Pybind11 upgrade

.ci/travis_build_linux.sh

@@ -12,13 +12,8 @@ set -x
 BUILDDIR=_build_travis
 mkdir -p $BUILDDIR
 
-PYTHON2="/usr/bin/python2"
 PYTHON3="/usr/bin/python3"
 
-$PYTHON2 -m pip install pip --upgrade --user
-$PYTHON2 -m pip install libNeuroML numpy==1.14 scipy==1.2 \
-    pyNeuroML python-libsbml --upgrade --user
-
 $PYTHON3 -m pip install pip --upgrade --user
 $PYTHON3 -m pip install libNeuroML pyNeuroML python-libsbml --upgrade --user
 
@@ -37,7 +32,6 @@ unset PYTHONPATH
 # many not be available. Therefore, it is neccessary to use fixed path for
 # python executable.
 
-$PYTHON2 -m compileall -q .
 $PYTHON3 -m compileall -q . 
 
 # Python3 with GSL in debug more.
@@ -67,14 +61,3 @@ $PYTHON3 -m compileall -q .
     export MOOSE_NUM_THREADS=3
     make coverage 
 )
-
-# GSL and python2, failure is allowed
-set +e
-(
-    mkdir -p $BUILDDIR && cd $BUILDDIR && \
-        cmake -DPYTHON_EXECUTABLE=$PYTHON2 -DCMAKE_INSTALL_PREFIX=/usr ..
-    $MAKE && MOOSE_NUM_THREADS=$NPROC ctest -j$NPROC --output-on-failure
-)
-set -e
-
-echo "All done"

.ci/travis_prepare_linux.sh

@@ -10,9 +10,8 @@ set -e -x
 apt update
 apt-get install -qq libxml2-dev libbz2-dev
 apt-get install -qq make cmake
-apt-get install -qq python-numpy python-matplotlib python-networkx python-pip
 apt-get install -qq python3-numpy python3-matplotlib python3-networkx python3-pip
-apt-get install -qq python-tk python3-tk
+apt-get install -qq python3-tk
 apt-get install -qq valgrind
 
 # Gsl
@@ -23,9 +22,9 @@ apt-get install -qq liblapack-dev
 apt-get install -qq libboost-all-dev
 
 # Dependencies for NML2
-apt-get install -qq python-scipy python3-scipy
-apt-get install -qq python-lxml python3-lxml
-apt-get install -qq python-setuptools python3-setuptools
+apt-get install -qq python3-scipy
+apt-get install -qq python3-lxml
+apt-get install -qq python3-setuptools
 
 # Install twine
 python3 -m pip install twine

CMakeLists.txt

@@ -3,6 +3,9 @@ cmake_minimum_required(VERSION 3.2.3 FATAL_ERROR)
 # Project to build MOOSE's python module.
 project(PyMOOSE)
 
+# minimum cxx standard required is 14
+set(CMAKE_CXX_STANDARD 14)
+
 # cmake related macros.
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 include(CheckCXXCompiler.cmake)
@@ -299,7 +302,7 @@ endif( WITH_BOOST )
 ######################### BUILD PYMOOSE ########################################
 
 if(NOT WITH_LEGACY_BINDING)
-    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/pybind11)
+    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/pybind11-2.6.1)
     add_subdirectory(pybind11)
 else()
     message(STATUS "Building legacy python binding.")

CheckCXXCompiler.cmake

@@ -1,13 +1,11 @@
 # Compiler check.
 # Must support c++14
-# If python2 is supported then we can not use c++17. 
 if(COMPILER_IS_TESTED)
     return()
 endif()
 
 ########################### COMPILER MACROS #####################################
 include(CheckCXXCompilerFlag)
-CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11 )
 CHECK_CXX_COMPILER_FLAG("-Wno-strict-aliasing" COMPILER_WARNS_STRICT_ALIASING )
 
 # Turn warning to error: Not all of the options may be supported on all
@@ -41,16 +39,4 @@ CHECK_CXX_COMPILER_FLAG( "-Wno-unused-but-set-variable"
 if(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
     add_definitions( "-Wno-unused-but-set-variable" )
 endif(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
-
-if(COMPILER_SUPPORTS_CXX11)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-    if(APPLE)
-        add_definitions( -mllvm -inline-threshold=1000 )
-    endif(APPLE)
-else(COMPILER_SUPPORTS_CXX11)
-    message(FATAL_ERROR "The compiler ${CMAKE_CXX_COMPILER} is too old. \n"
-      "Please use a compiler which has full c++11 support."
-      )
-endif(COMPILER_SUPPORTS_CXX11)
-
 set(COMPILER_IS_TESTED ON)

external/pybind11-2.6.1/.appveyor.yml

@@ -0,0 +1,37 @@
+version: 1.0.{build}
+image:
+- Visual Studio 2015
+test: off
+skip_branch_with_pr: true
+build:
+  parallel: true
+platform:
+- x86
+environment:
+  matrix:
+  - PYTHON: 36
+    CONFIG: Debug
+  - PYTHON: 27
+    CONFIG: Debug
+install:
+- ps: |
+    $env:CMAKE_GENERATOR = "Visual Studio 14 2015"
+    if ($env:PLATFORM -eq "x64") { $env:PYTHON = "$env:PYTHON-x64" }
+    $env:PATH = "C:\Python$env:PYTHON\;C:\Python$env:PYTHON\Scripts\;$env:PATH"
+    python -W ignore -m pip install --upgrade pip wheel
+    python -W ignore -m pip install pytest numpy --no-warn-script-location
+- ps: |
+    Start-FileDownload 'https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.zip'
+    7z x eigen-3.3.7.zip -y > $null
+    $env:CMAKE_INCLUDE_PATH = "eigen-3.3.7;$env:CMAKE_INCLUDE_PATH"
+build_script:
+- cmake -G "%CMAKE_GENERATOR%" -A "%CMAKE_ARCH%"
+    -DCMAKE_CXX_STANDARD=14
+    -DPYBIND11_WERROR=ON
+    -DDOWNLOAD_CATCH=ON
+    -DCMAKE_SUPPRESS_REGENERATION=1
+    .
+- set MSBuildLogger="C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
+- cmake --build . --config %CONFIG% --target pytest -- /m /v:m /logger:%MSBuildLogger%
+- cmake --build . --config %CONFIG% --target cpptest -- /m /v:m /logger:%MSBuildLogger%
+on_failure: if exist "tests\test_cmake_build" type tests\test_cmake_build\*.log*

external/pybind11-2.6.1/.clang-tidy

@@ -0,0 +1,13 @@
+FormatStyle: file
+
+Checks: '
+llvm-namespace-comment,
+modernize-use-override,
+readability-container-size-empty,
+modernize-use-using,
+modernize-use-equals-default,
+modernize-use-auto,
+modernize-use-emplace,
+'
+
+HeaderFilterRegex: 'pybind11/.*h'

external/pybind11-2.6.1/.cmake-format.yaml

@@ -0,0 +1,73 @@
+parse:
+  additional_commands:
+    pybind11_add_module:
+      flags:
+        - THIN_LTO
+        - MODULE
+        - SHARED
+        - NO_EXTRAS
+        - EXCLUDE_FROM_ALL
+        - SYSTEM
+
+format:
+  line_width: 99
+  tab_size: 2
+
+  # If an argument group contains more than this many sub-groups
+  # (parg or kwarg groups) then force it to a vertical layout.
+  max_subgroups_hwrap: 2
+
+  # If a positional argument group contains more than this many
+  # arguments, then force it to a vertical layout.
+  max_pargs_hwrap: 6
+
+  # If a cmdline positional group consumes more than this many
+  # lines without nesting, then invalidate the layout (and nest)
+  max_rows_cmdline: 2
+  separate_ctrl_name_with_space: false
+  separate_fn_name_with_space: false
+  dangle_parens: false
+
+  # If the trailing parenthesis must be 'dangled' on its on
+  # 'line, then align it to this reference: `prefix`: the start'
+  # 'of the statement,  `prefix-indent`: the start of the'
+  # 'statement, plus one indentation  level, `child`: align to'
+  # the column of the arguments
+  dangle_align: prefix
+  # If the statement spelling length (including space and
+  # parenthesis) is smaller than this amount, then force reject
+  # nested layouts.
+  min_prefix_chars: 4
+
+  # If the statement spelling length (including space and
+  # parenthesis) is larger than the tab width by more than this
+  # amount, then force reject un-nested layouts.
+  max_prefix_chars: 10
+
+  # If a candidate layout is wrapped horizontally but it exceeds
+  # this many lines, then reject the layout.
+  max_lines_hwrap: 2
+
+  line_ending: unix
+
+  # Format command names consistently as 'lower' or 'upper' case
+  command_case: canonical
+
+  # Format keywords consistently as 'lower' or 'upper' case
+  # unchanged is valid too
+  keyword_case: 'upper'
+
+  # A list of command names which should always be wrapped
+  always_wrap: []
+
+  # If true, the argument lists which are known to be sortable
+  # will be sorted lexicographically
+  enable_sort: true
+
+  # If true, the parsers may infer whether or not an argument
+  # list is sortable (without annotation).
+  autosort: false
+
+# Causes a few issues - can be solved later, possibly.
+markup:
+  enable_markup: false