musica 0.11.1.4__tar.gz → 0.12.1__tar.gz

{musica-0.11.1.4 → musica-0.12.1}/.dockerignore

@@ -17,4 +17,4 @@
 !pyproject.toml
 !LICENSE
 !README.md
-!wheelhouse
+!tutorials

{musica-0.11.1.4 → musica-0.12.1}/.github/workflows/docker.yml

@@ -26,7 +26,6 @@ jobs:
           - Dockerfile.openmp
           - Dockerfile.mpi
           - Dockerfile.mpi_openmp
-          - Dockerfile.python
           - Dockerfile.nvhpc
           - Dockerfile.coverage
         build_type: [Release, Debug]

musica-0.11.1.4/.github/workflows/clang_format.yml → musica-0.12.1/.github/workflows/format.yml

@@ -1,4 +1,4 @@
-name: Clang-Format
+name: Format Code with Clang-Format and autopep8
 
 on:
   push:
@@ -8,7 +8,7 @@ on:
 
 jobs:
   format:
-    name: Run Clang-Format
+    name: Run Formatting
     runs-on: ubuntu-latest
 
     steps:
@@ -21,10 +21,17 @@ jobs:
           ref: ${{ github.head_ref }}
           token: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: autopep8
+        uses: peter-evans/autopep8@v2
+        with:
+          args: --recursive --in-place --aggressive --aggressive --max-line-length 120 .
+
       - name: Run clang-format
         run: |
           find include -type f \( -name '*.hpp' -or -name '*.h' \) -exec clang-format -i --style=file --verbose {} +
           find src -type f \( -name '*.cpp' -or -name '*.c' \) -exec clang-format -i --style=file --verbose {} +
+          find musica -type f \( -name '*.cpp' -or -name '*.c' \) -exec clang-format -i --style=file --verbose {} +
+          find musica -type f \( -name '*.hpp' -or -name '*.h' \) -exec clang-format -i --style=file --verbose {} +
 
       - name: Check for changes
         id: check-changes
@@ -37,7 +44,7 @@ jobs:
         run: |
           git config --global user.name "GitHub Actions"
           git config --global user.email "actions@github.com"
-          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+          git commit -am "Auto-format code using Clang-Format and autopep8" || echo "No changes to commit"
 
       - name: Push changes to main-formatting branch
         if: steps.check-changes.outcome != 'success'
@@ -48,7 +55,7 @@ jobs:
         uses: peter-evans/create-pull-request@v6
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          commit-message: "Auto-format code using Clang-Format"
+          commit-message: "Auto-format code using Clang-Format and autopep8"
           title: "Auto-format code changes"
-          body: "This is an automated pull request to apply code formatting using Clang-Format."
+          body: "This is an automated pull request to apply code formatting using Clang-Format and autopep8."
           branch: main-formatting

{musica-0.11.1.4 → musica-0.12.1}/.github/workflows/gh_pages.yml

@@ -1,11 +1,8 @@
 # Build and deploy documentation to GitHub Pages
 name: GitHub Pages
 
-on:
+on: 
   push:
-    branches:
-      - main
-      - release
   pull_request:
   workflow_dispatch:
 
@@ -15,14 +12,7 @@ env:
 jobs:
   build-and-deploy:
     name: Build and deploy to gh-pages
-    runs-on: ubuntu-24.04
-    strategy:
-      matrix:
-        gcc-version: [13]
-    env:
-      CXX: g++-${{ matrix.gcc-version }}
-      CC: gcc-${{ matrix.gcc-version }}
-      FC: gfortran-${{ matrix.gcc-version }}
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
@@ -94,7 +84,8 @@ jobs:
       # _gh-pages/branch/$brname (transforming '/' into '--')
       - name: Build and copy documentation (branch)
         if: |
-          contains(github.event_name, 'push') &&
+          (contains(github.event_name, 'push') ||
+          contains(github.event_name, 'pull_request')) &&
           !contains(github.ref, env.DEFAULT_BRANCH)
         run: |
           set -x
@@ -102,10 +93,16 @@ jobs:
           id=$(docker create musica)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id
-          brname="${{github.ref}}"
-          brname="${brname##refs/heads/}"
+          # Determine branch name for deployment directory
+          if [ "${{ github.event_name }}" = "pull_request" ]; then
+            brname="${{ github.head_ref }}"
+          else
+            brname="${{ github.ref }}"
+            brname="${brname##refs/heads/}"
+          fi
           brdir=${brname//\//--}   # replace '/' with '--'
           rm -rf   _gh-pages/branch/${brdir}
+          mkdir -p _gh-pages/branch/${brdir}
           rsync -a tmpdocs/ _gh-pages/branch/${brdir}
 
       # Go through each branch in _gh-pages/branch/, if it's not a
@@ -156,4 +153,4 @@ jobs:
               repo: context.repo.repo,
               issue_number: context.payload.pull_request.number,
               body: commentBody
-            });
+            });

{musica-0.11.1.4 → musica-0.12.1}/.github/workflows/mac.yml

@@ -18,11 +18,9 @@ jobs:
     strategy:
       matrix:
         compiler:
-          - { cpp: g++-12, c: gcc-12, fc: gfortran-12}
           - { cpp: g++-13, c: gcc-13, fc: gfortran-13}
           - { cpp: g++-14, c: gcc-14, fc: gfortran-14}
-          - { cpp: clang++, c: clang, fc: gfortran-12}
-          - { cpp: g++-14, c: gcc-14, fc: gfortran-14}
+          - { cpp: clang++, c: clang, fc: gfortran-14}
         build_type: [Release]
     env:
       CC: ${{ matrix.compiler.c }}
@@ -32,6 +30,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: maxim-lobanov/setup-xcode@v1
+        with:
+          xcode-version: '16.4'
+
       - name: Install dependencies
         run: brew install netcdf netcdf-fortran
 

{musica-0.11.1.4 → musica-0.12.1}/.github/workflows/python-tests.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [windows-latest, macos-13, ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         # python versions: https://devguide.python.org/versions/
 
     runs-on: ${{ matrix.platform }}
@@ -23,6 +23,17 @@ jobs:
       with:
         submodules: true
 
+    - name: Install dependencies
+      if: matrix.platform == 'ubuntu-latest'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libnetcdf-dev netcdf-bin libnetcdff-dev liblapack-dev
+    
+    - name: Install dependencies
+      if: matrix.platform == 'macos-13'
+      run: |
+        brew install netcdf netcdf-fortran lapack
+
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
@@ -34,4 +45,4 @@ jobs:
       run: pip install --verbose .[test]
 
     - name: Test
-      run: pytest
+      run: pytest -s

{musica-0.11.1.4 → musica-0.12.1}/.github/workflows/python-wheels.yml

@@ -36,8 +36,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.12"]
+        include:
+          # Linux builds (supports cross-compilation via QEMU)
+          - os: ubuntu-latest
+            python-version: "3.13"
+            cibw_archs: "x86_64 aarch64 i686"
+          
+          # Windows builds (separate runners needed for different archs)
+          - os: windows-latest
+            python-version: "3.13"
+            cibw_archs: "AMD64 x86 ARM64"
+          
+          # macOS Intel
+          - os: macos-13  # Intel runner
+            python-version: "3.13"
+            cibw_archs: "x86_64"
+          
+          # macOS Apple Silicon
+          - os: macos-latest  # ARM64 runner
+            python-version: "3.13"
+            cibw_archs: "arm64"
 
     steps:
     - uses: actions/checkout@v4
@@ -47,21 +65,22 @@ jobs:
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+  
+    - name: Set up QEMU for cross-architecture builds
+      if: matrix.os == 'ubuntu-latest'
+      uses: docker/setup-qemu-action@v3
+      with:
+        platforms: all
 
     - name: CI Build Wheels
       uses: pypa/cibuildwheel@v2.17
       env:
-        CIBW_ENVIRONMENT_PASS_LINUX: CIBW_ARCHS
-        CIBW_ENVIRONMENT_LINUX: >
-          CUDA_PATH=/usr/local/cuda
-          PATH=/usr/local/cuda/bin:$PATH
-          LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
-          BUILD_GPU=1
+        CIBW_ARCHS: ${{ matrix.cibw_archs }}
 
     - name: Upload wheels
       uses: actions/upload-artifact@v4
       with:
-        name: cibw-wheels-${{ matrix.os }}-py${{ matrix.python-version }}
+        name: cibw-wheels-${{ matrix.os }}-${{ matrix.cibw_archs }}-py${{ matrix.python-version }}
         path: wheelhouse/*.whl
 
   upload_all:
@@ -87,4 +106,4 @@ jobs:
         merge-multiple: true
 
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@release/v1

{musica-0.11.1.4 → musica-0.12.1}/.github/workflows/ubuntu.yml

@@ -23,8 +23,8 @@ jobs:
           - { cpp: g++-14, c: gcc-14, fc: gfortran-14}
           - { cpp: clang++, c: clang, fc: gfortran-12}
         options: 
-          - {micm: ON, tuvx: OFF, python: ON}
-          - {micm: OFF, tuvx: ON, python: OFF}
+          - {micm: ON, tuvx: OFF, carma: OFF, python: ON}
+          - {micm: OFF, tuvx: ON, carma: OFF, python: OFF}
         build_type: [Release]
     env:
       CC: ${{ matrix.compiler.c }}
@@ -46,6 +46,7 @@ jobs:
                               -D MUSICA_GIT_TAG=${{ github.sha }} \
                               -D MUSICA_ENABLE_MICM=${{ matrix.options.micm }} \
                               -D MUSICA_ENABLE_TUVX=${{ matrix.options.tuvx }} \
+                              -D MUSICA_ENABLE_CARMA=${{ matrix.options.carma }} \
                               -D MUSICA_ENABLE_PYTHON_LIBRARY=${{ matrix.options.python }} \
                               -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 

{musica-0.11.1.4 → musica-0.12.1}/.github/workflows/windows.yml

@@ -14,6 +14,7 @@ concurrency:
 jobs:
   mingw:
     runs-on: windows-latest
+    continue-on-error: true 
     strategy:
       matrix:
         architecture: [x64]
@@ -24,10 +25,10 @@ jobs:
         uses: egor-tensin/setup-mingw@v2
         with:
           platform: ${{ matrix.architecture }}
-          version: 12.2.0 # https://github.com/egor-tensin/setup-mingw/issues/14
+          static: 0
 
       - name: Run Cmake 
-        run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --parallel
@@ -56,7 +57,7 @@ jobs:
         architecture: x86
 
     - name: Run CMake
-      run: cmake -S . -B build -A ${{ matrix.architecture }} -D MUSICA_GIT_TAG=${{ github.sha }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+      run: cmake -S . -B build -A ${{ matrix.architecture }} -D MUSICA_GIT_TAG=${{ github.sha }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel
@@ -69,7 +70,7 @@ jobs:
     continue-on-error: true 
     strategy:
       matrix:
-        version: [18.1.0, 19.1.0, 20.1.0]
+        version: [19.1.0, 20.1.0]
 
     steps:
       - uses: actions/checkout@v4
@@ -78,7 +79,7 @@ jobs:
         run: curl -fsSL -o LLVM${{ matrix.version }}.exe https://github.com/llvm/llvm-project/releases/download/llvmorg-${{ matrix.version }}/LLVM-${{ matrix.version }}-win64.exe ; 7z x LLVM${{ matrix.version }}.exe -y -o"C:/Program Files/LLVM"
 
       - name: Run CMake
-        run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --parallel
@@ -104,7 +105,7 @@ jobs:
           architecture: x86
 
       - name: Run CMake
-        run: cmake -S . -B build -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --config Debug --parallel
@@ -114,10 +115,15 @@ jobs:
 
   fortran:
     runs-on: windows-latest
+    continue-on-error: true 
     strategy:
       fail-fast: false
       matrix:
-        build_type: [Debug, Release]
+        # for some reason the debug build fails with an error in the python library
+        # something about the usage of mechanism configuration and variants causes missing type information
+        # This commit for mechanism configuration works: 903150064277e024b0afcfc879df419e1cefc87b
+        # This one doesn't: a3ef728c69f619f80c272d634bc2a17ca5ab4de9
+        build_type: [Release]
 
     steps:
       - name: Checkout code
@@ -135,12 +141,17 @@ jobs:
             mingw-w64-x86_64-cmake
             mingw-w64-x86_64-netcdf
             mingw-w64-x86_64-netcdf-fortran
+            mingw-w64-x86_64-lapack
           msystem: MINGW64
 
       - name: Add MSYS2 mingw64 to PATH
         shell: msys2 {0}
         run: echo "C:/msys64/mingw64/bin" >> $GITHUB_PATH
 
+      - name: Clean build directory
+        shell: msys2 {0}
+        run: rm -rf build
+
       - name: Configure with CMake
         shell: msys2 {0}
         run: |
@@ -149,6 +160,7 @@ jobs:
                               -D MUSICA_GIT_TAG=${{ github.sha }} \
                               -D MUSICA_ENABLE_MICM=ON \
                               -D MUSICA_ENABLE_TUVX=ON \
+                              -D MUSICA_ENABLE_CARMA=ON \
                               -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
                               -D MUSICA_BUILD_FORTRAN_INTERFACE=ON \
                               -D CMAKE_POLICY_VERSION_MINIMUM=3.5

{musica-0.11.1.4 → musica-0.12.1}/.gitignore

@@ -11,6 +11,13 @@ musica.cpython-*
 musica.egg-info
 **/*.mod
 
+.venv
+.pytest_cache
 **/*__pycache__*
 **/*.pyc
 wheelhouse
+
+error.json
+
+.ipynb_checkpoints
+configs/tuvx/output/

musica-0.12.1/.zenodo.json

@@ -0,0 +1,80 @@
+{
+  "title": "MUSICA: Multi-Scale Infrastructure for Chemistry and Aerosols",
+  "description": "MUSICA is a multi-language library for performing computational simulations in atmospheric chemistry.",
+  "license": {
+    "id": "Apache-2.0"
+  },
+  "creators": [
+    {
+      "name": "Dawson, Matthew",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    },
+    {
+      "name": "Gim, Jiwon",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    },
+    {
+      "name": "Fillmore, David",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    },
+    {
+      "name": "Shores, Kyle",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": "0000-0002-4272-5187"
+    },
+    {
+      "name": "Thind, Montek",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    },
+    {
+      "name": "Jian Sun",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    }
+  ],
+  "contributors": [
+    {
+      "name": "ACOM MUSICA Development Team",
+      "type": "ResearchGroup"
+    },
+    {
+      "name": "Angela Pak",
+      "type": "ProjectMember"
+    },
+    {
+      "name": "Aidan Winney",
+      "type": "ProjectMember"
+    },
+    {
+      "name": "Dee Grant",
+      "type": "Other"
+    },
+    {
+      "name": "Ward Fisher",
+      "type": "Other"
+    },
+    {
+      "name": "Qina Tan",
+      "type": "ProjectMember"
+    }
+  ],
+  "keywords": [
+    "atmospheric chemistry",
+    "chemical mechanisms",
+    "air quality modeling",
+    "photolysis",
+    "MICM",
+    "TUV-x"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "10.1175/BAMS-D-19-0331.1",
+      "relation": "cites",
+      "description": "The foundational MUSICA paper describing the scientific vision"
+    }
+  ]
+}

musica-0.12.1/AUTHORS.md

@@ -0,0 +1,59 @@
+# MUSICA Authors and Contributors
+
+This file acknowledges all individuals who have contributed to the MUSICA project.
+
+## Core Development Team
+
+The following individuals are the primary developers and maintainers of the MUSICA software:
+
+- **Matthew Dawson** (mattdawson@ucar.edu) - Core Developer
+- **Jiwon Gim** (jiwongim@ucar.edu) - Core Developer  
+- **David Fillmore** (fillmore@ucar.edu) - Core Developer
+- **Kyle Shores** (kshores@ucar.edu) - Core Developer
+- **Montek Thind** (mthind@ucar.edu) - Core Developer
+- **Jian Sun** - Core Developer
+
+## Scientific Leadership and Vision
+
+The scientific leadership and vision for MUSICA are provided by the authors of the [foundational paper](https://doi.org/10.1175/BAMS-D-19-0331.1). 
+This software implements that vision. For a full list of scientific authors, 
+please refer to our [CITATION.cff](CITATION.cff) file. To cite the software, use the Zenodo DOI from our latest release.
+
+## Additional Contributors
+
+<!-- Contributors will be added here as they join the project -->
+<!-- Format: -->
+<!-- - **Name** (affiliation) - Brief description of contribution -->
+
+- **Aidan Winney** - Documentation and Tutorials
+- **Angela Pak** - Documentation and Tutorials
+- **Dee Grant** - Improving the Python API
+- **Qina Tan** - Implementing the CUDA-based Rosenbrock solver
+
+## Recognition Policy
+
+We recognize contributors at different levels based on their involvement:
+
+- **Core Development Team**: Listed in `pyproject.toml`, `.zenodo.json` (creators), and this file
+- **Additional Contributors**: Listed in `.zenodo.json` (contributors) and this file
+- **All Contributors**: Automatically tracked by GitHub's contributor statistics
+
+See our [Contributing Guide](CONTRIBUTING.md) for more details on how contributions are recognized.
+
+## How to Contribute
+
+We welcome contributions from the community! Please see our [Contributing Guide](CONTRIBUTING.md) for information on how to get involved.
+
+## Acknowledgments
+
+We thank the broader atmospheric chemistry modeling community for their feedback, testing, and contributions to making MUSICA a robust and useful tool for scientific research.
+
+---
+
+## Citation Information
+
+For citation purposes, please refer to our [CITATION.cff](CITATION.cff) file for the appropriate citations based on your use case. The main citations are:
+
+1. **For the MUSICA vision and scientific framework**: [Pfister et al., 2020](https://doi.org/10.1175/BAMS-D-19-0331.1)
+2. **For the MUSICA software evaluation**: [Schwantes et al., 2022](https://doi.org/10.1029/2021MS002889)
+3. **For the software itself**: Use the Zenodo DOI from our latest release

{musica-0.11.1.4 → musica-0.12.1}/CITATION.cff

@@ -64,4 +64,4 @@ number: 10
 page: "E1743 - E1760"
 doi: "10.1175/BAMS-D-19-0331.1"
 url: "https://journals.ametsoc.org/view/journals/bams/101/10/bamsD190331.xml"
-version: 0.10.0
+version: 0.12.1

{musica-0.11.1.4 → musica-0.12.1}/CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.21)
 
 # must be on the same line so that pyproject.toml can correctly identify the version
-project(musica-distribution VERSION 0.11.1.4)
+project(musica-distribution VERSION 0.12.1)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${PROJECT_SOURCE_DIR}/cmake/SetDefaults.cmake)
@@ -29,6 +29,7 @@ option(MUSICA_ENABLE_MEMCHECK "Enable memory checking" OFF)
 option(MUSICA_BUILD_DOCS "Build the documentation" OFF)
 option(MUSICA_ENABLE_MICM "Enable MICM" ON)
 option(MUSICA_ENABLE_TUVX "Enable TUV-x" ON)
+option(MUSICA_ENABLE_CARMA "Enable CARMA" ON)
 option(MUSICA_ENABLE_PIC "Build the library with position independent code" OFF)
 option(MUSICA_ENABLE_COVERAGE "Enable code coverage output" OFF)
 option(MUSICA_BUNDLE_DEPENDENCIES "Bundle dependencies with the library" ON)
@@ -40,6 +41,9 @@ set(MUSICA_SET_MICM_DEFAULT_VECTOR_SIZE "4" CACHE STRING "Set MICM vector-ordere
 cmake_dependent_option(
   MUSICA_ENABLE_PYTHON_LIBRARY "Adds pybind11, a lightweight header-only library that exposes C++ types in Python and vice versa" OFF "MUSICA_BUILD_C_CXX_INTERFACE" OFF)
 
+cmake_dependent_option(
+  MUSICA_ONLY_PYTHON "Build only the Python bindings. This option is used when building Python wheels primarily" OFF "MUSICA_ENABLE_PYTHON_LIBRARY" OFF)
+
 ################################################################################
 # Projet wide setup variables 
 set(MUSICA_INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_INCLUDEDIR})
@@ -92,7 +96,7 @@ endif()
 # since sources are collected so that python libraries can target them directly,
 # we need to know if we are targeting Fortran before we collect the sources
 # otherwise cmake freaks out, and I don't know why, but this fixes it
-if(MUSICA_ENABLE_TUVX)
+if(MUSICA_ENABLE_TUVX OR MUSICA_ENABLE_CARMA)
     enable_language(Fortran)
 endif()
 

musica-0.12.1/CONTRIBUTING.md

@@ -0,0 +1,98 @@
+# Contributing to MUSICA
+
+We welcome contributions from the community! This guide outlines how you can contribute to the MUSICA project.
+
+## Getting Started
+
+### Development Setup
+
+1. **Clone the repository:**
+   ```bash
+   git clone https://github.com/NCAR/musica.git
+   cd musica
+   ```
+
+2. **Build the project:**
+   ```bash
+   mkdir build && cd build
+   ccmake ..
+   make
+   ```
+
+3. **Python development setup:**
+   ```bash
+   pip install -e .
+   ```
+
+For detailed developer options and dependency management, see our [Software Development Plan](docs/Software%20Development%20Plan.pdf).
+
+## Types of Contributions
+
+We appreciate all types of contributions:
+
+### Code Contributions
+- Bug fixes
+- New features
+- Performance improvements
+- Test coverage improvements
+
+### Documentation
+- README improvements
+- Code documentation
+- Tutorial and example updates
+- Wiki contributions
+
+### Testing and Validation
+- Bug reports with reproducible examples
+- Testing on different platforms
+- Validation against known results
+
+### Scientific Contributions
+- New chemical mechanisms
+- Algorithm improvements
+- Performance optimizations
+
+## Contribution Process
+
+1. **Fork the repository** and create a feature branch
+2. **Make your changes** following our coding standards
+3. **Add tests** for new functionality
+4. **Update documentation** as needed
+5. **Submit a pull request** with a clear description
+
+## Recognition Policy
+
+We believe in recognizing all contributors appropriately:
+
+### Core Development Team
+Contributors who make substantial, ongoing contributions to the codebase, architecture, or project direction will be listed as authors in:
+- `pyproject.toml` (for Python package metadata)
+- `.zenodo.json` (as "creators" for software citations)
+- `AUTHORS.md` (as core developers)
+
+### Additional Contributors  
+Contributors who make valuable but smaller contributions will be acknowledged in:
+- `.zenodo.json` (as "contributors" with appropriate type)
+- `AUTHORS.md` (in the Additional Contributors section)
+- GitHub's contributor list (automatic)
+
+## Development Guidelines
+
+### Code Standards
+- Follow existing code style and conventions
+- Include appropriate tests for new functionality
+- Document new features and APIs
+
+### Dependency Management
+We use CMake for C++ dependencies and pip for Python dependencies. See our [README](README.md#developer-options) for information about specifying dependency versions during development.
+
+### GPU Support
+If contributing GPU-related code, please test on appropriate hardware and follow our GPU build guidelines.
+
+## Questions?
+
+- Check our [documentation](https://ncar.github.io/musica/index.html)
+- Read our [Software Development Plan](docs/Software%20Development%20Plan.pdf)
+- Contact the maintainers at musica-support@ucar.edu
+
+Thank you for your interest in contributing to MUSICA!