Address shellcheck warnings (#600)

Co-authored-by: Mark Roberts <[email protected]>

.github/workflows/ci.yml

@@ -30,8 +30,8 @@ jobs:
         export JAVA_HOME=$HOME/.java/$JDK_DIR
         echo "JAVA_HOME=$JAVA_HOME" >> $GITHUB_ENV
         echo "$JAVA_HOME/bin" >> $GITHUB_PATH
-    - name: Install diffstat
-      run: sudo apt-get install diffstat
+    - name: Install diffstat and checkbashisms
+      run: sudo apt-get -y install diffstat devscripts
     - name: Install Carton
       uses: perl-actions/install-with-cpanm@v1
       with:

README_DEVELOPER.md

@@ -153,3 +153,9 @@ final data set, if this is still the case.
 Related, the test patches (<bid>.test.patch) stored in the repo are also not used. I think we
 should remove these as well. Source patches are manually minimized, but test patches are
 not -- these can be easily regenerated by running a diff between the buggy and fixed revisions.
+
+#### Style
+
+Because shell scripts are error-prone, we run a style checker on them.  CI will
+not pass if the style checker issues warnings.  Please address each warning by
+either correcting the problem or suppressing the warning.

framework/lib/test_generation/bin/_tool.source

@@ -24,6 +24,7 @@ die() {
 check_env() {
     local var="$1"
     local val
+    # shellcheck disable=SC2086
     val="$(eval echo \$$var)"
     [ -z "$val" ] && die "Variable $var not set!"
 }

framework/test/test_bug_mining.sh

@@ -7,7 +7,7 @@
 
 set -e
 
-HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -16,7 +16,6 @@ init
 BUG_MINING_FRAMEWORK_DIR="$BASE_DIR/framework/bug-mining"
 [ -d "$BUG_MINING_FRAMEWORK_DIR" ] || die "$BUG_MINING_FRAMEWORK_DIR does not exist"
 
-RESOURCES_INPUT_DIR="$HERE/resources/input/bug-mining"
 RESOURCES_OUTPUT_DIR="$HERE/resources/output/bug-mining"
 
 _check_output() {
@@ -233,8 +232,8 @@ test_analyze_project() {
     [ -s "$work_dir/$failing_tests" ] || die "No failing test cases has been reported"
 
     # Same number of failing tests
-    local actual_num_failing_tests; actual_num_failing_tests=$(grep -a "^--- " "$work_dir/$failing_tests" | wc -l)
-    local expected_num_failing_tests; expected_num_failing_tests=$(grep -a "^--- " "$RESOURCES_OUTPUT_DIR/$failing_tests" | wc -l)
+    local actual_num_failing_tests; actual_num_failing_tests=$(grep -c -a "^--- " "$work_dir/$failing_tests")
+    local expected_num_failing_tests; expected_num_failing_tests=$(grep -c -a "^--- " "$RESOURCES_OUTPUT_DIR/$failing_tests")
     if [ "$actual_num_failing_tests" -ne "$expected_num_failing_tests" ]; then
       echo "Expected failing tests:"
       grep -a "^--- " "$RESOURCES_OUTPUT_DIR/$failing_tests"

framework/test/test_cp.sh

@@ -5,7 +5,7 @@
 #
 ################################################################################
 
-HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1

framework/test/test_d4j_query.sh

@@ -5,14 +5,14 @@
 #
 ################################################################################
 
-HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
 init
 
-$BASE_DIR/framework/bin/defects4j query -p Collections -H >> $HERE"/temp"
-result=`diff $HERE/temp $HERE/resources/output/d4j-query/1`
+"$BASE_DIR"/framework/bin/defects4j query -p Collections -H >> "$HERE"/temp
+result=$(diff "$HERE"/temp "$HERE"/resources/output/d4j-query/1)
 
 [ "$result" == "" ] || die "query \"-p Collections\" -H failed: $result"
 

framework/test/test_export_command.sh

@@ -10,7 +10,7 @@
 #
 ################################################################################
 
-HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1

framework/test/test_fix_test_suite.sh

@@ -5,7 +5,7 @@
 #
 ################################################################################
 
-HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1

framework/test/test_gen_tests.sh

@@ -12,7 +12,7 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1

framework/test/test_monitor_test.sh

@@ -6,7 +6,7 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -18,11 +18,11 @@ vid=${bid}f
 work_dir=$TMP_DIR/$pid-$vid
 
 # Checkout buggy version
-defects4j checkout -p $pid -v $vid -w $work_dir || die "checkout program version $pid-$vid"
+defects4j checkout -p $pid -v $vid -w "$work_dir" || die "checkout program version $pid-$vid"
 
 actual="$(mktemp)"
 expected="resources/monitor.test.expected"
 # Compile buggy version
-defects4j monitor.test -t org.apache.commons.codec.binary.HexTest -w $work_dir > "$actual" || die "compile program version $pid-$vid"
+defects4j monitor.test -t org.apache.commons.codec.binary.HexTest -w "$work_dir" > "$actual" || die "compile program version $pid-$vid"
 
 cmp "$actual" "$expected" || die "compare actual vs. expected output: $actual vs. $expected"

framework/test/test_mutation_analysis.sh

@@ -7,7 +7,7 @@
 # TODO: There is some code duplication in this test script, which we can avoid
 # by extracting the mutation analysis workflow into a parameterized function. 
 
-HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -56,10 +56,10 @@ _check_mutation_result() {
 
     # Columns of summary (csv) file:
     # MutantsGenerated,MutantsRetained,MutantsCovered,MutantsKilled,MutantsLive,RuntimePreprocSeconds,RuntimeAnalysisSeconds
-    local act_mut_gen=$(tail -n1  "$summary_file" | cut -f1 -d',')
-    local act_mut_ret=$(tail -n1  "$summary_file" | cut -f2 -d',')
-    local act_mut_cov=$(tail -n1  "$summary_file" | cut -f3 -d',')
-    local act_mut_kill=$(tail -n1 "$summary_file" | cut -f4 -d',')
+    local act_mut_gen; act_mut_gen=$(tail -n1  "$summary_file" | cut -f1 -d',')
+    local act_mut_ret; act_mut_ret=$(tail -n1  "$summary_file" | cut -f2 -d',')
+    local act_mut_cov; act_mut_cov=$(tail -n1  "$summary_file" | cut -f3 -d',')
+    local act_mut_kill; act_mut_kill=$(tail -n1 "$summary_file" | cut -f4 -d',')
 
     [ "$act_mut_gen"  -eq "$exp_mut_gen" ] || die "Unexpected number of mutants generated (expected: $exp_mut_gen, actual: $act_mut_gen)!"
     [ "$act_mut_ret"  -eq "$exp_mut_ret" ] || die "Unexpected number of mutants retained (expected: $exp_mut_ret, actual: $act_mut_ret)!"

framework/test/test_mutation_cmd.sh

@@ -16,7 +16,7 @@ source test.include
 
 # Print usage message and exit
 usage() {
-    local known_pids=$(defects4j pids)
+    local known_pids; known_pids=$(defects4j pids)
     echo "usage: $0 -p <project id> [-b <bug id> ... | -b <bug id range> ... ]"
     echo "Project ids:"
     for pid in $known_pids; do
@@ -31,9 +31,10 @@ while getopts ":p:b:" opt; do
         p) PID="$OPTARG"
             ;;
         b) if [[ "$OPTARG" =~ ^[0-9]*\.\.[0-9]*$ ]]; then
+               # shellcheck disable=SC1083,2086
                 BUGS="$BUGS $(eval echo {$OPTARG})"
            else
-                BUGS="$BUGS $OPTARG"
+               BUGS="$BUGS $OPTARG"
            fi
             ;;
         \?)
@@ -59,20 +60,20 @@ init
 
 # Run all bugs, unless otherwise specified
 if [ "$BUGS" == "" ]; then
-    BUGS="$(get_bug_ids $BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE)"
+    BUGS="$(get_bug_ids "$BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE")"
 fi
 
 # Create log file
-script_name=$(echo $script | sed 's/\.sh$//')
-LOG="$TEST_DIR/${script_name}$(printf '_%s_%s' $PID $$).log"
-OUT_DIR="$TEST_DIR/${script_name}$(printf '_%s_%s' $PID $$).mutation_summary"
-mkdir -p $OUT_DIR
+script_name_without_sh=${script//.sh/}
+LOG="$TEST_DIR/${script_name_without_sh}$(printf '_%s_%s' "$PID" $$).log"
+OUT_DIR="$TEST_DIR/${script_name_without_sh}$(printf '_%s_%s' "$PID" $$).mutation_summary"
+mkdir -p "$OUT_DIR"
 
 # Reproduce all bugs (and log all results), regardless of whether errors occur
 HALT_ON_ERROR=0
 
 test_dir=$(mktemp -d)
-for bid in $(echo $BUGS); do
+for bid in $BUGS; do
     # Skip all bug ids that do not exist in the active-bugs csv
     if ! grep -q "^$bid," "$BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE"; then
         warn "Skipping bug ID that is not listed in active-bugs csv: $PID-$bid"
@@ -82,20 +83,20 @@ for bid in $(echo $BUGS); do
     # Test mutation analysis for the fixed version only.
     vid="${bid}f"
     work_dir="$test_dir/$PID-$vid"
-    defects4j checkout -p $PID -v "$vid" -w "$work_dir" || die "checkout: $PID-$vid"
+    defects4j checkout -p "$PID" -v "$vid" -w "$work_dir" || die "checkout: $PID-$vid"
     defects4j mutation -w "$work_dir" || die "mutation: $PID-$vid"
 
     cat "$work_dir/summary.csv" > "$OUT_DIR/$bid"
 done
-rm -rf $test_dir
+rm -rf "$test_dir"
 HALT_ON_ERROR=1
 
 # Print a summary of what went wrong
 if [ $ERROR != 0 ]; then
     printf '=%.s' $(seq 1 80) 1>&2
     echo 1>&2
     echo "The following errors occurred:" 1>&2
-    cat $LOG 1>&2
+    cat "$LOG" 1>&2
 fi
 
 # Indicate whether an error occurred

framework/test/test_sanity_check.sh

@@ -5,7 +5,7 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1

framework/test/test_style.sh

@@ -19,4 +19,3 @@ done
 for file in "$TOPLEVEL"/init.sh "$TOPLEVEL"/framework/lib/test_generation/bin/_tool.source ; do
     shellcheck -x -P SCRIPTDIR --format=gcc "$file"
 done
-

framework/test/test_tutorial.sh

@@ -5,7 +5,7 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1

framework/test/test_verify_bugs.sh

@@ -17,15 +17,15 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE="$(cd "$(dirname "$0")" && pwd)" || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
 init
 
 # Print usage message and exit
 usage() {
-    local known_pids=$(defects4j pids)
+    local known_pids; known_pids=$(defects4j pids)
     echo "usage: $0 -p <project id> [-b <bug id> ... | -b <bug id range> ... ] [-D]"
     echo "Project ids:"
     for pid in $known_pids; do
@@ -35,14 +35,14 @@ usage() {
 }
 
 # Run only relevant tests by default
-TEST_FLAG="-r"
+TEST_FLAG_OR_EMPTY="-r"
 # Debugging is off by default
 DEBUG=""
 
 # Check arguments
 while getopts ":p:b:AD" opt; do
     case $opt in
-        A) TEST_FLAG=""
+        A) TEST_FLAG_OR_EMPTY=""
             ;;
         D) DEBUG="-D"
             ;;
@@ -115,7 +115,7 @@ for bid in $BUGS ; do
         vid=${bid}$v
         defects4j checkout -p "$PID" -v "$vid" -w "$work_dir" || die "checkout: $PID-$vid"
         defects4j compile -w "$work_dir" || die "compile: $PID-$vid"
-        defects4j test $TEST_FLAG -w "$work_dir" || die "run relevant tests: $PID-$vid"
+        defects4j test $TEST_FLAG_OR_EMPTY -w "$work_dir" || die "run relevant tests: $PID-$vid"
 
         cat "$work_dir/failing_tests" > "$DIR_FAILING/$vid"
 
@@ -143,7 +143,7 @@ for bid in $BUGS ; do
 done
 
 if [ "$DEBUG" != "-D" ]; then
-    rm -rf $TMP_DIR
+    rm -rf "$TMP_DIR"
 fi
 HALT_ON_ERROR=1
 

init.sh

@@ -188,6 +188,7 @@ COVEREDCLASS_JAR="covered-class-${RANDOOP_VERSION}.jar"
 (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$RANDOOP_JAR" "randoop-current.jar")
 (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$REPLACECALL_JAR" "replacecall-current.jar")
 (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$COVEREDCLASS_JAR" "covered-class-current.jar")
+(cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/jacocoagent.jar" "jacocoagent.jar")
 
 ################################################################################
 #