musica 0.6.1__tar.gz

musica-0.6.1/.dockerignore

@@ -0,0 +1,14 @@
+# ignore all
+*
+
+# add things to copy
+!.git/
+!.gitmodules
+!CMakeLists.txt
+!cmake/
+!configs
+!docs/
+!fortran/
+!include/
+!lib/
+!src/

musica-0.6.1/.github/workflows/docker.yml

@@ -0,0 +1,60 @@
+name: Docker
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  docker-build-and-test:
+    name: Build and Test - ${{ matrix.dockerfile }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile
+          - Dockerfile.memcheck
+          - Dockerfile.fortran-intel
+          - Dockerfile.fortran-gcc
+          - Dockerfile.fortran-nvhpc
+          - Dockerfile.openmp
+          - Dockerfile.mpi
+          - Dockerfile.mpi_openmp
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Delete huge unnecessary tools folder
+        run: rm -rf /opt/hostedtoolcache
+
+      - name: Build Docker image
+        run: docker build -t tuvx -f docker/${{ matrix.dockerfile }} .
+
+      - name: Run tests in container
+        if: matrix.dockerfile != 'Dockerfile.coverage'
+        run: docker run --name test-container -t tuvx bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Run coverage tests in container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker run --name test-container -t tuvx bash -c 'make coverage ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Copy coverage from container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker cp test-container:build/coverage.info .
+
+      - name: Upload coverage report
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.info

musica-0.6.1/.github/workflows/mac.yml

@@ -0,0 +1,69 @@
+name: Mac
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  c_cxx:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        compiler:
+          - { cpp: g++-11, c: gcc-11}
+          - { cpp: g++-12, c: gcc-12}
+          - { cpp: g++-13, c: gcc-13}
+          - { cpp: clang++, c: clang}
+        build_type: [Release]
+    env:
+      CC: ${{ matrix.compiler.c }}
+      CXX: ${{ matrix.compiler.cpp }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+
+      - name: Build
+        run: cmake --build build --parallel
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+  fortran:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        gcc_version: [11, 12, 13]
+        build_type: [Release]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: brew install netcdf netcdf-fortran
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+
+      - name: Build
+        run: cmake --build build --parallel
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10

musica-0.6.1/.github/workflows/ubuntu.yml

@@ -0,0 +1,71 @@
+name: Ubuntu
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+  
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  c_cxx:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler:
+          - { cpp: g++-11, c: gcc-11}
+          - { cpp: g++-12, c: gcc-12}
+          - { cpp: g++-13, c: gcc-13}
+          - { cpp: clang++, c: clang}
+        build_type: [Release]
+    env:
+      CC: ${{ matrix.compiler.c }}
+      CXX: ${{ matrix.compiler.cpp }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+
+      - name: Build
+        run: cmake --build build --verbose --parallel
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+  fortran:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        gcc_version: [11, 12, 13]
+        build_type: [Release]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libnetcdf-dev netcdf-bin libnetcdff-dev
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+
+      - name: Build
+        run: cmake --build build --parallel
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10

musica-0.6.1/.github/workflows/windows.yml

@@ -0,0 +1,148 @@
+name: Windows
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  mingw:
+    runs-on: windows-2019
+    strategy:
+      matrix:
+        architecture: [x64]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up MinGW
+        uses: egor-tensin/setup-mingw@v2
+        with:
+          platform: ${{ matrix.architecture }}
+          version: 12.2.0 # https://github.com/egor-tensin/setup-mingw/issues/14
+      
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -G "MinGW Makefiles"  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+
+      - name: Build
+        run: cmake --build build --parallel
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C Debug --rerun-failed --output-on-failure . --verbose
+
+  msvc2019:
+    runs-on: windows-2019
+    strategy:
+      matrix:
+        build_type: [Release]
+        architecture: [Win32, x64]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      if: ${{ matrix.architecture == 'Win32' }}
+      with:
+        python-version: '3.x'
+        architecture: x86
+    - run: pip install -r python/requirements.txt
+
+    - name: Run CMake
+      run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+
+    - name: Build
+      run: cmake --build build --config ${{ matrix.build_type }} --parallel
+
+    - name: Test
+      run: cd build ; ctest -j 10 -C ${{ matrix.build_type }} --output-on-failure
+
+  msvc2022:
+    runs-on: windows-2022
+    strategy:
+      matrix:
+        build_type: [Release]
+        architecture: [Win32, x64]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      if: ${{ matrix.architecture == 'Win32' }}
+      with:
+        python-version: '3.x'
+        architecture: x86
+
+    - run: pip install -r python/requirements.txt
+
+    - name: Run CMake
+      run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+
+    - name: Build
+      run: cmake --build build --config ${{ matrix.build_type }} --parallel
+
+    - name: Test
+      run: cd build ; ctest -j 10 -C ${{ matrix.build_type }} --output-on-failure
+
+  clang:
+    runs-on: windows-2019
+    strategy:
+      matrix:
+        version: [11, 12, 13, 14, 15]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install Clang
+        run: curl -fsSL -o LLVM${{ matrix.version }}.exe https://github.com/llvm/llvm-project/releases/download/llvmorg-${{ matrix.version }}.0.0/LLVM-${{ matrix.version }}.0.0-win64.exe ; 7z x LLVM${{ matrix.version }}.exe -y -o"C:/Program Files/LLVM"
+
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
+      - 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_ENABLE_PYTHON_LIBRARY=ON
+
+      - name: Build
+        run: cmake --build build --parallel
+
+      - name: Test
+        run: cd build ; ctest -j 10 -C Debug --exclude-regex "test-unicode" --output-on-failure
+
+  clang-cl-11:
+    runs-on: windows-2019
+    strategy:
+      matrix:
+        architecture: [Win32, x64]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        if: ${{ matrix.architecture == 'Win32' }}
+        with:
+          python-version: '3.x'
+          architecture: x86
+
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
+      - name: Run CMake
+        run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+
+      - name: Build
+        run: cmake --build build --config Debug --parallel
+
+      - name: Test
+        run: cd build ; ctest -j 10 -C Debug --exclude-regex "test-unicode" --output-on-failure

musica-0.6.1/.gitignore

@@ -0,0 +1,10 @@
+# cmake and build stuff
+
+build/
+CMakeCache.txt
+CMakeFiles
+.DS_Store
+.vscode
+dist/
+musica.cpython-* 
+musica.egg-info

musica-0.6.1/.gitmodules

@@ -0,0 +1,10 @@
+[submodule "lib/micm"]
+	path = lib/micm
+	url = https://github.com/NCAR/micm.git
+[submodule "lib/tuv-x"]
+	path = lib/tuv-x
+	url = https://github.com/NCAR/tuv-x
+[submodule "lib/pybind11"]
+	path = lib/pybind11
+	url = https://github.com/pybind/pybind11
+	branch = stable

musica-0.6.1/CITATION.cff

@@ -0,0 +1,67 @@
+cff-version: 1.2.0
+message: "This Citation File Format (CFF) record describes how to cite MUSICA software."
+authors:
+  - family-names: Pfister
+    given-names: Gabriele G.
+  - family-names: Eastham
+    given-names: Sebastian D.
+  - family-names: Arellano
+    given-names: Avelino F.
+  - family-names: Aumont
+    given-names: Bernard
+  - family-names: Barsanti
+    given-names: Kelley C.
+  - family-names: Barth
+    given-names: Mary C.
+  - family-names: Conley
+    given-names: Andrew
+  - family-names: Davis
+    given-names: Nicholas A.
+  - family-names: Emmons
+    given-names: Louisa K.
+  - family-names: Fast
+    given-names: Jerome D.
+  - family-names: Fiore
+    given-names: Arlene M.
+  - family-names: Gaubert
+    given-names: Benjamin
+  - family-names: Goldhaber
+    given-names: Steve
+  - family-names: Granier
+    given-names: Claire
+  - family-names: Grell
+    given-names: Georg A.
+  - family-names: Guevara
+    given-names: Marc
+  - family-names: Henze
+    given-names: Daven K.
+  - family-names: Hodzic
+    given-names: Alma
+  - family-names: Liu
+    given-names: Xiaohong
+  - family-names: Marsh
+    given-names: Daniel R.
+  - family-names: Orlando
+    given-names: John J.
+  - family-names: Plane
+    given-names: John M. C.
+  - family-names: Polvani
+    given-names: Lorenzo M.
+  - family-names: Rosenlof
+    given-names: Karen H.
+  - family-names: Steiner
+    given-names: Allison L.
+  - family-names: Jacob
+    given-names: Daniel J.
+  - family-names: Brasseur
+    given-names: Guy P.
+title: "The Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICA)"
+journal: "Bulletin of the American Meteorological Society"
+year: 2020
+publisher: "American Meteorological Society"
+volume: 101
+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: 0.6.0

musica-0.6.1/CMakeLists.txt

@@ -0,0 +1,116 @@
+cmake_minimum_required(VERSION 3.21)
+
+project(
+  musica-distribution
+  VERSION 0.6.1
+)
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${CMAKE_CURRENT_LIST_DIR}/cmake)
+set(CMAKE_USER_MAKE_RULES_OVERRIDE ${CMAKE_MODULE_PATH}/SetDefaults.cmake)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING
+      "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel."
+      FORCE)
+endif(NOT CMAKE_BUILD_TYPE)
+
+include(GNUInstallDirs)
+
+################################################################################
+# Library options to build
+include(CMakeDependentOption)
+
+option(MUSICA_BUILD_C_CXX_INTERFACE "Use MUSICA" ON)
+option(MUSICA_BUILD_FORTRAN_INTERFACE "Use MUSICA-Fortran interface" OFF)
+option(MUSICA_ENABLE_INSTALL "Install the musica library" ON)
+option(MUSICA_ENABLE_TESTS "Builds tests that ensures each enabled MUSICA component can be used" ON)
+option(MUSICA_ENABLE_MPI "Enable MPI parallel support" OFF)
+option(MUSICA_ENABLE_OPENMP "Enable OpemMP support" OFF)
+option(MUSICA_ENABLE_MEMCHECK "Enable memory checking" OFF)
+
+cmake_dependent_option(
+  MUSICA_ENABLE_TUVX "Builds TUV-x, a photolysis calculator library" ON "MUSICA_BUILD_FORTRAN_INTERFACE" OFF)
+
+cmake_dependent_option(
+  MUSICA_ENABLE_MICM "Adds MICM, a model independent chemical mechanism solver" ON "MUSICA_BUILD_C_CXX_INTERFACE" OFF)
+
+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_CREATE_ENVIRONMENT_MODULE "Creates an Lmod environment module file that can be installed on the same machine this library is installed to." OFF "MUSICA_BUILD_C_CXX_INTERFACE" OFF)
+
+if(MUSICA_CREATE_ENVIRONMENT_MODULE)
+  set(MUSICA_INSTALL_MODULE_FILE_PATH "" CACHE STRING "This is the path of the modulefiles location that the Lmod files should be installed to.")
+  if(MUSICA_INSTALL_MODULE_FILE_PATH STREQUAL "")
+    message(FATAL_ERROR "MUSICA_INSTALL_MODULE_FILE_PATH is required but not set")
+  endif()
+endif()
+
+# shared libraries are required for python, but for some reason setting
+# BUILD_SHARED_LIBS to ON doesn't work on windows
+if (MUSICA_ENABLE_PYTHON_LIBRARY AND NOT WIN32) 
+  message(STATUS "Python requires shared libraries to be built. Enabling shared libraries.")
+  set(BUILD_SHARED_LIBS ON)
+endif()
+
+################################################################################
+# Projet wide setup variables 
+set(MUSICA_INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_INCLUDEDIR})
+set(MUSICA_MOD_DIR ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_INCLUDEDIR})
+set(MUSICA_LIB_DIR ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
+set(MUSICA_FORTRAN_SRC_DIR ${CMAKE_SOURCE_DIR}/fortran)
+
+# Add flags for various compilers
+if(${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
+  add_definitions(-DMUSICA_USING_INTEL)
+elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
+  add_definitions(-DMUSICA_USING_GNU)
+elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "PGI")
+  add_definitions(-DMUSICA_USING_PGI)
+endif()
+
+if(MUSICA_BUILD_C_CXX_INTERFACE)
+  # on ubuntu with clang, an incorrect version of the c++ standard library was being linked
+  if (${CMAKE_HOST_SYSTEM_NAME} MATCHES "Linux" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+      # If the compiler is Clang, use libc++
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
+  endif()
+
+  set(CMAKE_CXX_STANDARD 20)
+endif()
+
+################################################################################
+# Dependencies
+
+include(musica_util)
+
+# Add submodules
+checkout_submodules()
+
+include(dependencies)
+
+################################################################################
+# Tests
+if(MUSICA_ENABLE_TESTS)
+  enable_testing()
+endif()
+
+################################################################################
+# MUSICA
+if(MUSICA_BUILD_C_CXX_INTERFACE)
+  add_subdirectory(src)
+endif()
+
+################################################################################
+# MUSICA-Fortran
+if(MUSICA_BUILD_FORTRAN_INTERFACE)
+  add_subdirectory(fortran)
+endif()
+
+################################################################################
+# Musica python
+if(MUSICA_ENABLE_PYTHON_LIBRARY)
+  add_subdirectory(python)
+endif()