Add shellcheck and pre-commit to CI jobs

build_support/install_csa-libneurosim.sh

@@ -1,12 +1,16 @@
 #!/bin/bash
-# Install libneurosim
 set -euo pipefail
 
+NEUROSIM_INSTALL_PATH="${1:-${HOME}/.cache/libneurosim.install}"
+CSA_INSTALL_PATH="${1:-${HOME}/.cache/csa.install}"
+PYLIB_DIR="$(python3 -c "import sysconfig; print(sysconfig.get_path('include'))" | sed 's/include/lib/')" || true  # was "$1" before
+
+# Install libneurosim
 git clone "https://github.com/INCF/libneurosim.git" libneurosim.src
 pushd libneurosim.src
 ./autogen.sh
-./configure --prefix="${HOME}/.cache/libneurosim.install" --with-mpi --with-python=3
-make
+./configure --prefix="${NEUROSIM_INSTALL_PATH}" --with-mpi --with-python=3
+make -j"$(nproc)"
 make install
 popd || exit $?
 rm -rf libneurosim.src
@@ -17,7 +21,7 @@ pushd csa.src
 sed -i 's/lpyneurosim/lpy3neurosim/g' configure.ac
 sed -i 's/print __version__/print\(__version__\)/g' Makefile.am
 ./autogen.sh
-LDFLAGS="-L${1}" ./configure --with-libneurosim="${HOME}/.cache/libneurosim.install" --prefix="${HOME}/.cache/csa.install"
+LDFLAGS="${PYLIB_DIR:+-L${PYLIB_DIR}}" ./configure --with-libneurosim="${NEUROSIM_INSTALL_PATH}" --prefix="${CSA_INSTALL_PATH}"
 make
 make install
 popd || exit $?

build_support/install_music.sh

@@ -1,12 +1,13 @@
 #!/bin/bash
 set -euo pipefail
 
+MUSIC_INSTALL_PATH="${1:-${HOME}/.cache/music.install}"
 # Install current MUSIC version.
 git clone "https://github.com/INCF/MUSIC.git" music.src
 pushd music.src
 ./autogen.sh
-./configure --prefix="${HOME}/.cache/music.install"
-make
+./configure --prefix="${MUSIC_INSTALL_PATH}"
+make -j"$(nproc)"
 make install
 popd || exit $?
 rm -rf music.src

build_support/install_sionlib.sh

@@ -2,15 +2,16 @@
 set -euo pipefail
 
 SIONLIBVERSION="1.7.4"
+SIONLIB_INSTALL_PATH="${1:-${HOME}/.cache/csa.install}"
 
 # Install SIONlib
 wget --content-disposition "http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${SIONLIBVERSION}"
 tar xfz "sionlib-${SIONLIBVERSION}.tar.gz"
 mv sionlib sionlib.src
 pushd sionlib.src
-./configure --prefix="${HOME}/.cache/sionlib.install" --mpi=openmpi --enable-python=3 --disable-fortran --disable-parutils --disable-mic
+./configure --prefix="${SIONLIB_INSTALL_PATH}" --mpi=openmpi --enable-python=3 --disable-fortran --disable-parutils --disable-mic
 cd build-linux-gomp-openmpi
-make
+make -j"$(nproc)"
 make install
 popd || exit $?
 rm -rf "sionlib-${SIONLIBVERSION}.tar.gz" sionlib.src

examples/run_examples.sh

@@ -31,23 +31,28 @@ if ! python3 -c "import nest" >/dev/null 2>&1; then
     exit 1
 fi
 
-
 # set bash strict mode
 set -euo pipefail
+set -x
 IFS=$' \n\t'
 
+# current directory where all results are save is "basedir"
+basedir="$PWD"
+# source tree where all input scripts/data can be found is "sourcedir"
+sourcedir="$(realpath "$(dirname "$0")/..")"
+
 declare -a EXAMPLES
 if [ "${#}" -eq 0 ]; then
     # Find all examples that have a line containing "autorun=true"
     # The examples can be found in subdirectory nest and in the
     # examples installation path.
     EXAMPLELIST="$(mktemp examplelist.XXXXXXXXXX)"
     if [ -d "nest/" ] ; then
-        grep -rl --include='*.sli' 'autorun=true' nest/ >>"$EXAMPLELIST"
+        grep -rl --include='*.sli' 'autorun=true' "${sourcedir}/nest/" >>"$EXAMPLELIST" || true
     else
-        grep -rl --include='*.sli' 'autorun=true' examples/ >>"$EXAMPLELIST"
+        grep -rl --include='*.sli' 'autorun=true' "${sourcedir}/examples/" >>"$EXAMPLELIST" || true
     fi
-    find pynest/examples -name '*.py' >>"$EXAMPLELIST"
+    find "${sourcedir}/pynest/examples" -name '*.py' >>"$EXAMPLELIST" || true
     readarray -t EXAMPLES <"$EXAMPLELIST"  # append each example found above
     rm "$EXAMPLELIST"
 else
@@ -64,10 +69,34 @@ done
 MPLCONFIGDIR="$(pwd)/matplotlib/"
 export MPLCONFIGDIR
 
-time_format="  time: {real: %E, user: %U, system: %S}\n\
-  memory: {total: %K, max_rss: %M}"
+INFO_OS="$(uname -s)"
 
-basedir=$PWD
+# find "time" command
+if test "${INFO_OS:-}" = "Darwin"; then
+    if test -x "/usr/local/bin/gtime"; then
+        # https://www.man7.org/linux/man-pages/man1/time.1.html
+        alias time="/usr/local/bin/gtime -f '  time: {real: %E, user: %U, system: %S}\n  memory: {total: %K, max_rss: %M}' --quiet"
+    else
+        if command -v gtime >/dev/null; then
+            alias time="\$(command -v gtime) -f '  time: {real: %E, user: %U, system: %S}\n  memory: {total: %K, max_rss: %M}' --quiet"
+        elif command -v time >/dev/null; then
+            # bash built-in time does not have memory information and uses TIMEFORMAT env variable
+            TIMEFORMAT="  time: {real: %E, user: %U, system: %S}"
+            export TIMEFORMAT
+        else
+            echo "'time' does not work on macOS. Try 'brew install gnu-time' or provide a compatible command by different means."
+            exit 1;
+        fi
+    fi
+else
+    # bash built-in time does not have memory information and uses TIMEFORMAT env variable
+    TIMEFORMAT="  time: {real: %E, user: %U, system: %S}"
+    export TIMEFORMAT
+    if ! command -v time >/dev/null; then
+        echo "could not determine a 'time' command. aborting"
+        exit 1;
+    fi
+fi
 
 FAILURES=0
 START="${SECONDS}"
@@ -101,11 +130,9 @@ for i in "${EXAMPLES[@]}"; do
 
     export NEST_DATA_PATH="$output_dir"
     touch .start_example
-    sleep 1
+    #sleep 1  # why was this needed?!
     set +e
-    # The following line will not work on macOS. There, `brew install gnu-time` and use the commented-out line below.
-    /usr/bin/time -f "$time_format" --quiet sh -c "'$runner' '$example' >'$logfile' 2>&1" |& tee -a "$metafile"
-    # /usr/local/bin/gtime -f "$time_format" --quiet sh -c "'$runner' '$example' >'$logfile' 2>&1" | tee -a "$metafile" 2>&1
+    time sh -c "'$runner' '$example' >'$logfile' 2>&1" 2>&1 | tee -a "$metafile"
     ret=$?
     set -e
 
@@ -131,12 +158,12 @@ for i in "${EXAMPLES[@]}"; do
 
     unset NEST_DATA_PATH
     cd "$basedir"
-
+    exit 42
 done
 ELAPSED_TIME="$(( SECONDS - START ))"
 
 echo ">>> Longest running examples:"
-grep -Eo "real: [^,]+" example_logs/*/meta.yaml | sed -e 's/:real://' | sort -k2 -rg | head -n 15
+grep -Eo "real: [^,]+" example_logs/*/meta.yaml | sed -e 's/:real://' | sort -k2 -rg | head -n 15 || true
 
 echo ">>> RESULTS: ${FAILURES} failed /$(echo "${EXAMPLES[*]}" | wc -w) total"
 echo ">>> TOTAL TIME: $((ELAPSED_TIME/60)) min $((ELAPSED_TIME%60)) sec."

testsuite/do_tests.sh

@@ -157,8 +157,8 @@ if test "${HAVE_MPI}" = "true"; then
 fi
 
 # Under Mac OS X, suppress crash reporter dialogs. Restore old state at end.
-echo "INFO_OS=${INFO_OS}"
-if test "${INFO_OS}" = "Darwin"; then
+echo "INFO_OS=${INFO_OS:-}"
+if test "${INFO_OS:-}" = "Darwin"; then
     TEST_CRSTATE="$( defaults read com.apple.CrashReporter DialogType )" || true
     echo "TEST_CRSTATE=$TEST_CRSTATE"
     defaults write com.apple.CrashReporter DialogType server || echo "WARNING: Could not set CrashReporter DialogType!"
@@ -178,7 +178,7 @@ list_files() {
     # instead use list_files like
     #
     #   list_files <somedir> <some_pattern> | while read -r test_name; do ... done
-    if test "${INFO_OS}" = "Darwin"; then
+    if test "${INFO_OS:-}" = "Darwin"; then
         # ref https://stackoverflow.com/a/752893
         # Note that on GNU systems an additional '-r' would be needed for
         # xargs, which is not available here.
@@ -593,7 +593,7 @@ python3 "$(dirname "$0")/summarize_tests.py" "${REPORTDIR}"
 TESTSUITE_RESULT="$?"
 
 # Mac OS X: Restore old crash reporter state
-if test "${INFO_OS}" = "Darwin" ; then
+if test "${INFO_OS:-}" = "Darwin" ; then
     defaults write com.apple.CrashReporter DialogType "${TEST_CRSTATE}" || echo "WARNING: Could not reset CrashReporter DialogType to '${TEST_CRSTATE}'!"
 fi
 

testsuite/run_test.sh

@@ -173,7 +173,6 @@ run_test ()
     if test "x${unexpected_exitcode:-}" != x ; then
         echo "***"
         echo "*** An unexpected exit code usually hints at a bug in the test suite!"
-        ask_results
         exit 2
     fi