Merge branch 'master' of https://github.com/dilawar/moose-core

Author: Dilawar Singh

.github/main.workflow

@@ -0,0 +1,15 @@
+workflow "build pymoose" {
+  resolves = "build"
+  on = "push"
+}
+
+action "build" {
+  uses = "./"
+  args = "install"
+  env = {
+    CMAKE_GIT_REPO = "https://github.com/dilawar/moose-core",
+    CMAKE_INSTALL_DEPS_SCRIPT = ".travis/travis_prepare_linux.sh",
+    CMAKE_FLAGS = "-DCMAKE_INSTALL_PREFIX:PATH=/tmp/foo",
+    CMAKE_BUILD_THREADS = "4"
+  }
+}

.github/workflows/build.yml

@@ -0,0 +1,21 @@
+name: C/C++ CI
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install dependencies
+      run: |
+        sudo apt update
+        sudo apt install libgsl-dev g++ cmake python3-dev python3-numpy
+    - name: configure
+      run: mkdir -p build && cd build && cmake ..
+    - name: make
+      run: cd build && make
+    - name: ctest --output-on-failure
+      run: cd build && make check

CMakeLists.txt

@@ -1,5 +1,5 @@
-cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
-project(pymoose)
+cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
+project(MOOSE)
 
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules")
 include(CheckCXXCompiler.cmake)
@@ -333,8 +333,19 @@ endif( WITH_BOOST )
 
 
 ######################### BUILD PYMOOSE ########################################
+
+# 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})
+# See the cmake doc.
+# Till then, stay with the old macro.
+set(Python_ADDITIONAL_VERSIONS 2.7)
+find_package(PythonInterp 3.4)
+
 # This target is built by pymoose/CMakeLists.txt file.
-add_subdirectory( pymoose )
+add_subdirectory(pymoose)
+
 
 # always override debian default installation directory. It will be installed in
 # site-packages instead of dist-packages.

cmake_modules/FindNumPy.cmake

@@ -14,22 +14,26 @@
  */
 class ConcChanInfo
 {
-public:
-    ConcChanInfo();
-    ConcChanInfo( unsigned int my, unsigned int other,
-                  unsigned int chan, double perm, bool isSwapped )
-        : myPool( my ), otherPool( other ), chanPool( chan ),
-          swapped( isSwapped ),
-          permeability( perm )
-    {;}
+	public:
+		ConcChanInfo();
+		ConcChanInfo( unsigned int my, unsigned int other, 
+						unsigned int chan, double perm, bool isSwapped, bool _isLocal )
+				: myPool( my ), otherPool( other ), chanPool( chan ), 
+				swapped( isSwapped ),
+				isLocal( _isLocal ),
+				permeability( perm )
+		{;}
 
-    unsigned int myPool;
-    unsigned int otherPool;
-    unsigned int chanPool;
-    bool swapped;	// Flag records whether myPool/otherPool are
-    // swapped wrt inPool/outPool. System expects
-    // that inPool should be in same compt as chanPool.
-    double permeability;
+		unsigned int myPool; /// This is not Id, it is internal PoolIndex
+		/// Obtained using convertIdToPoolIndex.
+		unsigned int otherPool; /// Internal PoolIndex
+		unsigned int chanPool; /// Internal PoolIndex 
+		bool swapped;	// Flag records whether myPool/otherPool are 
+						// swapped wrt inPool/outPool. System expects
+						// that inPool should be in same compt as chanPool.
+		bool isLocal;	// Flag, records odd cases where the channel is
+						// entirely local to one compartment.
+		double permeability;
 };
 
 #endif // _CONC_CHAN_INFO_H