From c41707125e9fe6b6442042a198fc8ce88ebacd61 Mon Sep 17 00:00:00 2001
From: Michael Ernst <mernst@cs.washington.edu>
Date: Tue, 11 Nov 2025 15:42:41 -0800
Subject: [PATCH 1/6] Ask the user to install Python dependencies

---
 scripts/experiment-scripts/README.md          | 22 +++++++++++++++++++
 .../mutation-fig6-table3.sh                   |  4 ----
 scripts/experiment-scripts/mutation-fig7.sh   |  4 ----
 scripts/experiment-scripts/mutation-fig8-9.sh |  4 ----
 4 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/scripts/experiment-scripts/README.md b/scripts/experiment-scripts/README.md
index 1a27279..12303bd 100644
--- a/scripts/experiment-scripts/README.md
+++ b/scripts/experiment-scripts/README.md
@@ -15,6 +15,28 @@ evaluation.
 
 To set up the environment, refer to the `scripts/mutation-prerequisites.md` file.
 
+#### Python Dependencies
+
+Before running any experiment scripts, ensure the following Python packages are installed:
+
+* `pandas`
+* `matplotlib`
+* `seaborn`
+
+Install these packages using your preferred Python package manager. For example:
+
+**With pip:**
+
+```bash
+pip install pandas matplotlib seaborn
+```
+
+**With uv:**
+
+```bash
+uv pip install pandas matplotlib seaborn
+```
+
 ### Running Scripts
 
 To generate the desired figures or tables from the paper, run the corresponding
diff --git a/scripts/experiment-scripts/mutation-fig6-table3.sh b/scripts/experiment-scripts/mutation-fig6-table3.sh
index bdae0f6..b759734 100755
--- a/scripts/experiment-scripts/mutation-fig6-table3.sh
+++ b/scripts/experiment-scripts/mutation-fig6-table3.sh
@@ -37,10 +37,6 @@ GRT_TESTING_ROOT="$(realpath "$SCRIPT_DIR"/../)"
 
 . "$SCRIPT_DIR"/common.sh
 
-pip install pandas
-pip install matplotlib
-pip install seaborn
-
 # Clean up previous run artifacts.
 make -C "$GRT_TESTING_ROOT" clean
 rm -f "$GRT_TESTING_ROOT"/results/fig6-table3.pdf
diff --git a/scripts/experiment-scripts/mutation-fig7.sh b/scripts/experiment-scripts/mutation-fig7.sh
index 17e4368..08e563f 100755
--- a/scripts/experiment-scripts/mutation-fig7.sh
+++ b/scripts/experiment-scripts/mutation-fig7.sh
@@ -36,10 +36,6 @@ SCRIPT_DIR="$(CDPATH='' cd -- "$(dirname -- "$0")" && pwd -P)"
 GRT_TESTING_ROOT="$(realpath "$SCRIPT_DIR"/../)"
 . "$SCRIPT_DIR"/common.sh
 
-pip install pandas
-pip install matplotlib
-pip install seaborn
-
 # Clean up previous run artifacts
 make -C "$GRT_TESTING_ROOT" clean
 rm -f "$GRT_TESTING_ROOT"/results/fig7.pdf
diff --git a/scripts/experiment-scripts/mutation-fig8-9.sh b/scripts/experiment-scripts/mutation-fig8-9.sh
index 1863dbf..2ce3ec6 100755
--- a/scripts/experiment-scripts/mutation-fig8-9.sh
+++ b/scripts/experiment-scripts/mutation-fig8-9.sh
@@ -41,10 +41,6 @@ GRT_TESTING_ROOT="$(realpath "$SCRIPT_DIR"/../)"
 
 . "$SCRIPT_DIR"/common.sh
 
-pip install pandas
-pip install matplotlib
-pip install seaborn
-
 # Clean up previous run artifacts
 make -C "$GRT_TESTING_ROOT" clean
 rm -f "$GRT_TESTING_ROOT"/results/fig8-9.pdf

From 20d49c2349bd5e471bfc5f1f38e8d0d082b6906f Mon Sep 17 00:00:00 2001
From: Michael Ernst <mernst@cs.washington.edu>
Date: Tue, 11 Nov 2025 15:52:29 -0800
Subject: [PATCH 2/6] Rename `mutation-prerequisites.md` to `prerequisites.md`

---
 README.md                                     |  2 +-
 scripts/experiment-scripts/README.md          |  2 +-
 .../mutation-fig6-table3.sh                   |  2 +-
 scripts/experiment-scripts/mutation-fig7.sh   |  2 +-
 scripts/experiment-scripts/mutation-fig8-9.sh |  2 +-
 scripts/mutation-evosuite.sh                  |  2 +-
 scripts/mutation-prerequisites.md             | 22 --------
 scripts/mutation-randoop.sh                   |  2 +-
 scripts/prerequisites.md                      | 51 +++++++++++++++++++
 9 files changed, 58 insertions(+), 29 deletions(-)
 delete mode 100644 scripts/mutation-prerequisites.md
 create mode 100644 scripts/prerequisites.md

diff --git a/README.md b/README.md
index 3db580c..b91ea8c 100644
--- a/README.md
+++ b/README.md
@@ -13,7 +13,7 @@ Testing](GRT_Program-Analysis-Guided_Random_Testing.pdf)"
 
 ### Setup
 
-To set up the environment, refer to the `scripts/mutation-prerequisites.md` file.
+To set up the environment, refer to the `scripts/prerequisites.md` file.
 
 ### Running Scripts
 
diff --git a/scripts/experiment-scripts/README.md b/scripts/experiment-scripts/README.md
index 1a27279..e0fc01f 100644
--- a/scripts/experiment-scripts/README.md
+++ b/scripts/experiment-scripts/README.md
@@ -13,7 +13,7 @@ evaluation.
 
 ### Setup
 
-To set up the environment, refer to the `scripts/mutation-prerequisites.md` file.
+To set up the environment, refer to the `scripts/prerequisites.md` file.
 
 ### Running Scripts
 
diff --git a/scripts/experiment-scripts/mutation-fig6-table3.sh b/scripts/experiment-scripts/mutation-fig6-table3.sh
index bdae0f6..2101af3 100755
--- a/scripts/experiment-scripts/mutation-fig6-table3.sh
+++ b/scripts/experiment-scripts/mutation-fig6-table3.sh
@@ -28,7 +28,7 @@
 #------------------------------------------------------------------------------
 # Prerequisites:
 #------------------------------------------------------------------------------
-# See file `mutation-prerequisites.md`.
+# See file `prerequisites.md`.
 #
 #===============================================================================
 
diff --git a/scripts/experiment-scripts/mutation-fig7.sh b/scripts/experiment-scripts/mutation-fig7.sh
index 17e4368..b914c09 100755
--- a/scripts/experiment-scripts/mutation-fig7.sh
+++ b/scripts/experiment-scripts/mutation-fig7.sh
@@ -28,7 +28,7 @@
 #------------------------------------------------------------------------------
 # Prerequisites:
 #------------------------------------------------------------------------------
-# See file `mutation-prerequisites.md`.
+# See file `prerequisites.md`.
 #
 #===============================================================================
 
diff --git a/scripts/experiment-scripts/mutation-fig8-9.sh b/scripts/experiment-scripts/mutation-fig8-9.sh
index 1863dbf..fbf7b22 100755
--- a/scripts/experiment-scripts/mutation-fig8-9.sh
+++ b/scripts/experiment-scripts/mutation-fig8-9.sh
@@ -32,7 +32,7 @@
 #------------------------------------------------------------------------------
 # Prerequisites:
 #------------------------------------------------------------------------------
-# See file `mutation-prerequisites.md`.
+# See file `prerequisites.md`.
 #
 #===============================================================================
 
diff --git a/scripts/mutation-evosuite.sh b/scripts/mutation-evosuite.sh
index f1904ba..1243cd5 100755
--- a/scripts/mutation-evosuite.sh
+++ b/scripts/mutation-evosuite.sh
@@ -38,7 +38,7 @@ USAGE_STRING="usage: mutation-evosuite.sh [-h] [-v] [-r] [-o RESULTS_CSV] [-t to
 #------------------------------------------------------------------------------
 # Prerequisites:
 #------------------------------------------------------------------------------
-# See file `mutation-prerequisites.md`.
+# See file `prerequisites.md`.
 
 # Fail this script on errors.
 set -e
diff --git a/scripts/mutation-prerequisites.md b/scripts/mutation-prerequisites.md
deleted file mode 100644
index 861e610..0000000
--- a/scripts/mutation-prerequisites.md
+++ /dev/null
@@ -1,22 +0,0 @@
-# Prerequisites for running either mutation script
-
-1. Obtain the mutation programs, some dependencies, and the source code for the
-   subject programs:
-
-   ```sh
-   make -C scripts
-   ```
-
-2. If using Randoop, use the development version (the latest commit) rather than
-   a released version. Skip this step if only using EvoSuite.
-
-   ```sh
-   make -C scripts randoop-from-source
-   ```
-
-3. To get all subject programs, run:
-
-   ```sh
-   cd scripts
-   ./get-all-subject-src.sh
-   ```
diff --git a/scripts/mutation-randoop.sh b/scripts/mutation-randoop.sh
index 7d9614c..6093797 100755
--- a/scripts/mutation-randoop.sh
+++ b/scripts/mutation-randoop.sh
@@ -42,7 +42,7 @@ USAGE_STRING="usage: mutation-randoop.sh [-h] [-v] [-r] [-f features] [-a] [-o R
 #------------------------------------------------------------------------------
 # Prerequisites:
 #------------------------------------------------------------------------------
-# See file `mutation-prerequisites.md`.
+# See file `prerequisites.md`.
 
 # Fail this script on errors.
 set -e
diff --git a/scripts/prerequisites.md b/scripts/prerequisites.md
new file mode 100644
index 0000000..cb860f6
--- /dev/null
+++ b/scripts/prerequisites.md
@@ -0,0 +1,51 @@
+# Prerequisites for running the scripts
+
+## Java Versions Setup
+
+Different scripts require different Java versions:
+
+* **Defect scripts** (via [Defects4J](https://github.com/rjust/defects4j))
+require **Java 11**
+* **Mutation scripts** (via [Major](https://github.com/rjust/major))
+require **Java 8**
+
+To allow automatic switching between Java versions, set the following
+environment variables in your shell configuration file
+(e.g., `.bashrc`, `.zshrc`, or `.bash_profile`):
+
+```sh
+export JAVA8_HOME=/path/to/your/java8
+export JAVA11_HOME=/path/to/your/java11
+```
+
+## Required Tools
+
+* **Git** ≥ 1.9
+* **Subversion (svn)** ≥ 1.8
+* **Perl** ≥ 5.12
+* **cpanm** (Perl module installer)
+  To install `cpanm`:
+  ```sh
+  curl -L https://cpanmin.us | perl - App::cpanminus
+  ```
+
+## Obtaining Dependencies and Subject Programs
+
+```sh
+make -C scripts
+make -C scripts randoop-from-source
+cd scripts
+./get-all-subject-src.sh
+```
+
+## Adding Defects4J to PATH
+
+For defect detection scripts, add Defects4J's executables to your PATH in
+the shell session where you run the scripts:
+
+```sh
+export PATH=$PATH:"path2defects4j"/framework/bin
+```
+
+> "path2defects4j" points to the directory which Defects4J is in; it most
+likely will look like "currentdirectory/build/defects4j".

From 7869ca13b3c01c1f84c3f5acb7c7aa8df2352372 Mon Sep 17 00:00:00 2001
From: Michael Ernst <mernst@cs.washington.edu>
Date: Tue, 11 Nov 2025 15:56:51 -0800
Subject: [PATCH 3/6] Use standard Markdown item separator

---
 scripts/experiment-scripts/README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/scripts/experiment-scripts/README.md b/scripts/experiment-scripts/README.md
index 1a27279..dde74c6 100644
--- a/scripts/experiment-scripts/README.md
+++ b/scripts/experiment-scripts/README.md
@@ -26,17 +26,17 @@ shell script. For example, to generate **Figure 7**, use:
 
 Each script is documented at the top of the file with:
 
-- What it generates (figure/table)
-- What input parameters or configuration it expects
-- What output files it will produce and where
+* What it generates (figure/table)
+* What input parameters or configuration it expects
+* What output files it will produce and where
 
 ### Output
 
 Each experiment script writes its output to the `results/` directory. This includes:
 
-- `results/[experiment].csv`: the raw collected data from multiple
+* `results/[experiment].csv`: the raw collected data from multiple
   `mutation-randoop.sh` and/or `mutation-evosuite.sh` runs.
-- `results/[experiment].pdf`: the final rendered figure(s) and/or table(s) for
+* `results/[experiment].pdf`: the final rendered figure(s) and/or table(s) for
   the experiment.
 
 **Note:** Running an experiment script will overwrite any existing results for

From 77740de4e1ff4e607f33a7b951e3632a27f4e73e Mon Sep 17 00:00:00 2001
From: Michael Ernst <mernst@cs.washington.edu>
Date: Tue, 11 Nov 2025 16:02:49 -0800
Subject: [PATCH 4/6] Abstract out the generator name to reduce diffs

---
 scripts/mutation-evosuite.sh | 12 +++++++-----
 scripts/mutation-randoop.sh  | 12 +++++++-----
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/scripts/mutation-evosuite.sh b/scripts/mutation-evosuite.sh
index f1904ba..b563f1a 100755
--- a/scripts/mutation-evosuite.sh
+++ b/scripts/mutation-evosuite.sh
@@ -60,6 +60,8 @@ if [[ "$JAVA_VER" -ne 18 ]]; then
   exit 1
 fi
 
+Generator=EvoSuite
+generator=evosuite
 SCRIPT_DIR="$(CDPATH='' cd -- "$(dirname -- "$0")" && pwd -P)"
 MAJOR_HOME=$(realpath "${SCRIPT_DIR}/build/major/")               # Major home directory, for mutation testing
 EVOSUITE_JAR=$(realpath "${SCRIPT_DIR}/build/evosuite-1.2.0.jar") # EvoSuite jar file
@@ -391,7 +393,7 @@ EVOSUITE_BASE_COMMAND=(
 #===============================================================================
 # Build System Preparation
 #===============================================================================
-echo "Using EvoSuite to generate tests."
+echo "Using ${Generator} to generate tests."
 echo
 
 # Handle relative and absolute output files; make sure output file exists.
@@ -413,7 +415,7 @@ for i in $(seq 1 "$NUM_LOOP"); do
   FILE_SUFFIX="$SUBJECT_PROGRAM-EVOSUITE-$UUID"
 
   # Test directory for each iteration.
-  TEST_DIRECTORY="$SCRIPT_DIR/build/evosuite-tests/$FILE_SUFFIX"
+  TEST_DIRECTORY="$SCRIPT_DIR/build/$generator-tests/$FILE_SUFFIX"
   rm -rf "$TEST_DIRECTORY"
   mkdir -p "$TEST_DIRECTORY"
 
@@ -442,13 +444,13 @@ for i in $(seq 1 "$NUM_LOOP"); do
 
   cd "$RESULT_DIR"
 
-  EVOSUITE_COMMAND=(
+  GENERATOR_COMMAND=(
     "${EVOSUITE_BASE_COMMAND[@]}"
     -Dtest_dir="$TEST_DIRECTORY"
     -Dreport_dir="$REPORT_DIRECTORY"
   )
 
-  "${EVOSUITE_COMMAND[@]}"
+  "${GENERATOR_COMMAND[@]}"
 
   # After test generation, for JSAP-2.1, we need to remove the ant.jar from the classpath
   if [[ "$SUBJECT_PROGRAM" == "JSAP-2.1" ]]; then
@@ -459,7 +461,7 @@ for i in $(seq 1 "$NUM_LOOP"); do
   # Coverage & Mutation Analysis
   #===============================================================================
 
-  buildfile=build-evosuite.xml
+  buildfile="build-$generator.xml"
 
   echo
   echo "Compiling and mutating subject program..."
diff --git a/scripts/mutation-randoop.sh b/scripts/mutation-randoop.sh
index 7d9614c..d8ab624 100755
--- a/scripts/mutation-randoop.sh
+++ b/scripts/mutation-randoop.sh
@@ -64,6 +64,8 @@ if [[ "$JAVA_VER" -ne 18 ]]; then
   exit 1
 fi
 
+Generator=Randoop
+generator=randoop
 SCRIPT_DIR="$(CDPATH='' cd -- "$(dirname -- "$0")" && pwd -P)"
 MAJOR_HOME=$(realpath "${SCRIPT_DIR}/build/major/")                     # Major home directory, for mutation testing
 RANDOOP_JAR=$(realpath "${SCRIPT_DIR}/build/randoop-all-4.3.4.jar")     # Randoop jar file
@@ -478,7 +480,7 @@ fi
 #===============================================================================
 # Build System Preparation
 #===============================================================================
-echo "Using Randoop to generate tests."
+echo "Using ${Generator} to generate tests."
 echo
 
 # Handle relative and absolute output files; make sure output file exists.
@@ -510,7 +512,7 @@ for i in $(seq 1 "$NUM_LOOP"); do
     FILE_SUFFIX="$SUBJECT_PROGRAM-$FEATURE_NAME-$UUID"
 
     # Test directory for each iteration.
-    TEST_DIRECTORY="$SCRIPT_DIR/build/randoop-tests/$FILE_SUFFIX"
+    TEST_DIRECTORY="$SCRIPT_DIR/build/$generator-tests/$FILE_SUFFIX"
     rm -rf "$TEST_DIRECTORY"
     mkdir -p "$TEST_DIRECTORY"
 
@@ -588,12 +590,12 @@ for i in $(seq 1 "$NUM_LOOP"); do
     cd "$RESULT_DIR"
 
     # shellcheck disable=SC2086 # FEATURE_FLAG may contain multiple arguments.
-    RANDOOP_COMMAND=(
+    GENERATOR_COMMAND=(
       "${RANDOOP_BASE_COMMAND[@]}"
       --junit-output-dir="$TEST_DIRECTORY"
     )
 
-    "${RANDOOP_COMMAND[@]}"
+    "${GENERATOR_COMMAND[@]}"
 
     # Remove jacoco.exec file generated by Randoop
     rm -rf "$RESULT_DIR/jacoco.exec"
@@ -607,7 +609,7 @@ for i in $(seq 1 "$NUM_LOOP"); do
     # Coverage & Mutation Analysis
     #===============================================================================
 
-    buildfile=build-randoop.xml
+    buildfile="build-$generator.xml"
 
     echo
     echo "Compiling and mutating subject program..."

From c19bbd7cbd5edc1bef8f185583d1f6c802823386 Mon Sep 17 00:00:00 2001
From: Michael Ernst <mernst@cs.washington.edu>
Date: Tue, 25 Nov 2025 20:07:16 -0800
Subject: [PATCH 5/6] Formatting

---
 scripts/prerequisites.md | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/scripts/prerequisites.md b/scripts/prerequisites.md
index 4a313d7..c8aba8e 100644
--- a/scripts/prerequisites.md
+++ b/scripts/prerequisites.md
@@ -10,6 +10,7 @@
 * **Perl** ≥ 5.12
 * **cpanm** (Perl module installer)
   To install `cpanm`:
+
   ```sh
   curl -L https://cpanmin.us | perl - App::cpanminus
   ```
@@ -34,7 +35,9 @@ pip install pandas matplotlib seaborn
 
 ```sh
 uv pip install pandas matplotlib seaborn
-```## Obtaining Dependencies and Subject Programs
+```
+
+## Obtaining Dependencies and Subject Programs
 
 ```sh
 make -C scripts
@@ -52,8 +55,8 @@ the shell session where you run the scripts:
 export PATH=$PATH:"PATH2DEFECTS4J"/framework/bin
 ```
 
-> "PATH2DEFECTS4J" points to the directory which Defects4J is in; it most
->likely will look like "currentdirectory/build/defects4j".
+where "PATH2DEFECTS4J" points to the directory which Defects4J is in; it most
+likely will look like "currentdirectory/build/defects4j".
 
 ### Java Versions Setup
 

From 95a06f3fcdb00f5fa6d7f309f3838d19e2f039e4 Mon Sep 17 00:00:00 2001
From: Michael Ernst <mernst@cs.washington.edu>
Date: Tue, 25 Nov 2025 20:09:30 -0800
Subject: [PATCH 6/6] Remove duplication

---
 scripts/experiment-scripts/README.md | 22 ----------------------
 1 file changed, 22 deletions(-)

diff --git a/scripts/experiment-scripts/README.md b/scripts/experiment-scripts/README.md
index 4fbd1da..2bbf62e 100644
--- a/scripts/experiment-scripts/README.md
+++ b/scripts/experiment-scripts/README.md
@@ -14,28 +14,6 @@ figures and tables.
 
 To set up the environment, refer to the `scripts/prerequisites.md` file.
 
-#### Python Dependencies
-
-Before running any experiment scripts, ensure the following Python packages are installed:
-
-* `pandas`
-* `matplotlib`
-* `seaborn`
-
-Install these packages using your preferred Python package manager. For example:
-
-**With pip:**
-
-```bash
-pip install pandas matplotlib seaborn
-```
-
-**With uv:**
-
-```bash
-uv pip install pandas matplotlib seaborn
-```
-
 ### Running Scripts
 
 To generate the desired figures or tables from the paper, run the corresponding