version bump for nightly package.

.clang-format

@@ -4,6 +4,10 @@ SortIncludes: false
 ConstructorInitializerIndentWidth: 4
 AlignEscapedNewlinesLeft: true
 AlignTrailingComments: true
+AlignAfterOpenBracket: false
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: true
 AllowAllParametersOfDeclarationOnNextLine: false
 AllowShortFunctionsOnASingleLine: false
 AllowShortIfStatementsOnASingleLine: false
@@ -14,15 +18,12 @@ BreakBeforeBinaryOperators: false
 BreakBeforeTernaryOperators: true
 BreakConstructorInitializersBeforeComma: false
 BinPackParameters: true
-ColumnLimit:     80
+ColumnLimit: 90
 ConstructorInitializerAllOnOneLineOrOnePerLine: true
 DerivePointerBinding: true
-ExperimentalAutoDetectBinPacking: false
 IndentCaseLabels: true
 MaxEmptyLinesToKeep: 1
 NamespaceIndentation: None
-ObjCSpaceBeforeProtocolList: false
-PenaltyBreakBeforeFirstCallParameter: 1
 PenaltyBreakComment: 60
 PenaltyBreakString: 1000
 PenaltyBreakFirstLessLess: 120

.github/workflows/pymoose.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [2.7, 3.7, 3.8]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -19,8 +19,8 @@ jobs:
     - name: Install dependencies
       run: |
         export DEBIAN_FRONTEND=noninteractive
-        sudo -E apt install -y cmake libgsl-dev g++ gcc git 
-        sudo -E apt install python3-tk python-tk
+        sudo -E apt install -y cmake libboost-dev g++ gcc git 
+        sudo -E apt install python3-tk 
         python -m pip install numpy matplotlib --user
     - name: Build
       run: |

.github/workflows/windows.yml

@@ -0,0 +1,44 @@
+name: Windows Build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: "Setup Python ${{ matrix.python-version }}"
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    # Runs a set of commands using the runners shell
+    - name: Build using MSVS
+      shell: bash
+      run: |
+        mkdir build
+        cd build
+        PYTHON=$(which python)
+        $PYTHON -m pip install pip --upgrade
+        $PYTHON -m pip install numpy pytest matplotlib setuptools
+        cmake -DOPTION_PYTHON=ON -DOPTION_EXAMPLES=ON -DPython3_EXECUTABLE=$PYTHON ..
+        cmake --build . --config Release 
+        ctest -C Release
+
+    - name: Upload to PyPI
+      shell: bash
+      env:
+        SMOLDYN_PYPI_TOKEN: ${{ secrets.SMOLDYN_PYPI_TOKEN }}
+      run: |
+        cd build
+        python -m pip install twine --upgrade
+        python -m twine upload -u __token__ -p "$SMOLDYN_PYPI_TOKEN" *.whl --skip-existing || echo "Failed to upload"

CMakeLists.txt

@@ -1,23 +1,17 @@
-cmake_minimum_required(VERSION 3.2.3 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 # Project to build MOOSE's python module.
-project(PyMOOSE)
+project(PyMOOSE LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 # cmake related macros.
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
-include(CheckCXXCompiler.cmake)
-include(CheckIncludeFileCXX)
 
 # We find python executable here. Though mainly used inside pymoose. 
-# FIXME: When cmake 3.12 is widely available use the following:
-#   find_package(Python3 COMPONENTS Interpreter Numpy)
-#   set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
-set(Python_ADDITIONAL_VERSIONS 2.7)
-find_package(PythonInterp 3.5)
-if(NOT PYTHONINTERP_FOUND)
-  find_package(PythonInterp 2.7)
-endif()
-
+find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
+set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
 set(CMAKE_MACOSX_RPATH OFF)
 
 # NOTE: version should be changed in setup.py file.
@@ -55,19 +49,16 @@ option(DEBUG                "Build with debug support" OFF)
 option(GPROF                "Build for profiling using gprof" OFF)
 option(ENABLE_UNIT_TESTS    "Enable unit tests (DEBUG should also be ON)" OFF)
 option(WITH_MPI             "Enable Openmpi support" OFF)
-
-option(WITH_BOOST           "Enable boost. Prefer boost over stl" OFF)
-option(WITH_BOOST_ODE       "Use boost library ode2 library instead of GSL" OFF)
-option(WITH_GSL             "Use gsl-library. Alternative is WITH_BOOST" ON)
-
 option(WITH_ASAN            "Use AddressSanitizer in DEBUG mode." OFF)
-
 option(WITH_NSDF            "Enable NSDF support. Requires hdf5" OFF )
-
 option(WITH_LEGACY_BINDING  "Use legacy python-bindings" OFF)
 
 ############################ BUILD CONFIGURATION #################################
 
+# At least version 1.53 (odeint is part of this version)
+find_package(Boost 1.53 REQUIRED)
+include_directories(${Boost_INCLUDE_DIRS})
+
 # Default definitions.
 add_definitions(-DUSE_GENESIS_PARSER)
 if(DEBUG OR "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
@@ -99,12 +90,6 @@ if(WITH_ASAN AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
     set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address")
 endif()
 
-# Override default GSL solvers when BOOST is enabled.
-if(WITH_BOOST OR WITH_BOOST_ODE)
-    set(WITH_BOOST_ODE ON)
-    set(WITH_GSL OFF)
-endif()
-
 ################################### TARGETS ####################################
 
 link_directories(${CMAKE_BINARY_DIR})
@@ -120,35 +105,6 @@ set(STATIC_LIBRARIES "" )
 # Collect all shared libraries here.
 set(SYSTEM_SHARED_LIBS "")
 
-# BOOST ode library performs better than GSL and ideally should be made default.
-# Unfortunately Boost does not have a very good matrix library; it has ublas
-# which is not well maintained and emit a lot
-# of warning during compilation. Nonetheless, WITH_BOOST_ODE works fine and
-# produce results quicker than GSL. 
-if(WITH_GSL)
-    find_package(GSL 1.16 REQUIRED)
-    if(NOT GSL_FOUND)
-        message(FATAL_ERROR
-            "=====================================================================\n"
-            " FATAL gsl(>=1.16) not found.\n\n"
-            " MOOSE requires Gnu Scientific Library (GSL) 1.16 or higher. \n"
-            " Please install the `dev` or `devel` package e.g. \n"
-            "     $ sudo apt-get install libgsl0-dev \n"
-            "     $ sudo yum install libgsl-devel \n"
-            "     $ brew install gsl \n\n"
-            " Or build and install gsl from source code \n"
-            "     https://www.gnu.org/software/gsl/ \n"
-            " After installing gsl, rerun cmake.\n\n"
-            " If you install gsl in non-standard place, set the GSL_ROOT_DIR environment \n"
-            " variable. CMAKE use this to search for required files. \n"
-            "====================================================================\n"
-            )
-    endif(NOT GSL_FOUND)
-elseif(WITH_BOOST_ODE)
-    find_package(Boost 1.53 REQUIRED)
-    find_package(LAPACK REQUIRED)
-endif()
-
 
 # Openmpi
 if(WITH_MPI)
@@ -177,26 +133,6 @@ list(APPEND SYSTEM_SHARED_LIBS ${CMAKE_THREAD_LIBS_INIT})
 # These libraries could be static of dynamic. We need to discrimate between
 # these two types because of --whole-archive option. See
 # BhallaLab/moose-core#66,
-if(WITH_GSL)
-    if(GSL_STATIC_LIBRARIES)
-       message( STATUS "Using static libraries ${GSL_STATIC_LIBRARIES}" )
-       list(APPEND STATIC_LIBRARIES ${GSL_STATIC_LIBRARIES})
-    else( )
-       # message(DEBUG "Using gsl libraries: ${GSL_LIBRARIES}")
-       foreach(GSL_LIB ${GSL_LIBRARIES} )
-           if(GSL_LIB)
-               get_filename_component( GSL_LIB_EXT ${GSL_LIB} EXT )
-               if(GSL_LIB_EXT)
-                   if(GSL_LIB_EXT STREQUAL ".a" )
-                       list(APPEND STATIC_LIBRARIES ${GSL_LIB})
-                   else()
-                       list(APPEND SYSTEM_SHARED_LIBS ${GSL_LIB})
-                   endif( )
-               endif( )
-           endif( )
-       endforeach( )
-   endif( )
-endif()
 
 if(WITH_MPI)
     if(MPI_CXX_FOUND)

basecode/CMakeLists.txt

@@ -1,5 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
-include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
+cmake_minimum_required(VERSION 3.12)
 add_library(basecode
 	Element.cpp
 	DataElement.cpp
@@ -30,4 +29,3 @@ add_executable(test_globals testGlobals.cpp global.cpp)
 
 enable_testing()
 add_test(NAME cpp_test_globals  COMMAND $<TARGET_FILE:test_globals>)
-

biophysics/CMakeLists.txt

@@ -1,13 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
-include(${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
-
-if(WITH_GSL)
-    find_package(GSL 1.16)
-    include_directories(${GSL_INCLUDE_DIRS})
-elseif(WITH_BOOST_ODE)
-    find_package(Boost)
-    include_directories(${Boost_INCLUDE_DIRS})
-endif(WITH_GSL)
+cmake_minimum_required(VERSION 3.12)
 
 set(BIOPHYSICS_SRCS
     IntFire.cpp
@@ -57,3 +48,6 @@ set(BIOPHYSICS_SRCS
 
 add_library(biophysics ${BIOPHYSICS_SRCS})
 
+target_include_directories(biophysics PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/../external/odeint-v2/include)
+