Use POSIX syntax

Reduce bashisms. Downgrade shebangs from Bash to Dash (sh) in
POSIX-compliant shell scripts. Use the most portable shebang
(`#!/usr/bin/env <shell>`) to include the user $PATH in the
search path.

maintainer/CI/build_cmake.sh

@@ -7,8 +7,7 @@
 # notice and this notice are preserved. This file is offered as-is,
 # without any warranty.
 
-abort()
-{
+abort() {
  echo "An error occurred. Exiting..." >&2
  echo "Command that failed: ${BASH_COMMAND}" >&2
  exit 1
@@ -20,29 +19,29 @@ set -e
 # HELPER FUNCTIONS
 
 # output value of env variables
-function outp {
+outp() {
  for p in ${*}; do
  echo " ${p}=${!p}"
  done
 }
 
 # start a block
-function start {
+start() {
  echo "=================================================="
  echo "START ${1}"
  echo "=================================================="
 }
 
 # end a block
-function end {
+end() {
  echo "=================================================="
  echo "END ${1}"
  echo "=================================================="
 }
 
 # set a default value to empty environment variables
 # cast boolean values to true/false
-function set_default_value {
+set_default_value() {
  if [ "${#}" != 2 ]; then
  echo "set_default_value() takes 2 arguments (varname, default), got ${#}"
  exit 1
@@ -127,7 +126,7 @@ if [ -z "${cxx_flags}" ]; then
 fi
 
 if [ "${with_coverage}" = true ]; then
- bash <(curl -s https://codecov.io/env) &> /dev/null
+ bash <(curl -s https://codecov.io/env) 1>/dev/null 2>&1
 fi
 
 cmake_params="-DCMAKE_BUILD_TYPE=${build_type} -DWARNINGS_ARE_ERRORS=ON -DTEST_NP:INT=${check_procs} ${cmake_params}"
@@ -176,8 +175,8 @@ fi
 
 # load MPI module if necessary
 if [ -f "/etc/os-release" ]; then
- grep -q suse /etc/os-release && source /etc/profile.d/modules.sh && module load gnu-openmpi
- grep -q 'rhel\|fedora' /etc/os-release && for f in /etc/profile.d/*module*.sh; do source "${f}"; done && module load mpi
+ grep -q suse /etc/os-release && . /etc/profile.d/modules.sh && module load gnu-openmpi
+ grep -q 'rhel\|fedora' /etc/os-release && for f in /etc/profile.d/*module*.sh; do . "${f}"; done && module load mpi
 fi
 
 # CONFIGURE

maintainer/CI/dox_warnings.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 # Copyright (C) 2019 The ESPResSo project
 #
 # This file is part of ESPResSo.

maintainer/benchmarks/suite.sh

@@ -49,15 +49,15 @@ mkdir "${build_dir}"
 cd "${build_dir}"
 
 # check for unstaged changes
-if [ "$(git diff-index HEAD -- ${directories})" ]; then
+if [ ! -z "$(git status --porcelain -- ${directories})" ]; then
  echo "fatal: you have unstaged changes, please commit or stash them:"
  git diff-index --name-only HEAD -- ${directories}
  exit 1
 fi
 
 cleanup() {
  # restore files in source directory
- git checkout HEAD ${directories}
+ git checkout HEAD -- ${directories}
 }
 
 # prepare output files
@@ -69,7 +69,7 @@ EOF
 # run benchmarks
 for commit in ${commits}; do
  echo "### commit ${commit}" >> benchmarks.log
- git checkout ${commit} ${directories}
+ git checkout ${commit} -- ${directories}
  bash ../maintainer/benchmarks/runner.sh
  sed -ri "s/^/\"${commit}\",/" benchmarks.csv
  tail -n +2 benchmarks.csv >> benchmarks_suite.csv

maintainer/find_missing_header.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 # Copyright (C) 2012-2019 The ESPResSo project
 # Copyright (C) 2012 Olaf Lenz
 #

maintainer/gh_close_issue.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 # Copyright (C) 2019 The ESPResSo project
 #
 # This file is part of ESPResSo.

maintainer/gh_create_issue.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 # Copyright (C) 2019 The ESPResSo project
 #
 # This file is part of ESPResSo.

maintainer/gh_post_status.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 # Copyright (C) 2017,2019 The ESPResSo project
 #
 # This file is part of ESPResSo.

maintainer/missing_tests.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 # Copyright (C) 2017-2019 The ESPResSo project
 #
 # This file is part of ESPResSo.
@@ -18,14 +18,14 @@
 
 
 # Detect python tests that are not included in CMakeLists.txt. Run this script
-# in the folders for python, sample, tutorial and benchmark testsuite folders.
+# in the testsuite folders for python, sample, tutorial and benchmark tests.
 
 for T in *.py; do
  if grep -qF " ${T}" CMakeLists.txt; then
  continue
  else
- GIT_STATUS=$(git status --porcelain -- "${T}")
- if [[ ${GIT_STATUS} == ??* ]]; then
+ tracked_status=$(git ls-files -- "${T}")
+ if [ -z "${tracked_status}" ]; then
  echo "File '${T}' is not tracked."
  continue
  else

src/python/pypresso.cmakein

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/usr/bin/env sh
 # Copyright (C) 2010-2019 The ESPResSo project
 # 
 # Copying and distribution of this file, with or without modification,

testsuite/cmake/BashUnitTests.sh

@@ -107,7 +107,7 @@
 
 ## @brief Print message to stderr
 ## @param $1 Message to display
-function stderr() {
+stderr() {
  local message=$1
  echo "${message}" 1>&2
 }
@@ -116,7 +116,7 @@ function stderr() {
 ##
 ## If functions named `test_*` are already declared in the current environment,
 ## stop unit testing now. We don't want to run them and create side effects.
-function check_namespace() {
+check_namespace() {
  if [ ! -z "$(declare -F | sed -r 's/declare +-f +//' | grep -P '^test_')" ]; then
  stderr 'Functions named test_* already exist:'
  for test in $(declare -F | sed -r 's/declare +-f +//' | grep -P "^test_"); do
@@ -148,7 +148,7 @@ check_namespace
 ## variables](https://www.open-mpi.org/faq/?category=running#mpi-environmental-variables)
 ## that can easily be checked for.
 ## @returns 1 if MPI is used, 0 otherwise
-function detect_open_mpi() {
+detect_open_mpi() {
  if [ -z "${OMPI_COMM_WORLD_SIZE}" ] && [ -z "${OMPI_COMM_WORLD_RANK}" ] \
  && [ -z "${OMPI_COMM_WORLD_LOCAL_RANK}" ] && [ -z "${OMPI_UNIVERSE_SIZE}" ] \
  && [ -z "${OMPI_COMM_WORLD_LOCAL_SIZE}" ] && [ -z "${OMPI_COMM_WORLD_NODE_RANK}" ]; then
@@ -164,7 +164,7 @@ function detect_open_mpi() {
 ##
 ## @param $@ Command to run, possibly with modifiers
 ## @returns Error code returned by the command
-function try_catch() {
+try_catch() {
  detect_open_mpi || return 1
  (
  set -e # exit from current subshell on first error
@@ -178,7 +178,7 @@ function try_catch() {
 ## Run a command in a subshell, exiting the subshell on first error.
 ## @param $@ Command to run, possibly with modifiers
 ## @returns Error code returned by the command
-function try_catch_silent() {
+try_catch_silent() {
  detect_open_mpi || return 1
  (
  set -e # exit from current subshell on first error
@@ -193,7 +193,7 @@ function try_catch_silent() {
 ## logging stdout/stderr to the temporary file at #TMPNAME.
 ## @param $@ Command to run, possibly with modifiers
 ## @returns Error code returned by the command
-function try_catch_capture_output() {
+try_catch_capture_output() {
  detect_open_mpi || return 1
  rm -f "${TMPNAME}"
  (
@@ -207,7 +207,7 @@ function try_catch_capture_output() {
 
 ## @brief Run the set_up() function if it exists
 ## @returns Error code returned by setUp()
-function run_set_up() {
+run_set_up() {
  if [ "$(type -t set_up)" = "function" ]; then
  try_catch set_up
  local -r retcode=${?}
@@ -222,7 +222,7 @@ function run_set_up() {
 
 ## @brief Run the tear_down() function if it exists
 ## @returns Error code returned by tear_down()
-function run_tear_down() {
+run_tear_down() {
  rm -f "${TMPNAME}"
  if [ "$(type -t tear_down)" = "function" ]; then
  try_catch tear_down
@@ -236,7 +236,7 @@ function run_tear_down() {
 }
 
 ## @brief Run the tests
-function run_tests() {
+run_tests() {
  for test in $(declare -F | sed -r 's/declare +-f +//' | grep -P "^test_"); do
  start_test_block "${test#test_}"
  ${test}
@@ -273,22 +273,22 @@ function start_test_block() {
 ## @brief End a test
 ##
 ## Print a newline character and print all error messages in @ref error_log
-function end_test_block() {
+end_test_block() {
  echo ""
  for (( i=0; i<${#error_log[@]}; i++ )); do
  stderr " ${error_log[i]}"
  done
 }
 
 ## @brief Log a successful assertion
-function log_success() {
+log_success() {
  echo -n '.'
  total_tests=$((total_tests + 1))
 }
 
 ## @brief Log a failed assertion
 ## @param $* Description of the failure
-function log_failure() {
+log_failure() {
  local message="${*}"
  echo -n 'x'
  error_log+=("${message}")
@@ -307,7 +307,7 @@ function log_failure() {
 ## @{
 
 ## @brief Run the setup, tests, teardown
-function run_test_suite() {
+run_test_suite() {
  run_set_up
  run_tests
  run_tear_down
@@ -329,7 +329,7 @@ function run_test_suite() {
 ## @brief Check if a file exists
 ## @param $1 Filepath
 ## @param $2 Message on failure (optional)
-function assert_file_exists() {
+assert_file_exists() {
  local -r filepath="${1}"
  local message="${2}"
  if [ -z "${message}" ]; then
@@ -346,7 +346,7 @@ function assert_file_exists() {
 ## @param $1 Obtained result
 ## @param $2 Expected result
 ## @param $3 Message on failure (optional)
-function assert_string_equal() {
+assert_string_equal() {
  local -r result="${1}"
  local -r expected="${2}"
  local message="${3}"
@@ -364,7 +364,7 @@ function assert_string_equal() {
 ## @param $1 Obtained result
 ## @param $2 Expected result
 ## @param $3 Message on failure (optional)
-function assert_equal() {
+assert_equal() {
  local -r result="${1}"
  local -r expected="${2}"
  local message="${3}"
@@ -381,7 +381,7 @@ function assert_equal() {
 ## @brief Check if a variable is non-zero
 ## @param $1 Obtained result
 ## @param $2 Message on failure (optional)
-function assert_non_zero() {
+assert_non_zero() {
  local -r result="${1}"
  local message="${2}"
  if [ -z "${message}" ]; then
@@ -397,7 +397,7 @@ function assert_non_zero() {
 ## @brief Check if a variable is zero
 ## @param $1 Obtained result
 ## @param $2 Message on failure (optional)
-function assert_zero() {
+assert_zero() {
  local -r result="${1}"
  local message="${2}"
  if [ -z "${message}" ]; then
@@ -414,7 +414,7 @@ function assert_zero() {
 ##
 ## Cannot be used in a script run by Open MPI (see \ref TryCatch).
 ## @param $@ Command to run, possibly with modifiers
-function assert_return_code() {
+assert_return_code() {
  try_catch_capture_output "${@}"
  local -r retcode=${?}
  if [ "${retcode}" -eq "0" ]; then