Enable shell check scripts for existing scripts

.shellcheck_exclude_paths

@@ -1,9 +1,3 @@
-scripts/ci/circle/postCDashStatus.sh
-scripts/ci/circle/run.sh
-scripts/ci/gh-actions/check-branch-name.sh
-scripts/ci/gh-actions/get-changed-files.sh
-scripts/ci/gh-actions/macos-setup.sh
-scripts/ci/gh-actions/run.sh
 scripts/ci/scripts/github-prs-to-gitlab.sh
 scripts/ci/scripts/run-clang-format.sh
 scripts/ci/scripts/run-flake8.sh
@@ -15,18 +9,3 @@ scripts/developer/setup.sh
 scripts/docker/setup-user.sh
 scripts/runconf/runconf.sh
 scripts/runconf/runconf_olcf.sh
-testing/contract/lammps/build.sh
-testing/contract/lammps/config.sh
-testing/contract/lammps/install.sh
-testing/contract/lammps/setup.sh
-testing/contract/lammps/test.sh
-testing/contract/scorpio/build.sh
-testing/contract/scorpio/config.sh
-testing/contract/scorpio/install.sh
-testing/contract/scorpio/setup.sh
-testing/contract/scorpio/test.sh
-testing/contract/tau/build.sh
-testing/contract/tau/config.sh
-testing/contract/tau/install.sh
-testing/contract/tau/setup.sh
-testing/contract/tau/test.sh

scripts/ci/circle/postCDashStatus.sh

@@ -4,7 +4,7 @@ USER=${STATUS_ROBOT_NAME}
 TOKEN=${STATUS_ROBOT_KEY}
 COMMIT=${CIRCLE_SHA1}
 CDASH_STATUS_CONTEXT="cdash"
-SOURCE_DIR="$(readlink -f ${CIRCLE_WORKING_DIRECTORY}/source)"
+SOURCE_DIR="$(readlink -f "${CIRCLE_WORKING_DIRECTORY}"/source)"
 
 build_status_body() {
   cat <<EOF
@@ -18,8 +18,9 @@ EOF
 }
 
 PYTHON_SCRIPT="${SOURCE_DIR}/scripts/ci/findStatus.py"
-curl -u "${USER}:${TOKEN}" "${API_BASE}/commits/${COMMIT}/statuses" | python3 ${PYTHON_SCRIPT} --context ${CDASH_STATUS_CONTEXT}
-if [ $? -ne 0 ]
+curl -u "${USER}:${TOKEN}" "${API_BASE}/commits/${COMMIT}/statuses" | python3 "${PYTHON_SCRIPT}" --context ${CDASH_STATUS_CONTEXT}
+exit_status=$?
+if [ "$exit_status" -ne 0 ]
 then
   echo "Need to post a status for context ${CDASH_STATUS_CONTEXT}"
   postBody="$(build_status_body)"

scripts/ci/circle/run.sh

@@ -1,5 +1,6 @@
 #!/bin/bash --login
 
+# shellcheck source=/dev/null
 . /etc/profile.d/modules.sh
 
 # Parse the branch name used by the PR
@@ -8,8 +9,9 @@ REALBRANCH="${CIRCLE_BRANCH}"
 if [ -n "${CIRCLE_PR_NUMBER}" ]
 then
   APIURL="${API_BASE}/pulls/${CIRCLE_PR_NUMBER}"
-  RESULT="$(curl -s ${APIURL} | python3 -c "import sys, json; print(json.load(sys.stdin)['head']['ref'])" 2> /dev/null)"
-  if [ $? -eq 0 ]
+  RESULT="$(curl -s "${APIURL}" | python3 -c "import sys, json; print(json.load(sys.stdin)['head']['ref'])" 2> /dev/null)"
+  exit_status=$?
+  if [ "$exit_status" -eq 0 ]
   then
     REALBRANCH="$(echo "${RESULT}" | tr '/' '-')"
   fi
@@ -70,8 +72,9 @@ echo "**********Env End************"
 
 echo "**********CTest Begin**********"
 ${CTEST} --version
-echo ${CTEST} -VV -S ${CTEST_SCRIPT} -Ddashboard_full=OFF ${CTEST_STEP_ARGS}
-${CTEST} -VV -S ${CTEST_SCRIPT} -Ddashboard_full=OFF ${CTEST_STEP_ARGS}
+echo ${CTEST} -VV -S "${CTEST_SCRIPT}" -Ddashboard_full=OFF "${CTEST_STEP_ARGS}"
+# shellcheck disable=SC2086
+${CTEST} -VV -S "${CTEST_SCRIPT}" -Ddashboard_full=OFF ${CTEST_STEP_ARGS}
 RET=$?
 echo "**********CTest End************"
 

scripts/ci/gh-actions/check-branch-name.sh

@@ -4,7 +4,7 @@ if [ "${GITHUB_EVENT_NAME}" = "pull_request" ]
 then
   if [ -z "${BASE_REF}" ]
   then
-    BASE_REF="$(jq -r .pull_request.base.ref ${GITHUB_EVENT_PATH})"
+    BASE_REF="$(jq -r .pull_request.base.ref "${GITHUB_EVENT_PATH}")"
   fi
   echo "Base ref: ${BASE_REF}"
   echo "Head ref: ${GITHUB_HEAD_REF}"

scripts/ci/gh-actions/get-changed-files.sh

@@ -3,12 +3,12 @@
 case "${GITHUB_EVENT_NAME}"
 in
   pull_request)
-    BASE_SHA=$(jq -r .pull_request.base.sha ${GITHUB_EVENT_PATH})
-    HEAD_SHA=$(jq -r .pull_request.head.sha ${GITHUB_EVENT_PATH})
+    BASE_SHA=$(jq -r .pull_request.base.sha "${GITHUB_EVENT_PATH}")
+    HEAD_SHA=$(jq -r .pull_request.head.sha "${GITHUB_EVENT_PATH}")
     ;;
   push)
-    BASE_SHA=$(jq -r .before ${GITHUB_EVENT_PATH})
-    HEAD_SHA=$(jq -r .after ${GITHUB_EVENT_PATH})
+    BASE_SHA=$(jq -r .before "${GITHUB_EVENT_PATH}")
+    HEAD_SHA=$(jq -r .after "${GITHUB_EVENT_PATH}")
     ;;
   *)
     echo "Unable to get changed files from '${GITHUB_EVENT_NAME}' event"
@@ -20,11 +20,11 @@ echo "Base: ${BASE_SHA}"
 echo "Head: ${HEAD_SHA}"
 echo ""
 
-git fetch origin ${BASE_SHA}
+git fetch origin "${BASE_SHA}"
 
 echo ""
 echo "::group::All changed files"
-git diff --name-only ${BASE_SHA}...${HEAD_SHA} | tee all-changed-files.txt
+git diff --name-only "${BASE_SHA}"..."${HEAD_SHA}" | tee all-changed-files.txt
 
 echo "::group::Filtered changes"
 grep -v '^docs/' all-changed-files.txt | tee filtered-changed-files.txt

scripts/ci/gh-actions/macos-setup.sh

@@ -8,13 +8,13 @@ then
   echo "Error: GH_YML_MATRIX_COMPILER variable is not defined"
   exit 1
 fi
-XCODE_VER="$(echo ${GH_YML_MATRIX_COMPILER} | sed -e 's|_|.|g' -e 's|xcode||')"
-if [ ! -d /Applications/Xcode_${XCODE_VER}.app ]
+XCODE_VER="$(echo "${GH_YML_MATRIX_COMPILER}" | sed -e 's|_|.|g' -e 's|xcode||')"
+if [ ! -d "/Applications/Xcode_${XCODE_VER}.app" ]
 then
   echo "Error: XCode installation directory /Applications/Xcode_${XCODE_VER}.app does not exist"
   exit 2
 fi
-sudo xcode-select --switch /Applications/Xcode_${XCODE_VER}.app
+sudo xcode-select --switch "/Applications/Xcode_${XCODE_VER}.app"
 
 echo "Installing CMake"
 
@@ -36,7 +36,7 @@ brew install ninja
 
 echo "Installing GCC"
 brew install gcc
-sudo ln -v -s $(which gfortran-11) /usr/local/bin/gfortran
+sudo ln -v -s "$(which gfortran-11)" /usr/local/bin/gfortran
 
 echo "Installing blosc compression"
 brew install c-blosc

scripts/ci/gh-actions/run.sh

@@ -100,19 +100,19 @@ export ADIOS2_IP=127.0.0.1
 export OMP_NUM_THREADS=1
 
 # Load any additional setup scripts
-if [ -f gha/scripts/ci/setup-run/ci-${GH_YML_JOBNAME}.sh ]
+if [ -f "gha/scripts/ci/setup-run/ci-${GH_YML_JOBNAME}.sh" ]
 then
   SETUP_RUN_SCRIPT=gha/scripts/ci/setup-run/ci-${GH_YML_JOBNAME}.sh
-elif [ -f gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}-${GH_YML_MATRIX_COMPILER}-${GH_YML_MATRIX_PARALLEL}.sh ]
+elif [ -f "gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}-${GH_YML_MATRIX_COMPILER}-${GH_YML_MATRIX_PARALLEL}.sh" ]
 then
   SETUP_RUN_SCRIPT=gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}-${GH_YML_MATRIX_COMPILER}-${GH_YML_MATRIX_PARALLEL}.sh
-elif [ -f gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}-${GH_YML_MATRIX_COMPILER}.sh ]
+elif [ -f "gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}-${GH_YML_MATRIX_COMPILER}.sh" ]
 then
   SETUP_RUN_SCRIPT=gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}-${GH_YML_MATRIX_COMPILER}.sh
-elif [ -f gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}.sh ]
+elif [ -f "gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}.sh" ]
 then
   SETUP_RUN_SCRIPT=gha/scripts/ci/setup-run/ci-${GH_YML_MATRIX_OS}.sh
-elif [ -f gha/scripts/ci/setup-run/ci-${GH_YML_BASE_OS}.sh ]
+elif [ -f "gha/scripts/ci/setup-run/ci-${GH_YML_BASE_OS}.sh" ]
 then
   SETUP_RUN_SCRIPT=gha/scripts/ci/setup-run/ci-${GH_YML_BASE_OS}.sh
 fi
@@ -126,7 +126,8 @@ echo "::endgroup::"
 echo "::group::Job-run setup (if any)"
 if [ "${SETUP_RUN_SCRIPT:-UNSET}" != "UNSET" ]
 then
-  source ${SETUP_RUN_SCRIPT}
+  # shellcheck source=/dev/null
+  source "${SETUP_RUN_SCRIPT}"
 fi
 echo "::endgroup::"
 
@@ -139,7 +140,8 @@ echo "::group::CTest version"
 echo "::endgroup::"
 
 echo "::group::Execute job step"
-"${CTEST}" -VV -S ${CTEST_SCRIPT} -Ddashboard_full=OFF ${CTEST_STEP_ARGS}
+# shellcheck disable=SC2086
+"${CTEST}" -VV -S "${CTEST_SCRIPT}" -Ddashboard_full=OFF ${CTEST_STEP_ARGS}
 RET=$?
 echo "::endgroup::"
 

testing/contract/lammps/build.sh

@@ -3,6 +3,10 @@
 set -x
 set -e
 
-source $(dirname $(readlink -f ${BASH_SOURCE}))/setup.sh
+# shellcheck disable=SC1091
+source "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")/setup.sh"
 
-cmake --build ${build_dir} -j8
+# Fail if is not set
+build_dir="${build_dir:?}"
+
+cmake --build "${build_dir}" -j8

testing/contract/lammps/config.sh

@@ -3,17 +3,23 @@
 set -x
 set -e
 
-source $(dirname $(readlink -f ${BASH_SOURCE}))/setup.sh
+# shellcheck disable=SC1091
+source "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")/setup.sh"
 
-mkdir -p ${build_dir}
-cd ${build_dir}
+# Fail if is not set
+source_dir="${source_dir:?}"
+build_dir="${build_dir:?}"
+install_dir="${install_dir:?}"
+
+mkdir -p "${build_dir}"
+cd "${build_dir}"
 
 cmake \
-  -DCMAKE_INSTALL_PREFIX=${install_dir} \
+  -DCMAKE_INSTALL_PREFIX="${install_dir}" \
   -DBUILD_MPI=yes \
   -DBUILD_EXE=yes \
   -DBUILD_LIB=no \
   -DBUILD_DOC=no \
   -DLAMMPS_SIZES=smallbig \
   -DPKG_ADIOS=yes \
-  ${source_dir}/cmake
+  "${source_dir}/cmake"

testing/contract/lammps/install.sh

@@ -3,6 +3,10 @@
 set -x
 set -e
 
-source $(dirname $(readlink -f ${BASH_SOURCE}))/setup.sh
+# shellcheck disable=SC1091
+source "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")/setup.sh"
 
-cmake --install ${build_dir}
+# Fail if is not set
+build_dir="${build_dir:?}"
+
+cmake --install "${build_dir}"

testing/contract/lammps/setup.sh

@@ -1,7 +1,14 @@
-source_dir=$(readlink -f ${PWD})/source
-build_dir=$(readlink -f ${PWD})/build
-install_dir=$(readlink -f ${PWD})/install
-test_dir=$(readlink -f ${PWD})/test
+#!/bin/bash
+
+source_dir=$(readlink -f "${PWD}")/source
+build_dir=$(readlink -f "${PWD}")/build
+install_dir=$(readlink -f "${PWD}")/install
+test_dir=$(readlink -f "${PWD}")/test
+
+export source_dir
+export build_dir
+export install_dir
+export test_dir
 
 echo "source_dir  = \"${source_dir}\""
 echo "build_dir   = \"${build_dir}\""

testing/contract/lammps/test.sh

@@ -3,13 +3,18 @@
 set -x
 set -e
 
-source $(dirname $(readlink -f ${BASH_SOURCE}))/setup.sh
+# shellcheck disable=SC1091
+source "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")/setup.sh"
 
-mkdir -p ${test_dir}
-cd ${test_dir}
+# Fail if is not set
+install_dir="${install_dir:?}"
+test_dir="${test_dir:?}"
+
+mkdir -p "${test_dir}"
+cd "${test_dir}"
 cp -v /opt/adios2/source/testing/contract/lammps/{adios2_config.xml,check_results.sh,in.test} .
 
 
-mpiexec -np 4 --oversubscribe ${install_dir}/bin/lmp -in in.test
+mpiexec -np 4 --oversubscribe "${install_dir}/bin/lmp" -in in.test
 
 ./check_results.sh

testing/contract/scorpio/build.sh

@@ -3,6 +3,10 @@
 set -x
 set -e
 
-source $(dirname $(readlink -f ${BASH_SOURCE}))/setup.sh
+# shellcheck disable=SC1091
+source "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")/setup.sh"
 
-cmake --build ${build_dir} -j8
+# Fail if is not set
+build_dir="${build_dir:?}"
+
+cmake --build "${build_dir}" -j8

testing/contract/scorpio/config.sh

@@ -3,22 +3,28 @@
 set -x
 set -e
 
-source $(dirname $(readlink -f ${BASH_SOURCE}))/setup.sh
+# shellcheck disable=SC1091
+source "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")/setup.sh"
 
-mkdir -p ${build_dir}
-cd ${build_dir}
+# Fail if is not set
+source_dir="${source_dir:?}"
+build_dir="${build_dir:?}"
+install_dir="${install_dir:?}"
+
+mkdir -p "${build_dir}"
+cd "${build_dir}"
 
 export CC=mpicc
 export CXX=mpic++
 export FC=mpifort
 
 cmake \
-  -DCMAKE_INSTALL_PREFIX=${install_dir} \
+  -DCMAKE_INSTALL_PREFIX="${install_dir}" \
   -DFPHSA_NAME_MISMATCHED=ON \
   -DPIO_ENABLE_TESTS=ON \
   -DPIO_ENABLE_EXAMPLES=ON \
   -DWITH_NETCDF=OFF \
   -DWITH_PNETCDF=ON \
-  -DPnetCDF_PATH=$(spack location -i parallel-netcdf) \
+  -DPnetCDF_PATH="$(spack location -i parallel-netcdf)" \
   -DWITH_ADIOS2=ON \
-  ${source_dir}
+  "${source_dir}"

testing/contract/scorpio/install.sh

@@ -3,6 +3,10 @@
 set -x
 set -e
 
-source $(dirname $(readlink -f ${BASH_SOURCE}))/setup.sh
+# shellcheck disable=SC1091
+source "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")/setup.sh"
 
-cmake --install ${build_dir}
+# Fail if is not set
+build_dir="${build_dir:?}"
+
+cmake --install "${build_dir}"

testing/contract/scorpio/setup.sh

@@ -1,7 +1,14 @@
-source_dir=$(readlink -f ${PWD})/source
-build_dir=$(readlink -f ${PWD})/build
-install_dir=$(readlink -f ${PWD})/install
-test_dir=$(readlink -f ${PWD})/test
+#!/bin/bash
+
+source_dir=$(readlink -f "${PWD}")/source
+build_dir=$(readlink -f "${PWD}")/build
+install_dir=$(readlink -f "${PWD}")/install
+test_dir=$(readlink -f "${PWD}")/test
+
+export source_dir
+export build_dir
+export install_dir
+export test_dir
 
 echo "source_dir  = \"${source_dir}\""
 echo "build_dir   = \"${build_dir}\""

testing/contract/scorpio/test.sh

@@ -3,12 +3,17 @@
 set -x
 set -e
 
-source $(dirname $(readlink -f ${BASH_SOURCE}))/setup.sh
+# shellcheck disable=SC1091
+source "$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")/setup.sh"
 
-mkdir -p ${test_dir}
-cd ${test_dir}
+# Fail if is not set
+build_dir="${build_dir:?}"
+test_dir="${test_dir:?}"
 
-mpiexec --oversubscribe -np 4 ${build_dir}/examples/adios/example3 -v
+mkdir -p "${test_dir}"
+cd "${test_dir}"
+
+mpiexec --oversubscribe -np 4 "${build_dir}/examples/adios/example3" -v
 
 bpls -d example3_1.nc.bp.dir/example3_1.nc.bp.0 > 0.dump
 diff -u 0.dump /opt/adios2/source/testing/contract/scorpio/0.dump