Build updated

- Removed deprecated CMake version setting
- Removed python2: out of life. Only supporting Python>=3.8
- Removed pybind11: should be installed directly with pip
- Added MacOSX build workflow: to be tested

.ci/build_wheels_osx.sh

@@ -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

.ci/travis_build_linux.sh

@@ -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"

.github/workflows/pymoose.yml

@@ -3,13 +3,13 @@ name: Python package
 on: [push]
 
 jobs:
-  build:
-    name : Python Package
+  build-ubuntu:
+    name: Ubuntu Package
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10',3.11,3.12]
+        python-version: [3.8, 3.9, 3.10, 3.11, 3.12]
 
     steps:
     - uses: actions/checkout@v2
@@ -29,3 +29,28 @@ jobs:
     - name: Build
       run: |
          pip install .
+         
+  build-mac:
+    name: MacOSX Package
+    runs-on: macos-14
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, 3.10, 3.11, 3.12]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |        
+        sudo xcode-select --install
+        /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+        brew install micromamba
+        micromamba self-update
+        micromamba create -n moose numpy matplotlib vpython python3-tk libhdf5 doxygen gsl        
+        micromamba activate moose
+    - name: Build
+      run: |
+         pip install .

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.2.3 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.0 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

CONTRIBUTING.md

@@ -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.

INSTALL.md

@@ -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 ..
 

basecode/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
 add_library(basecode
 	Element.cpp

basecode/global.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);
 }
 

biophysics/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 include(${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 
 if(WITH_GSL)

builtins/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
 
 # NSDF5 support. Disabled by default.

devel/docker/travis/Dockerfile

@@ -13,7 +13,6 @@ RUN apt update && apt install -y cmake gcc g++ make valgrind \
         python-dev python3-dev \
         && rm -rf /var/lib/apt/lists/*
 
-RUN python2 -m pip --no-cache-dir install pyneuroml python-libsbml
 RUN python3 -m pip --no-cache-dir install pyneuroml python-libsbml
 WORKDIR /root
 RUN ls -ltrah

device/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 add_library(device
     PulseGen.cpp

diffusion/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 
 if(WITH_GSL)

examples/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 ADD_LIBRARY(examples
     Example.cpp

external/fmt/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
 
 add_library(fmt STATIC src/format.cc src/os.cc)
 target_include_directories(fmt PRIVATE include)

external/libsoda/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 
 find_package(Threads REQUIRED)