Windows build and NeuroML2 support

.clang-format

@@ -31,7 +31,6 @@ PenaltyReturnTypeOnItsOwnLine: 200
 PointerBindsToType: true
 SpacesBeforeTrailingComments: 2
 Cpp11BracedListStyle: true
-Standard:        Auto
 IndentWidth:     4
 TabWidth:        4
 UseTab:          Never

.github/workflows/pymoose.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}    
     strategy:      
       matrix:
-        os: [ubuntu-latest, macos-14]
+        os: [ubuntu-latest, macos-14, windows-latest]
         build_type: [Release]
         c_compiler: [clang]
         python-version: ["3.12"]
@@ -16,6 +16,8 @@ jobs:
             apt: 10
           - os: macos-14
             brew: 20
+          - os: windows-latest
+            winget: 30
     steps:
       - name: mamba-setup
         uses: mamba-org/setup-micromamba@v1
@@ -25,7 +27,10 @@ jobs:
           cache-downloads: true
           create-args: >-
             python=${{ matrix.python-version }}
+            pkg-config
+            clang
             hdf5
+            pybind11[global]
             graphviz
             pytables
             numpy
@@ -35,25 +40,41 @@ jobs:
             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 install libhdf5-dev libgsl0-dev graphviz-dev python3-lxml cmake doxygen
+        run: |
+          sudo apt-get -y install libhdf5-dev libgsl0-dev graphviz-dev python3-lxml doxygen libgsl-dev
       - if: ${{ matrix.brew }}
         run: |
           brew install gsl
           brew install hdf5
           brew install graphviz
-          brew install cmake
           brew install doxygen
-      - name: install python module dependencies via pip
-        run: |
-          pip install pybind11[global]
-          pip install python-libsbml
       - name: checkout
         uses: actions/checkout@v4          
-      - name: build and install
+      - name: build and install (non-windows)
+        if: runner.os != 'Windows' 
+        run: |
+          eval "$(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()"

AppleM1_Guide.md

@@ -0,0 +1,27 @@
+- 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
+          brew install hdf5
+          brew install graphviz
+          brew install cmake
+          brew install doxygen
+  ```
+
+- 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 hdf5 graphviz pytables numpy matplotlib vpython lxml doxygen setuptools wheel pybind11[global]
+```
+- Activate the moose environment: `micromamba activate moose`
+- Install libsbml: `pip install python-libsbml`
+- Install moose from github: `pip install git+https://github.com/BhallaLab/moose-core.git`