.sh
 delete mode 100644 bin/nightly_build/src/error_detector.py
 delete mode 100644 bin/nightly_build/src/parse_coverage.py
 delete mode 100644 bin/nightly_build/src/parse_regression.py
 delete mode 100755 bin/nightly_build/src/send_mail_html.sh
 create mode 100755 bin/wrapper_nightly_runs.sh

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
new file mode 100755
index 000000000..21d0ce025
--- /dev/null
+++ b/bin/nightly_build.py
@@ -0,0 +1,693 @@
+#!/usr/bin/python3
+"""
+Python Regression Build Automation Script
+
+This Python script serves the purpose of automating nightly regression builds for a software project. 
+The script is designed to handle the setup, execution, and reporting aspects of the regression testing process.
+
+Features:
+
+    1.  Nightly Regression Builds: The script is scheduled to run on a nightly basis, making and executing the regression builds.
+
+    2.  Markdown Report Generation: Upon completion of the regression tests, the script generates detailed reports in Markdown format. 
+        These reports provide comprehensive insights into the test results, including test cases executed, pass/fail status, and any encountered issues.    
+
+    3.  Email Notification: The script is configured to send out email notifications summarizing the regression test results. 
+        These emails serve as communication channels for stakeholders, providing them with timely updates on the software's regression status.
+
+Usage:
+
+- The script is designed to be scheduled and executed automatically on a nightly basis using task scheduling tools such as Cronjobs. To create a cronjob do the following:
+    1)  Open Terminal:
+
+        Open your terminal application. This is where you'll enter the commands to create and manage cron jobs.
+
+    2)  Access the Cron Table:
+
+        Type the following command and press Enter:
+
+        crontab -e
+
+        This command opens the crontab file in your default text editor. If it's your first time, you might be prompted to choose a text editor.
+
+    3)  Edit the Cron Table:
+        The crontab file will open in your text editor. Each line in this file represents a cron job. You can now add your new cron job.
+
+    4)  Syntax:
+
+        Our cron job has the following syntax:
+        0 3 * * * BASH_ENV=~/.bashrc bash -l -c "*WHERE YOUR CVW IS MUST PUT FULL PATH*/cvw/bin/wrapper_nightly_runs.sh > *WHERE YOU WANT TO STORE LOG FILES/cron.log 2>&1" 
+
+        This cronjob sources the .bashrc file and executes the wrapper script as a user. 
+
+    5)  Double check:
+
+        Execute the following command to see your cronjobs:
+        
+        crontab -l
+
+Dependencies:
+    Python:
+        - os
+        - shutil
+        - datetime from datetime
+        - re
+        - markdown
+        - subprocess
+
+    Bash:
+        - mutt (email sender)
+
+Conclusion:
+
+In summary, this Python script facilitates the automation of nightly regression builds, providing comprehensive reporting and email notification capabilities to ensure effective communication and monitoring of regression test results.
+"""
+
+import os
+import shutil
+from datetime import datetime
+import re
+import markdown
+import subprocess
+
+
+
+class FolderManager:
+    """A class for managing folders and repository cloning."""
+
+    def __init__(self):
+        """
+        Initialize the FolderManager instance.
+
+        Args:
+            base_dir (str): The base directory where folders will be managed and repository will be cloned.
+        """
+        env_extract_var = 'WALLY'
+        print(f"The environemntal variable is {env_extract_var}")
+        self.base_dir = os.environ.get(env_extract_var)
+        print(f"The base directory is: {self.base_dir}")
+        self.base_parent_dir = os.path.dirname(self.base_dir)
+
+        # print(f"The new WALLY vairable is: {os.environ.get('WALLY')}")
+        # print(f"The Base Directory is now : {self.base_dir}")
+        # print(f"The Base Parent Directory is now : {self.base_parent_dir}")
+
+    def create_preliminary_folders(self, folders):
+        """
+        Create preliminary folders if they do not exist. 
+        These folders are:
+            nightly_runs/repos/
+            nightly_runs/results/ 
+
+        Args:
+            folders (list): A list of folder names to be created.
+
+        Returns:
+            None
+        """
+        
+        for folder in folders:
+            folder_path = os.path.join(self.base_parent_dir, folder)
+            if not os.path.exists(folder_path):
+                os.makedirs(folder_path)
+
+    def create_new_folder(self, folders):
+        """
+        Create a new folder based on the current date if it does not already exist.
+
+        Args:
+            folder_name (str): The base name for the new folder.
+
+        Returns:
+            str: The path of the newly created folder if created, None otherwise.
+        """
+
+        todays_date = datetime.now().strftime("%Y-%m-%d")
+        return_folder_path = []
+        for folder in folders:
+            folder_path = os.path.join(self.base_parent_dir, folder, todays_date)
+            if not os.path.exists(folder_path):
+                os.makedirs(folder_path)
+                return_folder_path.append(folder_path)
+            else:
+                return_folder_path.append(None) # Folder already exists
+        
+        return return_folder_path
+
+    def clone_repository(self, folder, repo_url):
+        """
+        Clone a repository into the 'cvw' folder if it does not already exist.
+
+        Args:
+            repo_url (str): The URL of the repository to be cloned.
+
+        Returns:
+            None
+        """
+        todays_date = datetime.now().strftime("%Y-%m-%d")
+        repo_folder = os.path.join(self.base_parent_dir, folder, todays_date, 'cvw')
+        tmp_folder = os.path.join(repo_folder, "tmp") # temprorary files will be stored in here
+
+        if not os.path.exists(repo_folder):
+            os.makedirs(repo_folder)
+            os.system(f"git clone --recurse-submodules {repo_url} {repo_folder}")
+            os.makedirs(tmp_folder)
+    
+
+class TestRunner:
+    """A class for making, running, and formatting test results."""
+
+    def __init__(self): 
+        self.base_dir = os.environ.get('WALLY')
+        self.base_parent_dir = os.path.dirname(self.base_dir)
+        self.current_datetime = datetime.now()
+        #self.temp_dir = self.base_parent_dir
+        #print(f"Base Directory: {self.base_parent_dir}")
+        
+    def copy_setup_script(self, folder):
+        """
+        Copy the setup script to the destination folder.
+
+        The setup script will be copied from the base directory to a specific folder structure inside the base directory.
+
+        Args:
+            folder: the "nightly_runs/repos/"
+
+        Returns:
+            bool: True if the script is copied successfully, False otherwise.
+        """
+        # Get today's date in YYYY-MM-DD format
+        todays_date = datetime.now().strftime("%Y-%m-%d")
+
+        # Define the source and destination paths
+        source_script = os.path.join(self.base_dir, "setup_host.sh")
+        destination_folder = os.path.join(self.base_parent_dir, folder, todays_date, 'cvw')
+        
+        # Check if the source script exists
+        if not os.path.exists(source_script):
+            print(f"Error: Source script '{source_script}' not found.")
+            return False
+
+
+        # Check if the destination folder exists, create it if necessary
+        if not os.path.exists(destination_folder):
+            print(f"Error: Destination folder '{destination_folder}' not found.")
+            return False
+
+        # Copy the script to the destination folder
+        try:
+            shutil.copy(source_script, destination_folder)
+            #print(f"Setup script copied to: {destination_folder}")
+            return True
+        except Exception as e:
+            print(f"Error copying setup script: {e}")
+            return False
+
+
+    def set_env_var(self, folder):
+        """
+        Source a shell script.
+
+        Args:
+            script_path (str): Path to the script to be sourced.
+
+        Returns:
+            None
+        """
+        # find the new repository made
+        todays_date = datetime.now().strftime("%Y-%m-%d")
+        wally_path = os.path.join(self.base_parent_dir, folder, todays_date, 'cvw')
+
+        # set the WALLY environmental variable to the new repository
+        os.environ["WALLY"] = wally_path
+
+        self.base_dir = os.environ.get('WALLY')
+        self.base_parent_dir = os.path.dirname(self.base_dir)
+        self.temp_dir = self.base_parent_dir
+
+        # print(f"The new WALLY vairable is: {os.environ.get('WALLY')}")
+        # print(f"The Base Directory is now : {self.base_dir}")
+        # print(f"The Base Parent Directory is now : {self.base_parent_dir}")
+       
+    def execute_makefile(self, target=None):
+        """
+        Execute a Makefile with optional target.
+
+        Args:
+            makefile_path (str): Path to the Makefile.
+            target (str, optional): Target to execute in the Makefile.
+
+        Returns:
+            True if the tests were made
+            False if the tests didnt pass
+        """
+        # Prepare the command to execute the Makefile
+        make_file_path = os.path.join(self.base_dir, "sim")
+        os.chdir(make_file_path)
+
+        output_file = os.path.join(self.base_dir, "tmp", "make_output.log")
+
+        command = ["make"]
+
+        # Add target to the command if specified
+        if target:
+            command.append(target)
+        #print(f"The command is: {command}")
+
+        # Execute the command using subprocess and save the output into a file
+        with open(output_file, "w") as f:
+            formatted_datetime = self.current_datetime.strftime("%Y-%m-%d %H:%M:%S")
+            f.write(formatted_datetime)
+            f.write("\n\n")
+            result = subprocess.run(command, stdout=f, stderr=subprocess.STDOUT, text=True)
+        
+        # Execute the command using a subprocess and not save the output
+        #result = subprocess.run(command, text=True)
+
+        # Check the result
+        if result.returncode == 0:
+            #print(f"Makefile executed successfully{' with target ' + target if target else ''}.")
+            return True
+        else:
+            #print("Error executing Makefile.")
+            return False
+            
+    def run_tests(self, test_type=None, test_name=None, test_exctention=None):
+        """
+        Run a script through the terminal and save the output to a file.
+
+        Args:
+            test_name (str): The test name will allow the function to know what test to execute in the sim directory
+            test_type (str): The type such as python, bash, etc
+        Returns:
+            True and the output file location
+        """
+
+        # Prepare the function to execute the simulation
+        test_file_path = os.path.join(self.base_dir, "sim")
+        
+        output_file = os.path.join(self.base_dir, "tmp", f"{test_name}-output.log")
+        os.chdir(test_file_path)
+
+        if test_exctention:
+            command = [test_type, test_name, test_exctention]
+        else:
+            command = [test_type, test_name]
+
+        # Execute the command using subprocess and save the output into a file
+        with open(output_file, "w") as f:
+            formatted_datetime = self.current_datetime.strftime("%Y-%m-%d %H:%M:%S")
+            f.write(formatted_datetime)
+            f.write("\n\n")
+            result = subprocess.run(command, stdout=f, stderr=subprocess.STDOUT, text=True)
+        
+        # Check if the command executed successfully
+        if result.returncode or result.returncode == 0:
+            return True, output_file
+        else:
+            print("Error:", result.returncode)
+            return False, output_file
+
+
+    def clean_format_output(self, input_file, output_file=None):
+        """
+        Clean and format the output from tests.
+
+        Args:
+            input_file (str): Path to the input file with raw test results.
+            output_file (str): Path to the file where cleaned and formatted output will be saved.
+
+        Returns:
+            None
+        """
+        # Implement cleaning and formatting logic here
+
+        # Open up the file with only read permissions
+        with open(input_file, 'r') as input_file:
+            unlceaned_output = input_file.read()
+
+        # use something like this function to detect pass and fail
+        passed_configs = []
+        failed_configs = []
+
+        lines = unlceaned_output.split('\n')
+        index = 0
+
+        while index < len(lines):
+            # Remove ANSI escape codes
+            line = re.sub(r'\x1b\[[0-9;]*[mGK]', '', lines[index])  
+            #print(line)
+            if "Success" in line:
+                passed_configs.append(line.split(':')[0].strip())
+            elif "passed lint" in line:
+                #print(line)
+                passed_configs.append(line.split(' ')[0].strip())
+                #passed_configs.append(line) # potentially use a space
+            elif "failed lint" in line:
+                failed_configs.append(line.split(' ')[0].strip(), "no log file")
+                #failed_configs.append(line)
+
+            elif "Failures detected in output" in line:
+                try:
+                    config_name = line.split(':')[0].strip()
+                    log_file = os.path.abspath("logs/"+config_name+".log")
+                    #print(f"The log file saving to: {log_file} in the current working directory: {os.getcwd()}") 
+                    failed_configs.append((config_name, log_file))
+                except:
+                    failed_configs.append((config_name, "Log file not found"))
+            
+
+            index += 1
+
+        # alphabetically sort the configurations
+        if len(passed_configs) != 0:
+            passed_configs.sort()
+
+        if len(failed_configs) != 0:
+            failed_configs.sort()
+        #print(f"The passed configs are: {passed_configs}")
+        #print(f"The failed configs are {failed_configs}")
+        return passed_configs, failed_configs
+
+    def rewrite_to_markdown(self, test_name, passed_configs, failed_configs):
+        """
+        Rewrite test results to markdown format.
+
+        Args:
+            input_file (str): Path to the input file with cleaned and formatted output.
+            markdown_file (str): Path to the markdown file where test results will be saved.
+
+        Returns:
+            None
+        """
+        # Implement markdown rewriting logic here
+        timestamp = datetime.now().strftime("%Y-%m-%d")
+
+        output_directory = os.path.join(self.base_parent_dir, "../../results", timestamp)
+        os.chdir(output_directory)
+        current_directory = os.getcwd()
+        output_file = os.path.join(current_directory, f"{test_name}.md")
+        #print("Current directory:", current_directory)
+        #print("Output File:", output_file)
+
+        with open(output_file, 'w') as md_file:
+       
+            # Title
+            md_file.write(f"\n\n# Regression Test Results - {timestamp}\n\n")
+            #md_file.write(f"\n\n<div class=\"regression\">\n# Regression Test Results - {timestamp}\n</div>\n\n")
+
+            # File Path
+            md_file.write(f"\n**File:** {output_file}\n\n")
+
+            if failed_configs:
+                md_file.write("## Failed Configurations\n\n")
+                for config, log_file in failed_configs:
+                    md_file.write(f"- <span class=\"failure\" style=\"color: red;\">{config}</span> ({log_file})\n")
+                md_file.write("\n")
+            else:
+                md_file.write("## Failed Configurations\n")
+                md_file.write(f"No Failures\n")
+            
+            md_file.write("\n## Passed Configurations\n")
+            for config in passed_configs:
+                md_file.write(f"- <span class=\"success\" style=\"color: green;\">{config}</span>\n")
+
+    def combine_markdown_files(self, passed_tests, failed_tests, test_list, total_number_failures, total_number_success, test_type="default", markdown_file=None):
+        """
+        First we want to display the server properties like:
+            - Server full name
+            - Operating System
+
+        Combine the markdown files and format them to display all of the failures at the top categorized by what kind of test it was
+        Then display all of the successes.
+
+        Args:
+            passed_tests (list): a list of successful tests
+            failed_tests (list): a list of failed tests
+            test_list (list): a list of the test names. 
+            markdown_file (str): Path to the markdown file where test results will be saved.
+
+        Returns:
+            None
+        """
+        timestamp = datetime.now().strftime("%Y-%m-%d")
+
+        output_directory = os.path.join(self.base_parent_dir, "../../results", timestamp)
+        os.chdir(output_directory)
+        current_directory = os.getcwd()
+        output_file = os.path.join(current_directory, "results.md")
+        
+
+        with open(output_file, 'w') as md_file:
+            # Title
+            md_file.write(f"\n\n# Nightly Test Results - {timestamp}\n\n")
+            # Host information
+            try:
+                # Run hostname command
+                hostname = subprocess.check_output(['hostname', '-A']).strip().decode('utf-8')
+                md_file.write(f"**Host name:** {hostname}")
+                md_file.write("\n")
+                # Run uname command to get OS information
+                os_info = subprocess.check_output(['uname', '-a']).strip().decode('utf-8')
+                md_file.write(f"\n**Operating System Information:** {os_info}")
+                md_file.write("\n")
+            except subprocess.CalledProcessError as e:
+                # Handle if the command fails
+                md_file.write(f"Failed to identify host and Operating System information: {str(e)}")
+            
+            # Which tests did we run
+            md_file.write(f"\n**Tests made:** `make {test_type}`\n")
+
+            # File Path
+            md_file.write(f"\n**File:** {output_file}\n\n") # *** needs to be changed
+            md_file.write(f"**Total Successes: {total_number_success}**\n")
+            md_file.write(f"**Total Failures: {total_number_failures}**\n")
+
+            # Failed Tests
+            md_file.write(f"\n\n## Failed Tests")
+            md_file.write(f"\nTotal failed tests: {total_number_failures}")
+            for (test_item, item) in zip(test_list, failed_tests):
+                md_file.write(f"\n\n### {test_item[1]} test")
+                md_file.write(f"\n**General Information**\n")
+                md_file.write(f"\n* Test type: {test_item[0]}\n")
+                md_file.write(f"\n* Test name: {test_item[1]}\n")
+                md_file.write(f"\n* Test extension: {test_item[2]}\n\n")
+                md_file.write(f"**Failed Tests:**\n")
+
+                
+
+                if len(item) == 0:
+                    md_file.write("\n")
+                    md_file.write(f"* <span class=\"no-failure\" style=\"color: green;\">No failures</span>\n")
+                    md_file.write("\n")
+                else:
+                    for failed_test in item:
+                        config = failed_test[0]
+                        log_file = failed_test[1]
+
+                        md_file.write("\n")
+                        md_file.write(f"* <span class=\"failure\" style=\"color: red;\">{config}</span> ({log_file})\n")
+                        md_file.write("\n")
+            # Successfull Tests
+
+            md_file.write(f"\n\n## Successfull Tests")
+            md_file.write(f"\n**Total successfull tests: {total_number_success}**")
+            for (test_item, item) in zip(test_list, passed_tests):
+                md_file.write(f"\n\n### {test_item[1]} test")
+                md_file.write(f"\n**General Information**\n")
+                md_file.write(f"\n* Test type: {test_item[0]}")
+                md_file.write(f"\n* Test name: {test_item[1]}")
+                md_file.write(f"\n* Test extension: {test_item[2]}\n\n")
+                md_file.write(f"\n**Successfull Tests:**\n")
+
+                
+
+                if len(item) == 0:
+                    md_file.write("\n")
+                    md_file.write(f"* <span class=\"no-successes\" style=\"color: red;\">No successes</span>\n")
+                    md_file.write("\n")
+                else:
+                    for passed_tests in item:
+                        config = passed_tests
+                        
+                        md_file.write("\n")
+                        md_file.write(f"* <span class=\"success\" style=\"color: green;\">{config}</span>\n")
+                        md_file.write("\n")
+                    
+                    
+
+    def convert_to_html(self, markdown_file="results.md", html_file="results.html"):
+        """
+        Convert markdown file to HTML.
+
+        Args:
+            markdown_file (str): Path to the markdown file.
+            html_file (str): Path to the HTML file where converted output will be saved.
+
+        Returns:
+            None
+        """
+        # Implement markdown to HTML conversion logic here
+        todays_date = self.current_datetime.strftime("%Y-%m-%d")
+        markdown_file_path = os.path.join(self.base_parent_dir, "../../results", todays_date) 
+        os.chdir(markdown_file_path)
+
+        with open(markdown_file, 'r') as md_file:
+            md_content = md_file.read()
+            html_content = markdown.markdown(md_content)
+        
+        with open(html_file, 'w') as html_file:
+            html_file.write(html_content)
+        
+
+ 
+    def send_email(self, sender_email=None, receiver_emails=None, subject="Nightly Regression Test"):
+        """
+        Send email with HTML content.
+
+        Args:
+            self: The instance of the class.
+            sender_email (str): The sender's email address. Defaults to None.
+            receiver_emails (list[str]): List of receiver email addresses. Defaults to None.
+            subject (str, optional): Subject of the email. Defaults to "Nightly Regression Test".
+
+        Returns:
+            None
+        """
+
+        # check if there are any emails
+        if not receiver_emails:
+            print("No receiver emails provided.")
+            return
+        # grab thge html file
+        todays_date = self.current_datetime.strftime("%Y-%m-%d")
+        html_file_path = os.path.join(self.base_parent_dir, "../../results", todays_date) 
+        os.chdir(html_file_path)
+        html_file = "results.html"
+
+        with open(html_file, 'r') as html_file:
+                body = html_file.read()
+
+    
+        
+
+        for receiver_email in receiver_emails:
+            # Compose the mutt command for each receiver email
+            command = [
+                'mutt',
+                '-s', subject,
+                '-e', 'set content_type=text/html',
+                '-e', 'my_hdr From: James Stine <james.stine@okstate.edu>',
+                '--', receiver_email
+            ]
+            
+            # Open a subprocess to run the mutt command
+            process = subprocess.Popen(command, stdin=subprocess.PIPE)
+            
+            # Write the email body to the subprocess
+            process.communicate(body.encode('utf-8'))
+
+
+#############################################
+#                 SETUP                     #
+#############################################
+folder_manager = FolderManager() # creates the object
+
+# setting the path on where to clone new repositories of cvw
+path = folder_manager.create_preliminary_folders(["nightly_runs/repos/", "nightly_runs/results/"])
+new_folder = folder_manager.create_new_folder(["nightly_runs/repos/", "nightly_runs/results/"])
+
+# clone the cvw repo
+folder_manager.clone_repository("nightly_runs/repos/", "https://github.com/openhwgroup/cvw.git")
+
+
+        
+#############################################
+#                 SETUP                     #
+#############################################
+
+test_runner = TestRunner() # creates the object
+test_runner.set_env_var("nightly_runs/repos/") # ensures that the new WALLY environmental variable is set correctly
+
+
+#############################################
+#              MAKE TESTS                   #
+#############################################
+
+
+# target = "wally-riscv-arch-test"
+target = "all"
+if test_runner.execute_makefile(target = target):
+   print(f"The {target} tests were made successfully")
+
+#############################################
+#               RUN TESTS                   #
+#############################################
+
+
+test_list = [["python", "regression-wally", "-nightly"], ["bash", "lint-wally", "-nightly"], ["bash", "coverage", "--search"]]
+output_log_list = [] # a list where the output markdown file lcoations will be saved to
+total_number_failures = 0  # an integer where the total number failures from all of the tests will be collected
+total_number_success = 0    # an integer where the total number of sucess will be collected
+
+total_failures = []
+total_success = []
+
+for test_type, test_name, test_exctention in test_list:
+    print("--------------------------------------------------------------")
+    print(f"Test type: {test_type}")
+    print(f"Test name: {test_name}")
+    print(f"Test extenction: {test_exctention}")
+
+    check, output_location = test_runner.run_tests(test_type=test_type, test_name=test_name, test_exctention=test_exctention)
+    print(check)
+    print(output_location)
+    if check: # this checks if the test actually ran successfully
+        output_log_list.append(output_location)
+        
+        # format tests to markdown
+        try:
+            passed, failed = test_runner.clean_format_output(input_file = output_location)
+        except:
+            print("There was an error cleaning the data")
+
+        print(f"The # of failures are for {test_name}: {len(failed)}")
+        total_number_failures+= len(failed)
+        total_failures.append(failed)
+
+        print(f"The # of sucesses are for {test_name}: {len(passed)}")
+        total_number_success += len(passed)
+        total_success.append(passed)
+        test_runner.rewrite_to_markdown(test_name, passed, failed)
+
+print(f"The total sucesses are: {total_number_success}")
+print(f"The total failures are: {total_number_failures}")
+
+
+
+
+    
+
+#############################################
+#               FORMAT TESTS                #
+#############################################
+
+# Combine multiple markdown files into one file
+
+test_runner.combine_markdown_files(passed_tests = total_success, failed_tests = total_failures, test_list = test_list, total_number_failures = total_number_failures, total_number_success = total_number_success, test_type=target, markdown_file=None)
+
+
+#############################################
+#             WRITE MD TESTS                #
+#############################################
+test_runner.convert_to_html()
+
+
+
+#############################################
+#                SEND EMAIL                 #
+#############################################
+
+sender_email = 'james.stine@okstate.edu'
+receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu']
+test_runner.send_email(sender_email=sender_email, receiver_emails=receiver_emails)
\ No newline at end of file
diff --git a/bin/nightly_build/nightly_build_v13_beta.sh b/bin/nightly_build/nightly_build_v13_beta.sh
deleted file mode 100755
index 2e0ca42d4..000000000
--- a/bin/nightly_build/nightly_build_v13_beta.sh
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/bin/bash
-
-# set WALLY path
-WALLY=$(dirname ${BASH_SOURCE[0]:-$0})
-export WALLY=$(cd "$WALLY/../../" && pwd)
-echo "WALLY is set to: $WALLY"
-
-# Going to nightly runs
-cd $WALLY/../
-
-# check if directories exist
-if [ ! -d "build-results" ]; then
-    echo "Directory does not exist, creating it..."
-    mkdir -p "build-results"
-    if [ $? -eq 0 ]; then
-        echo "Directory created successfully."
-    else
-        echo "Failed to create directory."
-        exit 1
-    fi
-else
-    echo "Directory already exists."
-fi
-
-if [ ! -d "logs" ]; then
-    echo "Directory does not exist, creating it..."
-    mkdir -p "logs"
-    if [ $? -eq 0 ]; then
-        echo "Directory created successfully."
-    else
-        echo "Failed to create directory."
-        exit 1
-    fi
-else
-    echo "Directory already exists."
-fi
-
-# setup source okstate file
-echo "Sourcing setup files"
-source $WALLY/setup_host.sh
-source $WALLY/../setup-files/setup_tools.sh
-
-# Navigate to the gir repo
-cd $WALLY
-
-# pull the repository
-echo "Pulling submodules"
-#git pull --recurse-submodules origin main
-
-# build the regression tests
-echo "Building the regression tests"
-cd sim
-#if make wally-riscv-arch-test; then
-#if make all; then
-#	echo "Make successfull"
-#else
-#	echo "Make failed"
-#	cd $WALLY/..
-	# add the the regression result and the coverage result that there was an error in making the tests
-#	python $WALLY/bin/nightly_build/src/error_detector.py --tag make -o $WALLY/../build-results/regression_results.md
-#	python $WALLY/bin/nightly_build/src/error_detector.py --tag make -o $WALLY/../build-results/coverage_results.md
-
-	# exit the program
-	#exit 1
-#fi
-
-# execute the simulation / regression tests and save output to a file
-echo "running the regression test"
-#./regression-wally > $WALLY/../logs/regression_output.log 2>&1
-
-echo "running coverage tests"
-#./coverage > $WALLY/../logs/coverage_output.log 2>&1
-
-
-# run the Python script to parse the output and generate the log file
-echo "Parsing output data from the regression test"
-cd $WALLY/../
-
-python $WALLY/bin/nightly_build/src/parse_regression.py -i $WALLY/../logs/regression_output.log -o $WALLY/../build-results/regression_results.md
-
-python $WALLY/bin/nightly_build/src/parse_coverage.py -i $WALLY/../logs/coverage_output.log -o $WALLY/../build-results/coverage_results.md
-
-# email update
-cd $WALLY/bin/nightly_build/src/
-./send_mail_html.sh
diff --git a/bin/nightly_build/src/error_detector.py b/bin/nightly_build/src/error_detector.py
deleted file mode 100644
index c239032e9..000000000
--- a/bin/nightly_build/src/error_detector.py
+++ /dev/null
@@ -1,37 +0,0 @@
-import argparse
-import datetime
-
-def add_failure_to_markdown(tag, output_file, input_file = None):
-    # Get the current date and time
-    current_datetime = datetime.datetime.now()
-    formatted_datetime = current_datetime.strftime("%Y-%m-%d %H:%M:%S")
-
-    # Create the failure message based on the provided tag and input content
-    if tag == "make":
-        failure_message = f"# {tag.capitalize()} riscof comilation failure - {formatted_datetime}\n\n"
-        failure_message += f"The error was due to a problem in compiling the the riscof tests:\n\n"
-        if input_file != None:
-            failure_message += f"The particular error: {input_file}\n\n"
-    else:
-        failure_message = f"# {tag.capitalize()} Failure - {formatted_datetime}\n\n"
-        failure_message += f":\n\n"
-
-    # Append the failure message to the specified output file
-    with open(output_file, "a") as file:
-        file.write(failure_message)
-
-    print(f"Failure information added to {output_file}.")
-
-if __name__ == "__main__":
-    # Set up argparse
-    parser = argparse.ArgumentParser(description="Add failure information to Markdown file.")
-    parser.add_argument("--tag", required=True, help="Specify the tag for the failure type (e.g., 'make', 'custom').")
-    parser.add_argument("-i", required=False, help="Specify the input file containing failure details.")
-    parser.add_argument("-o", required=True, help="Specify the output file to write the failure information.")
-
-    # Parse command-line arguments
-    args = parser.parse_args()
-
-    # Call the function with the specified tag, input file, and output file
-    add_failure_to_markdown(args.tag,  args.o)
-
diff --git a/bin/nightly_build/src/parse_coverage.py b/bin/nightly_build/src/parse_coverage.py
deleted file mode 100644
index 33811b0a1..000000000
--- a/bin/nightly_build/src/parse_coverage.py
+++ /dev/null
@@ -1,95 +0,0 @@
-import os
-import argparse
-from datetime import datetime
-import re
-from colorama import init, Fore, Style
-
-def parse_regression_output(output):
-    passed_configs = []
-    failed_configs = []
-
-    lines = output.split('\n')
-    index = 0
-
-    while index < len(lines):
-        # Remove ANSI escape codes
-        line = re.sub(r'\x1b\[[0-9;]*[mGK]', '', lines[index])  
-        if "Success" in line:
-            passed_configs.append(line.split(':')[0].strip())
-        elif "Failures detected in output" in line:
-            try:
-                config_name = line.split(':')[0].strip()
-                log_file = os.path.abspath(config_name+".log") 
-                failed_configs.append((config_name, log_file))
-            except:
-                failed_configs.append((config_name, "Log file not found"))
-
-        index += 1
-
-    # alphabetically sort the configurations
-    passed_configs.sort()
-    failed_configs.sort()
-    return passed_configs, failed_configs
-
-def write_to_markdown(passed_configs, failed_configs, output_file):
-    timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
-
-    with open(output_file, 'a') as md_file:
-        md_file.write(f"\n\n# Coverage Test Results - {timestamp}\n\n")
-
-        md_file.write("\n## Failed Configurations\n")
-        for config, log_file in failed_configs:
-            md_file.write(f"- <span class=\"failure\" style=\"color: red;\">{config}</span> ({log_file})\n")
-            if len(failed_configs) == 0:
-                md_file.write(" - no failures\n")
-
-        md_file.write("\n## Passed Configurations\n")
-        for config in passed_configs:
-            md_file.write(f"- <span class=\"success\" style=\"color: green;\">{config}</span>\n")
-
-
-def write_new_markdown(passed_configs, failed_configs):
-    timestamp = datetime.now().strftime("%Y-%m-%d")
-    output_file = f"/home/thkidd/nightly_runs/build-results/builds/coverage/wally_coverage_{timestamp}.md"
-    
-    with open(output_file, 'w') as md_file:
-        # Title
-        md_file.write(f"\n\n# Coverage Test Results - {timestamp}\n\n")
-        
-        ## File path
-        md_file.write(f"\n**File:** {output_file}\n")
-
-        md_file.write("\n## Failed Configurations\n")
-        # add in if there were no failures
-        if len(failed_configs) == 0:
-            md_file.write(f"No Failures\n")
-        
-        for config, log_file in failed_configs:
-                md_file.write(f"- <span class=\"failure regression\" style=\"color: red;\">{config}</span> ({log_file})\n")
-
-        md_file.write("\n## Passed Configurations\n")
-        for config in passed_configs:
-            md_file.write(f"- <span class=\"success regression\" style=\"color: green;\">{config}</span>\n")
-
-
-
-
-if __name__ == "__main__":
-    init(autoreset=True)  # Initialize colorama
-    parser = argparse.ArgumentParser(description='Parse regression test output and append to a markdown file.')
-    parser.add_argument('-i', '--input', help='Input file containing regression test output', required=True)
-    parser.add_argument('-o', '--output', help='Output markdown file', default='regression_results.md')
-    args = parser.parse_args()
-
-    with open(args.input, 'r') as input_file:
-        regression_output = input_file.read()
-
-    passed_configs, failed_configs = parse_regression_output(regression_output)
-    write_to_markdown(passed_configs, failed_configs, args.output)
-
-    print(f"Markdown file updated: {args.output}")
-
-    write_new_markdown(passed_configs, failed_configs)
-
-    print("New markdown file created")
-
diff --git a/bin/nightly_build/src/parse_regression.py b/bin/nightly_build/src/parse_regression.py
deleted file mode 100644
index 0d8c9467d..000000000
--- a/bin/nightly_build/src/parse_regression.py
+++ /dev/null
@@ -1,102 +0,0 @@
-import argparse
-import os
-from datetime import datetime
-import re
-from colorama import init, Fore, Style
-
-def parse_regression_output(output):
-    passed_configs = []
-    failed_configs = []
-
-    lines = output.split('\n')
-    index = 0
-
-    while index < len(lines):
-        # Remove ANSI escape codes
-        line = re.sub(r'\x1b\[[0-9;]*[mGK]', '', lines[index])  
-        #print("The cleaned line: ", line)
-        if "Success" in line:
-            passed_configs.append(line.split(':')[0].strip())
-        elif "Failures detected in output" in line:
-            try:
-                config_name = line.split(':')[0].strip()
-                log_file = os.path.abspath(config_name+".log") 
-                failed_configs.append((config_name, log_file))
-            except:
-                failed_configs.append((config_name, "Log file not found"))
-        elif "Timeout" in line:
-            try:
-                config_name = line.split(':')[0].strip()
-                log_file = os.path.abspath(config_name+".log")
-                failed_configs.append((config_name, log_file))
-            except:
-                failed_configs.append((config_name, "Log file not found"))
-        index += 1
-    
-    # alphabetically sort the configurations
-    passed_configs.sort()
-    failed_configs.sort()
-    return passed_configs, failed_configs
-
-def write_to_markdown(passed_configs, failed_configs, output_file):
-    timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
-    with open(output_file, 'a') as md_file:
-        md_file.write(f"\n\n<div class=\"regression\">\n# Regression Test Results - {timestamp}\n</div>\n\n")
-        #md_file.write(f"\n\n# Regression Test Results - {timestamp}\n\n")
-
-        if failed_configs:
-            md_file.write("## Failed Configurations\n")
-            for config, log_file in failed_configs:
-                md_file.write(f"- <span class=\"failure regression\" style=\"color: red;\">{config}</span> ({log_file})\n")
-            md_file.write("\n")
-        else:
-            md_file.write("## No Failed Configurations\n")
-
-        md_file.write("\n## Passed Configurations\n")
-        for config in passed_configs:
-            md_file.write(f"- <span class=\"success regression\" style=\"color: green;\">{config}</span>\n")
-
-def write_new_markdown(passed_configs, failed_configs):
-    timestamp = datetime.now().strftime("%Y-%m-%d")
-    output_file = f"/home/thkidd/nightly_runs/build-results/builds/regression/wally_regression_{timestamp}.md"
-    with open(output_file, 'w') as md_file:
-       
-        # Title
-        md_file.write(f"\n\n# Regression Test Results - {timestamp}\n\n")
-        #md_file.write(f"\n\n<div class=\"regression\">\n# Regression Test Results - {timestamp}\n</div>\n\n")
-
-        # File Path
-        md_file.write(f"\n**File:** {output_file}\n\n")
-
-        if failed_configs:
-            md_file.write("## Failed Configurations\n\n")
-            for config, log_file in failed_configs:
-                md_file.write(f"- <span class=\"failure regression\" style=\"color: red;\">{config}</span> ({log_file})\n")
-            md_file.write("\n")
-        else:
-            md_file.write("## Failed Configurations\n")
-            md_file.write(f"No Failures\n")
-        
-        md_file.write("\n## Passed Configurations\n")
-        for config in passed_configs:
-            md_file.write(f"- <span class=\"success regression\" style=\"color: green;\">{config}</span>\n")
-
-if __name__ == "__main__":
-    init(autoreset=True)  # Initialize colorama
-    parser = argparse.ArgumentParser(description='Parse regression test output and append to a markdown file.')
-    parser.add_argument('-i', '--input', help='Input file containing regression test output', required=True)
-    parser.add_argument('-o', '--output', help='Output markdown file containing formatted file', default='regression_results.md')
-    args = parser.parse_args()
-
-    with open(args.input, 'r') as input_file:
-        regression_output = input_file.read()
-
-    passed_configs, failed_configs = parse_regression_output(regression_output)
-    write_to_markdown(passed_configs, failed_configs, args.output)
-
-    print(f"Markdown file updated: {args.output}")
-
-    write_new_markdown(passed_configs, failed_configs)
-
-    print("New markdown file created")
-
diff --git a/bin/nightly_build/src/send_mail_html.sh b/bin/nightly_build/src/send_mail_html.sh
deleted file mode 100755
index 5c3735a3a..000000000
--- a/bin/nightly_build/src/send_mail_html.sh
+++ /dev/null
@@ -1,79 +0,0 @@
-current_date=$(date "+%Y-%m-%d")
-email_address="thomas.kidd@okstate.edu"
-#email_address="WALLY-REGRESSION@LISTSERV.OKSTATE.EDU"
-subject="WALLY regression and coverage test report"
-attachments=""
-html_body=""
-host_name=$(hostname) 
-os_info=$(lsb_release -a 2>/dev/null)
-script_location=$WALLY/bin/nightly_build/
-
-html_body="<div id='system-info'>
-    <h3>System Information</h3>
-    <p><strong>Server Name:</strong> $host_name@okstate.edu</p>  
-    <p><strong>Operating System:</strong> $os_info</p>
-    <p><strong>Script Origin:</strong> $script_location</p>
-</div>
-
-<p>Testing sending HTML content through mutt</p>"
-
-# Iterate through the files and concatenate their content to the body
-for file in $WALLY/../build-results/builds/*/wally_*_"$current_date"*.md; do
-    attachments+=" -a $file"
-
-    # Convert Markdown to HTML using pandoc
-    html_content=$(pandoc "$file")
-
-    # add the file full path
-    # html_body+="<p>File: $file</p>"
-    # Append the HTML content to the body
-    html_body+="$html_content"
-done
-echo "Sending email"
-
-# Get server hostname and OS information
-host_name=$(hostname)
-os_info=$(uname -a)
-
-# Define HTML body content
-
-# Use mutt to send the email with HTML body
-#mutt -e "my_hdr From:James Stine <james.stine@okstate.edu>" -s "$subject" $attachments \
-mutt -e "my_hdr From:Thomas Kidd <thomas.kidd@okstate.edu>" -s "$subject"  \
-    -e "set content_type=text/html" -- $email_address <<EOF
-<html>
-<head>
-    <meta charset="UTF-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>Nightly Build Results - $current_date</title>
-    <style>
-        body {
-            font-family: 'Helvetica Neue', Arial, sans-serif;
-            margin: 20px;
-            padding: 20px;
-            background-color: #f4f4f4;
-        }
-        h1, h3, p {
-            color: #333;
-        }
-        #system-info {
-            border: 1px solid #ddd;
-            padding: 15px;
-            margin-bottom: 20px;
-            background-color: #fff;
-            border-radius: 5px;
-            box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
-        }
-<!--	.success { color: green; } -->
-<!--    .failure { color: red; }   -->
-
-    </style>
-</head>
-<body>
-    <h1 id="test-results---$current_date">Test Results - $current_date</h1>
-    
-    $html_body
-</body>
-</html>
-EOF
-
diff --git a/bin/wrapper_nightly_runs.sh b/bin/wrapper_nightly_runs.sh
new file mode 100755
index 000000000..219e765df
--- /dev/null
+++ b/bin/wrapper_nightly_runs.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+date
+
+
+# Variables
+LOG=$HOME/nightly_runs/logs/from_wrapper.log    # you can store your log file where you would like
+PYTHON_SCRIPT=$HOME/nightly_runs/cvw/bin/       # cvw can be anywhere you would like it. Make sure to point your variable there
+SETUP_SCRIPT=$HOME/nightly_runs/cvw/            # cvw can be anywhere you would like it. Make sure to point your variable there
+
+
+
+date > $LOG 2>&1
+
+echo "Current directory"
+pwd
+
+cd $SETUP_SCRIPT
+echo "Current directory"
+pwd
+
+echo "Sourcing setup_host"
+source ./setup_host.sh >> $LOG 2>&1
+echo "Sourcing setup_tools"
+
+cd $PYTHON_SCRIPT
+pwd
+echo "Running python file"
+python nightly_build.py >> $LOG 2>&1

From 4c84b9d819aa2637c8f19d5e7d68e167a5a14c50 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Fri, 23 Feb 2024 14:54:03 -0600
Subject: [PATCH 10/20] updated nightly build, but ran into buildroot errors

---
 bin/nightly_build.py        | 13 ++++++++-----
 bin/wrapper_nightly_runs.sh |  1 -
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index 21d0ce025..7848198d2 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -615,8 +615,8 @@ test_runner.set_env_var("nightly_runs/repos/") # ensures that the new WALLY envi
 #############################################
 
 
-# target = "wally-riscv-arch-test"
-target = "all"
+target = "wally-riscv-arch-test"
+# target = "all"
 if test_runner.execute_makefile(target = target):
    print(f"The {target} tests were made successfully")
 
@@ -640,8 +640,8 @@ for test_type, test_name, test_exctention in test_list:
     print(f"Test extenction: {test_exctention}")
 
     check, output_location = test_runner.run_tests(test_type=test_type, test_name=test_name, test_exctention=test_exctention)
-    print(check)
-    print(output_location)
+    print(f"Did the tests run?: {check}")
+    print(f"The tests log files are saved to: {output_location}")
     if check: # this checks if the test actually ran successfully
         output_log_list.append(output_location)
         
@@ -689,5 +689,8 @@ test_runner.convert_to_html()
 #############################################
 
 sender_email = 'james.stine@okstate.edu'
-receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu']
+# sender_email = 'thomas.kidd@okstate.edu'
+
+# receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu']
+receiver_emails = ['thomas.kidd@okstate.edu']
 test_runner.send_email(sender_email=sender_email, receiver_emails=receiver_emails)
\ No newline at end of file
diff --git a/bin/wrapper_nightly_runs.sh b/bin/wrapper_nightly_runs.sh
index 219e765df..55d2da04f 100755
--- a/bin/wrapper_nightly_runs.sh
+++ b/bin/wrapper_nightly_runs.sh
@@ -20,7 +20,6 @@ pwd
 
 echo "Sourcing setup_host"
 source ./setup_host.sh >> $LOG 2>&1
-echo "Sourcing setup_tools"
 
 cd $PYTHON_SCRIPT
 pwd

From 9ccc93ff0e0c0e973beb875ea7c27a4af26ced57 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Mon, 4 Mar 2024 18:21:03 -0600
Subject: [PATCH 11/20] over rides TIMEOUT on -nightly tag for regression since
 buildroot is not working

---
 bin/nightly_build.py | 45 ++++++++++++++++++++++++++++++++++++++------
 1 file changed, 39 insertions(+), 6 deletions(-)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index 7848198d2..166b8b9f9 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -228,7 +228,29 @@ class TestRunner:
         # print(f"The new WALLY vairable is: {os.environ.get('WALLY')}")
         # print(f"The Base Directory is now : {self.base_dir}")
         # print(f"The Base Parent Directory is now : {self.base_parent_dir}")
-       
+
+    def change_time_dur(self, time_duriation=1):
+        
+        # Prepare the command to execute the Makefile
+        make_file_path = os.path.join(self.base_dir, "sim")
+        os.chdir(make_file_path)
+        file_path = "regression-wally"
+        line_number = 450 # TIMEOUT_DUR = 1 day at this line in regression-wally 
+        new_line = f"        TIMEOUT_DUR = {60*time_duriation}"
+
+        with open(file_path, 'r') as file:
+            lines = file.readlines()
+
+        if line_number < 1 or line_number > len(lines):
+            print("Error: Line number out of range.")
+            return False
+
+        lines[line_number - 1] = new_line + '\n'
+
+        with open(file_path, 'w') as file:
+            file.writelines(lines)
+            return True
+
     def execute_makefile(self, target=None):
         """
         Execute a Makefile with optional target.
@@ -610,13 +632,24 @@ test_runner = TestRunner() # creates the object
 test_runner.set_env_var("nightly_runs/repos/") # ensures that the new WALLY environmental variable is set correctly
 
 
+#############################################
+#             TMP SETUP                     #
+#############################################
+
+"""
+The goal of this section is to replace the TIMEOUT_DUR for regression tests.
+
+"""
+if test_runner.change_time_dur():
+    print("The regression-wally file was successfully changed")
+
 #############################################
 #              MAKE TESTS                   #
 #############################################
 
 
-target = "wally-riscv-arch-test"
-# target = "all"
+# target = "wally-riscv-arch-test"
+target = "all"
 if test_runner.execute_makefile(target = target):
    print(f"The {target} tests were made successfully")
 
@@ -691,6 +724,6 @@ test_runner.convert_to_html()
 sender_email = 'james.stine@okstate.edu'
 # sender_email = 'thomas.kidd@okstate.edu'
 
-# receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu']
-receiver_emails = ['thomas.kidd@okstate.edu']
-test_runner.send_email(sender_email=sender_email, receiver_emails=receiver_emails)
\ No newline at end of file
+receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu', "sarah.harris@unlv.edu"]
+# receiver_emails = ['thomas.kidd@okstate.edu']
+test_runner.send_email(sender_email=sender_email, receiver_emails=receiver_emails)

From 22947e5b5eefece7b0308b4282a7444d9f841d8a Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Tue, 5 Mar 2024 14:26:35 -0600
Subject: [PATCH 12/20] udpated readme by adding how to add crontab section

---
 README.md     |  8 +++++++
 setup_host.sh | 58 +++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100644 setup_host.sh

diff --git a/README.md b/README.md
index f0b1a9f4b..d75e8fb98 100644
--- a/README.md
+++ b/README.md
@@ -128,4 +128,12 @@ If you want to implement your own version of the chip, your tool and license com
 Startups can expect to spend more than $1 million on CAD tools to get a chip to market. Commercial CAD tools are not realistically available to individuals without a university or company connection.
 
 
+## Adding Cron Job for nightly builds
+
+If you want to add a cronjob you can do the following:
+1) `crontab -e`
+2) add this code:
+```
+0 3 * * * BASH_ENV=~/.bashrc bash -l -c "PATH_TO_CVW/cvw/bin/wrapper_nightly_runs.sh > PATH_TO_LOG_FOLDER/cron.log"
+```
 
diff --git a/setup_host.sh b/setup_host.sh
new file mode 100644
index 000000000..55854a71c
--- /dev/null
+++ b/setup_host.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+# setup.sh
+# David_Harris@hmc.edu and kekim@hmc.edu 1 December 2021
+# Set up tools for riscv-wally
+
+echo "Executing Wally setup.sh"
+
+# Path to Wally repository
+WALLY=$(dirname ${BASH_SOURCE[0]:-$0})
+export WALLY=$(cd "$WALLY" && pwd)
+echo \$WALLY set to ${WALLY}
+
+# Path to RISC-V Tools
+export RISCV=/opt/riscv   # change this if you installed the tools in a different location
+
+# Tools
+# GCC
+#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RISCV/riscv-gnu-toolchain/lib:$RISCV/riscv-gnu-toolchain/riscv64-unknown-elf/lib
+#export PATH=$PATH:$RISCV/riscv-gnu-toolchain/bin:$RISCV/riscv-gnu-toolchain/riscv64-unknown-elf/bin      # GCC tools
+# Spike
+#export LD_LIBRARY_PATH=$RISCV/lib:$LD_LIBRARY_PATH
+export PATH=$PATH:$RISCV/bin
+# utility functions in Wally repository
+export PATH=$WALLY/bin:$PATH    
+# Verilator
+export PATH=$RICKV/verilator:$PATH # Change this for your path to Verilator
+# ModelSim/Questa (vsim)
+# Note: 2022.1 complains on cache/sram1p1r1w about StoredData cannot be driven by multiple always_ff blocks.  Ues 2021.2 for now
+#export PATH=/cad/mentor/questa_sim-2022.1_1/questasim/bin:$PATH    # Change this for your path to Modelsim 
+#export PATH=/cad/mentor/questa_sim-2021.2_1/questasim/bin:$PATH    # Change this for your path to Modelsim, or delete
+#export MGLS_LICENSE_FILE=1717@solidworks.eng.hmc.edu # Change this to your Siemens license server
+#export PATH=/cad/synopsys/SYN/bin:$PATH  # Change this for your path to Design Compiler
+#export SNPSLMD_LICENSE_FILE=27020@134.173.38.184 # Change this to your license manager file
+
+# Imperas; put this in if you are using it
+#export PATH=$RISCV/imperas-riscv-tests/riscv-ovpsim-plus/bin/Linux64:$PATH  
+#export LD_LIBRARY_PATH=$RISCV/imperas_riscv_tests/riscv-ovpsim-plus/bin/Linux64:$LD_LIBRARY_PATH # remove if no imperas
+
+export MODSIM=/opt/ModelSim/questasim
+export PATH=$PATH:$MODSIM/bin
+export LD_LIBRARY_PATH=/usr/lib:/lib
+export MGC_DOC_PATH=$MODSIM/docs
+export MGC_PDF_READER=evince
+export MGC_HTML_BROWSER=firefox
+export MGLS_LICENSE_FILE=1717@trelaina.ecen.okstate.edu
+export IMPERASD_LICENSE_FILE=2700@trelaina.ecen.okstate.edu
+
+export IDV=$RISCV/ImperasDV-OpenHW
+if [ -e "$IDV" ]; then
+#    echo "Imperas exists"
+    export IMPERAS_HOME=$IDV/Imperas
+    export IMPERAS_PERSONALITY=CPUMAN_DV_ASYNC
+    export ROOTDIR=${WALLY}/..
+    source ${IMPERAS_HOME}/bin/setup.sh
+    setupImperas ${IMPERAS_HOME}
+    export PATH=$IDV/scripts/cvw:$PATH
+fi

From 4addee0fc0b450ac9102dc9e6b41ff08d385c380 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Sat, 9 Mar 2024 14:21:04 -0600
Subject: [PATCH 13/20] updated nightly runs with try statement in email
 sending

---
 bin/nightly_build.py        | 69 +++++++++++++++++++------------------
 bin/wrapper_nightly_runs.sh |  7 ++--
 2 files changed, 39 insertions(+), 37 deletions(-)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index 166b8b9f9..ee4988736 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -36,7 +36,7 @@ Usage:
     4)  Syntax:
 
         Our cron job has the following syntax:
-        0 3 * * * BASH_ENV=~/.bashrc bash -l -c "*WHERE YOUR CVW IS MUST PUT FULL PATH*/cvw/bin/wrapper_nightly_runs.sh > *WHERE YOU WANT TO STORE LOG FILES/cron.log 2>&1" 
+        0 3 * * * BASH_ENV=~/.bashrc bash -l -c "*WHERE YOUR CVW IS MUST PUT FULL PATH*/cvw/bin/wrapper_nightly-runs.sh > *WHERE YOU WANT TO STORE LOG FILES/cron.log 2>&1" 
 
         This cronjob sources the .bashrc file and executes the wrapper script as a user. 
 
@@ -96,8 +96,8 @@ class FolderManager:
         """
         Create preliminary folders if they do not exist. 
         These folders are:
-            nightly_runs/repos/
-            nightly_runs/results/ 
+            nightly-runs/repos/
+            nightly-runs/results/ 
 
         Args:
             folders (list): A list of folder names to be created.
@@ -171,7 +171,7 @@ class TestRunner:
         The setup script will be copied from the base directory to a specific folder structure inside the base directory.
 
         Args:
-            folder: the "nightly_runs/repos/"
+            folder: the "nightly-runs/repos/"
 
         Returns:
             bool: True if the script is copied successfully, False otherwise.
@@ -592,35 +592,36 @@ class TestRunner:
 
     
         
-
-        for receiver_email in receiver_emails:
-            # Compose the mutt command for each receiver email
-            command = [
-                'mutt',
-                '-s', subject,
-                '-e', 'set content_type=text/html',
-                '-e', 'my_hdr From: James Stine <james.stine@okstate.edu>',
-                '--', receiver_email
-            ]
-            
-            # Open a subprocess to run the mutt command
-            process = subprocess.Popen(command, stdin=subprocess.PIPE)
-            
-            # Write the email body to the subprocess
-            process.communicate(body.encode('utf-8'))
-
-
+        try:
+            for receiver_email in receiver_emails:
+                # Compose the mutt command for each receiver email
+                command = [
+                    '/usr/bin/mutt',
+                    '-s', subject,
+                    '-e', 'set content_type=text/html',
+                    '-e', 'my_hdr From: James Stine <james.stine@okstate.edu>',
+                    '--', receiver_email
+                ]
+                try:
+                    # Open a subprocess to run the mutt command
+                    process = subprocess.Popen(command, stdin=subprocess.PIPE)
+                    # Write the email body to the subprocess
+                    process.communicate(body.encode('utf-8'))
+                except expression as identifier:
+                    print(f"Error sending email: {identifier}")
+        except expression as identifier:
+            print(f"Error sending email: {identifier}")
 #############################################
 #                 SETUP                     #
 #############################################
 folder_manager = FolderManager() # creates the object
 
 # setting the path on where to clone new repositories of cvw
-path = folder_manager.create_preliminary_folders(["nightly_runs/repos/", "nightly_runs/results/"])
-new_folder = folder_manager.create_new_folder(["nightly_runs/repos/", "nightly_runs/results/"])
+path = folder_manager.create_preliminary_folders(["nightly-runs/repos/", "nightly-runs/results/"])
+new_folder = folder_manager.create_new_folder(["nightly-runs/repos/", "nightly-runs/results/"])
 
 # clone the cvw repo
-folder_manager.clone_repository("nightly_runs/repos/", "https://github.com/openhwgroup/cvw.git")
+folder_manager.clone_repository("nightly-runs/repos/", "https://github.com/openhwgroup/cvw.git")
 
 
         
@@ -629,7 +630,7 @@ folder_manager.clone_repository("nightly_runs/repos/", "https://github.com/openh
 #############################################
 
 test_runner = TestRunner() # creates the object
-test_runner.set_env_var("nightly_runs/repos/") # ensures that the new WALLY environmental variable is set correctly
+test_runner.set_env_var("nightly-runs/repos/") # ensures that the new WALLY environmental variable is set correctly
 
 
 #############################################
@@ -650,8 +651,8 @@ if test_runner.change_time_dur():
 
 # target = "wally-riscv-arch-test"
 target = "all"
-if test_runner.execute_makefile(target = target):
-   print(f"The {target} tests were made successfully")
+# if test_runner.execute_makefile(target = target):
+#    print(f"The {target} tests were made successfully")
 
 #############################################
 #               RUN TESTS                   #
@@ -671,7 +672,7 @@ for test_type, test_name, test_exctention in test_list:
     print(f"Test type: {test_type}")
     print(f"Test name: {test_name}")
     print(f"Test extenction: {test_exctention}")
-
+ 
     check, output_location = test_runner.run_tests(test_type=test_type, test_name=test_name, test_exctention=test_exctention)
     print(f"Did the tests run?: {check}")
     print(f"The tests log files are saved to: {output_location}")
@@ -683,16 +684,16 @@ for test_type, test_name, test_exctention in test_list:
             passed, failed = test_runner.clean_format_output(input_file = output_location)
         except:
             print("There was an error cleaning the data")
-
+ 
         print(f"The # of failures are for {test_name}: {len(failed)}")
         total_number_failures+= len(failed)
         total_failures.append(failed)
-
+ 
         print(f"The # of sucesses are for {test_name}: {len(passed)}")
         total_number_success += len(passed)
         total_success.append(passed)
         test_runner.rewrite_to_markdown(test_name, passed, failed)
-
+ 
 print(f"The total sucesses are: {total_number_success}")
 print(f"The total failures are: {total_number_failures}")
 
@@ -724,6 +725,6 @@ test_runner.convert_to_html()
 sender_email = 'james.stine@okstate.edu'
 # sender_email = 'thomas.kidd@okstate.edu'
 
-receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu', "sarah.harris@unlv.edu"]
-# receiver_emails = ['thomas.kidd@okstate.edu']
+# receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu', 'sarah.harris@unlv.edu', 'nlucio@hmc.edu']
+receiver_emails = ['thomas.kidd@okstate.edu']
 test_runner.send_email(sender_email=sender_email, receiver_emails=receiver_emails)
diff --git a/bin/wrapper_nightly_runs.sh b/bin/wrapper_nightly_runs.sh
index 55d2da04f..e6d198fcd 100755
--- a/bin/wrapper_nightly_runs.sh
+++ b/bin/wrapper_nightly_runs.sh
@@ -3,9 +3,9 @@ date
 
 
 # Variables
-LOG=$HOME/nightly_runs/logs/from_wrapper.log    # you can store your log file where you would like
-PYTHON_SCRIPT=$HOME/nightly_runs/cvw/bin/       # cvw can be anywhere you would like it. Make sure to point your variable there
-SETUP_SCRIPT=$HOME/nightly_runs/cvw/            # cvw can be anywhere you would like it. Make sure to point your variable there
+LOG=$HOME/nightly-runs/logs/from_wrapper.log    # you can store your log file where you would like
+PYTHON_SCRIPT=$HOME/nightly-runs/cvw/bin/       # cvw can be anywhere you would like it. Make sure to point your variable there
+SETUP_SCRIPT=$HOME/nightly-runs/cvw/            # cvw can be anywhere you would like it. Make sure to point your variable there
 
 
 
@@ -25,3 +25,4 @@ cd $PYTHON_SCRIPT
 pwd
 echo "Running python file"
 python nightly_build.py >> $LOG 2>&1
+echo "Finished"

From 0e3341c1dc692be85042dabe5564594adc88bdbe Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Sat, 9 Mar 2024 16:27:35 -0600
Subject: [PATCH 14/20] added argstrings to make it a better CLI tool

---
 bin/nightly_build.py        | 226 ++++++++++++++++++++----------------
 bin/wrapper_nightly_runs.sh |   2 +-
 2 files changed, 128 insertions(+), 100 deletions(-)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index ee4988736..ff92704d0 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -54,6 +54,7 @@ Dependencies:
         - re
         - markdown
         - subprocess
+        - argparse
 
     Bash:
         - mutt (email sender)
@@ -69,6 +70,8 @@ from datetime import datetime
 import re
 import markdown
 import subprocess
+import argparse
+
 
 
 
@@ -83,7 +86,7 @@ class FolderManager:
             base_dir (str): The base directory where folders will be managed and repository will be cloned.
         """
         env_extract_var = 'WALLY'
-        print(f"The environemntal variable is {env_extract_var}")
+        # print(f"The environemntal variable is {env_extract_var}")
         self.base_dir = os.environ.get(env_extract_var)
         print(f"The base directory is: {self.base_dir}")
         self.base_parent_dir = os.path.dirname(self.base_dir)
@@ -611,120 +614,145 @@ class TestRunner:
                     print(f"Error sending email: {identifier}")
         except expression as identifier:
             print(f"Error sending email: {identifier}")
-#############################################
-#                 SETUP                     #
-#############################################
-folder_manager = FolderManager() # creates the object
-
-# setting the path on where to clone new repositories of cvw
-path = folder_manager.create_preliminary_folders(["nightly-runs/repos/", "nightly-runs/results/"])
-new_folder = folder_manager.create_new_folder(["nightly-runs/repos/", "nightly-runs/results/"])
-
-# clone the cvw repo
-folder_manager.clone_repository("nightly-runs/repos/", "https://github.com/openhwgroup/cvw.git")
 
 
-        
-#############################################
-#                 SETUP                     #
-#############################################
 
-test_runner = TestRunner() # creates the object
-test_runner.set_env_var("nightly-runs/repos/") # ensures that the new WALLY environmental variable is set correctly
+def main():
+    #############################################
+    #                 ARG PARSER                #
+    #############################################
+
+    parser = argparse.ArgumentParser(description='Nightly Verification Testing for WALLY.')
+
+    parser.add_argument('--path', help='specify the path for where the nightly repositories will be cloned ex: "nightly-runs')
+    parser.add_argument('--repository', help='specify which github repository you want to clone')
+    parser.add_argument('--target', help='types of tests you can make are: all, wally-riscv-arch-test')
+    parser.add_argument('--send_email', help='do you want to send emails: "yes" or "y"')
+    
+    args = parser.parse_args()
+
+    # file paths for where the results and repos will be saved: repos and results can be changed to whatever
+    repos_path = f"{args.path}/repos/"
+    results_path = f"{args.path}/results/"
+    #############################################
+    #                 SETUP                     #
+    #############################################
+    folder_manager = FolderManager() # creates the object
+
+    # setting the path on where to clone new repositories of cvw
+    folder_manager.create_preliminary_folders([repos_path, results_path])
+    new_folder = folder_manager.create_new_folder([repos_path, results_path])
+
+    # clone the cvw repo
+    folder_manager.clone_repository(repos_path, args.repository)
+            
+    #############################################
+    #                 SETUP                     #
+    #############################################
+
+    test_runner = TestRunner() # creates the object
+    test_runner.set_env_var(repos_path) # ensures that the new WALLY environmental variable is set correctly
 
 
-#############################################
-#             TMP SETUP                     #
-#############################################
+    #############################################
+    #             TMP SETUP                     #
+    #############################################
 
-"""
-The goal of this section is to replace the TIMEOUT_DUR for regression tests.
-
-"""
-if test_runner.change_time_dur():
-    print("The regression-wally file was successfully changed")
-
-#############################################
-#              MAKE TESTS                   #
-#############################################
-
-
-# target = "wally-riscv-arch-test"
-target = "all"
-# if test_runner.execute_makefile(target = target):
-#    print(f"The {target} tests were made successfully")
-
-#############################################
-#               RUN TESTS                   #
-#############################################
-
-
-test_list = [["python", "regression-wally", "-nightly"], ["bash", "lint-wally", "-nightly"], ["bash", "coverage", "--search"]]
-output_log_list = [] # a list where the output markdown file lcoations will be saved to
-total_number_failures = 0  # an integer where the total number failures from all of the tests will be collected
-total_number_success = 0    # an integer where the total number of sucess will be collected
-
-total_failures = []
-total_success = []
-
-for test_type, test_name, test_exctention in test_list:
-    print("--------------------------------------------------------------")
-    print(f"Test type: {test_type}")
-    print(f"Test name: {test_name}")
-    print(f"Test extenction: {test_exctention}")
- 
-    check, output_location = test_runner.run_tests(test_type=test_type, test_name=test_name, test_exctention=test_exctention)
-    print(f"Did the tests run?: {check}")
-    print(f"The tests log files are saved to: {output_location}")
-    if check: # this checks if the test actually ran successfully
-        output_log_list.append(output_location)
-        
-        # format tests to markdown
-        try:
-            passed, failed = test_runner.clean_format_output(input_file = output_location)
-        except:
-            print("There was an error cleaning the data")
- 
-        print(f"The # of failures are for {test_name}: {len(failed)}")
-        total_number_failures+= len(failed)
-        total_failures.append(failed)
- 
-        print(f"The # of sucesses are for {test_name}: {len(passed)}")
-        total_number_success += len(passed)
-        total_success.append(passed)
-        test_runner.rewrite_to_markdown(test_name, passed, failed)
- 
-print(f"The total sucesses are: {total_number_success}")
-print(f"The total failures are: {total_number_failures}")
+    """
+    The goal of this section is to replace the TIMEOUT_DUR for regression tests.
 
+    """
+    if test_runner.change_time_dur(time_duriation=2):
+        pass
+    else:
+        print("Error occured changing the TIMEOUT duration in './regression-wally'")
 
+    #############################################
+    #              MAKE TESTS                   #
+    #############################################
 
 
     
+    # if test_runner.execute_makefile(target = args.target):
+    #    print(f"The {args.target} tests were made successfully")
 
-#############################################
-#               FORMAT TESTS                #
-#############################################
-
-# Combine multiple markdown files into one file
-
-test_runner.combine_markdown_files(passed_tests = total_success, failed_tests = total_failures, test_list = test_list, total_number_failures = total_number_failures, total_number_success = total_number_success, test_type=target, markdown_file=None)
+    #############################################
+    #               RUN TESTS                   #
+    #############################################
 
 
-#############################################
-#             WRITE MD TESTS                #
-#############################################
-test_runner.convert_to_html()
+    test_list = [["python", "regression-wally", "-nightly"], ["bash", "lint-wally", "-nightly"], ["bash", "coverage", "--search"]]
+    output_log_list = [] # a list where the output markdown file lcoations will be saved to
+    total_number_failures = 0  # an integer where the total number failures from all of the tests will be collected
+    total_number_success = 0    # an integer where the total number of sucess will be collected
+
+    total_failures = []
+    total_success = []
+
+    for test_type, test_name, test_exctention in test_list:
+        print("--------------------------------------------------------------")
+        print(f"Test type: {test_type}")
+        print(f"Test name: {test_name}")
+        print(f"Test extention: {test_exctention}")
+    
+        check, output_location = test_runner.run_tests(test_type=test_type, test_name=test_name, test_exctention=test_exctention)
+        print(f"Did the tests run?: {check}")
+        print(f"The tests log files are saved to: {output_location}")
+        if check: # this checks if the test actually ran successfully
+            output_log_list.append(output_location)
+            
+            # format tests to markdown
+            try:
+                passed, failed = test_runner.clean_format_output(input_file = output_location)
+            except:
+                print("There was an error cleaning the data")
+    
+            print(f"The # of failures are for {test_name}: {len(failed)}")
+            total_number_failures+= len(failed)
+            total_failures.append(failed)
+    
+            print(f"The # of sucesses are for {test_name}: {len(passed)}")
+            total_number_success += len(passed)
+            total_success.append(passed)
+            test_runner.rewrite_to_markdown(test_name, passed, failed)
+    
+    print(f"The total sucesses are: {total_number_success}")
+    print(f"The total failures are: {total_number_failures}")
 
 
 
-#############################################
-#                SEND EMAIL                 #
-#############################################
 
-sender_email = 'james.stine@okstate.edu'
-# sender_email = 'thomas.kidd@okstate.edu'
+        
 
-# receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu', 'sarah.harris@unlv.edu', 'nlucio@hmc.edu']
-receiver_emails = ['thomas.kidd@okstate.edu']
-test_runner.send_email(sender_email=sender_email, receiver_emails=receiver_emails)
+    #############################################
+    #               FORMAT TESTS                #
+    #############################################
+
+    # Combine multiple markdown files into one file
+
+    test_runner.combine_markdown_files(passed_tests = total_success, failed_tests = total_failures, test_list = test_list, total_number_failures = total_number_failures, total_number_success = total_number_success, test_type=args.target, markdown_file=None)
+
+
+    #############################################
+    #             WRITE MD TESTS                #
+    #############################################
+    test_runner.convert_to_html()
+
+
+
+    #############################################
+    #                SEND EMAIL                 #
+    #############################################
+
+    sender_email = 'james.stine@okstate.edu'
+
+    receiver_emails = ['thomas.kidd@okstate.edu', 'james.stine@okstate.edu', 'harris@g.hmc.edu', 'rose.thompson10@okstate.edu', 'sarah.harris@unlv.edu', 'nlucio@hmc.edu']
+    testing_emails = ['thomas.kidd@okstate.edu']
+    
+    if (args.send_email == "yes" or args.send_email == "y"):
+        test_runner.send_email(sender_email=sender_email, receiver_emails=receiver_emails)
+    if (args.send_email == "test"):
+        test_runner.send_email(sender_email=sender_email, receiver_emails=testing_emails)
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/bin/wrapper_nightly_runs.sh b/bin/wrapper_nightly_runs.sh
index e6d198fcd..91e57d091 100755
--- a/bin/wrapper_nightly_runs.sh
+++ b/bin/wrapper_nightly_runs.sh
@@ -24,5 +24,5 @@ source ./setup_host.sh >> $LOG 2>&1
 cd $PYTHON_SCRIPT
 pwd
 echo "Running python file"
-python nightly_build.py >> $LOG 2>&1
+python nightly_build.py --path "nightly-runs" --repository "https://github.com/openhwgroup/cvw" --target "all" --send_email "yes" >> $LOG 2>&1
 echo "Finished"

From 0caed8f8c6c335a0d61564c5fa9225e6f2264879 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Sat, 9 Mar 2024 19:23:24 -0600
Subject: [PATCH 15/20] undo changing TIMEOUT duration for regression-wally

---
 bin/nightly_build.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index ff92704d0..fdb04e9d5 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -662,10 +662,10 @@ def main():
     The goal of this section is to replace the TIMEOUT_DUR for regression tests.
 
     """
-    if test_runner.change_time_dur(time_duriation=2):
-        pass
-    else:
-        print("Error occured changing the TIMEOUT duration in './regression-wally'")
+    # if test_runner.change_time_dur(time_duriation=2):
+    #     pass
+    # else:
+    #     print("Error occured changing the TIMEOUT duration in './regression-wally'")
 
     #############################################
     #              MAKE TESTS                   #

From c8df291d488a9f08bb22c6fbf2d2b947d9483927 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Sat, 9 Mar 2024 14:21:04 -0600
Subject: [PATCH 16/20] updated nightly runs with try statement in email
 sending

---
 bin/nightly_build.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index fdb04e9d5..63c7a9808 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -37,6 +37,7 @@ Usage:
 
         Our cron job has the following syntax:
         0 3 * * * BASH_ENV=~/.bashrc bash -l -c "*WHERE YOUR CVW IS MUST PUT FULL PATH*/cvw/bin/wrapper_nightly-runs.sh > *WHERE YOU WANT TO STORE LOG FILES/cron.log 2>&1" 
+        0 3 * * * BASH_ENV=~/.bashrc bash -l -c "*WHERE YOUR CVW IS MUST PUT FULL PATH*/cvw/bin/wrapper_nightly-runs.sh > *WHERE YOU WANT TO STORE LOG FILES/cron.log 2>&1" 
 
         This cronjob sources the .bashrc file and executes the wrapper script as a user. 
 
@@ -101,6 +102,8 @@ class FolderManager:
         These folders are:
             nightly-runs/repos/
             nightly-runs/results/ 
+            nightly-runs/repos/
+            nightly-runs/results/ 
 
         Args:
             folders (list): A list of folder names to be created.
@@ -175,6 +178,7 @@ class TestRunner:
 
         Args:
             folder: the "nightly-runs/repos/"
+            folder: the "nightly-runs/repos/"
 
         Returns:
             bool: True if the script is copied successfully, False otherwise.

From 7f65718297d6734200fb5aa613075f738f1db0e8 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Sat, 9 Mar 2024 20:18:55 -0600
Subject: [PATCH 17/20] fixed documentation typo

---
 bin/nightly_build.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index 63c7a9808..38cfa74fc 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -36,8 +36,7 @@ Usage:
     4)  Syntax:
 
         Our cron job has the following syntax:
-        0 3 * * * BASH_ENV=~/.bashrc bash -l -c "*WHERE YOUR CVW IS MUST PUT FULL PATH*/cvw/bin/wrapper_nightly-runs.sh > *WHERE YOU WANT TO STORE LOG FILES/cron.log 2>&1" 
-        0 3 * * * BASH_ENV=~/.bashrc bash -l -c "*WHERE YOUR CVW IS MUST PUT FULL PATH*/cvw/bin/wrapper_nightly-runs.sh > *WHERE YOU WANT TO STORE LOG FILES/cron.log 2>&1" 
+        0 3 * * * BASH_ENV=~/.bashrc bash -l -c "*WHERE YOUR CVW IS MUST PUT FULL PATH*/cvw/bin/wrapper_nightly_runs.sh > *WHERE YOU WANT TO STORE LOG FILES/cron.log 2>&1" 
 
         This cronjob sources the .bashrc file and executes the wrapper script as a user. 
 

From e568f931878151740f29b8abaea83426accdaa4b Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Wed, 13 Mar 2024 13:56:05 -0500
Subject: [PATCH 18/20] typo fixes

---
 bin/nightly_build.py | 173 ++++++++++++++++++++++++++-----------------
 1 file changed, 105 insertions(+), 68 deletions(-)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index 38cfa74fc..c4cbc0e77 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -55,6 +55,7 @@ Dependencies:
         - markdown
         - subprocess
         - argparse
+        - logging
 
     Bash:
         - mutt (email sender)
@@ -71,7 +72,30 @@ import re
 import markdown
 import subprocess
 import argparse
+import logging
 
+# Logger
+
+# Set up the logger
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+
+# Create a file handler
+file_handler = logging.FileHandler('../../logs/nightly_build.log')
+file_handler.setLevel(logging.DEBUG)
+
+# Create a console handler
+console_handler = logging.StreamHandler()
+console_handler.setLevel(logging.INFO)
+
+# Create a formatter and add it to the handlers
+formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
+file_handler.setFormatter(formatter)
+console_handler.setFormatter(formatter)
+
+# Add the handlers to the logger
+logger.addHandler(file_handler)
+logger.addHandler(console_handler)
 
 
 
@@ -86,14 +110,12 @@ class FolderManager:
             base_dir (str): The base directory where folders will be managed and repository will be cloned.
         """
         env_extract_var = 'WALLY'
-        # print(f"The environemntal variable is {env_extract_var}")
         self.base_dir = os.environ.get(env_extract_var)
-        print(f"The base directory is: {self.base_dir}")
         self.base_parent_dir = os.path.dirname(self.base_dir)
 
-        # print(f"The new WALLY vairable is: {os.environ.get('WALLY')}")
-        # print(f"The Base Directory is now : {self.base_dir}")
-        # print(f"The Base Parent Directory is now : {self.base_parent_dir}")
+        logger.info(f"Base directory: {self.base_dir}")
+        logger.info(f"Parent Base directory: {self.base_parent_dir}")
+
 
     def create_preliminary_folders(self, folders):
         """
@@ -115,6 +137,7 @@ class FolderManager:
             folder_path = os.path.join(self.base_parent_dir, folder)
             if not os.path.exists(folder_path):
                 os.makedirs(folder_path)
+        logger.info(f"Preliminary folders created: {folders}")
 
     def create_new_folder(self, folders):
         """
@@ -136,7 +159,7 @@ class FolderManager:
                 return_folder_path.append(folder_path)
             else:
                 return_folder_path.append(None) # Folder already exists
-        
+        logger.info(f"New folder created. Path: {folder_path}")
         return return_folder_path
 
     def clone_repository(self, folder, repo_url):
@@ -157,7 +180,8 @@ class FolderManager:
             os.makedirs(repo_folder)
             os.system(f"git clone --recurse-submodules {repo_url} {repo_folder}")
             os.makedirs(tmp_folder)
-    
+
+        logger.info(f"Repository cloned: {repo_url}")
 
 class TestRunner:
     """A class for making, running, and formatting test results."""
@@ -166,8 +190,9 @@ class TestRunner:
         self.base_dir = os.environ.get('WALLY')
         self.base_parent_dir = os.path.dirname(self.base_dir)
         self.current_datetime = datetime.now()
-        #self.temp_dir = self.base_parent_dir
-        #print(f"Base Directory: {self.base_parent_dir}")
+
+        logger.info("Test runner object is initialized")
+        
         
     def copy_setup_script(self, folder):
         """
@@ -180,7 +205,7 @@ class TestRunner:
             folder: the "nightly-runs/repos/"
 
         Returns:
-            bool: True if the script is copied successfully, False otherwise.
+            bool: True if the script is copied successfuly, False otherwise.
         """
         # Get today's date in YYYY-MM-DD format
         todays_date = datetime.now().strftime("%Y-%m-%d")
@@ -191,22 +216,22 @@ class TestRunner:
         
         # Check if the source script exists
         if not os.path.exists(source_script):
-            print(f"Error: Source script '{source_script}' not found.")
+            logger.error(f"Error: Source script '{source_script}' not found.")
             return False
 
 
         # Check if the destination folder exists, create it if necessary
         if not os.path.exists(destination_folder):
-            print(f"Error: Destination folder '{destination_folder}' not found.")
+            logger.error(f"Error: Destination folder '{destination_folder}' not found.")
             return False
 
         # Copy the script to the destination folder
         try:
             shutil.copy(source_script, destination_folder)
-            #print(f"Setup script copied to: {destination_folder}")
+            logger.info(f"Setup script copied to: {destination_folder}")
             return True
         except Exception as e:
-            print(f"Error copying setup script: {e}")
+            logger.error(f"Error copying setup script: {e}")
             return False
 
 
@@ -231,15 +256,19 @@ class TestRunner:
         self.base_parent_dir = os.path.dirname(self.base_dir)
         self.temp_dir = self.base_parent_dir
 
-        # print(f"The new WALLY vairable is: {os.environ.get('WALLY')}")
-        # print(f"The Base Directory is now : {self.base_dir}")
-        # print(f"The Base Parent Directory is now : {self.base_parent_dir}")
+        logger.info(f"Tests are going to be ran from: {self.base_dir}")
+        logger.info(f"WALLY environmental variable is: {os.environ.get('WALLY')}")
+    
 
     def change_time_dur(self, time_duriation=1):
         
         # Prepare the command to execute the Makefile
         make_file_path = os.path.join(self.base_dir, "sim")
-        os.chdir(make_file_path)
+        logger.info(f"Make file path is set to: {make_file_path}")
+        try:
+            os.chdir(make_file_path)
+        except Exception as e:
+            logger.error(f"Error nagivating to the make file path. Error: {e}")
         file_path = "regression-wally"
         line_number = 450 # TIMEOUT_DUR = 1 day at this line in regression-wally 
         new_line = f"        TIMEOUT_DUR = {60*time_duriation}"
@@ -248,13 +277,14 @@ class TestRunner:
             lines = file.readlines()
 
         if line_number < 1 or line_number > len(lines):
-            print("Error: Line number out of range.")
+            logger.error("Error: Line number out of range.")
             return False
 
         lines[line_number - 1] = new_line + '\n'
 
         with open(file_path, 'w') as file:
             file.writelines(lines)
+            logger.info(f"Timeduration in ./regression-wally has been changed to: {time_duriation*60} seconds")
             return True
 
     def execute_makefile(self, target=None):
@@ -280,7 +310,9 @@ class TestRunner:
         # Add target to the command if specified
         if target:
             command.append(target)
-        #print(f"The command is: {command}")
+            logger.info(f"Command used: {command[0]} {command[1]}")
+        else:
+            logger.info(f"Command used: {command[0]}")
 
         # Execute the command using subprocess and save the output into a file
         with open(output_file, "w") as f:
@@ -294,10 +326,10 @@ class TestRunner:
 
         # Check the result
         if result.returncode == 0:
-            #print(f"Makefile executed successfully{' with target ' + target if target else ''}.")
+            logger.info(f"Tests have been made with tag target: {target}")
             return True
         else:
-            #print("Error executing Makefile.")
+            logger.error(f"Error making the tests. Target: {target}")
             return False
             
     def run_tests(self, test_type=None, test_name=None, test_exctention=None):
@@ -319,8 +351,11 @@ class TestRunner:
 
         if test_exctention:
             command = [test_type, test_name, test_exctention]
+            logger.info(f"Command used to run tests: {test_type} {test_name} -{test_exctention}")
         else:
             command = [test_type, test_name]
+            logger.info(f"Command used to run tests: {test_type} {test_name}")
+
 
         # Execute the command using subprocess and save the output into a file
         with open(output_file, "w") as f:
@@ -329,11 +364,12 @@ class TestRunner:
             f.write("\n\n")
             result = subprocess.run(command, stdout=f, stderr=subprocess.STDOUT, text=True)
         
-        # Check if the command executed successfully
+        # Check if the command executed successfuly
         if result.returncode or result.returncode == 0:
+            logger.info(f"Test ran successfuly. Test type: {test_type}, test name: {test_name}, test extention: {test_exctention}")
             return True, output_file
         else:
-            print("Error:", result.returncode)
+            logger.error(f"Error making test. Test type: {test_type}, test name: {test_name}, test extention: {test_exctention}")
             return False, output_file
 
 
@@ -364,11 +400,10 @@ class TestRunner:
         while index < len(lines):
             # Remove ANSI escape codes
             line = re.sub(r'\x1b\[[0-9;]*[mGK]', '', lines[index])  
-            #print(line)
+            
             if "Success" in line:
                 passed_configs.append(line.split(':')[0].strip())
             elif "passed lint" in line:
-                #print(line)
                 passed_configs.append(line.split(' ')[0].strip())
                 #passed_configs.append(line) # potentially use a space
             elif "failed lint" in line:
@@ -379,7 +414,6 @@ class TestRunner:
                 try:
                     config_name = line.split(':')[0].strip()
                     log_file = os.path.abspath("logs/"+config_name+".log")
-                    #print(f"The log file saving to: {log_file} in the current working directory: {os.getcwd()}") 
                     failed_configs.append((config_name, log_file))
                 except:
                     failed_configs.append((config_name, "Log file not found"))
@@ -393,8 +427,7 @@ class TestRunner:
 
         if len(failed_configs) != 0:
             failed_configs.sort()
-        #print(f"The passed configs are: {passed_configs}")
-        #print(f"The failed configs are {failed_configs}")
+        logger.info(f"Cleaned test results. Passed configs {passed_configs}. Failed configs: {failed_configs}")
         return passed_configs, failed_configs
 
     def rewrite_to_markdown(self, test_name, passed_configs, failed_configs):
@@ -415,8 +448,7 @@ class TestRunner:
         os.chdir(output_directory)
         current_directory = os.getcwd()
         output_file = os.path.join(current_directory, f"{test_name}.md")
-        #print("Current directory:", current_directory)
-        #print("Output File:", output_file)
+        
 
         with open(output_file, 'w') as md_file:
        
@@ -440,7 +472,9 @@ class TestRunner:
             for config in passed_configs:
                 md_file.write(f"- <span class=\"success\" style=\"color: green;\">{config}</span>\n")
 
-    def combine_markdown_files(self, passed_tests, failed_tests, test_list, total_number_failures, total_number_success, test_type="default", markdown_file=None):
+        logger.info("writing test outputs to markdown")
+
+    def combine_markdown_files(self, passed_tests, failed_tests, test_list, total_number_failures, total_number_success, test_type="default", markdown_file=None, args=None):
         """
         First we want to display the server properties like:
             - Server full name
@@ -479,6 +513,9 @@ class TestRunner:
                 os_info = subprocess.check_output(['uname', '-a']).strip().decode('utf-8')
                 md_file.write(f"\n**Operating System Information:** {os_info}")
                 md_file.write("\n")
+
+                md_file.write(f"\n**Command used to execute test:** python nightly_build.py --path {args.path} --repository {args.repository} --target {args.target} --send_email {args.send_email}")
+                md_file.write("\n")
             except subprocess.CalledProcessError as e:
                 # Handle if the command fails
                 md_file.write(f"Failed to identify host and Operating System information: {str(e)}")
@@ -516,17 +553,17 @@ class TestRunner:
                         md_file.write("\n")
                         md_file.write(f"* <span class=\"failure\" style=\"color: red;\">{config}</span> ({log_file})\n")
                         md_file.write("\n")
-            # Successfull Tests
+            # Successful Tests
 
-            md_file.write(f"\n\n## Successfull Tests")
-            md_file.write(f"\n**Total successfull tests: {total_number_success}**")
+            md_file.write(f"\n\n## Successful Tests")
+            md_file.write(f"\n**Total successful tests: {total_number_success}**")
             for (test_item, item) in zip(test_list, passed_tests):
                 md_file.write(f"\n\n### {test_item[1]} test")
                 md_file.write(f"\n**General Information**\n")
                 md_file.write(f"\n* Test type: {test_item[0]}")
                 md_file.write(f"\n* Test name: {test_item[1]}")
                 md_file.write(f"\n* Test extension: {test_item[2]}\n\n")
-                md_file.write(f"\n**Successfull Tests:**\n")
+                md_file.write(f"\n**Successful Tests:**\n")
 
                 
 
@@ -542,7 +579,8 @@ class TestRunner:
                         md_file.write(f"* <span class=\"success\" style=\"color: green;\">{config}</span>\n")
                         md_file.write("\n")
                     
-                    
+        logger.info("Combining markdown files")
+
 
     def convert_to_html(self, markdown_file="results.md", html_file="results.html"):
         """
@@ -567,7 +605,7 @@ class TestRunner:
         with open(html_file, 'w') as html_file:
             html_file.write(html_content)
         
-
+        logger.info("Converting markdown file to html file.")
  
     def send_email(self, sender_email=None, receiver_emails=None, subject="Nightly Regression Test"):
         """
@@ -585,7 +623,7 @@ class TestRunner:
 
         # check if there are any emails
         if not receiver_emails:
-            print("No receiver emails provided.")
+            logger.ERROR("No receiver emails provided.")
             return
         # grab thge html file
         todays_date = self.current_datetime.strftime("%Y-%m-%d")
@@ -613,10 +651,11 @@ class TestRunner:
                     process = subprocess.Popen(command, stdin=subprocess.PIPE)
                     # Write the email body to the subprocess
                     process.communicate(body.encode('utf-8'))
+                    logger.info("Sent email")
                 except expression as identifier:
-                    print(f"Error sending email: {identifier}")
+                    logger.error(f"Error sending email with error: {identifier}")
         except expression as identifier:
-            print(f"Error sending email: {identifier}")
+            logger.error(f"Error sending email with error: {identifier}")
 
 
 
@@ -634,6 +673,11 @@ def main():
     
     args = parser.parse_args()
 
+    logger.info(f"path: {args.path}")
+    logger.info(f"repository: {args.repository}")
+    logger.info(f"target: {args.target}")
+    logger.info(f"send_email: {args.send_email}")
+
     # file paths for where the results and repos will be saved: repos and results can be changed to whatever
     repos_path = f"{args.path}/repos/"
     results_path = f"{args.path}/results/"
@@ -649,9 +693,7 @@ def main():
     # clone the cvw repo
     folder_manager.clone_repository(repos_path, args.repository)
             
-    #############################################
-    #                 SETUP                     #
-    #############################################
+
 
     test_runner = TestRunner() # creates the object
     test_runner.set_env_var(repos_path) # ensures that the new WALLY environmental variable is set correctly
@@ -665,19 +707,18 @@ def main():
     The goal of this section is to replace the TIMEOUT_DUR for regression tests.
 
     """
-    # if test_runner.change_time_dur(time_duriation=2):
-    #     pass
-    # else:
-    #     print("Error occured changing the TIMEOUT duration in './regression-wally'")
+    if test_runner.change_time_dur(time_duriation=2):
+        pass
+    else:
+        logger.error("Error occured changing the TIMEOUT duration in './regression-wally'")
 
     #############################################
     #              MAKE TESTS                   #
     #############################################
 
-
-    
-    # if test_runner.execute_makefile(target = args.target):
-    #    print(f"The {args.target} tests were made successfully")
+    if args.target != "no":
+        # test_runner.execute_makefile(target = "deriv")
+        test_runner.execute_makefile(target = args.target)
 
     #############################################
     #               RUN TESTS                   #
@@ -693,34 +734,30 @@ def main():
     total_success = []
 
     for test_type, test_name, test_exctention in test_list:
-        print("--------------------------------------------------------------")
-        print(f"Test type: {test_type}")
-        print(f"Test name: {test_name}")
-        print(f"Test extention: {test_exctention}")
-    
+        
         check, output_location = test_runner.run_tests(test_type=test_type, test_name=test_name, test_exctention=test_exctention)
-        print(f"Did the tests run?: {check}")
-        print(f"The tests log files are saved to: {output_location}")
-        if check: # this checks if the test actually ran successfully
+
+        if check: # this checks if the test actually ran successfuly
             output_log_list.append(output_location)
-            
+            logger.info(f"{test_name} ran successfuly. Output location: {output_location}")
             # format tests to markdown
             try:
                 passed, failed = test_runner.clean_format_output(input_file = output_location)
+                logger.info(f"{test_name} has been formatted to markdown")
             except:
-                print("There was an error cleaning the data")
+                logger.ERROR(f"Error occured with formatting {test_name}")
     
-            print(f"The # of failures are for {test_name}: {len(failed)}")
+            logger.info(f"The # of failures are for {test_name}: {len(failed)}")
             total_number_failures+= len(failed)
             total_failures.append(failed)
     
-            print(f"The # of sucesses are for {test_name}: {len(passed)}")
+            logger.info(f"The # of sucesses are for {test_name}: {len(passed)}")
             total_number_success += len(passed)
             total_success.append(passed)
             test_runner.rewrite_to_markdown(test_name, passed, failed)
     
-    print(f"The total sucesses are: {total_number_success}")
-    print(f"The total failures are: {total_number_failures}")
+    logger.info(f"The total sucesses for all tests ran are: {total_number_success}")
+    logger.info(f"The total failures for all tests ran are: {total_number_failures}")
 
 
 
@@ -733,7 +770,7 @@ def main():
 
     # Combine multiple markdown files into one file
 
-    test_runner.combine_markdown_files(passed_tests = total_success, failed_tests = total_failures, test_list = test_list, total_number_failures = total_number_failures, total_number_success = total_number_success, test_type=args.target, markdown_file=None)
+    test_runner.combine_markdown_files(passed_tests = total_success, failed_tests = total_failures, test_list = test_list, total_number_failures = total_number_failures, total_number_success = total_number_success, test_type=args.target, markdown_file=None, args=args)
 
 
     #############################################
@@ -758,4 +795,4 @@ def main():
         test_runner.send_email(sender_email=sender_email, receiver_emails=testing_emails)
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()

From 90026a5da15b7be23e0ca2f891eedd4eeca4347b Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Wed, 13 Mar 2024 22:13:20 -0500
Subject: [PATCH 19/20] showing commands used for executing each specific test

---
 bin/nightly_build.py | 74 ++++++++++++++++++++++----------------------
 setup_host.sh        | 58 ----------------------------------
 2 files changed, 37 insertions(+), 95 deletions(-)
 delete mode 100644 setup_host.sh

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index c4cbc0e77..a82c1496f 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -358,12 +358,14 @@ class TestRunner:
 
 
         # Execute the command using subprocess and save the output into a file
-        with open(output_file, "w") as f:
-            formatted_datetime = self.current_datetime.strftime("%Y-%m-%d %H:%M:%S")
-            f.write(formatted_datetime)
-            f.write("\n\n")
-            result = subprocess.run(command, stdout=f, stderr=subprocess.STDOUT, text=True)
-        
+        try:
+            with open(output_file, "w") as f:
+                formatted_datetime = self.current_datetime.strftime("%Y-%m-%d %H:%M:%S")
+                f.write(formatted_datetime)
+                f.write("\n\n")
+                result = subprocess.run(command, stdout=f, stderr=subprocess.STDOUT, text=True)
+        except Exception as e:
+            logger.error("There was an error in running the tests in the run_tests function: {e}")
         # Check if the command executed successfuly
         if result.returncode or result.returncode == 0:
             logger.info(f"Test ran successfuly. Test type: {test_type}, test name: {test_name}, test extention: {test_exctention}")
@@ -530,13 +532,10 @@ class TestRunner:
 
             # Failed Tests
             md_file.write(f"\n\n## Failed Tests")
-            md_file.write(f"\nTotal failed tests: {total_number_failures}")
+            md_file.write(f"\n**Total failed tests: {total_number_failures}**")
             for (test_item, item) in zip(test_list, failed_tests):
                 md_file.write(f"\n\n### {test_item[1]} test")
-                md_file.write(f"\n**General Information**\n")
-                md_file.write(f"\n* Test type: {test_item[0]}\n")
-                md_file.write(f"\n* Test name: {test_item[1]}\n")
-                md_file.write(f"\n* Test extension: {test_item[2]}\n\n")
+                md_file.write(f"\n**Command used:** {test_item[0]} {test_item[1]} {test_item[2]}\n\n")
                 md_file.write(f"**Failed Tests:**\n")
 
                 
@@ -559,10 +558,7 @@ class TestRunner:
             md_file.write(f"\n**Total successful tests: {total_number_success}**")
             for (test_item, item) in zip(test_list, passed_tests):
                 md_file.write(f"\n\n### {test_item[1]} test")
-                md_file.write(f"\n**General Information**\n")
-                md_file.write(f"\n* Test type: {test_item[0]}")
-                md_file.write(f"\n* Test name: {test_item[1]}")
-                md_file.write(f"\n* Test extension: {test_item[2]}\n\n")
+                md_file.write(f"\n**Command used:** {test_item[0]} {test_item[1]} {test_item[2]}\n\n")
                 md_file.write(f"\n**Successful Tests:**\n")
 
                 
@@ -707,7 +703,7 @@ def main():
     The goal of this section is to replace the TIMEOUT_DUR for regression tests.
 
     """
-    if test_runner.change_time_dur(time_duriation=2):
+    if test_runner.change_time_dur(time_duriation=1):
         pass
     else:
         logger.error("Error occured changing the TIMEOUT duration in './regression-wally'")
@@ -736,26 +732,29 @@ def main():
     for test_type, test_name, test_exctention in test_list:
         
         check, output_location = test_runner.run_tests(test_type=test_type, test_name=test_name, test_exctention=test_exctention)
+        try:
+            if check: # this checks if the test actually ran successfuly
+                output_log_list.append(output_location)
+                logger.info(f"{test_name} ran successfuly. Output location: {output_location}")
+                # format tests to markdown
+                try:
+                    passed, failed = test_runner.clean_format_output(input_file = output_location)
+                    logger.info(f"{test_name} has been formatted to markdown")
+                except:
+                    logger.ERROR(f"Error occured with formatting {test_name}")
 
-        if check: # this checks if the test actually ran successfuly
-            output_log_list.append(output_location)
-            logger.info(f"{test_name} ran successfuly. Output location: {output_location}")
-            # format tests to markdown
-            try:
-                passed, failed = test_runner.clean_format_output(input_file = output_location)
-                logger.info(f"{test_name} has been formatted to markdown")
-            except:
-                logger.ERROR(f"Error occured with formatting {test_name}")
-    
-            logger.info(f"The # of failures are for {test_name}: {len(failed)}")
-            total_number_failures+= len(failed)
-            total_failures.append(failed)
-    
-            logger.info(f"The # of sucesses are for {test_name}: {len(passed)}")
-            total_number_success += len(passed)
-            total_success.append(passed)
-            test_runner.rewrite_to_markdown(test_name, passed, failed)
+                logger.info(f"The # of failures are for {test_name}: {len(failed)}")
+                total_number_failures+= len(failed)
+                total_failures.append(failed)
+
+                logger.info(f"The # of sucesses are for {test_name}: {len(passed)}")
+                total_number_success += len(passed)
+                total_success.append(passed)
+                test_runner.rewrite_to_markdown(test_name, passed, failed)
     
+        except Exception as e:
+            logger.error("There was an error in running the tests: {e}")
+
     logger.info(f"The total sucesses for all tests ran are: {total_number_success}")
     logger.info(f"The total failures for all tests ran are: {total_number_failures}")
 
@@ -769,9 +768,10 @@ def main():
     #############################################
 
     # Combine multiple markdown files into one file
-
-    test_runner.combine_markdown_files(passed_tests = total_success, failed_tests = total_failures, test_list = test_list, total_number_failures = total_number_failures, total_number_success = total_number_success, test_type=args.target, markdown_file=None, args=args)
-
+    try:
+        test_runner.combine_markdown_files(passed_tests = total_success, failed_tests = total_failures, test_list = test_list, total_number_failures = total_number_failures, total_number_success = total_number_success, test_type=args.target, markdown_file=None, args=args)
+    except Exception as e:
+        logger.error(f"Error combining the markdown tests called from main: {e}")
 
     #############################################
     #             WRITE MD TESTS                #
diff --git a/setup_host.sh b/setup_host.sh
deleted file mode 100644
index 55854a71c..000000000
--- a/setup_host.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/bash
-
-# setup.sh
-# David_Harris@hmc.edu and kekim@hmc.edu 1 December 2021
-# Set up tools for riscv-wally
-
-echo "Executing Wally setup.sh"
-
-# Path to Wally repository
-WALLY=$(dirname ${BASH_SOURCE[0]:-$0})
-export WALLY=$(cd "$WALLY" && pwd)
-echo \$WALLY set to ${WALLY}
-
-# Path to RISC-V Tools
-export RISCV=/opt/riscv   # change this if you installed the tools in a different location
-
-# Tools
-# GCC
-#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RISCV/riscv-gnu-toolchain/lib:$RISCV/riscv-gnu-toolchain/riscv64-unknown-elf/lib
-#export PATH=$PATH:$RISCV/riscv-gnu-toolchain/bin:$RISCV/riscv-gnu-toolchain/riscv64-unknown-elf/bin      # GCC tools
-# Spike
-#export LD_LIBRARY_PATH=$RISCV/lib:$LD_LIBRARY_PATH
-export PATH=$PATH:$RISCV/bin
-# utility functions in Wally repository
-export PATH=$WALLY/bin:$PATH    
-# Verilator
-export PATH=$RICKV/verilator:$PATH # Change this for your path to Verilator
-# ModelSim/Questa (vsim)
-# Note: 2022.1 complains on cache/sram1p1r1w about StoredData cannot be driven by multiple always_ff blocks.  Ues 2021.2 for now
-#export PATH=/cad/mentor/questa_sim-2022.1_1/questasim/bin:$PATH    # Change this for your path to Modelsim 
-#export PATH=/cad/mentor/questa_sim-2021.2_1/questasim/bin:$PATH    # Change this for your path to Modelsim, or delete
-#export MGLS_LICENSE_FILE=1717@solidworks.eng.hmc.edu # Change this to your Siemens license server
-#export PATH=/cad/synopsys/SYN/bin:$PATH  # Change this for your path to Design Compiler
-#export SNPSLMD_LICENSE_FILE=27020@134.173.38.184 # Change this to your license manager file
-
-# Imperas; put this in if you are using it
-#export PATH=$RISCV/imperas-riscv-tests/riscv-ovpsim-plus/bin/Linux64:$PATH  
-#export LD_LIBRARY_PATH=$RISCV/imperas_riscv_tests/riscv-ovpsim-plus/bin/Linux64:$LD_LIBRARY_PATH # remove if no imperas
-
-export MODSIM=/opt/ModelSim/questasim
-export PATH=$PATH:$MODSIM/bin
-export LD_LIBRARY_PATH=/usr/lib:/lib
-export MGC_DOC_PATH=$MODSIM/docs
-export MGC_PDF_READER=evince
-export MGC_HTML_BROWSER=firefox
-export MGLS_LICENSE_FILE=1717@trelaina.ecen.okstate.edu
-export IMPERASD_LICENSE_FILE=2700@trelaina.ecen.okstate.edu
-
-export IDV=$RISCV/ImperasDV-OpenHW
-if [ -e "$IDV" ]; then
-#    echo "Imperas exists"
-    export IMPERAS_HOME=$IDV/Imperas
-    export IMPERAS_PERSONALITY=CPUMAN_DV_ASYNC
-    export ROOTDIR=${WALLY}/..
-    source ${IMPERAS_HOME}/bin/setup.sh
-    setupImperas ${IMPERAS_HOME}
-    export PATH=$IDV/scripts/cvw:$PATH
-fi

From 7ed2d0c13d0b8d34387544cd90b8ff52b3c59c27 Mon Sep 17 00:00:00 2001
From: Thomas Kidd <thomas.kidd@okstate.edu>
Date: Wed, 13 Mar 2024 22:40:00 -0500
Subject: [PATCH 20/20] typo fix for displaying commands in email

---
 bin/nightly_build.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/nightly_build.py b/bin/nightly_build.py
index a82c1496f..8f806d119 100755
--- a/bin/nightly_build.py
+++ b/bin/nightly_build.py
@@ -351,7 +351,7 @@ class TestRunner:
 
         if test_exctention:
             command = [test_type, test_name, test_exctention]
-            logger.info(f"Command used to run tests: {test_type} {test_name} -{test_exctention}")
+            logger.info(f"Command used to run tests: {test_type} {test_name} {test_exctention}")
         else:
             command = [test_type, test_name]
             logger.info(f"Command used to run tests: {test_type} {test_name}")