Add shellcheck and pre-commit to CI jobs

.cppcheck_suppressions

@@ -34,4 +34,3 @@ duplicateCondition:./
 nullPointer:./
 missingInclude:./
 uninitvar:./
-

.github/ISSUE_TEMPLATE/bug_report.md

@@ -31,7 +31,7 @@ If applicable, add screenshots to help explain your problem.
  - NEST-Version: [e.g. nest-2.18, or git hash]
  - Installation: [e.g. conda packet, apt, with/out MPI, ...]
    (in case you compiled the source code manually, provide the
-    "Installation Summary" that you see at the end of the 
+    "Installation Summary" that you see at the end of the
     cmake step)
 
 **Additional context**

.github/styles/nest-styles/Ampersands.yml

@@ -5,4 +5,3 @@ level: warning
 nonword: true
 tokens:
   - '\w+\s&\s\w+'
-

.github/styles/nest-styles/Annotations.yml

@@ -8,4 +8,3 @@ tokens:
   - FIXME
   - TODO
   - NOTE
-

.github/styles/nest-styles/Capitalization.yml

@@ -4,4 +4,3 @@ message: "'%s' should be in sentence case"
 level: warning
 scope: heading
 match: $sentence
-

.github/styles/nest-styles/CommasPerSentence.yml

@@ -4,4 +4,3 @@ extends: occurrence
 scope: sentence
 max: 3
 token: ','
-

.github/styles/nest-styles/ComplexWords.yml

@@ -118,4 +118,3 @@ swap:
   transmit: "'send'"
   utilization: "'use'"
   utilize: "'use'"
-

.github/styles/nest-styles/ListCapitalize.yml

@@ -6,4 +6,3 @@ scope: list
 nonword: true
 tokens:
   - '^[a-z].+'
-

.github/styles/nest-styles/Negative.yml

@@ -9,4 +9,3 @@ tokens:
   - don't
   - doesn't
   - hasn't
-

.github/styles/nest-styles/NotEasy.yml

@@ -8,4 +8,3 @@ tokens:
   - just
   - easily
   - simply
-

.github/styles/nest-styles/ParagraphLength.yml

@@ -5,4 +5,3 @@ scope: paragraph.rst
 level: suggestion
 max: 150
 token: \b(\w+)\b
-

.github/styles/nest-styles/PassiveVoice.yml

@@ -182,4 +182,3 @@ tokens:
   - woven
   - written
   - wrung
-

.github/styles/nest-styles/Pronouns.yml

@@ -13,4 +13,3 @@ tokens:
   - hers
   - himself
   - herself
-

.github/styles/nest-styles/SentenceLength.yml

@@ -5,4 +5,3 @@ scope: sentence
 level: suggestion
 max: 25
 token: \b(\w+)\b
-

.github/styles/nest-styles/Slash.yml

@@ -5,4 +5,3 @@ ignorecase: true
 level: error
 tokens:
   - '\w+/\w+'
-

.github/styles/nest-styles/Spelling.yml

@@ -4,4 +4,3 @@ message: "Did you really mean '%s'?"
 level: error
 ignore:
   - vocab.txt
-

.github/styles/nest-styles/Units.yml

@@ -4,4 +4,3 @@ message: "Add a space between a numeral and a unit of measure."
 level: error
 tokens:
   - '\d+(?:MB|Gbit|GB|kbps|KB|kb)'
-

.github/styles/nest-styles/Wordiness.yml

@@ -118,4 +118,3 @@ swap:
   with regard to: regarding
   with respect to: about or on
   with the exception of: except for
-

.github/workflows/nestbuildmatrix.yml

@@ -33,6 +33,63 @@ jobs:
           files=$(find . \( -iname "*.h" -o -iname "*.c" -o -iname "*.cc" -o -iname "*.cpp" \) -not -path "./thirdparty/*")
           diff -u <(cat ${files}) <(clang-format ${files})
 
+  shellcheck:
+    runs-on: "ubuntu-20.04"
+    steps:
+      - name: "Checkout repository content"
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        with:
+          fetch-depth: 0
+
+      - name: "Install Linux system dependencies"
+        run: |
+          sudo apt-get update
+          sudo apt-get install shellcheck
+
+      - name: "Run shellcheck..."
+        run: |
+          shellcheck --version
+          find . -iname "*.sh" -o -iname "*.sh.in" | xargs shellcheck
+
+  pre-commit-hooks:
+    runs-on: "ubuntu-20.04"
+    steps:
+      - name: "Checkout repository content"
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        with:
+          fetch-depth: 0
+
+      - name: "Set up Python 3.x"
+        uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # v4.7.0
+        with:
+          python-version: 3.9
+
+      - name: "Install dependencies"
+        run: |
+          pip install pre-commit
+
+      - name: "Run pre-commit checks..."
+        run: |
+          pre-commit run --all-files
+
+  no-crlf:
+    # While pre-commit-hook mixed-line-endings could check for this, it would
+    # be incompatible with "git smudge", as users may decide to use any
+    # formatting in their editor consistently.
+    # https://github.com/pre-commit/pre-commit-hooks?tab=readme-ov-file#mixed-line-ending
+    #
+    # This check makes sure the files in the repository are always consistent
+    # in their line endings, i.e. new line, and not carriage return+line feed.
+    runs-on: "ubuntu-20.04"
+    steps:
+      - name: "Checkout repository content"
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        with:
+          fetch-depth: 0
+
+      - name: "Check all files for broken line endings…"
+        run: '! find . -not -type d -exec file "{}" ";" | grep CRLF'
+
   cppcheck:
     runs-on: "ubuntu-22.04"
     steps:
@@ -509,7 +566,7 @@ jobs:
   build_linux:
     if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
     runs-on: ${{ matrix.os }}
-    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8]
+    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8, shellcheck, pre-commit-hooks, cppcheck, no-crlf]
     env:
       CXX_FLAGS: "-pedantic -Wextra -Woverloaded-virtual -Wno-unknown-pragmas"
       NEST_VPATH: "build"
@@ -654,7 +711,7 @@ jobs:
           CMAKE_C_COMPILER_LAUNCHER: ccache
           CMAKE_CXX_COMPILER_LAUNCHER: ccache
         run: |
-          mkdir -p "$NEST_VPATH/reports" "$NEST_RESULT"
+          mkdir -pv "$NEST_VPATH/reports" "$NEST_RESULT"
 
           if [ "$xNEST_BUILD_COMPILER" = "CLANG" ]; then
               export CC=clang-11
@@ -676,9 +733,9 @@ jobs:
               -Dwith-ltdl=${{ contains(matrix.use, 'ltdl') && 'ON' || 'OFF' }} \
               -Dwith-readline=${{ contains(matrix.use, 'readline') && 'ON' || 'OFF' }} \
               -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
-              -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
-              -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
-              -Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' || 'OFF' }} \
+              -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && "{$HOME}/.cache/sionlib.install" || 'OFF' }} \
+              -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && "${HOME}/.cache/libneurosim.install" || 'OFF' }} \
+              -Dwith-music=${{ contains(matrix.use, 'music') && "${HOME}/.cache/music.install" || 'OFF' }} \
               ..
 
       - name: "Add GCC problem matcher"
@@ -703,7 +760,7 @@ jobs:
       - name: "Initialize Matplotlibrc"
         run: |
           # initialize matplotlib backend
-          mkdir -p $HOME/.matplotlib
+          mkdir -pv $HOME/.matplotlib
           echo "backend : svg" > $HOME/.matplotlib/matplotlibrc
 
       - name: "Run NEST testsuite"
@@ -727,7 +784,7 @@ jobs:
   build_macos:
     if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
     runs-on: ${{ matrix.os }}
-    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8]
+    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8, shellcheck, pre-commit-hooks, cppcheck, no-crlf]
     env:
       CXX_FLAGS: "-pedantic -Wextra -Woverloaded-virtual -Wno-unknown-pragmas"
       NEST_VPATH: "build"
@@ -789,7 +846,7 @@ jobs:
 
       - name: "Configure NEST build"
         run: |
-          mkdir -p "$NEST_VPATH/reports" "$NEST_RESULT"
+          mkdir -pv "$NEST_VPATH/reports" "$NEST_RESULT"
 
           cd "$NEST_VPATH"
           cmake \
@@ -832,7 +889,7 @@ jobs:
       - name: "Initialize Matplotlibrc"
         run: |
           # initialize matplotlib backend
-          mkdir -p $HOME/.matplotlib
+          mkdir -pv $HOME/.matplotlib
           echo "backend : svg" > $HOME/.matplotlib/matplotlibrc
 
       - name: "Run NEST testsuite"

.pre-commit-config.yaml

@@ -1,35 +1,44 @@
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
-    hooks:
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-      - id: check-yaml
-
-  - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.16.3
-    hooks:
-      - id: gitleaks
-
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: ["--profile", "black", "--thirdparty", "nest"]
-
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
-    hooks:
-      - id: black
-        language_version: python3
-
-  - repo: https://github.com/koalaman/shellcheck-precommit
-    rev: v0.9.0
-    hooks:
-      - id: shellcheck
-
-  - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v17.0.4
-    hooks:
-      - id: clang-format
-        types_or: [c++]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: forbid-submodules
+      - id: mixed-line-ending
+      - id: fix-byte-order-marker
+
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.16.3
+    hooks:
+      - id: gitleaks
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--thirdparty", "nest"]
+
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+        language_version: python3
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+        # explicitly add input files that are not "*.sh"
+        args: [ # note that these differ from arguments in .github/workflows/nestbuildmatrix.yml
+          "bin/nest_vars.sh.in",   # testsuite/do_tests.sh:112 requires this for `. "${PREFIX}/bin/nest_vars.sh"`
+        ]
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v17.0.4
+    hooks:
+      - id: clang-format
+        types_or: [c++]
+
+exclude: 'build/.*|thirdparty/.*'

CONTRIBUTING.md

@@ -7,12 +7,11 @@ The NEST Simulator is a scientific tool and as such it is never finished and con
 
 
 Visit the [contributing to NEST docs](https://nest-simulator.readthedocs.io/en/latest/developer_space/index.html) for details
-on 
+on
 
 * development workflow
 * reporing bugs and issues
 * making changes to the code or documentation
 * code review policies
 
 and much more!
-

SECURITY.md

@@ -36,4 +36,3 @@ severity and further handling via [Security
 Advisories](https://github.com/nest/nest-simulator/security/advisories)
 or as normal [Issue](https://github.com/nest/nest-simulator/issues) in
 non-critical cases.
-

bin/nest-config.in

@@ -29,31 +29,32 @@ Known values for OPTION are:
 
 EOF
 
-    exit $1
+    exit "${1}"
 }
 
 if test $# -eq 0; then
     usage 1
 fi
 
-cflags=false
-libs=false
-
 while test $# -gt 0; do
     case "$1" in
-    -*=*) optarg=`echo "$1" | sed 's/[-_a-zA-Z0-9]*=//'` ;;
-    *) optarg= ;;
+    -*=*)
+        optarg="$(echo "$1" | sed 's/[-_a-zA-Z0-9]*=//')"
+        ;;
+    *)
+        optarg=
+        ;;
     esac
 
     case "$1" in
     --prefix=*)
-        prefix=$optarg
+        prefix="${optarg}"
         ;;
     --prefix)
-        echo $prefix
+        echo "${prefix}"
         ;;
     --exec-prefix)
-        echo $exec_prefix
+        echo "${exec_prefix}"
         ;;
     --version)
         echo "@NEST_VERSION@"
@@ -68,7 +69,7 @@ while test $# -gt 0; do
         echo "@ALL_CXXFLAGS@"
         ;;
     --libs)
-        echo "-L$prefix/@CMAKE_INSTALL_LIBDIR@/nest @MODULE_LINK_LIBS@"
+        echo "-L${prefix}/@CMAKE_INSTALL_LIBDIR@/nest @MODULE_LINK_LIBS@"
         ;;
     --compiler)
         echo "@CMAKE_CXX_COMPILER@"
@@ -99,8 +100,7 @@ while test $# -gt 0; do
         echo "@CMAKE_INSTALL_LIBDIR@"
         ;;
     *)
-        usage
-        exit 1
+        usage 1
         ;;
     esac
     shift