0.7.1 release (#190)

* Start on test_micm_box_model.F90. * Start on test_micm_box_model.F90. * In test_micm_box_model, create micm_t solver. * Initialize some variables. * Use configs/analytical. * Use configs/analytical. * Added micm solve. * Start on Chapter 2. * Literal include for test_micm_box_model. * Literal include json configs. * Updated CMakeLists.txt. * Add config file description. * Tutorial Chapter 2. * Tutorial Chapter 2. * Minor formatting. * Minor formatting. * Added link to MICM docs, test program output. * Start on tutorial CMakeLists.txt. * Created MUSICA/tutorial subdir. * Added MUSICA_INCLUDE_DIR and MUSICA_LIBRARY_DIR. * Switch to MUSICA_INSTALL_DIR/include /lib. * Include musicaConfig.cmake. * Include addtional cmake files. * Added Fortran to CMakeList LANGUAGES. * Added target_link_directories and libraries. * Added find_package(musica). * Comment use_package(musica_fortran), not working. * Added cmake usage comments. * Restored find_package for musica and musica_fortran. * Start on Tutorial Chapter 0 text. * Added literal include of Ch 0 CMakeLists.txt. * Chapter 0 intro. * Tutorial Chapter 0. * update cmake options * set vector matrix dimension * Use music-fortran instead of musica_fortran. * Added test_micm_box_model executable. * Updated test_micm_box_model with new micm solve. * Added deallocate( micm ) in test_micm_box_model. * Auto-format code using Clang-Format (#170) Co-authored-by: GitHub Actions <actions@github.com> * pypi version badge * fair software checklist badge * compilation flag for grid cells, vector matrix dimension * c api for vector ordered matrix * add vector matrix test * update fortran api * chage the build type * update python wrapper * resolve memory leak * fix intel docker * tuvx on * micm git tag * edit erorr * opdate the option name for open mp * remove open mp fortran in c tests * edit comment * Removed find_package lines in this version. * replace unique ptr T to T * replace tempalte with auto * Add profiles for TUV-x (#171) * add profiles for TUV-x * update TUV-x commit * split tuvx source into separate headers and modules * split TUV-x interface into separate modules * allow grid creation * fix grid updates * update fortran tuvx wrapper * address cross-compiler issue * fix invalid free * update actions * fix grid map ownership problem * finish profile and profile_map * address review comments * Auto-format code using Clang-Format * add map header * expose solver type enum to python * back to template * back to template * enum for solver type * enum solver type for fortran * add fortran 2023 feature comment * pass num grid cells to constructor * code clean up * space uniformly * specify enabled languages in top level cmake * comment out the tuvx openmp tests * revert back * revert back * Added tutorial/demo.f90 as a unit test. * Auto-format code using Clang-Format * Set demo.f90 path with PROJECT_SOURCE_DIR. * Added tutorial dir .dockerignore. * add radiator wrapper * working-on file of radiator header * fix typos, and incomplete parts * code clean up * add radiator src * fix bugs * fix bugs * Moved tutorial subdir to fortran/test/tutorial. * Removed demo_c executable. * Updated docs. * fix bugs in c sources * fix bugs in f90 sources * fix bugs * temp add radiator test * fix bugs * passed test * incomplete test * temp file for transfer * working version * fix test * fix bugs * fix fortran bugs * add radiator fortran test * test tag * add fortran test * add tests back: * fix docker integration * revert cmake * clean up * code cleanup * code clean up * revert back to main branch * 159 create an action to publish to pypi when we make a release (#184) * testing automated pypi release * trying to appropriately name the wheels * only need one version of python to build wheels for all other versions * trying to get macos to build successfully * excluding universal2 arch build for macos * seeing if arm64 works * trying to skip musllinux * trying to choose linux architecture support * trying to skip musllinux again * adding intel based mac build * trying to set the osx deployment target * trying a different way * that wasn't it * trying to force a minimum of 10.15 for macos? * setting action trigger * undoing version change * correcting project name * Address review comments * fix tuvx git tag * Python error checking (#189) * adding error checking, some debug statements for the python wrapper * adding error checking to python, updating micm tag * getting tests to pass * correcting a fortran test * newest tuvx commit * I don't know what's wrong with nvidia * Updating citation version number --------- Co-authored-by: David Fillmore <fillmore@ucar.edu> Co-authored-by: Jiwon Gim <jiwongim@ucar.edu> Co-authored-by: David Fillmore <1524012+dwfncar@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: Matt Dawson <mattldawson@gmail.com> Co-authored-by: Jiwon Gim <55209567+boulderdaze@users.noreply.github.com>
NCAR · Aug 7, 2024 · 98410c6 · 98410c6
1 parent bd9019f
commit 98410c6
Show file tree

Hide file tree

Showing 77 changed files with 7,933 additions and 1,365 deletions.
diff --git a/.dockerignore b/.dockerignore
@@ -16,4 +16,4 @@
 !python/
 !pyproject.toml
 !LICENSE
-!README.md
+!README.md
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,85 @@
+name: Publish Python Package
+
+on:
+  workflow_dispatch:
+  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: ${{ matrix.python-version }}
+
+    - uses: pypa/cibuildwheel@v2.17
+      env:
+        CIBW_ARCHS_MACOS: arm64 x86_64
+        CIBW_SKIP: cp27-* cp34-* cp35-* cp36-* *musllinux*
+        CIBW_BUILD: cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*
+
+    - name: Verify clean directory
+      run: git diff --exit-code
+      shell: bash
+
+    - name: Upload wheels
+      uses: actions/upload-artifact@v4
+      with:
+        name: cibw-wheels-${{ matrix.os }}-py${{ matrix.python-version }}
+        path: wheelhouse/*.whl
+
+  upload_all:
+    name: Upload release
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/musica
+    permissions:
+      id-token: write
+
+    steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+
+    - uses: actions/download-artifact@v4
+      with:
+        pattern: cibw-*
+        path: dist
+        merge-multiple: true
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -55,7 +55,7 @@ jobs:
     strategy:
       matrix:
         gcc_version: [12, 13, 14]
-        build_type: [Release]
+        build_type: [Debug, Release]
     env:
       CXX: g++-${{ matrix.gcc_version }}
       CC: gcc-${{ matrix.gcc_version }}

diff --git a/CITATION.cff b/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: 0.7.0
+version: 0.7.1
diff --git a/CMakeLists.txt b/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)
 

diff --git a/README.md b/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
 

diff --git a/cmake/dependencies.cmake b/cmake/dependencies.cmake
@@ -51,7 +51,7 @@ 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 v3.5.0)
+  set_git_default(MICM_GIT_TAG 6b1c58a9be14095e3f3c6df403c91c4e800f23de)
 
   FetchContent_Declare(micm
       GIT_REPOSITORY ${MICM_GIT_REPOSITORY}
@@ -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 674ee1e72853bb44d23c36602fa73c955b2f021d)
 
   FetchContent_Declare(tuvx
     GIT_REPOSITORY ${TUVX_GIT_REPOSITORY}

diff --git a/cmake/test_util.cmake b/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}")

diff --git a/configs/chapman/species.json b/configs/chapman/species.json
@@ -3,7 +3,7 @@
         {
             "name": "M",
             "type": "CHEM_SPEC",
-            "tracer type": "CONSTANT"
+            "tracer type": "THIRD_BODY"
         },
         {
             "name": "O2",

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -9,7 +9,6 @@ RUN dnf -y update \
         gfortran \
         gdb \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

diff --git a/docker/Dockerfile.fortran-gcc b/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 \
@@ -13,7 +13,6 @@ RUN dnf -y update \
     git \
     hdf5-devel \
     json-devel \
-    lapack-devel \
     lcov \
     libcurl-devel \
     m4 \
@@ -38,6 +37,7 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
+             -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
              -D MUSICA_BUILD_FORTRAN_INTERFACE=ON \
              -D MUSICA_ENABLE_MEMCHECK=ON \
     && cd build \

diff --git a/docker/Dockerfile.fortran-gcc.integration b/docker/Dockerfile.fortran-gcc.integration
@@ -14,7 +14,6 @@ RUN dnf -y update \
     git \
     hdf5-devel \
     json-devel \
-    lapack-devel \
     lcov \
     libcurl-devel \
     m4 \
@@ -50,6 +49,7 @@ 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
diff --git a/docker/Dockerfile.fortran-intel b/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
diff --git a/docker/Dockerfile.fortran-nvhpc b/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
diff --git a/docker/Dockerfile.memcheck b/docker/Dockerfile.memcheck
@@ -1,13 +1,14 @@
 FROM fedora:35
 
+ARG BUILD_TYPE=Debug
+
 RUN dnf -y update \
     && dnf -y install \
         cmake \
         gcc-c++ \
         gfortran \
         gdb \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \
@@ -22,7 +23,7 @@ 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 

diff --git a/docker/Dockerfile.mpi b/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 \
@@ -14,7 +16,6 @@ RUN sudo dnf -y install \
         gcc-c++ \
         gfortran \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \
@@ -38,9 +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_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 \

diff --git a/docker/Dockerfile.mpi_openmp b/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 \
@@ -14,7 +16,6 @@ RUN sudo dnf -y install \
         gcc-c++ \
         gfortran \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \
@@ -38,10 +39,10 @@ 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 \

diff --git a/docker/Dockerfile.openmp b/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 \
@@ -14,7 +16,6 @@ RUN sudo dnf -y install \
         gcc-c++ \
         gfortran \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \
@@ -37,9 +38,9 @@ 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++ \