merge master branch

.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"

.ci/travis_prepare_osx.sh

@@ -45,3 +45,4 @@ $PYTHON3 -m pip install matplotlib --user --upgrade
 $PYTHON3 -m pip install pyNeuroML libNeuroML --user
 $PYTHON3 -m pip install scipy --user
 $PYTHON3 -m pip install pylint --user
+$PYTHON3 -m pip install pytest --user

.clang-format

@@ -0,0 +1,48 @@
+---
+AccessModifierOffset: -4
+SortIncludes: false
+ConstructorInitializerIndentWidth: 4
+AlignEscapedNewlinesLeft: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortFunctionsOnASingleLine: false
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakTemplateDeclarations: true
+AlwaysBreakBeforeMultilineStrings: true
+BreakBeforeBinaryOperators: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BinPackParameters: true
+ColumnLimit:     80
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+DerivePointerBinding: true
+ExperimentalAutoDetectBinPacking: false
+IndentCaseLabels: true
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 60
+PenaltyBreakString: 1000
+PenaltyBreakFirstLessLess: 120
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerBindsToType: true
+SpacesBeforeTrailingComments: 2
+Cpp11BracedListStyle: true
+IndentWidth:     4
+TabWidth:        4
+UseTab:          Never
+BreakBeforeBraces: Stroustrup
+IndentFunctionDeclarationAfterType: true
+SpacesInParentheses: false
+SpacesInAngles:  false
+SpaceInEmptyParentheses: false
+SpacesInCStyleCastParentheses: false
+SpaceAfterControlStatementKeyword: false
+SpaceBeforeAssignmentOperators: true
+ContinuationIndentWidth: 4
+Standard : C++11
+...
+

.github/workflows/package.yml

@@ -0,0 +1,113 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build_wheel:
+    runs-on: ${{ matrix.os }}    
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-14, macos-15, windows-latest]
+        build_type: [Release]
+        c_compiler: [clang]
+        python-version: ['3.11']
+        # python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.21.3
+
+      - name: MacOS dpendencies
+        if: ${{ runner.os == 'macOS' }}
+        run: |
+          brew install gsl
+          brew install hdf5          
+      - name: Windows dependencies
+        if: ${{ runner.os == 'Windows' }}
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: moose
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pkg-config
+            clang
+            hdf5
+            pybind11[global]
+            graphviz
+            pytables
+            numpy
+            matplotlib
+            vpython
+            lxml
+            doxygen
+            setuptools
+            wheel
+            meson
+            ninja
+            meson-python
+            gsl
+            cibuildwheel
+          post-cleanup: all
+          generate-run-shell: false            
+
+      - name: Linux package
+        if: runner.os == 'Linux'
+        env:
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_BEFORE_ALL: 'uname -a'
+          CIBW_BEFORE_ALL_LINUX: >
+            yum install -y epel-release &&
+            yum install -y pkgconfig &&
+            yum install -y gsl-devel &&
+            yum install -y hdf5-devel
+          CIBW_BUILD: '*-manylinux_x86_64'
+          CIBW_SKIP: 'pp*'
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
+          CIBW_MANYLINUX_PYPY_X86_64_IMAGE: manylinux_2_28          
+        run: |
+          python -m cibuildwheel --output-dir wheelhouse
+          ls wheelhouse
+      - name: MacOS package
+        if: runner.os == 'macOS'
+        env:
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_BEFORE_ALL: 'uname -a'
+          CIBW_BEFORE_ALL_MACOS: >
+            brew uninstall pkg-config || :
+              brew uninstall [email protected] || :
+                brew install gsl hdf5 meson ninja cmake &&
+            export PKG_CONFIG=`which pkg-config` &&
+            echo "<<<<<<<<<#########################################>>>>>>>>>>" &&
+            echo "$$$$$ `pkg-config --libs gsl`" &&
+            echo "@@@@@ `pkg-config --cflags gsl`"
+          CIBW_ARCHS: 'arm64'
+          CIBW_BUILD: '*-macosx_arm64'
+          CIBW_SKIP: 'pp* cp38*'
+        run: |
+          export "MACOSX_DEPLOYMENT_TARGET=$(echo ${{ matrix.os }} | cut -c 7-8).0"  # required because gsl2.8 has minimum target of 14.0
+          python -m cibuildwheel --output-dir wheelhouse
+          ls wheelhouse
+      - name: Windows package
+        if: runner.os == 'Windows' 
+        env:
+          CIBW_BEFORE_ALL: 'uname -a'
+          CIBW_BUILD: '*-win_*'
+          CIBW_SKIP: '*-win32 pp*'
+        run: |
+          micromamba shell hook -s powershell | Out-String | Invoke-Expression
+          micromamba activate moose
+          python -m cibuildwheel --output-dir wheelhouse
+          dir wheelhouse
+      - name: Upload packages
+        if: github.ref == 'refs/heads/main'
+        uses: xresloader/upload-to-github-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          file: "wheelhouse/pymoose*.whl"

.github/workflows/pymoose.yml

@@ -1,27 +1,80 @@
-name: Python package
+name: Build install test
 
 on: [push]
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}    
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [2.7, 3.7, 3.8]
-
+        os: [ubuntu-22.04, macos-14, windows-latest]
+        build_type: [Release]
+        c_compiler: [clang]
+        python-version: ["3.12"]
+        include:
+          - os: ubuntu-22.04
+            apt: 10
+          - os: macos-14
+            brew: 20
+          - os: windows-latest
+            winget: 30
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        export DEBIAN_FRONTEND=noninteractive
-        sudo -E apt install -y cmake libgsl-dev g++ gcc git 
-        sudo -E apt install python3-tk python-tk
-        python -m pip install numpy matplotlib --user
-    - name: Build
-      run: |
-        python setup.py install
+      - name: mamba-setup
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: moose
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pkg-config
+            clang
+            hdf5
+            pybind11[global]
+            graphviz
+            pytables
+            numpy
+            matplotlib
+            vpython
+            lxml
+            doxygen
+            setuptools
+            wheel
+            meson
+            ninja
+            meson-python
+            gsl
+          post-cleanup: all
+          generate-run-shell: false            
+      - name: Display Python version
+        run: |          
+          python -c "import sys; print(sys.version)"
+      - if: ${{ matrix.apt }}
+        run: |
+          sudo apt-get update
+          sudo apt-get -y install libgsl0-dev libgsl-dev libhdf5-dev
+      - if: ${{ matrix.brew }}
+        run: |
+          brew install gsl
+          brew install hdf5
+      - name: checkout
+        uses: actions/checkout@v4          
+      - name: Build and install (non-windows)
+        if: runner.os != 'Windows' 
+        run: |
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate moose
+          python -c "import sys; print('#' * 60, sys.version)"
+          pip install python-libsbml
+          pip install .
+          python -c "import moose; moose.le()"
+      - name: Build and install (windows)
+        if: runner.os == 'Windows' 
+        run: |
+          micromamba shell hook -s powershell | Out-String | Invoke-Expression
+          micromamba activate moose
+          python -c "import sys; print('#' * 60, sys.version)"
+          pip install python-libsbml
+          pip install .
+          python -c "import moose; moose.le()"

.gitlab-ci.yml

@@ -17,6 +17,12 @@ build:
     - python3 -m pip install python-libsbml --user --upgrade
     - python3 -m pip install pyneuroml --user --upgrade
     - python3 -m pip install sympy scipy --user --upgrade
+    - python3 -m pip install pytest --user --upgrade
     - python3 setup.py build test 
     - python3 setup.py install --user
-    - python3 -c "import moose; moose.test()"
+    - python3 -c "import moose.tests; moose.tests.test()"
+
+  except:
+      - pybind11
+      - devel
+

AUTHORS

@@ -2,11 +2,11 @@
 
 Upinder S. Bhalla 	Primary Architect, rdesigneur
 HarshaRani. G.V         MOOSE Website, SBML support, GUI
-Dilawar Singh    	Multithreading, GSoC, Packaging, Maintenance, BOOST solvers
+Subhasis Ray            Lead Developer, Python interface, Packaging, Maintenance
 
 # Past developers
 
-Subhasis Ray 	        Python interface, GUI
+Dilawar Singh    	Multithreading, GSoC, Packaging, Maintenance, BOOST solvers
 Niraj Dudani 	        Neuronal solver
 Aditya Gilra 	        NeuroML support
 Aviral Goel 	        Moogli

AppleM1Build.md

@@ -0,0 +1,23 @@
+# Building MOOSE on MacOS with Apple M1 CPU
+- Install homebrew: https://brew.sh/
+- Set up required development environment
+  - Install command line tools for XCode
+  - Install build dependencies by running these commands in a terminal
+  ```
+          brew install gsl
+  ```
+
+- Install anaconda/miniconda/micromamba/miniforge. For example, for micromamba, run
+```
+"${SHELL}" <(curl -L micro.mamba.pm/install.sh)
+```
+
+  in command line
+- Update micromamba: `micromamba self-update`
+- Restart terminal and create an environment with necessary packages: 
+
+```
+micromamba create -n moose numpy matplotlib vpython lxml meson ninja meson-python gsl setuptools pybind11[global] pkg-config -c conda-forge
+```
+- Activate the moose environment: `micromamba activate moose`
+- Install moose from github: `pip install git+https://github.com/BhallaLab/moose-core.git`