sty: Apply shellcheck diff

git grep -l '^#\( *shellcheck \|!\(/bin/\|/usr/bin/env \)\(sh\|bash\|dash\|ksh\)\)' \
    | xargs shellcheck -f diff
    | git apply

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py38" /usr/bin/run_pytests.sh
+docker run --rm=false -t -v "$WORKDIR":/work -v "$HOME"/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py38" /usr/bin/run_pytests.sh

@@ -8,21 +8,21 @@ arr=$@
 tmp_var=$( IFS=$' '; echo "${arr[*]}" )
 example_id=${tmp_var//[^A-Za-z0-9_-]/_}
 
-mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id} ${WORKDIR}/tests ${WORKDIR}/crashfiles
-echo "[logging]" > ${HOME}/.nipype/nipype.cfg
-echo "workflow_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
-echo "interface_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
-echo "utils_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
-echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
-echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
+mkdir -p "${HOME}"/.nipype "${WORKDIR}"/logs/example_"${example_id}" "${WORKDIR}"/tests "${WORKDIR}"/crashfiles
+echo "[logging]" > "${HOME}"/.nipype/nipype.cfg
+echo "workflow_level = DEBUG" >> "${HOME}"/.nipype/nipype.cfg
+echo "interface_level = DEBUG" >> "${HOME}"/.nipype/nipype.cfg
+echo "utils_level = DEBUG" >> "${HOME}"/.nipype/nipype.cfg
+echo "log_to_file = true" >> "${HOME}"/.nipype/nipype.cfg
+echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> "${HOME}"/.nipype/nipype.cfg
 
-echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
-echo 'crashfile_format = txt' >> ${HOME}/.nipype/nipype.cfg
+echo '[execution]' >> "${HOME}"/.nipype/nipype.cfg
+echo 'crashfile_format = txt' >> "${HOME}"/.nipype/nipype.cfg
 
 if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then
-echo '[monitoring]' >> ${HOME}/.nipype/nipype.cfg
-echo 'enabled = true' >> ${HOME}/.nipype/nipype.cfg
-echo 'sample_frequency = 3' >> ${HOME}/.nipype/nipype.cfg
+echo '[monitoring]' >> "${HOME}"/.nipype/nipype.cfg
+echo 'enabled = true' >> "${HOME}"/.nipype/nipype.cfg
+echo 'sample_frequency = 3' >> "${HOME}"/.nipype/nipype.cfg
 fi
 
 # Set up coverage
@@ -35,9 +35,9 @@ coverage run /src/nipype/tools/run_examples.py $@
 exit_code=$?
 
 if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then
-cp resource_monitor.json 2>/dev/null ${WORKDIR}/logs/example_${example_id}/ || :
+cp resource_monitor.json 2>/dev/null "${WORKDIR}"/logs/example_"${example_id}"/ || :
 fi
 # Collect crashfiles and generate xml report
-coverage xml -o ${WORKDIR}/tests/smoketest_${example_id}.xml
-find /work -maxdepth 1 -name "crash-*" -exec mv {} ${WORKDIR}/crashfiles/ \;
+coverage xml -o "${WORKDIR}"/tests/smoketest_"${example_id}".xml
+find /work -maxdepth 1 -name "crash-*" -exec mv {} "${WORKDIR}"/crashfiles/ \;
 exit $exit_code

@@ -9,32 +9,32 @@ WORKDIR=${WORK:-/work}
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
 # Create necessary directories
-mkdir -p ${WORKDIR}/tests ${WORKDIR}/crashfiles ${WORKDIR}/logs/py${PYTHON_VERSION}
+mkdir -p "${WORKDIR}"/tests "${WORKDIR}"/crashfiles "${WORKDIR}"/logs/py"${PYTHON_VERSION}"
 
 # Create a nipype config file
-mkdir -p ${HOME}/.nipype
-echo '[logging]' > ${HOME}/.nipype/nipype.cfg
-echo 'log_to_file = true' >> ${HOME}/.nipype/nipype.cfg
-echo "log_directory = ${WORKDIR}/logs/py${PYTHON_VERSION}" >> ${HOME}/.nipype/nipype.cfg
+mkdir -p "${HOME}"/.nipype
+echo '[logging]' > "${HOME}"/.nipype/nipype.cfg
+echo 'log_to_file = true' >> "${HOME}"/.nipype/nipype.cfg
+echo "log_directory = ${WORKDIR}/logs/py${PYTHON_VERSION}" >> "${HOME}"/.nipype/nipype.cfg
 
-echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
-echo 'crashfile_format = txt' >> ${HOME}/.nipype/nipype.cfg
+echo '[execution]' >> "${HOME}"/.nipype/nipype.cfg
+echo 'crashfile_format = txt' >> "${HOME}"/.nipype/nipype.cfg
 
 if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then
-echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg
+echo 'resource_monitor = true' >> "${HOME}"/.nipype/nipype.cfg
 fi
 
 # Run tests using pytest
 export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}
-py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}.xml \
+py.test -v --junitxml="${WORKDIR}"/tests/pytests_py"${PYTHON_VERSION}".xml \
 --cov nipype --cov-config /src/nipype/.coveragerc \
---cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml \
+--cov-report xml:"${WORKDIR}"/tests/coverage_py"${PYTHON_VERSION}".xml \
 -n auto \
--c ${TESTPATH}/pytest.ini ${TESTPATH}
+-c "${TESTPATH}"/pytest.ini "${TESTPATH}"
 exit_code=$?
 
 # Collect crashfiles
-find ${WORKDIR} -maxdepth 1 -name "crash-*" -exec mv {} ${WORKDIR}/crashfiles/ \;
+find "${WORKDIR}" -maxdepth 1 -name "crash-*" -exec mv {} "${WORKDIR}"/crashfiles/ \;
 
 echo "Unit tests finished with exit code ${exit_code}"
 exit ${exit_code}

@@ -4,15 +4,15 @@
 
 set -e
 
-USAGE="usage: $(basename $0) [-h] [-b] [-m]"
+USAGE="usage: $(basename "$0") [-h] [-b] [-m]"
 
 function Help {
 cat <<USAGE
 Generate base and/or main Dockerfiles for Nipype.
 
 Usage:
 
-$(basename $0) [-h] [-b] [-m]
+$(basename "$0") [-h] [-b] [-m]
 
 Options:
 

@@ -8,7 +8,7 @@ source tools/ci/env.sh
 set -eu
 
 # Required variables
-echo CHECK_TYPE = $CHECK_TYPE
+echo CHECK_TYPE = "$CHECK_TYPE"
 
 set -x
 

@@ -7,15 +7,15 @@ source tools/ci/env.sh
 set -eu
 
 # Required variables
-echo SETUP_REQUIRES = $SETUP_REQUIRES
+echo SETUP_REQUIRES = "$SETUP_REQUIRES"
 
 set -x
 
 python -m pip install --upgrade pip virtualenv
 virtualenv --python=python virtenv
 source tools/ci/activate.sh
 python --version
-python -m pip install -U $SETUP_REQUIRES
+python -m pip install -U "$SETUP_REQUIRES"
 which python
 which pip
 

@@ -8,8 +8,8 @@ source tools/ci/env.sh
 set -eu
 
 # Required variables
-echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
-echo DEPENDS = $DEPENDS
+echo EXTRA_PIP_FLAGS = "$EXTRA_PIP_FLAGS"
+echo DEPENDS = "$DEPENDS"
 
 set -x
 
@@ -18,7 +18,7 @@ if [ -n "$EXTRA_PIP_FLAGS" ]; then
 fi
 
 if [ -n "$DEPENDS" ]; then
-pip install ${EXTRA_PIP_FLAGS} --prefer-binary ${!DEPENDS}
+pip install "${EXTRA_PIP_FLAGS}" --prefer-binary "${!DEPENDS}"
 fi
 
 set +eux

@@ -51,22 +51,22 @@ else
 fi
 
 # Clean working copy
-TMP=`mktemp -d`
-hub clone conda-forge/$FEEDSTOCK $TMP/$FEEDSTOCK
-pushd $TMP/$FEEDSTOCK
+TMP=$(mktemp -d)
+hub clone conda-forge/"$FEEDSTOCK" "$TMP"/"$FEEDSTOCK"
+pushd "$TMP"/"$FEEDSTOCK"
 
 # Get user fork, move to a candidate release branch, detecting if new branch
 hub fork
 git fetch --all
-if git checkout -t $_USER/$BRANCH; then
+if git checkout -t "$_USER"/"$BRANCH"; then
 NEW_PR=false
 else
 NEW_PR=true
-git checkout -b $BRANCH origin/main
+git checkout -b "$BRANCH" origin/main
 fi
 
 # Calculate hash
-SHA256=`curl -sSL https://.com/$SRCREPO/archive/$REF.tar.gz | sha256sum | cut -d\ -f 1`
+SHA256=$(curl -sSL https://.com/"$SRCREPO"/archive/"$REF".tar.gz | sha256sum | cut -d\ -f 1)
 
 URL_BASE="https://.com/$CIRCLE_PROJECT_USERNAME/{{ name }}/archive"
 if $RELEASE; then
@@ -87,7 +87,7 @@ sed -i \
 # Bump branch
 git add recipe/meta.yaml
 git commit -m "$COMMIT_MSG"
-git push -u $_USER $BRANCH
+git push -u "$_USER" "$BRANCH"
 
 if $NEW_PR; then
 hub pull-request -b conda-forge:main -F - <<END
@@ -117,4 +117,4 @@ fi
 
 # Remove working copy
 popd
-rm -rf $TMP/$FEEDSTOCK
+rm -rf "$TMP"/"$FEEDSTOCK"

@@ -26,11 +26,11 @@ for ARG; do
 done
 
 RET=0
-for i in `seq $NLOOPS`; do
+for i in $(seq "$NLOOPS"); do
 sh -c "$CMD"
 RET="$?"
 if [ "$RET" -eq 0 ]; then break; fi
-if [ "$i" -ne "$NLOOPS" ]; then sleep $TOSLEEP; fi
+if [ "$i" -ne "$NLOOPS" ]; then sleep "$TOSLEEP"; fi
 done
 
 exit $RET