Reduce duplication

Author: mernst

scripts/experiment-scripts/README.md

@@ -10,33 +10,11 @@ These scripts execute various configurations of the mutation analysis and defect
 detection driver scripts, collect results, and generate the corresponding
 figures and tables.
 
-### Setup
+## Setup
 
 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:**
-
-```sh
-pip install pandas matplotlib seaborn
-```
-
-**With uv:**
-
-```sh
-uv pip install pandas matplotlib seaborn
-```
-
-### Running Scripts
+## Running Scripts
 
 To generate the desired figures or tables from the paper, run the corresponding
 shell script. For example, to generate **Figure 7**, use:
@@ -45,7 +23,7 @@ shell script. For example, to generate **Figure 7**, use:
 ./mutation-fig7.sh
 ```
 
-* To generate **Table 4 (defect detection)**:
+To generate **Table 4 (defect detection)**:
 
 ```sh
 ./defects4j-table4.sh
@@ -57,7 +35,7 @@ Each script is documented at the top of its file with:
 * What input parameters or configuration it expects
 * What output files it will produce and where
 
-### Output
+## Output
 
 Each experiment script writes its output to the `results/` directory. This includes:
 

scripts/experiment-scripts/defects4j-table4.sh

@@ -42,11 +42,8 @@ if [ -z "$PYTHON_EXECUTABLE" ]; then
   exit 1
 fi
 
-# Clean up previous run artifacts
-rm -rf "$GRT_TESTING_ROOT"/build/defects4j-src/*
-rm -rf "$GRT_TESTING_ROOT"/build/randoop-tests/*
-rm -rf "$GRT_TESTING_ROOT"/build/evosuite-tests/*
-rm -rf "$GRT_TESTING_ROOT"/build/evosuite-report/*
+# Clean up previous run artifacts.
+make -C "$GRT_TESTING_ROOT" clean
 rm -f "$GRT_TESTING_ROOT"/results/table4.pdf
 rm -f "$GRT_TESTING_ROOT"/results/table4.csv
 

scripts/experiment-scripts/mutation-fig7.sh

@@ -37,7 +37,7 @@ SCRIPT_NAME=$(basename -- "$0")
 GRT_TESTING_ROOT="$(realpath "$SCRIPT_DIR"/../)"
 . "$SCRIPT_DIR"/common.sh
 
-# Clean up previous run artifacts
+# Clean up previous run artifacts.
 make -C "$GRT_TESTING_ROOT" clean
 rm -f "$GRT_TESTING_ROOT"/results/fig7.pdf
 rm -f "$GRT_TESTING_ROOT"/results/fig7.csv

scripts/experiment-scripts/mutation-fig8-9.sh

@@ -42,7 +42,7 @@ GRT_TESTING_ROOT="$(realpath "$SCRIPT_DIR"/../)"
 
 . "$SCRIPT_DIR"/common.sh
 
-# Clean up previous run artifacts
+# Clean up previous run artifacts.
 make -C "$GRT_TESTING_ROOT" clean
 rm -f "$GRT_TESTING_ROOT"/results/fig8-9.pdf
 rm -f "$GRT_TESTING_ROOT"/results/fig8-9.csv

scripts/mutation-randoop.sh

@@ -561,10 +561,11 @@ for i in $(seq 1 "$NUM_LOOP"); do
     exec 1>> "$RESULT_DIR"/mutation_output.txt 2>&1
   fi
 
-  # We cd into the result directory because Randoop generates jacoco.exec in the
-  # directory in which it is run. This is a concurrency issue since multiple
-  # runs will output a jacoco file to the exact same spot. Each result directory
-  # is unique to each instance of this script.
+  # We cd into the result directory (which is unique to each execution
+  # of this script) because Randoop generates `jacoco.exec` in the
+  # directory in which it is run. Otherwise, there would be a
+  # concurrency issue since multiple runs will output a jacoco file to
+  # the exact same spot.
   cd "$RESULT_DIR"
 
   GENERATOR_COMMAND=(

scripts/prerequisites.md

@@ -73,6 +73,6 @@ export JAVA11_HOME=/path/to/your/java11
 This is needed because different scripts require different Java versions:
 
 * **Defect scripts** (via [Defects4J](https://github.com/rjust/defects4j))
-require **Java 11**.
+  require **Java 11**.
 * **Mutation scripts** (via [Major](https://github.com/rjust/major))
-require **Java 8**.
+  require **Java 8**.