Merge branch 'main' into release

.github/workflows/docker.yml

@@ -27,6 +27,8 @@ jobs:
           - Dockerfile.mpi
           - Dockerfile.mpi_openmp
           - Dockerfile.python
+          - Dockerfile.pip
+        build_type: [Release, Debug]
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
@@ -37,10 +39,10 @@ jobs:
         run: rm -rf /opt/hostedtoolcache
 
       - name: Build Docker image
-        run: docker build -t musica -f docker/${{ matrix.dockerfile }} .
+        run: docker build -t musica -f docker/${{ matrix.dockerfile }} . --build-arg MUSICA_GIT_TAG=${{ github.sha }} --build-arg BUILD_TYPE=${{ matrix.build_type }}
 
       - name: Run tests in container
-        if: matrix.dockerfile != 'Dockerfile.coverage'
+        if: matrix.dockerfile != 'Dockerfile.coverage' && matrix.dockerfile != 'Dockerfile.pip'
         run: docker run --name test-container -t musica bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
 
       - name: Run coverage tests in container

.github/workflows/mac.yml

@@ -18,10 +18,11 @@ jobs:
     strategy:
       matrix:
         compiler:
-          - { cpp: g++-11, c: gcc-11, fc: gfortran-11}
           - { 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}
         build_type: [Release]
     env:
       CC: ${{ matrix.compiler.c }}
@@ -44,6 +45,7 @@ jobs:
             cmake -S . -B build \
                 -D CMAKE_CXX_FLAGS=-Wl,-ld_classic \
                 -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                -D MUSICA_GIT_TAG=${{ github.sha }} \
                 -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
                 -D Python3_EXECUTABLE=$PYTHON_PATH 
 
@@ -57,6 +59,7 @@ jobs:
             cmake -S . -B build \
                 -D CMAKE_CXX_FLAGS=-Wl,-ld_classic \
                 -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                -D MUSICA_GIT_TAG=${{ github.sha }} \
                 -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
                 -D Python3_EXECUTABLE=$PYTHON_PATH \
                 -D CMAKE_OSX_SYSROOT=""
@@ -73,7 +76,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        gcc_version: [11, 12, 13]
+        gcc_version: [13, 14]
         build_type: [Release]
     env:
       FC: gfortran-${{ matrix.gcc_version }}
@@ -85,7 +88,7 @@ jobs:
         run: brew install netcdf netcdf-fortran
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+        run: cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
 
       - name: Build
         run: cmake --build build --verbose --parallel 10

.github/workflows/pep8.yml

@@ -15,7 +15,7 @@ jobs:
       - name: autopep8
         uses: peter-evans/autopep8@v2
         with:
-          args: --recursive --in-place --aggressive --aggressive .
+          args: --recursive --in-place --aggressive --aggressive --max-line-length 120 .
 
       - name: Check for changes
         id: check-changes

.github/workflows/pip.yml

@@ -34,4 +34,4 @@ jobs:
       run: pip install --verbose .[test]
 
     - name: Test
-      run: python -m unittest discover -s python/test
+      run: python -m unittest discover -v -s python/test

.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: 
-          - {python: ON, tuvx: OFF}
-          - {python: OFF, tuvx: ON}
+          - {micm: ON, tuvx: OFF, python: ON}
+          - {micm: OFF, tuvx: ON, python: OFF}
         build_type: [Release]
     env:
       CC: ${{ matrix.compiler.c }}
@@ -40,21 +40,31 @@ jobs:
           sudo apt-get install -y liblapack-dev libblas-dev build-essential libnetcdf-dev libnetcdff-dev
           sudo apt-get install -y python3-numpy
 
-      - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=${{ matrix.options.python }} -D MUSICA_ENABLE_TUVX=${{ matrix.matrix.options.tuvx }}
+      - name: Run Cmake
+        # TUV-x doesn't work with gcc 13
+        if: matrix.compiler.fc != 'gfortran-13' && matrix.options.tuvx != 'ON'
+        run: |
+          cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                              -D MUSICA_GIT_TAG=${{ github.sha }} \
+                              -D MUSICA_ENABLE_MICM=${{ matrix.options.micm }} \
+                              -D MUSICA_ENABLE_TUVX=${{ matrix.options.tuvx }} \
+                              -D MUSICA_ENABLE_PYTHON_LIBRARY=${{ matrix.options.python }}
 
       - name: Build
+        if: matrix.compiler.fc != 'gfortran-13' && matrix.options.tuvx != 'ON'
         run: cmake --build build --verbose
 
       - name: Run tests
+        if: matrix.compiler.fc != 'gfortran-13' && matrix.options.tuvx != 'ON'
         run: |
           cd build
           ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
   fortran:
     runs-on: ubuntu-24.04
+    continue-on-error: true
     strategy:
       matrix:
-        gcc_version: [12, 13, 14]
+        gcc_version: [14]
         build_type: [Debug, Release]
     env:
       CXX: g++-${{ matrix.gcc_version }}
@@ -70,7 +80,7 @@ jobs:
           sudo apt-get install -y libnetcdf-dev netcdf-bin libnetcdff-dev liblapack-dev libblas-dev
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
 
       - name: Build
         run: cmake --build build --verbose --parallel 1

.github/workflows/windows.yml

@@ -30,7 +30,7 @@ jobs:
       - run: pip install numpy
 
       - name: Run Cmake 
-        run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+        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
 
       - name: Build
         run: cmake --build build --parallel
@@ -61,7 +61,7 @@ jobs:
     - run: pip install numpy
 
     - 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_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+      run: cmake -S . -B build -G "Visual Studio 17 2022" -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
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel
@@ -86,7 +86,7 @@ jobs:
       - run: pip install numpy
 
       - 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_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+        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
 
       - name: Build
         run: cmake --build build --parallel
@@ -115,7 +115,7 @@ jobs:
       - run: pip install numpy
 
       - name: Run CMake
-        run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+        run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
       - name: Build
         run: cmake --build build --config Debug --parallel

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: 0.7.3
+version: 0.8.0

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 0.7.3)
+project(musica-distribution VERSION 0.8.0)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${CMAKE_MODULE_PATH}/SetDefaults.cmake)

cmake/dependencies.cmake

@@ -20,6 +20,17 @@ if (MUSICA_BUILD_FORTRAN_INTERFACE)
   pkg_check_modules(netcdfc IMPORTED_TARGET REQUIRED netcdf)
 endif()
 
+# ##############################################################################
+# yaml-cpp
+
+FetchContent_Declare(
+  yaml-cpp
+  GIT_REPOSITORY https://github.com/jbeder/yaml-cpp/
+  GIT_TAG 0.8.0
+  GIT_PROGRESS NOT
+  ${FETCHCONTENT_QUIET})
+FetchContent_MakeAvailable(yaml-cpp)
+
 ################################################################################
 # google test
 if(MUSICA_ENABLE_TESTS)
@@ -51,7 +62,7 @@ endif()
 if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE)
 
   set_git_default(MICM_GIT_REPOSITORY https://github.com/NCAR/micm.git)
-  set_git_default(MICM_GIT_TAG 6b1c58a9be14095e3f3c6df403c91c4e800f23de)
+  set_git_default(MICM_GIT_TAG v3.6.0)
 
   FetchContent_Declare(micm
       GIT_REPOSITORY ${MICM_GIT_REPOSITORY}
@@ -75,7 +86,7 @@ if (MUSICA_ENABLE_TUVX AND MUSICA_BUILD_C_CXX_INTERFACE)
   set(TUVX_INSTALL_INCLUDE_DIR ${MUSICA_INSTALL_INCLUDE_DIR} CACHE STRING "" FORCE)
 
   set_git_default(TUVX_GIT_REPOSITORY https://github.com/NCAR/tuv-x.git)
-  set_git_default(TUVX_GIT_TAG 674ee1e72853bb44d23c36602fa73c955b2f021d)
+  set_git_default(TUVX_GIT_TAG v0.10.0)
 
   FetchContent_Declare(tuvx
     GIT_REPOSITORY ${TUVX_GIT_REPOSITORY}

cmake/test_util.cmake

@@ -41,7 +41,7 @@ function(create_standard_test_cxx)
   include(CMakeParseArguments)
   cmake_parse_arguments(${prefix} " " "${singleValues}" "${multiValues}" ${ARGN})
   add_executable(test_${TEST_NAME} ${TEST_SOURCES})
-  target_link_libraries(test_${TEST_NAME} PUBLIC musica::musica GTest::gtest_main)
+  target_link_libraries(test_${TEST_NAME} PUBLIC musica::musica GTest::gtest_main yaml-cpp)
   if(MUSICA_ENABLE_OPENMP)
     target_link_libraries(test_${TEST_NAME} PUBLIC OpenMP::OpenMP_CXX)
   endif()

configs/analytical/reactions.json

@@ -7,14 +7,26 @@
       "reactions":
       [
         {
-          "type": "ARRHENIUS", "A": 0.00012, "B": 7, "C" : 75, "D": 50, "E": 0.5,
-          "reactants": {"B": {"qty": 1}},
-          "products": {"C": {"yield": 1}}
+          "type": "USER_DEFINED",
+          "MUSICA name" : "reaction 2",
+          "reactants": {"E": {"qty": 1}},
+          "products": {"F": {"yield": 1}}
+        },
+        {
+          "type": "USER_DEFINED",
+          "MUSICA name" : "reaction 1",
+          "reactants": {"D": {"qty": 1}},
+          "products": {"E": {"yield": 1}}
         },
         {
           "type": "ARRHENIUS", "A": 0.004, "C" : 50,
           "reactants": {"A": {"qty": 1}},
           "products": {"B": {"yield": 1}}
+        },
+        {
+          "type": "ARRHENIUS", "A": 0.012, "B": -2, "C" : 75, "D": 50, "E": 1.0e-6,
+          "reactants": {"B": {"qty": 1}},
+          "products": {"C": {"yield": 1}}
         }
       ]
     }

configs/analytical/species.json

@@ -9,6 +9,15 @@
     },
     {
       "name": "C", "type": "CHEM_SPEC"
+    },
+    {
+      "name": "D", "type": "CHEM_SPEC"
+    },
+    {
+      "name": "E", "type": "CHEM_SPEC"
+    },
+    {
+      "name": "F", "type": "CHEM_SPEC"
     }
   ]
 }

configs/chapman/reactions.json

@@ -14,7 +14,7 @@
                             "yield": 2.0
                         }
                     },
-                    "MUSICA name": "R1"
+                    "MUSICA name": "jO2"
                 },
                 {
                     "type": "ARRHENIUS",
@@ -37,7 +37,7 @@
                         "O": {},
                         "O2": {}
                     },
-                    "MUSICA name": "R3"
+                    "MUSICA name": "jO3->O"
                 },
                 {
                     "type": "ARRHENIUS",
@@ -62,7 +62,7 @@
                         "O1D": {},
                         "O2": {}
                     },
-                    "MUSICA name": "R5"
+                    "MUSICA name": "jO3->O1D"
                 },
                 {
                     "type": "ARRHENIUS",

docker/Dockerfile

@@ -1,5 +1,6 @@
-FROM fedora:35
+FROM fedora:latest
 
+ARG MUSICA_GIT_TAG=main
 ARG BUILD_TYPE=Release
 
 RUN dnf -y update \
@@ -15,6 +16,7 @@ RUN dnf -y update \
         json-devel \
         python \
         valgrind \
+        tree \
     && dnf clean all
 
 # Copy the musica code
@@ -25,6 +27,7 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
+             -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
     && cd build \
     && make install -j 8 
 

docker/Dockerfile.docs

@@ -1,4 +1,7 @@
-FROM fedora:37
+FROM fedora:latest
+
+ARG MUSICA_GIT_TAG=main
+ARG BUILD_TYPE=Release
 
 RUN dnf -y update \
     && dnf -y install \
@@ -17,7 +20,8 @@ RUN dnf -y update \
 
 COPY . /musica/
 
-RUN pip3 install -r /musica/docs/requirements.txt
+RUN python3 -m pip install --upgrade pip setuptools \
+    && python3 -m pip install -r /musica/docs/requirements.txt
 
 ARG SUFFIX=""
 ENV SWITCHER_SUFFIX=$SUFFIX
@@ -28,6 +32,8 @@ RUN mkdir /build \
       && cd /build \
       && cmake -D MUSICA_BUILD_DOCS=ON \
                -D MUSICA_ENABLE_TUVX=OFF \
+                -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
+                -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
                /musica \
       && make docs
 

docker/Dockerfile.fortran-gcc

@@ -1,5 +1,6 @@
-FROM fedora:35
+FROM fedora:latest
 
+ARG MUSICA_GIT_TAG=main
 ARG BUILD_TYPE=Release
 
 RUN dnf -y update \

docker/Dockerfile.fortran-gcc.integration

@@ -1,4 +1,4 @@
-FROM fedora:35
+FROM fedora:latest
 
 ARG MUSICA_GIT_TAG=main
 ARG BUILD_TYPE=Release
@@ -38,6 +38,7 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
+              -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
     && cd build \
     && make install -j