Merge remote-tracking branch 'upstream/master' into separated-checks

Author: terhorstd

Diff for: .github/workflows/nestbuildmatrix.yml

@@ -438,14 +438,14 @@ jobs:
           # --force-reinstall required to ensure executable is linked from bin dir in PATH
           python -m pip install --force-reinstall clang-format==13.0
           python -c "import setuptools; print('package location:', setuptools.__file__)"
-          python -m pip install --force-reinstall --upgrade scipy numpy pytest pytest-timeout pytest-xdist mpi4py cython matplotlib terminaltables pandoc 'junitparser>=2'
+          python -m pip install --force-reinstall --upgrade scipy 'junitparser>=2' numpy pytest pytest-timeout pytest-xdist mpi4py cython matplotlib terminaltables pandoc pandas
           python -c "import pytest; print('package location:', pytest.__file__)"
           pip list
 
       - name: "Find changed files"
         run: |
           echo "CHANGED_FILES<<EOF" >> $GITHUB_ENV
-          echo "$(git diff --name-only ${{ github.event.before }}..${{ github.event.after }})" >> $GITHUB_ENV
+          echo "$(git diff --name-only ${{ github.event.pull_request.base.sha }}..${{ github.event.after }})" >> $GITHUB_ENV
           echo 'EOF' >> $GITHUB_ENV
           echo "GITHUB_ENV = $GITHUB_ENV"
           cat $GITHUB_ENV
@@ -557,7 +557,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           python -c "import setuptools; print('package location:', setuptools.__file__)"
-          python -m pip install --force-reinstall --upgrade scipy 'junitparser>=2' numpy pytest pytest-timeout pytest-xdist mpi4py cython matplotlib terminaltables pandoc
+          python -m pip install --force-reinstall --upgrade scipy 'junitparser>=2' numpy pytest pytest-timeout pytest-xdist mpi4py cython matplotlib terminaltables pandoc pandas
           python -c "import pytest; print('package location:', pytest.__file__)"
           pip list
 
@@ -647,7 +647,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           python -c "import setuptools; print('package location:', setuptools.__file__)"
-          python -m pip install --force-reinstall --upgrade scipy 'junitparser>=2' numpy pytest pytest-timeout pytest-xdist mpi4py cython matplotlib terminaltables pandoc
+          python -m pip install --force-reinstall --upgrade scipy 'junitparser>=2' numpy pytest pytest-timeout pytest-xdist mpi4py cython matplotlib terminaltables pandoc pandas
           python -c "import pytest; print('package location:', pytest.__file__)"
           pip list
 

Diff for: .gitignore

@@ -32,8 +32,6 @@ cmake_install.cmake
 CMakeDoxygenDefaults.cmake
 
 # generated files
-doc/fulldoc.conf
-doc/normaldoc.conf
 bin/nest-config
 bin/nest_vars.sh
 libnestutil/config.h

Diff for: CMakeLists.txt

@@ -82,6 +82,10 @@ set( with-includes OFF CACHE STRING "Add additional include paths [default=OFF].
 set( with-defines OFF CACHE STRING "Additional defines, e.g. '-DXYZ=1' [default=OFF]. Separate multiple defines by ';'." )
 set( with-version-suffix "" CACHE STRING "Set a user defined version suffix [default='']." )
 
+# documentation build configuration
+set( with-userdoc OFF CACHE STRING "Build user documentation [default=OFF]")
+set( with-devdoc OFF CACHE STRING "Build developer documentation [default=OFF]")
+
 ################################################################################
 ##################      Project Directory variables           ##################
 ################################################################################
@@ -96,13 +100,6 @@ set( CMAKE_INSTALL_DATADIR "share/${PROJECT_NAME}" CACHE STRING "Relative direct
 ##################           Find utility programs            ##################
 ################################################################################
 
-# needed for pynest test suite
-if ( ${with-python} STREQUAL "ON" )
-  find_program( NOSETESTS NAMES nosetests )
-endif ()
-
-# needed for target doc and fulldoc
-find_package( Doxygen )
 find_program( SED NAMES sed gsed )
 
 ################################################################################
@@ -156,6 +153,8 @@ nest_process_with_mpi4py()
 nest_process_with_boost()
 nest_process_target_bits_split()
 nest_process_version_suffix()
+nest_process_userdoc()
+nest_process_devdoc()
 
 nest_get_color_flags()
 set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${NEST_C_COLOR_FLAGS}" )
@@ -344,11 +343,6 @@ configure_file(
     "${PROJECT_BINARY_DIR}/bin/nest_vars.sh" @ONLY
 )
 
-configure_file(
-    "${PROJECT_SOURCE_DIR}/doc/normaldoc.conf.in"
-    "${PROJECT_BINARY_DIR}/doc/normaldoc.conf" @ONLY
-)
-
 configure_file(
     "${PROJECT_SOURCE_DIR}/doc/fulldoc.conf.in"
     "${PROJECT_BINARY_DIR}/doc/fulldoc.conf" @ONLY
@@ -368,8 +362,4 @@ install( FILES LICENSE README.md
     DESTINATION ${CMAKE_INSTALL_DOCDIR}
     )
 
-add_custom_target( install-nodoc
-  COMMAND $(MAKE) NEST_INSTALL_NODOC=true install
-)
-
 nest_print_config_summary()

Diff for: CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contribute to NEST
 
-The NEST simulator is a scientific tool and as such it is never finished and constantly changing to meet the needs of novel neuroscientific endeavors. Here you find the most important information on how you can contribute to NEST. This document is an excerpt from our [Contributing to NEST documentation](https://nest-simulator.readthedocs.io/en/latest/contribute/index.html), which provides more detailed information.
+The NEST Simulator is a scientific tool and as such it is never finished and constantly changing to meet the needs of novel neuroscientific endeavors. Here you find the most important information on how you can contribute to NEST. This document is an excerpt from our [Contributing to NEST documentation](https://nest-simulator.readthedocs.io/en/latest/contribute/index.html), which provides more detailed information.
 
 
 * Make sure you have a [GitHub account](https://github.com/signup/free)

Diff for: SECURITY.md

@@ -1,7 +1,7 @@
 
 # Security Policy
 
-The NEST simulator is research oriented software and as such is expected to
+The NEST Simulator is research oriented software and as such is expected to
 run mainly in well protected environments. In case it is found that this
 software can be used to violate security mechanisms, developers will try to
 provide patches that mitigate the risk of this misuse.

Diff for: bin/nest-config.in

@@ -16,6 +16,8 @@ Known values for OPTION are:
   --cflags              print pre-processor and compiler flags
   --includes            print includes
   --compiler            print the compiler used to compile NEST
+  --compiler-name       Print the compiler name used to compile NEST
+  --compiler-version    Print the compiler version used to compile NEST
   --python-executable   print full path to Python interpreter used
   --python-version      print Python version string for interpreter
   --static-libraries    print "ON" if configured for static libraries, "OFF" otherwise
@@ -71,6 +73,12 @@ while test $# -gt 0; do
     --compiler)
         echo "@CMAKE_CXX_COMPILER@"
         ;;
+    --compiler-name)
+        echo "@CMAKE_CXX_COMPILER_ID@"
+        ;;
+    --compiler-version)
+        echo "@CMAKE_CXX_COMPILER_VERSION@"
+        ;;
     --python-executable)
         echo "@Python_EXECUTABLE@"
         ;;

Diff for: build_support/check_code_style.sh

@@ -28,13 +28,11 @@ unset FILE_TO_BE_CHECKED
 GIT_START_SHA=master             # If 'file=' is not specified all changed files in the commit range
 GIT_END_SHA=HEAD                 # '<master>..<HEAD>' are processed.
 
-VERA=vera++                      # The names of the static code analysis tools executables.
 CPPCHECK=cppcheck                # CPPCHECK version 1.69 or later is required!
 CLANG_FORMAT=clang-format        # CLANG-FORMAT version 13 is required!
 PEP8=pycodestyle
 PYCODESTYLE_IGNORES="E121,E123,E126,E226,E24,E704,W503,W504"
 
-PERFORM_VERA=true                # Perform VERA++ analysis.
 PERFORM_CPPCHECK=false           # Skip CPPCHECK analysis.
 PERFORM_CLANG_FORMAT=true        # Perform CLANG-FORMAT analysis.
 PERFORM_PEP8=true                # Perform PEP8 analysis.
@@ -103,9 +101,6 @@ Options:
     --git-end=Git_SHA_value          Hash value (Git SHA) at which Git ends the diff.
                                      Default: --git-start=HEAD
 
-    --vera++=exe                     The name of the VERA++ executable.
-                                     Default: --vera++=vera++
-
     --cppcheck=exe                   The name of the CPPCHECK executable.
                                      Default: --cppcheck=cppcheck
                                      Note: CPPCHECK version 1.69 or later is required.
@@ -119,9 +114,6 @@ Options:
     --pep8=exe                       The name of the PEP8 executable.
                                      Default: --pep8=pycodestyle
 
-    --perform-vera=on/off            Turn on/off VERA++ analysis.
-                                     Default: --perform-vera=on
-
     --perform-cppcheck=on/off        Turn on/off CPPCHECK analysis.
                                      Default: --perform-cppcheck=off
 
@@ -164,9 +156,6 @@ while test $# -gt 0 ; do
       --git-end=*)
           GIT_END_SHA="$( echo "$1" | sed 's/^--git-end=//' )"
           ;;
-      --vera++=*)
-          VERA="$( echo "$1" | sed 's/^--vera++=//' )"
-          ;;
       --cppcheck=*)
           CPPCHECK="$( echo "$1" | sed 's/^--cppcheck=//' )"
           ;;
@@ -176,20 +165,6 @@ while test $# -gt 0 ; do
       --pep8=*)
           PEP8="$( echo "$1" | sed 's/^--pep8=//' )"
           ;;
-      --perform-vera=*)
-          value="$( echo "$1" | sed 's/^--perform-vera=//' )"
-          case "$value" in
-            on)
-                PERFORM_VERA=true
-            ;;
-            off)
-                PERFORM_VERA=false
-            ;;
-            *)
-                error_unknown_option "$1"
-            ;;
-          esac
-          ;;
       --perform-cppcheck=*)
           value="$( echo "$1" | sed 's/^--perform-cppcheck=//' )"
           case "$value" in
@@ -239,7 +214,7 @@ while test $# -gt 0 ; do
   shift
 done
 
-if ! $PERFORM_VERA && ! $PERFORM_CPPCHECK && ! $PERFORM_CLANG_FORMAT && ! $PERFORM_PEP8; then
+if ! $PERFORM_CPPCHECK && ! $PERFORM_CLANG_FORMAT && ! $PERFORM_PEP8; then
   error_no_analysis
 fi
 
@@ -248,13 +223,6 @@ fi
 EXTENDED_REGEX_PARAM=r
 /bin/sh -c "echo 'hello' | sed -${EXTENDED_REGEX_PARAM} 's/[aeou]/_/g' "  >/dev/null 2>&1 || EXTENDED_REGEX_PARAM=E
 
-# Verify the VERA++ installation.
-if $PERFORM_VERA; then
-  $VERA ./nest/main.cpp >/dev/null 2>&1 || error_exit "Failed to verify the VERA++ installation. Executable: $VERA"
-  $VERA --profile nest ./nest/main.cpp >/dev/null 2>&1 || error_exit \
-  "Failed to verify the VERA++ installation. The profile 'nest' could not be found. See https://nest-simulator.readthedocs.io/en/latest/contribute/coding_guidelines_cpp.html#vera-profile-nest"
-fi
-
 # Verify the CPPCHECK installation. CPPCHECK version 1.69 or later is required.
 # Previous versions of CPPCHECK halted on sli/tokenutils.cc (see https://github.com/nest/nest-simulator/pull/79)
 if $PERFORM_CPPCHECK; then
@@ -303,15 +271,14 @@ fi
 RUNS_ON_CI=false
 
 unset NEST_VPATH               # These command line arguments are placeholders and not required here.
-IGNORE_MSG_VERA=false          # They are needed when running the static code analysis script within
 IGNORE_MSG_CPPCHECK=false      # the CI build environment.
 IGNORE_MSG_CLANG_FORMAT=false
 IGNORE_MSG_PYCODESTYLE=false
 
 ./build_support/static_code_analysis.sh "$RUNS_ON_CI" "$INCREMENTAL" "$file_names" "$NEST_VPATH" \
-"$VERA" "$CPPCHECK" "$CLANG_FORMAT" "$PEP8" \
-"$PERFORM_VERA" "$PERFORM_CPPCHECK" "$PERFORM_CLANG_FORMAT" "$PERFORM_PEP8" \
-"$IGNORE_MSG_VERA" "$IGNORE_MSG_CPPCHECK" "$IGNORE_MSG_CLANG_FORMAT" "$IGNORE_MSG_PYCODESTYLE" \
+"$CPPCHECK" "$CLANG_FORMAT" "$PEP8" \
+"$PERFORM_CPPCHECK" "$PERFORM_CLANG_FORMAT" "$PERFORM_PEP8" \
+"$IGNORE_MSG_CPPCHECK" "$IGNORE_MSG_CLANG_FORMAT" "$IGNORE_MSG_PYCODESTYLE" \
 "$PYCODESTYLE_IGNORES"
 if [ $? -gt 0 ]; then
     exit $?

Diff for: build_support/ci_build.sh

@@ -45,7 +45,7 @@ if [ "$xNEST_BUILD_TYPE" = "STATIC_CODE_ANALYSIS" ]; then
     echo "+               S T A T I C   C O D E   A N A L Y S I S                       +"
     echo "+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +"
 
-    echo "MSGBLD0010: Initializing VERA++ static code analysis."
+    echo "MSGBLD0010: Initializing static code analysis."
     export PYTHON_EXECUTABLE="$(which python3)"
     export PYTHON_INCLUDE_DIR="`python3 -c "import sysconfig; print(sysconfig.get_path('include'))"`"
     export PYLIB_BASE="lib`basename $PYTHON_INCLUDE_DIR`"
@@ -54,9 +54,6 @@ if [ "$xNEST_BUILD_TYPE" = "STATIC_CODE_ANALYSIS" ]; then
     echo "--> Detected PYTHON_LIBRARY=$PYTHON_LIBRARY"
     echo "--> Detected PYTHON_INCLUDE_DIR=$PYTHON_INCLUDE_DIR"
     CONFIGURE_PYTHON="-DPYTHON_EXECUTABLE=$PYTHON_EXECUTABLE -DPYTHON_LIBRARY=$PYTHON_LIBRARY -DPYTHON_INCLUDE_DIR=$PYTHON_INCLUDE_DIR"
-    # Add the NEST profile to the VERA++ profiles.
-    sudo cp build_support/vera++.profile /usr/lib/vera++/profiles/nest
-    echo "MSGBLD0020: VERA++ initialization completed."
     if [ ! -f "$HOME/.cache/bin/cppcheck" ]; then
         echo "MSGBLD0030: Installing CPPCHECK version 1.69."
         # Build cppcheck version 1.69
@@ -92,21 +89,18 @@ if [ "$xNEST_BUILD_TYPE" = "STATIC_CODE_ANALYSIS" ]; then
     # Set the command line arguments for the static code analysis script and execute it.
 
     # The names of the static code analysis tools executables.
-    VERA=vera++
     CPPCHECK=cppcheck
     CLANG_FORMAT=clang-format
     PEP8=pycodestyle
     PYCODESTYLE_IGNORES="E121,E123,E126,E226,E24,E704,W503,W504"
 
     # Perform or skip a certain analysis.
-    PERFORM_VERA=true
     PERFORM_CPPCHECK=true
     PERFORM_CLANG_FORMAT=true
     PERFORM_PEP8=true
 
     # The following command line parameters indicate whether static code analysis error messages
     # will cause the CI build to fail or are ignored.
-    IGNORE_MSG_VERA=false
     IGNORE_MSG_CPPCHECK=true
     IGNORE_MSG_CLANG_FORMAT=false
     IGNORE_MSG_PYCODESTYLE=false
@@ -117,9 +111,9 @@ if [ "$xNEST_BUILD_TYPE" = "STATIC_CODE_ANALYSIS" ]; then
 
     chmod +x build_support/static_code_analysis.sh
     ./build_support/static_code_analysis.sh "$RUNS_ON_CI" "$INCREMENTAL" "$file_names" "$NEST_VPATH" \
-    "$VERA" "$CPPCHECK" "$CLANG_FORMAT" "$PEP8" \
-    "$PERFORM_VERA" "$PERFORM_CPPCHECK" "$PERFORM_CLANG_FORMAT" "$PERFORM_PEP8" \
-    "$IGNORE_MSG_VERA" "$IGNORE_MSG_CPPCHECK" "$IGNORE_MSG_CLANG_FORMAT" "$IGNORE_MSG_PYCODESTYLE" \
+    "$CPPCHECK" "$CLANG_FORMAT" "$PEP8" \
+    "$PERFORM_CPPCHECK" "$PERFORM_CLANG_FORMAT" "$PERFORM_PEP8" \
+    "$IGNORE_MSG_CPPCHECK" "$IGNORE_MSG_CLANG_FORMAT" "$IGNORE_MSG_PYCODESTYLE" \
     "$PYCODESTYLE_IGNORES"
 
     exit $?
@@ -291,6 +285,7 @@ echo "MSGBLD0236: $(pwd)\$ cmake \
     -DCMAKE_CXX_FLAGS=\"$CXX_FLAGS\" \
     -Dwith-optimize=ON \
     -Dwith-warning=ON \
+    -Dwith-userdoc=OFF \
     $CONFIGURE_BOOST \
     $CONFIGURE_OPENMP \
     $CONFIGURE_MPI \