Impurity annotation

.github/workflows/make.yml

@@ -19,5 +19,8 @@ jobs:
         run: sudo apt -y install shfmt shellcheck devscripts
       - name: Install markdownlint
         run: npm install markdownlint-cli2 --global
+      - name: Install Python `uv`
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
       - name: style check
-        run: make style-check
+        run: |
+          make style-check

.gitignore

@@ -16,7 +16,13 @@ Thumbs.db
 
 # subdirectory with source repositories
 tests/src
-subject-programs/src
+subject-programs/src-grt/
+subject-programs/src-upstream/
+# temporary
+subject-programs/src-upstream-OLD/
+subject-programs/src-upstream-GOOD/
+subject-programs/src-grt-SAVE/
+subject-programs/files.diff
 
 # subdirectory created by scripts/mutation-randoop.sh and scripts/mutation-evosuite.sh
 scripts/jarfiles
@@ -25,11 +31,8 @@ scripts/build/
 scripts/results/
 checkbashisms
 
-# output from runnin jacoco
+# output from running jacoco
 jacoco.exec
 
-# For code formatting
+# Obtained via Git
 .plume-scripts
-.markdownlint-cli2.yaml
-.pymarkdown
-.ruff.toml

.python-version

@@ -1 +1 @@
-3.14
+3.10

pyproject.toml

@@ -1,3 +1,7 @@
+[build-system]
+requires = ["uv_build >= 0.9.11, <0.10.0"]
+build-backend = "uv_build"
+
 [project]
 name = "grt-testing"
 version = "0.1.0"
@@ -13,5 +17,7 @@ dependencies = [
 [dependency-groups]
 dev = [
     "pymarkdownlnt>=0.9.33",
+    "pyyaml>=6.0.3",
     "ty>=0.0.1a31",
 ]
+# dynamic = ["version"]

scripts/Makefile

@@ -1,6 +1,7 @@
 MAKEFILE_DIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
 
 all: \
+    build/checker-framework/checker/dist/checker-qual.jar \
     build/evosuite-1.2.0.jar \
     build/evosuite-standalone-runtime-1.2.0.jar \
     build/hamcrest-core-1.3.jar \
@@ -64,13 +65,21 @@ build/junit-4.12.jar:
 
 build/hamcrest-core-1.3.jar:
 	mkdir -p build
-	cp ../subject-programs/hamcrest-core-1.3.jar build/
+	cp ../subject-programs/jars/hamcrest-core-1.3.jar build/
 
 build/major/bin/ant-replacecall:
 	LATEST_RELEASE=$$(curl -s https://api.github.com/repos/randoop/grt-replacecall/releases/latest | grep -o '"tag_name": "[^"]*' | cut -d'"' -f4) && \
 	wget "https://github.com/randoop/grt-replacecall/releases/download/$${LATEST_RELEASE}/ant-replacecall" && \
 	mv ant-replacecall build/major/bin/
 
+build/checker-framework/checker/dist/checker-qual.jar:
+	mkdir -p build
+	CFVER=3.50.0 && \
+	cd build && wget "https://github.com/typetools/checker-framework/releases/download/checker-framework-$${CFVER}/checker-framework-$${CFVER}.zip" && \
+	unzip -o checker-framework-$${CFVER}.zip && \
+	rm -rf checker-framework && \
+	mv checker-framework-$${CFVER} checker-framework
+
 build/defects4j:
 	mkdir -p build
 	cd build && git clone https://github.com/rjust/defects4j && cd defects4j && cpanm --installdeps . && ./init.sh

scripts/mutation-evosuite.sh

@@ -172,7 +172,7 @@ echo
 SRC_BASE_DIR="$(realpath "$SCRIPT_DIR/../subject-programs/src/$SUBJECT_PROGRAM")"
 
 # Path to the jar file of the subject program.
-SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/$SUBJECT_PROGRAM.jar")
+SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/jars/$SUBJECT_PROGRAM.jar")
 
 # Number of classes in given jar file.
 NUM_CLASSES=$(jar -tf "$SRC_JAR" | grep -c '.class')
@@ -318,7 +318,7 @@ case "$SUBJECT_PROGRAM" in
       "$SRC_BASE_DIR/lib/jaxen-core.jar" \
       "$SRC_BASE_DIR/lib/jaxen-jdom.jar" \
       "$SRC_BASE_DIR/lib/saxpath.jar" \
-      "$SCRIPT_DIR/../subject-programs/jaxen-1.1.6.jar"
+      "$SCRIPT_DIR/../subject-programs/jars/jaxen-1.1.6.jar"
     ;;
 
   "joda-time-2.3")

scripts/mutation-randoop.sh

@@ -56,12 +56,12 @@ set -o pipefail
 Generator=Randoop
 generator=randoop
 SCRIPT_DIR="$(CDPATH='' cd -- "$(dirname -- "$0")" && pwd -P)"
-SCRIPT_NAME=$(basename -- "$0")
-MAJOR_HOME=$(realpath "${SCRIPT_DIR}/build/major/")                     # Major home directory, for mutation testing
-RANDOOP_JAR=$(realpath "${SCRIPT_DIR}/build/randoop-all-4.3.4.jar")     # Randoop jar file
-JACOCO_AGENT_JAR=$(realpath "${SCRIPT_DIR}/build/jacocoagent.jar")      # For Bloodhound
-JACOCO_CLI_JAR=$(realpath "${SCRIPT_DIR}/build/jacococli.jar")          # For coverage report generation
-REPLACECALL_JAR=$(realpath "${SCRIPT_DIR}/build/replacecall-4.3.4.jar") # For replacing undesired method calls
+MAJOR_HOME=$(realpath "${SCRIPT_DIR}/build/major/")                                                # Major home directory, for mutation testing
+RANDOOP_JAR=$(realpath "${SCRIPT_DIR}/build/randoop-all-4.3.4.jar")                                # Randoop jar file
+JACOCO_AGENT_JAR=$(realpath "${SCRIPT_DIR}/build/jacocoagent.jar")                                 # For Bloodhound
+JACOCO_CLI_JAR=$(realpath "${SCRIPT_DIR}/build/jacococli.jar")                                     # For coverage report generation
+REPLACECALL_JAR=$(realpath "${SCRIPT_DIR}/build/replacecall-4.3.4.jar")                            # For replacing undesired method calls
+CHECKER_QUAL_JAR=$(realpath "${SCRIPT_DIR}/build/checker-framework/checker/dist/checker-qual.jar") # For Randoop Impurity
 
 . "$SCRIPT_DIR/defs.sh" # Define shell functions.
 
@@ -70,6 +70,7 @@ require_file "$RANDOOP_JAR"
 require_file "$JACOCO_AGENT_JAR"
 require_file "$JACOCO_CLI_JAR"
 require_file "$REPLACECALL_JAR"
+require_file "$CHECKER_QUAL_JAR"
 
 usejdk8
 JAVA_VER=$(java -version 2>&1 | awk -F '"' '/version/ {print $2}' | awk -F '.' '{sub("^$", "0", $2); print ($1=="1")?$2:$1}')
@@ -219,8 +220,18 @@ echo
 # Path to the base directory of the source code.
 SRC_BASE_DIR="$(realpath "$SCRIPT_DIR/../subject-programs/src/$SUBJECT_PROGRAM")"
 
-# Path to the jar file of the subject program.
-SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/$SUBJECT_PROGRAM.jar")
+if [[ " ${RANDOOP_FEATURES[*]} " =~ " GRT_FUZZING " ]]; then
+  # If randoop features contain "GRT_FUZZING", use annotated subject program jar.
+  ANNOTATED_JAR="$SCRIPT_DIR/../subject-programs/annotated-jars/$SUBJECT_PROGRAM.jar"
+  if [ ! -f "$ANNOTATED_JAR" ]; then
+    echo "${SCRIPT_NAME}: error: GRT_FUZZING enabled but annotated JAR not found: $ANNOTATED_JAR" >&2
+    exit 2
+  fi
+  SRC_JAR=$(realpath "$ANNOTATED_JAR")
+else
+  # Else, use the original subject program jar.
+  SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/jars/$SUBJECT_PROGRAM.jar")
+fi
 
 # Number of classes in given jar file.
 NUM_CLASSES=$(jar -tf "$SRC_JAR" | grep -c '.class')
@@ -353,7 +364,7 @@ case "$SUBJECT_PROGRAM" in
       "$SRC_BASE_DIR/lib/jaxen-core.jar" \
       "$SRC_BASE_DIR/lib/jaxen-jdom.jar" \
       "$SRC_BASE_DIR/lib/saxpath.jar" \
-      "$SCRIPT_DIR/../subject-programs/jaxen-1.1.6.jar"
+      "$SCRIPT_DIR/../subject-programs/jars/jaxen-1.1.6.jar"
     ;;
 
   "joda-time-2.3")
@@ -456,7 +467,7 @@ RANDOOP_BASE_COMMAND=(
   -Xbootclasspath/a:"$JACOCO_AGENT_JAR:$REPLACECALL_JAR"
   -javaagent:"$JACOCO_AGENT_JAR"
   -javaagent:"$REPLACECALL_COMMAND"
-  -classpath "$RANDOOP_CLASSPATH:$RANDOOP_JAR"
+  -classpath "$RANDOOP_CLASSPATH:$RANDOOP_JAR:$CHECKER_QUAL_JAR"
   randoop.main.Main
   gentests
   --testjar="$TARGET_JAR"

subject-programs/README

@@ -1,3 +1,8 @@
+Run Python scripts in this directory via:
+
+uv run SCRIPTNAME
+
+
 This directory contains compiled versions (jar files) of projects that the GRT
 paper used as subject programs.  The paper's Table II lists 32 projects.  We
 have located 30 of them.