musica 0.7.0__tar.gz → 0.7.1__tar.gz

{musica-0.7.0 → musica-0.7.1}/.dockerignore

@@ -16,4 +16,4 @@
 !python/
 !pyproject.toml
 !LICENSE
-!README.md
+!README.md

musica-0.7.1/.github/workflows/release.yml

@@ -0,0 +1,86 @@
+name: Publish Python Package
+
+on:
+  workflow_dispatch:
+  push:
+  # release:
+  #   types:
+  #     - published
+
+jobs:
+  build_sdist:
+    name: Build SDist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - name: Build SDist
+      run: pipx run build --sdist
+
+    - name: Check metadata
+      run: pipx run twine check dist/*
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-sdist
+        path: dist/*.tar.gz
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - uses: pypa/cibuildwheel@v2.17
+      env:
+        CIBW_ARCHS_MACOS: arm64 
+        CIBW_SKIP: cp27-* cp34-* cp35-* cp36-* *musllinux*
+        CIBW_BUILD: cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*
+
+    - name: Verify clean directory
+      run: git diff --exit-code
+      shell: bash
+
+    - name: Upload wheels
+      uses: actions/upload-artifact@v4
+      with:
+        name: cibw-wheels-${{ matrix.os }}-py${{ matrix.python-version }}
+        path: wheelhouse/*.whl
+
+  upload_all:
+    name: Upload release
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/<your-pypi-project-name>
+    permissions:
+      id-token: write
+
+    steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+
+    - uses: actions/download-artifact@v4
+      with:
+        pattern: cibw-*
+        path: dist
+        merge-multiple: true
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

{musica-0.7.0 → musica-0.7.1}/.github/workflows/ubuntu.yml

@@ -55,7 +55,7 @@ jobs:
     strategy:
       matrix:
         gcc_version: [12, 13, 14]
-        build_type: [Release]
+        build_type: [Debug, Release]
     env:
       CXX: g++-${{ matrix.gcc_version }}
       CC: gcc-${{ matrix.gcc_version }}

{musica-0.7.0 → musica-0.7.1}/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 0.7.0)
+project(musica-distribution VERSION 0.7.1)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${CMAKE_MODULE_PATH}/SetDefaults.cmake)
@@ -30,6 +30,8 @@ option(MUSICA_BUILD_DOCS "Build the documentation" OFF)
 option(MUSICA_ENABLE_MICM "Enable MICM" ON)
 option(MUSICA_ENABLE_TUVX "Enable TUV-x" ON)
 
+set(MUSICA_SET_MICM_VECTOR_MATRIX_SIZE "1" CACHE STRING "Set MICM vector-ordered matrix dimension")
+
 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)
 

{musica-0.7.0 → musica-0.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: musica
-Version: 0.7.0
+Version: 0.7.1
 Summary: MUSICA is a Python library for performing computational simulations in atmospheric chemistry.
 Home-page: https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
 Author-Email: Matthew Dawsom <mattdawson@ucar.edu>, Jiwon Gim <jiwongim@ucar.edu>, David Fillmore <fillmore@ucar.edu>, Kyle Shores <kshores@ucar.edu>
@@ -220,6 +220,8 @@ Description-Content-Type: text/markdown
 [![windows](https://github.com/NCAR/musica/actions/workflows/windows.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/windows.yml)
 [![pip](https://github.com/NCAR/musica/actions/workflows/pip.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/pip.yml)
 [![DOI](https://zenodo.org/badge/550370528.svg)](https://zenodo.org/doi/10.5281/zenodo.7458559)
+[![PyPI version](https://badge.fury.io/py/musica.svg)](https://pypi.org/p/musica)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=22322&r=123)
 
 Multi-Scale Infrastructure for Chemistry and Aerosols
 

{musica-0.7.0 → musica-0.7.1}/README.md

@@ -7,6 +7,8 @@
 [![windows](https://github.com/NCAR/musica/actions/workflows/windows.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/windows.yml)
 [![pip](https://github.com/NCAR/musica/actions/workflows/pip.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/pip.yml)
 [![DOI](https://zenodo.org/badge/550370528.svg)](https://zenodo.org/doi/10.5281/zenodo.7458559)
+[![PyPI version](https://badge.fury.io/py/musica.svg)](https://pypi.org/p/musica)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=22322&r=123)
 
 Multi-Scale Infrastructure for Chemistry and Aerosols
 

{musica-0.7.0 → musica-0.7.1}/cmake/dependencies.cmake

@@ -60,6 +60,7 @@ if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE)
   )
   set(MICM_ENABLE_TESTS OFF)
   set(MICM_ENABLE_EXAMPLES OFF)
+  set(MICM_DEFAULT_VECTOR_MATRIX_SIZE ${MUSICA_SET_MICM_VECTOR_MATRIX_SIZE})
 
   FetchContent_MakeAvailable(micm)
 endif()
@@ -74,7 +75,7 @@ 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 v0.9.0)
+  set_git_default(TUVX_GIT_TAG 80f896a0fb591987c2a79209377bd6f599b4fb6f)
 
   FetchContent_Declare(tuvx
     GIT_REPOSITORY ${TUVX_GIT_REPOSITORY}

{musica-0.7.0 → musica-0.7.1}/cmake/test_util.cmake

@@ -43,7 +43,7 @@ function(create_standard_test_cxx)
   add_executable(test_${TEST_NAME} ${TEST_SOURCES})
   target_link_libraries(test_${TEST_NAME} PUBLIC musica::musica GTest::gtest_main)
   if(MUSICA_ENABLE_OPENMP)
-    target_link_libraries(test_${TEST_NAME} PUBLIC OpenMP::OpenMP_CXX OpenMP::OpenMP_Fortran)
+    target_link_libraries(test_${TEST_NAME} PUBLIC OpenMP::OpenMP_CXX)
   endif()
   if(NOT DEFINED TEST_WORKING_DIRECTORY)
     set(TEST_WORKING_DIRECTORY "${CMAKE_BINARY_DIR}")

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.fortran-gcc

@@ -1,6 +1,6 @@
 FROM fedora:35
 
-ARG BUILD_TYPE=release
+ARG BUILD_TYPE=Release
 
 RUN dnf -y update \
   && dnf -y install \

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.fortran-gcc.integration

@@ -50,6 +50,7 @@ RUN cd musica/fortran/test/fetch_content_integration \
         -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
         -D MUSICA_ENABLE_MICM=ON \
         -D MUSICA_ENABLE_TUVX=OFF \
+        -D MUSICA_ENABLE_MEMCHECK=ON \
     && make -j
 
 WORKDIR musica/fortran/test/fetch_content_integration/build

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.fortran-intel

@@ -12,6 +12,7 @@ ARG MUSICA_GIT_TAG=main
 RUN apt update \
     && apt -y install \
     cmake \
+    cmake-curses-gui \
     curl \
     gcc \
     gfortran \
@@ -50,7 +51,7 @@ COPY . musica
 RUN cd musica \
     && cmake -S . \
              -B build \
-             -D CMAKE_BUILD_TYPE=Release \
+             -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
     && cd build \
     && make install -j
 
@@ -65,8 +66,7 @@ RUN cd musica/fortran/test/fetch_content_integration \
         -D CMAKE_BUILD_TYPE=Release \
         -D CMAKE_EXE_LINKER_FLAGS="-Wl,--copy-dt-needed-entries" \
         -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
+        -D MUSICA_ENABLE_MEMCHECK=ON \
     && make -j
 
-WORKDIR musica/fortran/test/fetch_content_integration/build
-RUN cp -r /musica/build/_deps/tuvx-src/examples/ .
-RUN cp -r /musica/build/_deps/tuvx-src/data/ .
+WORKDIR musica/fortran/test/fetch_content_integration/build

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.fortran-nvhpc

@@ -66,6 +66,7 @@ RUN cd musica/fortran/test/fetch_content_integration \
         -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
         -D CMAKE_EXE_LINKER_FLAGS="-Wl,--copy-dt-needed-entries" \
         -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
+        -D MUSICA_ENABLE_MEMCHECK=ON \
     && make -j
 
 WORKDIR musica/fortran/test/fetch_content_integration/build

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.memcheck

@@ -1,5 +1,7 @@
 FROM fedora:35
 
+ARG BUILD_TYPE=Debug
+
 RUN dnf -y update \
     && dnf -y install \
         cmake \
@@ -22,7 +24,7 @@ COPY . musica
 RUN cd musica \
     && cmake -S . \
              -B build \
-             -D CMAKE_BUILD_TYPE=Debug \
+             -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
              -D MUSICA_ENABLE_MEMCHECK=ON \
     && cd build \
     && make install -j 8 

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.mpi

@@ -1,5 +1,7 @@
 FROM fedora:35
 
+ARG BUILD_TYPE=Debug
+
 RUN dnf -y update \
     && dnf install -y sudo \
     && adduser test_user \
@@ -38,9 +40,9 @@ RUN sudo chown -R test_user.test_user musica
 RUN cd musica \
     && cmake -S . \
              -B build \
-             -D CMAKE_BUILD_TYPE=debug \
-             -D ENABLE_TESTS=ON \
-             -D ENABLE_MPI=ON \
+             -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
+             -D MUSICA_ENABLE_TESTS=ON \
+             -D MUSICA_ENABLE_MPI=ON \
              -D CMAKE_Fortran_COMPILER=/usr/lib64/openmpi/bin/mpif90 \
              -D CMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc \
              -D CMAKE_CXX_COMPILER=/usr/lib64/openmpi/bin/mpicxx \

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.mpi_openmp

@@ -1,5 +1,7 @@
 FROM fedora:35
 
+ARG BUILD_TYPE=Debug
+
 RUN dnf -y update \
     && dnf install -y sudo \
     && adduser test_user \
@@ -38,10 +40,10 @@ RUN sudo chown -R test_user.test_user musica
 RUN cd musica \
     && cmake -S . \
              -B build \
-             -D CMAKE_BUILD_TYPE=debug \
-             -D ENABLE_MPI=ON \
-             -D ENABLE_OPENMP=ON \
-             -D ENABLE_TESTS=ON \
+             -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
+             -D MUSICA_ENABLE_MPI=ON \
+             -D MUSICA_ENABLE_OPENMP=ON \
+             -D MUSICA_ENABLE_TESTS=ON \
              -D CMAKE_Fortran_COMPILER=/usr/lib64/openmpi/bin/mpif90 \
              -D CMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc \
              -D CMAKE_CXX_COMPILER=/usr/lib64/openmpi/bin/mpicxx \

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.openmp

@@ -1,5 +1,7 @@
 FROM fedora:35
 
+ARG BUILD_TYPE=Debug
+
 RUN dnf -y update \
     && dnf install -y sudo \
     && adduser test_user \
@@ -37,9 +39,9 @@ RUN sudo chown -R test_user.test_user musica
 RUN cd musica \
     && cmake -S . \
              -B build \
-             -D CMAKE_BUILD_TYPE=debug \
-             -D ENABLE_OPENMP:BOOL=TRUE \
-             -D ENABLE_TESTS=ON \
+             -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
+             -D MUSICA_ENABLE_OPENMP=ON \
+             -D MUSICA_ENABLE_TESTS=ON \
              -D CMAKE_Fortran_COMPILER=/usr/lib64/openmpi/bin/mpif90 \
              -D CMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc \
              -D CMAKE_CXX_COMPILER=/usr/lib64/openmpi/bin/mpic++ \

{musica-0.7.0 → musica-0.7.1}/docker/Dockerfile.python

@@ -1,5 +1,7 @@
 FROM fedora:latest
 
+ARG BUILD_TYPE=Release
+
 RUN dnf -y update \
     && dnf -y install \
         cmake \
@@ -45,7 +47,7 @@ RUN pip install -r requirements.txt
 RUN cd musica \
     && cmake -S . \
              -B build \
-             -D CMAKE_BUILD_TYPE=Release \
+             -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
              -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
              -D MUSICA_ENABLE_TUVX=OFF \
     && cd build \

musica-0.7.1/docs/source/tutorial/chapter0.rst

@@ -0,0 +1,40 @@
+Chapter 0
+=========
+
+The MUSICA CMake Package
+------------------------
+
+The MUSICA library installs with `CMake` ``musica`` and ``musica_fortran``
+packages to facilitate linking
+to higher level libraries and host models that have CMake build systems.
+
+A minimal ``CMakeLists.txt`` file designed to link the ``musica_fortran`` library
+to a Fortran program ``demo_f.f90`` is exhibited below
+
+  .. literalinclude:: ../../../fortran/test/tutorial/CMakeLists.txt
+    :language: cmake
+
+These `CMake` directives are essentially equivalent to compilation on the command line via
+
+.. code-block:: bash
+
+  gfortran -o demo_f demo_f.f90 -I<MUSICA_DIR>/include -L<MUSICA_DIR>/lib -lmusica-fortran -lmusica -lstdc++
+
+``<MUSICA_DIR>`` is the full path of the MUSICA installation directory,
+specified by the option ``CMAKE_INSTALL_PREFIX``
+during the `cmake` configuration process.
+
+Common practice is to create a ``build`` subdir (relative to the top level ``CMakeLists.txt`` file, say).
+
+.. code-block:: bash
+
+  mkdir build
+  cd build
+
+The ``cmake`` could then be invoked with:
+
+.. code-block:: bash
+
+  cmake -DMUSICA_INSTALL_DIR <MUSICA_DIR> ..
+  cmake --build .
+

musica-0.7.1/docs/source/tutorial/chapter2.rst

@@ -0,0 +1,65 @@
+Chapter 2
+=========
+
+An MICM Box Model Fortran Example
+---------------------------------
+
+In this next MUSICA Fortran example,
+we will setup a MICM solver, starting with a set of MICM configuration files,
+and run the solver for a single integration time step.
+
+The MICM configuration is specified in a top-level ``config.json`` file,
+which simply lists the chemical species configuration file followed by
+the reactions configuration file.
+
+  .. literalinclude:: ../../../configs/analytical/config.json
+    :language: json
+
+For this example, we will have a system of three chemical species
+`A`, `B`, and `C`, defined in the JSON file ``species.json`` as follows:
+
+  .. literalinclude:: ../../../configs/analytical/species.json
+    :language: json
+
+The ``reactions.json`` specifies a mechanism, or a set of reactions for the system.
+Here, we will introduce two Arrhenius type reactions, the first
+with `B` evolving to `C`, and specifying all five reaction parameters,
+and the second reaction with `A` evolving to `B` and using only two reaction parameters. 
+The mechanism configuration might then be set up as:
+
+  .. literalinclude:: ../../../configs/analytical/reactions.json
+    :language: json
+
+More information on MICM configurations and reactions can be found in the MICM documentation
+at `https://ncar.github.io/micm/user_guide/`_
+
+The Fortran example code is shown below in full: 
+
+  .. literalinclude:: ../../../fortran/test/fetch_content_integration/test_micm_box_model.F90
+    :language: f90
+
+From the ``musica_util`` module we need the Fortran types
+``error_t``, ``string_t``, and ``mapping_t``.
+A pointer to a ``musica_micm::micm_t`` will serve as the interface to the MICM solver
+(in the example the pointer name is ``micm``).
+Note that the ``config_path`` in the code sample has been set to ``configs/analytical``,
+so that subdir should be created relative to the main program and contain
+the MICM JSON configuration files,
+or otherwise the ``config_path`` should be modified appropriately.
+The initial species concentrations are initialized in the ``concentrations`` array,
+which is an argument to the MICM solver.
+
+Finally, a single time step solution is obtained through a call to ``micm%solve``,
+after which the updated concentrations may be displayed.
+
+.. code-block:: bash
+
+  $ ./test_micm_box_model
+    Creating MICM solver...
+    Species Name:A, Index:           1
+    Species Name:B, Index:           2
+    Species Name:C, Index:           3
+    Solving starts...
+    After solving, concentrations  0.38  1.61E-009  2.62
+  $
+

{musica-0.7.0 → musica-0.7.1}/docs/source/tutorial/tutorial.rst

@@ -6,4 +6,6 @@ Tutorial
    :maxdepth: 1
    :caption: Contents:
 
+   chapter0.rst
    chapter1.rst
+   chapter2.rst

{musica-0.7.0 → musica-0.7.1}/fortran/CMakeLists.txt

@@ -63,10 +63,7 @@ if (MUSICA_ENABLE_MICM)
   )
 endif()
 if (MUSICA_ENABLE_TUVX)
-  target_sources(musica-fortran
-    PRIVATE
-      tuvx.F90
-  )
+  add_subdirectory(tuvx)
 endif()
 
 # Add flags for gfortran