Require C++17 (#1893)

* flex: require >= 2.6 to avoid register keyword.
* flex/c++ standard documentation and fixes.
* Use std:: prefix on cout, endl, istream, ostream etc.
* drop gcc5 and gcc6, do not explicitly specify default cmake option values.
* Use newer python patch versions and target macOS 10.14 instead of 10.9.
* Dockerfile: newer flex 
* Dockerfile_gpu: base on `latest-x86_64`

* C++17 in submodules.
  *  Require C++17 in CoreNEURON too -> BlueBrain/CoreNeuron#834.
  *  Require C++17 in InterViews too->  iv#43 & Bump to C++17 iv#44.
  *  Require C++17 in NMODL too -> BlueBrain/nmodl#889 

Co-authored-by: Alexandru Săvulescu <[email protected]>

.clang-format.changes

@@ -1,3 +1,3 @@
 SortIncludes: false
-Standard: c++14
-StatementMacros: [MKDLL, MKDLLdec, MKDLLif, MKDLLvp, MKDLLvpf]
+Standard: c++17
+StatementMacros: [MKDLL, MKDLLdec, MKDLLif, MKDLLvp, MKDLLvpf]

.github/workflows/neuron-ci.yml

@@ -43,12 +43,14 @@ jobs:
       matrix:
         os: [ macOS-10.15, ubuntu-18.04]
         config:
-          - { matrix_eval : "CC=gcc CXX=g++" ,      build_mode: "cmake",      cmake_option: "-DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_CORENEURON=ON" }
-          - { matrix_eval : "CC=gcc-8 CXX=g++-8",   build_mode: "setuptools"  }
-          - { matrix_eval : "CC=gcc-5 CXX=g++-5",   build_mode: "cmake",      cmake_option: "-DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_CORENEURON=ON" }
-          - { matrix_eval : "CC=gcc-6 CXX=g++-6",   build_mode: "cmake",      cmake_option: "-DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_CORENEURON=OFF" }
-          - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "cmake",      cmake_option: "-DNRN_ENABLE_PYTHON=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_CORENEURON=ON" }
-          - { matrix_eval : "CC=gcc-8 CXX=g++-8",   build_mode: "cmake",      python_dynamic : ON }
+        # GitHub Actions's ubuntu-18.04 image should provide g++ versions 9 and
+        # 10 even though those are not available in vanilla Ubuntu 18.04
+          - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "setuptools"}
+          - { matrix_eval : "CC=gcc-8 CXX=g++-8",   build_mode: "cmake"}
+          - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "cmake", python_dynamic: ON}
+          - { matrix_eval : "CC=gcc-7 CXX=g++-7" ,  build_mode: "cmake", cmake_option: "-DNRN_ENABLE_CORENEURON=ON"}
+          - { matrix_eval : "CC=gcc-7 CXX=g++-7",   build_mode: "cmake", cmake_option: "-DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_CORENEURON=ON"}
+          - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", cmake_option: "-DNRN_ENABLE_PYTHON=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_CORENEURON=ON"}
         include:
           - os: ubuntu-22.04
             config:
@@ -79,10 +81,11 @@ jobs:
       - name: Install homebrew packages
         if: startsWith(matrix.os, 'macOS')
         run: |
-          brew install ccache coreutils doxygen mpich ninja xz
+          brew install ccache coreutils doxygen flex mpich ninja xz
           brew unlink mpich
           brew install openmpi
           brew install --cask xquartz
+          echo /usr/local/opt/flex/bin >> $GITHUB_PATH
           # Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
           echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV
           echo CTEST_PARALLEL_LEVEL=3 >> $GITHUB_ENV
@@ -97,7 +100,7 @@ jobs:
             openmpi-bin patchelf
           # The sanitizer builds use ubuntu 22.04
           if [[ "${{matrix.os}}" == "ubuntu-18.04" ]]; then
-            sudo apt-get install g++-5 g++-6 g++-8 g++-9
+            sudo apt-get install g++-7 g++-8
           fi
           # Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
           echo CMAKE_BUILD_PARALLEL_LEVEL=2 >> $GITHUB_ENV
@@ -165,7 +168,7 @@ jobs:
         run:  |
           # OS related
           if [ "$RUNNER_OS" == "Linux" ]; then
-            eval $MATRIX_EVAL;
+            export ${MATRIX_EVAL};
             export SHELL="/bin/bash"
           else
             export CXX=${CXX:-g++};

CMakeLists.txt

@@ -24,7 +24,7 @@ project(
 # =============================================================================
 # CMake common project settings
 # =============================================================================
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
@@ -251,7 +251,7 @@ include(cmake/SanitizerHelper.cmake)
 # Find required packages
 # =============================================================================
 find_package(BISON REQUIRED)
-find_package(FLEX REQUIRED)
+find_package(FLEX 2.6 REQUIRED)
 
 # When shipping the wheels we want to link readline libs statically.
 if(NRN_WHEEL_STATIC_READLINE)

azure-pipelines.yml

@@ -140,19 +140,19 @@ stages:
         matrix:
           Python37:
             python.version: '3.7'
-            python.org.version: '3.7.7'
+            python.org.version: '3.7.9'
             python.installer.name: 'macosx10.9.pkg'
           Python38:
             python.version: '3.8'
-            python.org.version: '3.8.2'
+            python.org.version: '3.8.10'
             python.installer.name: 'macosx10.9.pkg'
           Python39:
             python.version: '3.9'
-            python.org.version: '3.9.0'
+            python.org.version: '3.9.13'
             python.installer.name: 'macosx10.9.pkg'
           Python310:
             python.version: '3.10'
-            python.org.version: '3.10.0'
+            python.org.version: '3.10.5'
             python.installer.name: 'macos11.pkg'
 
       steps:
@@ -186,8 +186,10 @@ stages:
         inputs:
           secureFile: 'readline7.0.tar.gz'
 
+      # 10.14 is required for full C++17 support, see:
+      # https://cibuildwheel.readthedocs.io/en/stable/cpp_standards
       - script: |
-          export MACOSX_DEPLOYMENT_TARGET=10.9
+          export MACOSX_DEPLOYMENT_TARGET=10.14
           export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH
           export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
           export NRN_BUILD_FOR_UPLOAD=1

bin/nrnivmodl_makefile_cmake.in

@@ -65,7 +65,7 @@ endif
 ifeq ($(origin CXX), default)
     CXX = @CMAKE_CXX_COMPILER@
 endif
-CXXFLAGS = @BUILD_TYPE_CXX_FLAGS@ @CMAKE_CXX_FLAGS@ @CMAKE_CXX14_STANDARD_COMPILE_OPTION@
+CXXFLAGS = @BUILD_TYPE_CXX_FLAGS@ @CMAKE_CXX_FLAGS@ @CMAKE_CXX17_STANDARD_COMPILE_OPTION@
 CXXCOMPILE = $(CXX) $(CXXFLAGS) @NRN_COMPILE_DEFS_STRING@ @NRN_COMPILE_FLAGS_STRING@
 CXX_LINK_EXE = $(CXX) $(CXXFLAGS) @CMAKE_EXE_LINKER_FLAGS@ @NRN_LINK_FLAGS_STRING@
 CXX_LINK_SHARED = $(CXX) $(CXXFLAGS) @CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS@ @CMAKE_SHARED_LIBRARY_CXX_FLAGS@ @CMAKE_SHARED_LINKER_FLAGS@

cmake/CompilerHelper.cmake

@@ -54,9 +54,3 @@ else()
   set(USING_PGI_COMPILER_TRUE "#")
   set(USING_PGI_COMPILER_FALSE "")
 endif()
-
-if(CMAKE_CXX_COMPILER_ID MATCHES "PGI")
-  # CMake adds strict standard complaint PGI flag "-A" which breaks compilation of old codes (e.g.
-  # spdlog, fmt)
-  set(CMAKE_CXX14_STANDARD_COMPILE_OPTION --c++14)
-endif()

docs/install/install_instructions.md

@@ -198,8 +198,8 @@ from source.
 In order to build NEURON from source, the following packages must be available:
 
 - Bison
-- Flex
-- C/C++ compiler suite
+- Flex >= 2.6
+- C/C++ compiler suite supporting C++17
 - CMake 3.15.0
 
 The following packages are optional (see build options):

packaging/python/Dockerfile

@@ -12,14 +12,25 @@ RUN yum -y install \
     curl \
     unzip \
     bison \
-    flex \
     autoconf \
     automake \
     openssh-server \
     libtool
+
+# required for rpmbuild
+RUN yum -y install \
+    gettext \
+    gcc-c++ \
+    help2man \
+    rpm-build
 
 WORKDIR /root
 
+# newer flex with rpmbuild (manylinux2014 based on Centos7 currently has flex < 2.6)
+RUN rpmbuild --rebuild https://vault.centos.org/8-stream/AppStream/Source/SPackages/flex-2.6.1-9.el8.src.rpm \
+    && yum install -y /root/rpmbuild/RPMS/x86_64/flex-2.6.1-9.el7.x86_64.rpm \
+    && rm -rf rpmbuild
+
 RUN wget http://ftpmirror.gnu.org/ncurses/ncurses-6.2.tar.gz \
     && tar -xvzf ncurses-6.2.tar.gz \
     && cd ncurses-6.2  \

packaging/python/Dockerfile_gpu

@@ -1,4 +1,4 @@
-FROM neuronsimulator/neuron_wheel
+FROM neuronsimulator/neuron_wheel:latest-x86_64
 LABEL authors="Pramod Kumbhar, Olli Lupton, Fernando Pereira, Alexandru Savulescu"
 
 WORKDIR /root

src/ivoc/apwindow.cpp

@@ -563,7 +563,7 @@ void OcGlyph::def_size(Coord& w, Coord& h) const {
     }
 }
 
-void OcGlyph::save(ostream&) {
+void OcGlyph::save(std::ostream&) {
     printf("OcGlyph::save (not implemented for relevant class)\n");
 }
 

src/ivoc/axis.cpp

@@ -21,7 +21,7 @@
     GAxisItem(Glyph* g)
         : GraphItem(g) {}
     virtual ~GAxisItem(){};
-    virtual void save(ostream&, Coord, Coord) {}
+    virtual void save(std::ostream&, Coord, Coord) {}
     virtual void erase(Scene* s, GlyphIndex i, int type) {
         if (type & GraphItem::ERASE_AXIS) {
             s->remove(i);
@@ -85,7 +85,7 @@ void Axis::size(float& min, float& max) {
     max = float(amax_);
 }
 
-void Axis::save(ostream& o) {
+void Axis::save(std::ostream& o) {
     char buf[256];
     int c;
     if (d_ == Dimension_X) {
@@ -103,7 +103,7 @@ void Axis::save(ostream& o) {
             nminor_,
             invert_,
             number_);
-    o << buf << endl;
+    o << buf << std::endl;
 }
 
 void Axis::update(Observable*) {}

src/ivoc/axis.h

@@ -20,7 +20,7 @@ class Axis: public Glyph, public Observer {
          int invert = 0,
          bool number = true);
     virtual ~Axis();
-    virtual void save(ostream&);
+    virtual void save(std::ostream&);
     virtual void update(Observable*);
     virtual void size(float&, float&);
 

src/ivoc/epsprint.cpp

@@ -30,12 +30,12 @@ save 20 dict begin\n\
 \n\
 ";
 
-EPSPrinter::EPSPrinter(ostream* o)
+EPSPrinter::EPSPrinter(std::ostream* o)
     : Printer(o) {}
 
 EPSPrinter::~EPSPrinter() {}
 
-void EPSPrinter::eps_prolog(ostream& out, Coord width, Coord height, const char* creator) {
+void EPSPrinter::eps_prolog(std::ostream& out, Coord width, Coord height, const char* creator) {
     int bbw = int(width);
     int bbh = int(height);
     // need to describe it as EPSF = "encapsulated postscript"

src/ivoc/epsprint.h

@@ -5,10 +5,10 @@
 
 class EPSPrinter: public Printer {
   public:
-    EPSPrinter(ostream*);
+    EPSPrinter(std::ostream*);
     virtual ~EPSPrinter();
 
-    virtual void eps_prolog(ostream&,
+    virtual void eps_prolog(std::ostream&,
                             Coord width,
                             Coord height,
                             const char* creator = "InterViews");