Merge pull request #45 from terhorstd/add_shellcheck

Add shellcheck

.github/workflows/Tests.yml

@@ -10,12 +10,18 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v2
+
     - name: Install ${{ matrix.envmodules }}
-      run: sudo apt-get install ${{ matrix.envmodules }}
+      run: sudo apt install ${{ matrix.envmodules }}
+
+    - name: Install test dependencies
+      run: sudo apt install shellcheck
+
     - name: Install BATS
       run: |
         ./build.sh configure || true
-        echo "y" | ./build.sh bats
+        ./build.sh -s bats
+
     - name: Run BATS
       run: |
         source /etc/profile

plans/Builder/unstable/ebrains

@@ -38,7 +38,7 @@ build_install () {
         log_status ">>> build and install ${PACKAGE}..."
 	set -x
 	if [ -d "${TARGET}" ]; then
-                read -p "sure you want to delete ${TARGET}? (ctrl-c for NO)"
+                read -rp "sure you want to delete ${TARGET}? (ctrl-c for NO)"
                 rm -vrf "${TARGET}"
         fi
 	#git clone --depth 1 -b "${VARIANT}" "[email protected]:INM-6/${PACKAGE}.git" "${TARGET}"

plans/Builder/unstable/master

@@ -38,7 +38,7 @@ build_install () {
         log_status ">>> build and install ${PACKAGE}..."
 	set -x
 	if [ -d "${TARGET}" ]; then
-                read -p "sure you want to delete ${TARGET}? (ctrl-c for NO)"
+                read -rp "sure you want to delete ${TARGET}? (ctrl-c for NO)"
                 rm -vrf "${TARGET}"
         fi
 	git clone --depth 1 -b "${VARIANT}" "https://github.com/INM-6/${PACKAGE}.git" "${TARGET}"

plans/LFPy/2.2dev0/default

@@ -43,7 +43,7 @@ build_install () {
 
         # --target "${TARGET}"
 	# is a subset of --root
-	pip install ${CONFIGURE_OPTIONS:-} \
+	pip install "${CONFIGURE_OPTIONS:-}" \
 	    --root "${TARGET}" \
             --cache-dir "${PACKAGE_CACHE}" \
             --src "${SOURCE}" \

plans/cmake/3.18.0/default

@@ -25,8 +25,8 @@ build_package () {
 	log_status ">>> build"
 	cd "${BUILD}"
 	set -x
-	"${SOURCE}/bootstrap" --prefix="${TARGET}" --parallel=${MAKE_THREADS:-$(nproc)} |& tee "${LOG}/bootstrap.log"
-	make -j ${MAKE_THREADS:-$(nproc)} |& tee "${LOG}/make.log"
+	"${SOURCE}/bootstrap" --prefix="${TARGET}" --parallel="${MAKE_THREADS:-$(nproc)}" |& tee "${LOG}/bootstrap.log"
+	make -j "${MAKE_THREADS:-$(nproc)}" |& tee "${LOG}/make.log"
 	set +x
 }
 

plans/cmake/3.18.1/default

@@ -26,9 +26,9 @@ build_package () {
 	log_status ">>> build"
 	cd "${BUILD}"
 	set -x
-	"${SOURCE}/bootstrap" --prefix="${TARGET}" --parallel=${MAKE_THREADS:-$(nproc)} |& tee "${LOG}/bootstrap.log"
+	"${SOURCE}/bootstrap" --prefix="${TARGET}" --parallel="${MAKE_THREADS:-$(nproc)}" |& tee "${LOG}/bootstrap.log"
 	#./bootstrap --prefix="${TARGET}" --srcdir="${SOURCE}" |& tee "${LOG}/bootstrap.log"
-	make -j ${MAKE_THREADS:-$(nproc)} |& tee "${LOG}/make.log"
+	make -j "${MAKE_THREADS:-$(nproc)}" |& tee "${LOG}/make.log"
 	set +x
 }
 

plans/elephant/0.2.0/default

@@ -46,6 +46,8 @@ build_install () {
 
         # --target "${TARGET}"
 	# is a subset of --root
+	# CONFIGURE_OPTIONS variable needs to be split, so no quotes
+	# shellcheck disable=SC2086
 	pip install ${CONFIGURE_OPTIONS:-} \
 	    --root "${TARGET}" \
             --cache-dir "${PACKAGE_CACHE}" \

plans/elephant/0.8.0/default

@@ -46,6 +46,8 @@ build_install () {
 
         # --target "${TARGET}"
 	# is a subset of --root
+	# CONFIGURE_OPTIONS variable needs to be split, so no quotes
+	# shellcheck disable=SC2086
 	pip install ${CONFIGURE_OPTIONS:-} \
 	    --root "${TARGET}" \
             --cache-dir "${PACKAGE_CACHE}" \

plans/environment-modules/4.7.1/default

@@ -23,13 +23,15 @@ URL=https://github.com/cea-hpc/modules/releases/download/v${VERSION}/modules-${V
 # this checksum was not officially provided, but taken from downloaded tar-ball
 SHA256SUM=ee7ecd62bbbde6d51e30788a97800c39e72515b6a910839fb84041b35ba42b4d
 
-CONFIGURE_OPTIONS="--modulefilesdir '$MODULE_INSTALL_PATH'  --enable-color --disable-example-modulefiles"
+CONFIGURE_OPTIONS=("--modulefilesdir" "$MODULE_INSTALL_PATH"  "--enable-color" "--disable-example-modulefiles")
 
 build_package () {
 	log_status ">>> in-tree build ${PACKAGE}/${VERSION}/${VARIANT}..."
 	cd "${SOURCE}"
 	set -x
-	"./configure" --prefix="${TARGET}" ${CONFIGURE_OPTIONS:-} 2>&1 | tee "${LOG}/configure.log"
-	make -j ${MAKE_THREADS:-$(nproc)} 2>&1 | tee "${LOG}/make.log"
+	# CONFIGURE_OPTIONS variable needs to be split, so no quotes
+	# shellcheck disable=SC2086
+	"./configure" --prefix="${TARGET}" "${CONFIGURE_OPTIONS[@]}" 2>&1 | tee "${LOG}/configure.log"
+	make -j "${MAKE_THREADS:-$(nproc)}" 2>&1 | tee "${LOG}/make.log"
 	set +x
 }

plans/fairgraph/0.5.1/default

@@ -43,6 +43,8 @@ build_install () {
 
         # --target "${TARGET}"
 	# is a subset of --root
+	# CONFIGURE_OPTIONS variable needs to be split, so no quotes
+	# shellcheck disable=SC2086
 	pip install ${CONFIGURE_OPTIONS:-} \
 	    --root "${TARGET}" \
             --cache-dir "${PACKAGE_CACHE}" \

plans/fairgraph/0.5.1/git

@@ -35,7 +35,7 @@ source_prepare() {
 build_prepare() {
 	log_status ">>> prepare build"
         if [ -d "${BUILD}" ]; then
-                read -p "sure you want to delete ${BUILD}? (ctrl-c for NO)"
+                read -rp "sure you want to delete ${BUILD}? (ctrl-c for NO)"
                 rm -vrf "${BUILD}"
         fi
         mkdir -pv "${BUILD}"
@@ -55,6 +55,8 @@ build_prepare() {
 	# is a subset of --root
 	cd "${BUILD}"
 
+	# CONFIGURE_OPTIONS variable needs to be split, so no quotes
+	# shellcheck disable=SC2086
 	pip install ${CONFIGURE_OPTIONS:-} \
 	    --root "${TARGET}" \
             --cache-dir "${PACKAGE_CACHE}" \
@@ -75,6 +77,8 @@ build_package () {
 
         # --target "${TARGET}"
 	# is a subset of --root
+	# CONFIGURE_OPTIONS variable needs to be split, so no quotes
+	# shellcheck disable=SC2086
 	pip install ${CONFIGURE_OPTIONS:-} \
 	    --root "${TARGET}" \
             --cache-dir "${PACKAGE_CACHE}" \

plans/gsl/2.6/default

@@ -19,13 +19,11 @@
 # SPDX-License-Identifier: GPL-3.0-or-later
 #
 PACKAGE=gsl
-VERSION=${1:-2.6}
-SUFFIX=${2:-}
 URL=ftp://ftp.gnu.org/gnu/${PACKAGE}/${PACKAGE}-${VERSION}.tar.gz
 GPG_VERIFY_KEY=../gsl_key.txt
 
 build_install() {
-	make install |& tee ${LOG}/make-install.log
-	awk 'BEGIN {f=2;x=0}; /^-------/{x=1;if (f>0) f--} f*x' ${LOG}/make-install.log  >${TARGET}/ConfigurationSummary.txt
+	make install |& tee "${LOG}/make-install.log"
+	awk 'BEGIN {f=2;x=0}; /^-------/{x=1;if (f>0) f--} f*x' "${LOG}/make-install.log"  >"${TARGET}/ConfigurationSummary.txt"
 }
 

plans/hybridLFPy/0.1.3/default

@@ -44,6 +44,8 @@ build_install () {
 
         # --target "${TARGET}"
 	# is a subset of --root
+	# CONFIGURE_OPTIONS variable needs to be split, so no quotes
+	# shellcheck disable=SC2086
 	pip install ${CONFIGURE_OPTIONS:-} \
 	    --root "${TARGET}" \
             --cache-dir "${PACKAGE_CACHE}" \

plans/nest-simulator/2.14.0/default

@@ -24,4 +24,5 @@ DOI=10.5281/zenodo.882971
 MD5SUM=a214b61da740c9252f3dfea5ed804441 
 SHA256SUM=afaf7d53c2d5305fac1257759cc0ea6d62c3cebf7d5cc4a07d4739af4dbb9caf
 
+# shellcheck source=plans/nest-simulator/common
 source "$(dirname "${PLAN}")/../common"

plans/nest-simulator/2.16.0/default

@@ -28,4 +28,5 @@ MD5SUM=327c1d1edea9580cde1bc1deaa7f63f3 # GitHub release tarball
 SHA256SUM=abfeb61719dec54da9477be035bef1d9d764f4e7663f63f6a6d9211f967e0490
 log_warning "!!! NOTE: Building from release tar-ball, which is different from the DOI version!"
 
+# shellcheck source=plans/nest-simulator/common
 source "$(dirname "${PLAN}")/../common"

plans/nest-simulator/2.18.0/default

@@ -24,4 +24,5 @@ DOI=10.5281/zenodo.2605422
 MD5SUM=5d04f99bb8d1fa13a5796ef12500ec99
 SHA256SUM=7295c936fbdd5486395b06f54f0d4d35d9a1b6ee50b7b844186ec2c92de641d1
 
+# shellcheck source=plans/nest-simulator/common
 source "$(dirname "${PLAN}")/../common"

plans/nest-simulator/2.20.0/Python3-CN-gsl2.6

@@ -32,5 +32,6 @@ MD5SUM=d3fc815b6a6db187468350cc971fed0b
 SHA256SUM=40e33187c22d6e843d80095b221fa7fd5ebe4dbc0116765a91fc5c425dd0eca4
 log_warning "!!! NOTE: Building from release tar-ball, which is different from the DOI version!"
 
-CMAKEFLAGS="-Dwith-python=3 -Dwith-gsl=ON"
+CONFIGURE_OPTIONS="-Dwith-python=3 -Dwith-gsl=ON"
+# shellcheck source=plans/nest-simulator/common
 source "$(dirname "${PLAN}")/../common"

plans/nest-simulator/2.20.0/default

@@ -31,12 +31,13 @@ URL='https://github.com/nest/nest-simulator/archive/v2.20.0.tar.gz'
 MD5SUM=d3fc815b6a6db187468350cc971fed0b
 SHA256SUM=40e33187c22d6e843d80095b221fa7fd5ebe4dbc0116765a91fc5c425dd0eca4
 
-CMAKEFLAGS="-Dwith-python=OFF"
-if which python; then
-	PYTHON="$(which python3)"
-	CMAKEFLAGS="-Dwith-python=3"
+CONFIGURE_OPTIONS="-Dwith-python=OFF"
+if command -v python; then
+	PYTHON="$(command -v python3)"
+	CONFIGURE_OPTIONS="-Dwith-python=3"
 fi
 
-CMAKEFLAGS+=" -Dwith-boost=ON"
+CONFIGURE_OPTIONS+=" -Dwith-boost=ON"
 
+# shellcheck source=plans/nest-simulator/common
 source "$(dirname "${PLAN}")/../common"

plans/nest-simulator/2.20.0/py3.8-gsl2.6

@@ -32,5 +32,6 @@ MD5SUM=d3fc815b6a6db187468350cc971fed0b
 SHA256SUM=40e33187c22d6e843d80095b221fa7fd5ebe4dbc0116765a91fc5c425dd0eca4
 log_warning "!!! NOTE: Building from release tar-ball, which is different from the DOI version!"
 
-CMAKEFLAGS="-Dwith-python=3 -Dwith-gsl=ON"
+CONFIGURE_OPTIONS="-Dwith-python=3 -Dwith-gsl=ON"
+# shellcheck source=plans/nest-simulator/common
 source "$(dirname "${PLAN}")/../common"

plans/nest-simulator/2.20.1/default

@@ -26,12 +26,13 @@ URL="https://github.com/nest/nest-simulator/archive/v${VERSION}.tar.gz"
 MD5SUM=fd9aaebedd1d5ace9e7b4c5ae867f1fd
 SHA256SUM=df3d32b5899d5d444f708037b290f889ac6ff8eae6b7be9e9faee2c0d660d8e5
 
-CMAKEFLAGS="-Dwith-python=OFF"
-if which python; then
-	PYTHON="$(which python3)"
-	CMAKEFLAGS="-Dwith-python=3"
+CONFIGURE_OPTIONS="-Dwith-python=OFF"
+if command -v python; then
+	PYTHON="$(command -v python3)"
+	CONFIGURE_OPTIONS="-Dwith-python=3"
 fi
 
-CMAKEFLAGS+=" -Dwith-boost=ON"
+CONFIGURE_OPTIONS+=" -Dwith-boost=ON"
 
+# shellcheck source=plans/nest-simulator/common
 source "$(dirname "${PLAN}")/../common"

plans/nest-simulator/3.0/default

@@ -25,4 +25,5 @@ MD5SUM=5f369b65512bbb9a7031529ed18776e4
 SHA256SUM=d481ea67f3251fe3aadf5252ab0a999172f0cd5536c5985366d271d772e686e6
 
 
+# shellcheck source=plans/nest-simulator/common
 source "$(dirname "${PLAN}")/../common"

plans/nest-simulator/common

@@ -26,8 +26,10 @@ build_package () {
 	log_status ">>> build"
 	cd "${BUILD}"
 	set -x
-	cmake ${CMAKEFLAGS} -DCMAKE_INSTALL_PREFIX:PATH="$TARGET" "$SOURCE" 2>&1 | tee "${LOG}/cmake.log"
-	make -j ${MAKE_THREADS:-$(nproc)} 2>&1 | tee "${LOG}/make.log"
+	# CONFIGURE_OPTIONS variable needs to be split, so no quotes
+	# shellcheck disable=SC2086
+	cmake ${CONFIGURE_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH="$TARGET" "$SOURCE" 2>&1 | tee "${LOG}/cmake.log"
+	make -j "${MAKE_THREADS:-$(nproc)}" 2>&1 | tee "${LOG}/make.log"
 	set +x
 }
 

plans/snakemake/5.27.4/default

@@ -46,6 +46,7 @@ build_install () {
 
         # --target "${TARGET}"
 	# is a subset of --root
+	# shellcheck disable=SC2086
 	pip3 install ${CONFIGURE_OPTIONS:-} \
 	    --root "${TARGET}" \
             --cache-dir "${PACKAGE_CACHE}" \

plans/tree/1.8.0/default

@@ -29,7 +29,7 @@ log_warning "WARNING: This build re-assigns \$TARGET path to $TARGET, because tr
 build_prepare() {
 	log_status ">>> prepare build"
 	if [ -d "${BUILD}" ]; then
-		read -p "sure you want to delete ${BUILD}? (ctrl-c for NO)"
+		read -rp "sure you want to delete ${BUILD}? (ctrl-c for NO)"
 		rm -vrf "${BUILD}"
 	fi
 	# tree specific:

tests/static-checks.bats

@@ -0,0 +1,9 @@
+#!/usr/bin/env bats
+
+@test "pass shellcheck static code analysis" {
+	# Covered by strict mode (set -euo pipefail)
+	# SC2164: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
+	# SC2034: <variablename> appears unused. Verify it or export it.
+	export SHELLCHECK_OPTS='--exclude=SC2034,SC2164'
+	shellcheck $(find plans/ -type f -not -name "*.txt" -a -not -name "*.module" )
+}