Merge branch 'master' into add-hpc-docs

jessica-mitchell · Jan 31, 2023 · 94083b2 · 94083b2
2 parents 5d511ad + 4872b8c
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diff --git a/.clang-tidy b/.clang-tidy
@@ -0,0 +1 @@
+Checks: '-*,modernize-use-nullptr,modernize-use-override,bugprone,modernize-redundant-void-arg'
diff --git a/.github/workflows/jsc-push.yml b/.github/workflows/jsc-push.yml
@@ -0,0 +1,25 @@
+name: Mirror to JSC
+
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+  sync_to_jsc:
+    runs-on: ubuntu-latest
+    if: ${{ github.repository_owner == 'nest' }}
+    steps:
+      - name: sycnmaster
+        uses: wei/git-sync@v3
+        with:
+          source_repo: "nest/nest-simulator"
+          source_branch: "master"
+          destination_repo: "https://ghpusher:${{ secrets.JSC_GITLAB_TOKEN }}@gitlab.jsc.fz-juelich.de/nest/nest-simulator.git"
+          destination_branch: "master"
+      - name: synctags
+        uses: wei/git-sync@v3
+        with:
+          source_repo: "nest/nest-simulator"
+          source_branch: "refs/tags/v*"
+          destination_repo: "https://ghpusher:${{ secrets.JSC_GITLAB_TOKEN }}@gitlab.jsc.fz-juelich.de/nest/nest-simulator.git"
+          destination_branch: "refs/tags/v*"
diff --git a/.github/workflows/nestbuildmatrix.yml b/.github/workflows/nestbuildmatrix.yml
@@ -70,14 +70,14 @@ 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 '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
 
       - 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
@@ -171,7 +171,7 @@ 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
 
@@ -245,7 +245,7 @@ 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 --git a/.gitignore b/.gitignore
@@ -14,10 +14,6 @@ pynest/pynestkernel.cxx
 *.o
 *.pyc
 
-Makefile
-
-build/
-install/
 examples/example_logs/
 
 /libnestutil/config.h
@@ -35,8 +31,6 @@ cmake_install.cmake
 CMakeDoxygenDefaults.cmake
 
 # generated files
-doc/fulldoc.conf
-doc/normaldoc.conf
 bin/nest-config
 bin/nest_vars.sh
 libnestutil/config.h

diff --git a/CMakeLists.txt b/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 )
 
 ################################################################################
@@ -131,8 +128,6 @@ get_target_triple( NEST_TARGET_TRIPLE NEST_TARGET_ARCH NEST_TARGET_VENDOR NEST_T
 nest_process_with_python()
 include( GNUInstallDirs )
 nest_post_process_with_python()
-nest_process_with_optimize()
-nest_process_with_debug()
 nest_process_with_std()
 nest_process_with_intel_compiler_flags()
 nest_process_with_warning()
@@ -156,6 +151,14 @@ nest_process_with_mpi4py()
 nest_process_with_boost()
 nest_process_target_bits_split()
 nest_process_version_suffix()
+nest_process_userdoc()
+nest_process_devdoc()
+
+# These two function calls must come last, as to prevent unwanted interactions of the newly set flags
+# with detection/compilation operations carried out in earlier functions. The optimize/debug flags set
+# using these functions should only apply to the compilation of NEST.
+nest_process_with_optimize()
+nest_process_with_debug()
 
 nest_get_color_flags()
 set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${NEST_C_COLOR_FLAGS}" )
@@ -276,10 +279,9 @@ foreach ( def ${SIONLIB_DEFINES} )
     set( ALL_CXXFLAGS "${ALL_CXXFLAGS} ${def}" )
 endforeach ()
 
-# all libraries
-set( ALL_LIBS
+# libraries required to link extension modules
+set( MODULE_LINK_LIBS
   "-lnestutil"
-  "-lnest"
   "-lsli"
   "-lnestkernel"
   "${OpenMP_CXX_FLAGS}"
@@ -293,9 +295,15 @@ set( ALL_LIBS
   "${BOOST_LIBRARIES}" )
 
 if ( with-libraries )
-  set( ALL_LIBS "${ALL_LIBS};${with-libraries}" )
+  set( MODULE_LINK_LIBS "${MODULE_LINK_LIBS};${with-libraries}" )
 endif ()
-string( REPLACE ";" " " ALL_LIBS "${ALL_LIBS}" )
+string( REPLACE ";" " " MODULE_LINK_LIBS "${MODULE_LINK_LIBS}" )
+
+# libraries requied to link NEST
+set( ALL_LIBS
+  "-lnest"
+  ${MODULE_LINK_LIBS} )
+
 
 # all includes
 set( ALL_INCLUDES_tmp
@@ -339,11 +347,6 @@ 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
@@ -363,8 +366,4 @@ 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 --git a/CONTRIBUTING.md b/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 --git a/SECURITY.md b/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 --git a/bin/nest-config.in b/bin/nest-config.in
@@ -12,10 +12,12 @@ Known values for OPTION are:
 
   --prefix              NEST install prefix for architecture-independent files
   --exec-prefix         NEST install prefix for architecture-dependent files
-  --libs                print library linking information
+  --libs                print library linking information for extension modules
   --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
@@ -66,11 +68,17 @@ while test $# -gt 0; do
         echo "@ALL_CXXFLAGS@"
         ;;
     --libs)
-        echo "-L$prefix/@CMAKE_INSTALL_LIBDIR@/nest @ALL_LIBS@"
+        echo "-L$prefix/@CMAKE_INSTALL_LIBDIR@/nest @MODULE_LINK_LIBS@"
         ;;
     --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 --git a/bin/nest-server b/bin/nest-server
@@ -3,7 +3,7 @@
 DAEMON="${NEST_SERVER_DAEMON:-0}"
 HOST="${NEST_SERVER_HOST:-127.0.0.1}"
 LOGFILE="${NEST_SERVER_LOGFILE:-/tmp/nest-server.log}"
-PORT="${NEST_SERVER_PORT:-5000}"
+PORT="${NEST_SERVER_PORT:-52425}"
 STDOUT="${NEST_SERVER_STDOUT:-0}"
 
 usage() {
@@ -22,7 +22,7 @@ usage() {
   echo "  -d                 daemonize the server process"
   echo "  -h <HOST>          use hostname/IP address <HOST> for the server [default: 127.0.0.1]"
   echo "  -o                 print NEST outputs to the console"
-  echo "  -p <PORT>          use port <PORT> for opening the socket [default: 5000]"
+  echo "  -p <PORT>          use port <PORT> for opening the socket [default: 52425]"
 }
 
 log() {

diff --git a/bin/nest-server-mpi b/bin/nest-server-mpi
@@ -9,7 +9,7 @@ Usage:
 Options:
   -h --help     display usage information and exit
   --host HOST   use hostname/IP address HOST for server [default: 127.0.0.1]
-  --port PORT   use port PORT for opening the socket [default: 5000]
+  --port PORT   use port PORT for opening the socket [default: 52425]
 
 """
 
@@ -25,6 +25,10 @@ import sys
 import nest
 import nest.server
 
+import os
+
+HOST = os.getenv("NEST_SERVER_HOST", "127.0.0.1")
+PORT = os.getenv("NEST_SERVER_PORT", "52425")
 
 comm = MPI.COMM_WORLD.Clone()
 rank = comm.Get_rank()
@@ -38,7 +42,7 @@ def log(call_name, msg):
 if rank == 0:
     print("==> Starting NEST Server Master on rank 0", flush=True)
     nest.server.set_mpi_comm(comm)
-    nest.server.run_mpi_app(host=opt['--host'], port=opt['--port'])
+    nest.server.run_mpi_app(host=opt.get('--host', HOST), port=opt.get('--port', PORT))
 
 else:
     print(f"==> Starting NEST Server Worker on rank {rank}", flush=True)

diff --git a/build_support/check_code_style.sh b/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 --git a/build_support/check_copyright_headers.py b/build_support/check_copyright_headers.py
@@ -35,7 +35,7 @@
 printed to stderr using the helper function eprint(). Messages meant
 for the summary at the end of static_code_analysis.sh are printed to
 stdout instead so they can be more easily captured and only printed if
-errors occured.
+errors occurred.
 
 """