BhallaLab
diff --git a/‎.ci/build_wheels_osx.sh‎
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diff --git a/‎.ci/travis_build_linux.sh‎
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diff --git a/‎.github/workflows/pymoose.yml‎
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diff --git a/‎CMakeLists.txt‎
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diff --git a/‎CONTRIBUTING.md‎
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diff --git a/‎CheckCXXCompiler.cmake‎
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diff --git a/‎INSTALL.md‎
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diff --git a/‎basecode/CMakeLists.txt‎
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diff --git a/‎basecode/global.cpp‎
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diff --git a/‎biophysics/CMakeLists.txt‎
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@@ -11,7 +11,6 @@ export PATH=/usr/local/bin:$PATH
 brew update || echo "Failed to update brew"
 brew install gsl  || brew upgrade gsl 
 brew upgrade python3 || echo "Failed to upgrade python3"
-brew upgrade python2 || echo "Failed to upgrade python2"
 brew upgrade python || echo "Failed to upgrade python"
 
 # Following are to remove numpy; It is breaking the build on Xcode9.4.
@@ -48,7 +47,7 @@ for _py in 3 2; do
     $PYTHON -m pip install numpy --upgrade --user
     $PYTHON -m pip install twine  --upgrade  --user
 
-    PLATFORM=$($PYTHON -c "import distutils.util; print(distutils.util.get_platform())")
+    PLATFORM=$($PYTHON -c "import sysconfig; print(sysconfig.get_platform())")
 
     ( 
         cd $MOOSE_SOURCE_DIR
 
@@ -12,12 +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 +33,6 @@ 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.
@@ -68,13 +63,5 @@ $PYTHON3 -m compileall -q .
     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"
@@ -4,28 +4,37 @@ on: [push]
 
 jobs:
   build:
-    name : Python Package
-
-    runs-on: ubuntu-latest
-    strategy:
+    runs-on: ${{ matrix.os }}    
+    strategy:      
       matrix:
-        python-version: [3.8, 3.9, '3.10',3.11,3.12]
-
+        os: [ubuntu-latest, macos-14]
+        build_type: [Release]
+        c_compiler: [clang]
+        python-version: ["3.12"]
+        include:
+          - os: ubuntu-latest
+            apt: 10
+          - os: macos-14
+            brew: 20
     steps:
     - uses: actions/checkout@v2
+    - if: ${{ matrix.apt }}
+      run: sudo apt-get install libhdf5-dev libgsl0-dev
+    - if: ${{ matrix.brew }}
+      run: |
+        brew install gsl
+        brew install hdf5      
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+      shell: bash
       run: |
-        export DEBIAN_FRONTEND=noninteractive
-        sudo -E apt clean
-        sudo -E apt update
-        sudo -E apt install -y cmake libgsl-dev g++ gcc git 
-        sudo -E apt install python3-tk
-        sudo -E apt install -y libhdf5-dev doxygen
-        python -m pip install numpy matplotlib vpython --user
+        "${SHELL}" <(curl -L micro.mamba.pm/install.sh)
+        micromamba self-update
+        micromamba create -n moose python=${{ matrix.python-version }} graphviz lxml cmake numpy matplotlib vpython hdf5 pytables doxygen -c conda-forge
+        eval "$(micromamba shell hook --shell bash)"
+        micromamba activate moose
+        pip install python-libsbml
+        pip install pyneuroml
     - name: Build
       run: |
-         pip install .
+        pip install .
+         
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.2.3 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
 
 # Project to build MOOSE's python module.
 project(PyMOOSE)
@@ -317,13 +317,18 @@ endif( WITH_BOOST )
 
 ######################### BUILD PYMOOSE ########################################
 
-if(NOT WITH_LEGACY_BINDING)
-    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/pybind11)
-    add_subdirectory(pybind11)
-else()
-    message(STATUS "Building legacy python binding.")
-    add_subdirectory(pymoose)
-endif()
+# pybind11 should be installed as a dependency.
+# It can be easily done with `pip install pybind11`
+# See: https://pybind11.readthedocs.io/en/stable/installing.html
+# - Subha, Mon Apr 22 14:26:58 IST 2024
+
+# if(NOT WITH_LEGACY_BINDING)
+#     add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/pybind11)
+#     add_subdirectory(pybind11)
+# else()
+#     message(STATUS "Building legacy python binding.")
+#     add_subdirectory(pymoose)
+# endif()
 
 
 # always override debian default installation directory. It will be installed in
 
@@ -1,5 +1,10 @@
-To contribute, fork this repo and submit your changes via a pull-request.
-Before sending pull-request, check the following:
+We use the `fork-and-pull` workflow for moose development.
 
-- [ ] Software builds locally
-- [ ] `ctest --output-on-failure` passes all tests.
+To contribute:
+1. Fork this repo on github
+2. Make the changes you want to contribute
+3. Check that moose builds locally on your version
+4. Check all tests pass `ctest --output-on-failure` passes all tests (TODO: cleanup/fix/update the tests)
+5. Submit your changes via a pull-request.
+
+After this the repository admin will check your pull request and merge it to the main branch.
@@ -7,8 +7,12 @@ 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 )
+if(WIN32)
+        CHECK_CXX_COMPILER_FLAG("/std:c++14" COMPILER_SUPPORTS_CXX14 )
+else(WIN32)
+        CHECK_CXX_COMPILER_FLAG("-std=c++14" COMPILER_SUPPORTS_CXX14 )
+        CHECK_CXX_COMPILER_FLAG("-Wno-strict-aliasing" COMPILER_WARNS_STRICT_ALIASING )
+endif(WIN32)
 
 # Turn warning to error: Not all of the options may be supported on all
 # versions of compilers. be careful here.
@@ -42,15 +46,19 @@ 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 "${CMAKE_CXX_FLAGS} -std=c++11")
+if(COMPILER_SUPPORTS_CXX14)
+    if(WIN32)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /std:c++14")
+    else(WIN32)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
+    endif(WIN32)
     if(APPLE)
         add_definitions( -mllvm -inline-threshold=1000 )
     endif(APPLE)
-else(COMPILER_SUPPORTS_CXX11)
+else(COMPILER_SUPPORTS_CXX14)
     message(FATAL_ERROR "The compiler ${CMAKE_CXX_COMPILER} is too old. \n"
-      "Please use a compiler which has full c++11 support."
+      "Please use a compiler which has full c++14 support."
       )
-endif(COMPILER_SUPPORTS_CXX11)
+endif(COMPILER_SUPPORTS_CXX14)
 
 set(COMPILER_IS_TESTED ON)
@@ -1,7 +1,7 @@
 # Building MOOSE 
 
 To build `MOOSE` from source, you need `cmake` and `python-setuptools`. We
-recommend to use Python 3.5 or higher. Python 2.7 is also supported. 
+recommend to use Python 3.8 or higher. 
 
 Before running the following command to build and install, make sure that
 followings are installed.
@@ -15,7 +15,7 @@ On Ubuntu-16.04 or higher, these dependencies can be installed with:
 sudo apt-get install python-pip python-numpy cmake libgsl-dev g++
 ```
 
-Now use `pip` to download and install the `pymoose`.
+Now use `pip` to download and install `pymoose` from the [github repository](https://github.com/BhallaLab/moose-core).
 
 ```
 $ pip install git+https://github.com/BhallaLab/moose-core --user
@@ -41,6 +41,12 @@ from github.
 This will build moose, `ctest` will run few tests to check if build process was
 successful.
 
+To rebuild, delete the `_build` directory and the generated `_temp__build/` directory and recreate the `_build` directory:
+
+    $ cd ..; rm -rf _build; rm -rf _temp__build
+    
+and continue the steps following that described above.
+
 To make in debug mode use:
     $ cmake -DCMAKE_BUILD_TYPE=Debug ..
 
 
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.20)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
 add_library(basecode
 	Element.cpp
 
@@ -226,7 +226,7 @@ string moosePathToColumnName(const string& path, char delim, size_t maxParents)
 string toString(double x)
 {
     char buffer[50];
-    sprintf(buffer, "%.17g", x);
+    snprintf(buffer, sizeof buffer, "%.17g", x);
     return string(buffer);
 }
 
 
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.20)
 include(${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 
 if(WITH_GSL)
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-cmake_minimum_required(VERSION 2.8)`
	`1`	`+cmake_minimum_required(VERSION 3.20)`
`2`	`2`	`include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )`
`3`	`3`	`add_library(basecode`
`4`	`4`	`Element.cpp`
Original file line number	Diff line number	Diff line change
`@@ -226,7 +226,7 @@ string moosePathToColumnName(const string& path, char delim, size_t maxParents)`
`226`	`226`	`string toString(double x)`
`227`	`227`	`{`
`228`	`228`	`char buffer[50];`
`229`		`- sprintf(buffer, "%.17g", x);`
	`229`	`+ snprintf(buffer, sizeof buffer, "%.17g", x);`
`230`	`230`	`return string(buffer);`
`231`	`231`	`}`
`232`	`232`