musica 0.10.1__tar.gz → 0.11.1.1__tar.gz

{musica-0.10.1 → musica-0.11.1.1}/.dockerignore

@@ -13,7 +13,7 @@
 !include/
 !lib/
 !src/
-!python/
+!musica/
 !pyproject.toml
 !LICENSE
 !README.md

{musica-0.10.1 → musica-0.11.1.1}/.github/workflows/docker.yml

@@ -13,7 +13,7 @@ concurrency:
 
 jobs:
   docker-build-and-test:
-    name: Build and Test - ${{ matrix.dockerfile }}
+    name: Build and Test - ${{ matrix.dockerfile }} - ${{ matrix.build_type }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -27,7 +27,8 @@ jobs:
           - Dockerfile.mpi
           - Dockerfile.mpi_openmp
           - Dockerfile.python
-          - Dockerfile.pip
+          - Dockerfile.nvhpc
+          - Dockerfile.coverage
         build_type: [Release, Debug]
     steps:
       - name: Checkout code
@@ -42,7 +43,7 @@ jobs:
         run: docker build -t musica -f docker/${{ 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' && matrix.dockerfile != 'Dockerfile.pip'
+        if: matrix.dockerfile != 'Dockerfile.coverage' && matrix.dockerfile != 'Dockerfile.nvhpc'
         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

{musica-0.10.1 → musica-0.11.1.1}/.github/workflows/gh_pages.yml

@@ -1,7 +1,13 @@
 # Build and deploy documentation to GitHub Pages
 name: GitHub Pages
 
-on: [ push, pull_request ]
+on:
+  push:
+    branches:
+      - main
+      - release
+  pull_request:
+  workflow_dispatch:
 
 env:
   DEFAULT_BRANCH: "release"
@@ -132,3 +138,22 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: _gh-pages/
           force_orphan: true
+
+  comment-doc-link:
+    name: Comment documentation link on PR
+    if: ${{ github.event_name == 'pull_request' && github.event.action == 'opened' }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Post documentation link
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const branchName = context.payload.pull_request.head.ref;
+            const docLink = `https://ncar.github.io/musica/branch/${branchName}/`;
+            const commentBody = `📄 Documentation for this branch is available at: [${docLink}](${docLink})`;
+            await github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.payload.pull_request.number,
+              body: commentBody
+            });

{musica-0.10.1 → musica-0.11.1.1}/.github/workflows/python-tests.yml

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

musica-0.10.1/.github/workflows/release.yml → musica-0.11.1.1/.github/workflows/python-wheels.yml

@@ -43,20 +43,20 @@ jobs:
     - uses: actions/checkout@v4
       with:
         submodules: true
-
+    
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: pypa/cibuildwheel@v2.17
+    - name: CI Build Wheels
+      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
+        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
 
     - name: Upload wheels
       uses: actions/upload-artifact@v4

{musica-0.10.1 → musica-0.11.1.1}/.github/workflows/windows.yml

@@ -74,13 +74,13 @@ jobs:
     continue-on-error: true 
     strategy:
       matrix:
-        version: [11, 12, 13, 14, 15]
+        version: [12.0.0, 13.0.0, 14.0.0, 15.0.0, 16.0.0, 17.0.1, 18.1.0, 19.1.0, 20.1.0]
 
     steps:
       - uses: actions/checkout@v4
 
       - 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"
+        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"
 
       - uses: actions/setup-python@v5
       - run: pip install numpy

{musica-0.10.1 → musica-0.11.1.1}/.gitignore

@@ -1,6 +1,7 @@
 # cmake and build stuff
 
 build/
+install/
 CMakeCache.txt
 CMakeFiles
 .DS_Store
@@ -11,4 +12,5 @@ musica.egg-info
 **/*.mod
 
 **/*__pycache__*
-**/*.pyc
+**/*.pyc
+wheelhouse

{musica-0.10.1 → musica-0.11.1.1}/CMakeLists.txt

@@ -1,10 +1,10 @@
 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 0.10.1)
+project(musica-distribution VERSION 0.11.1.1)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
-set(CMAKE_USER_MAKE_RULES_OVERRIDE ${CMAKE_MODULE_PATH}/SetDefaults.cmake)
+set(CMAKE_USER_MAKE_RULES_OVERRIDE ${PROJECT_SOURCE_DIR}/cmake/SetDefaults.cmake)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
 if(NOT CMAKE_BUILD_TYPE)
@@ -30,21 +30,15 @@ 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_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)
 
-set(MUSICA_SET_MICM_VECTOR_MATRIX_SIZE "4" CACHE STRING "Set MICM vector-ordered matrix dimension")
+set(MUSICA_GPU_TYPE "None" CACHE STRING "The GPU type being targeted")
 
-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)
+set(MUSICA_SET_MICM_DEFAULT_VECTOR_SIZE "4" CACHE STRING "Set MICM vector-ordered matrix dimension")
 
 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()
+  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)
 
 ################################################################################
 # Projet wide setup variables 
@@ -64,6 +58,23 @@ elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "PGI")
   list(APPEND musica_compile_definitions MUSICA_USING_PGI)
 endif()
 
+# Set the C++ standard library if it is not already set
+if(NOT CMAKE_CXX_STANDARD_LIBRARIES)
+  if(${CMAKE_CXX_COMPILER_ID} MATCHES "GNU")
+    set(CMAKE_CXX_STANDARD_LIBRARIES "-lstdc++")
+  elseif(${CMAKE_CXX_COMPILER_ID} MATCHES "Intel")
+    set(CMAKE_CXX_STANDARD_LIBRARIES "-lstdc++")
+  elseif(${CMAKE_CXX_COMPILER_ID} MATCHES "IBM")
+    set(CMAKE_CXX_STANDARD_LIBRARIES "-lstdc++")
+  elseif(${CMAKE_CXX_COMPILER_ID} MATCHES "NVHPC")
+    set(CMAKE_CXX_STANDARD_LIBRARIES "-lstdc++")
+  elseif(${CMAKE_CXX_COMPILER_ID} MATCHES "Clang")
+    set(CMAKE_CXX_STANDARD_LIBRARIES "-lstdc++") # use GNU standard library
+  else()
+    set(CMAKE_CXX_STANDARD_LIBRARIES "-lstdc++") # default to most common name
+  endif()
+endif()
+
 if(MUSICA_BUILD_C_CXX_INTERFACE)
   # must be global so that it also applies to dependencies like google test, unless we want
   # to set it for each target
@@ -89,15 +100,24 @@ set(MEMCHECK_SUPPRESS "--suppressions=${PROJECT_SOURCE_DIR}/valgrind.supp")
 ################################################################################
 # Dependencies
 
-include(dependencies)
-
-if(MUSICA_BUILD_DOCS)
-  add_subdirectory(docs)
+if(MUSICA_BUNDLE_DEPENDENCIES)
+  include(${PROJECT_SOURCE_DIR}/cmake/dependencies.cmake)
 endif()
 
 ################################################################################
 # Tests
 if(MUSICA_ENABLE_TESTS)
+  if(MUSICA_ENABLE_COVERAGE)
+    include(CodeCoverage)
+    append_coverage_compiler_flags()
+    setup_target_for_coverage_lcov(
+        NAME coverage
+        EXECUTABLE "ctest"
+        EXCLUDE "${PROJECT_SOURCE_DIR}/test/*"
+        BASE_DIRECTORY "${PROJECT_SOURCE_DIR}/src")
+    
+  endif()
+  
   enable_testing()
 endif()
 
@@ -107,6 +127,10 @@ if(MUSICA_BUILD_C_CXX_INTERFACE)
   add_subdirectory(src)
 endif()
 
+if(MUSICA_BUILD_DOCS)
+  add_subdirectory(docs)
+endif()
+
 ################################################################################
 # MUSICA-Fortran
 if(MUSICA_BUILD_FORTRAN_INTERFACE)
@@ -116,11 +140,11 @@ endif()
 ################################################################################
 # Musica python
 if(MUSICA_ENABLE_PYTHON_LIBRARY)
-  add_subdirectory(python)
+  add_subdirectory(musica)
 endif()
 
 ################################################################################
 ###
 # Configure and display a summary file for how musica was built.
 ###
-include(summary)
+include(${PROJECT_SOURCE_DIR}/cmake/summary.cmake)

{musica-0.10.1 → musica-0.11.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: musica
-Version: 0.10.1
+Version: 0.11.1.1
 Summary: MUSICA is a Python library for performing computational simulations in atmospheric chemistry.
 Author-Email: Matthew Dawsom <mattdawson@ucar.edu>, Jiwon Gim <jiwongim@ucar.edu>, David Fillmore <fillmore@ucar.edu>, Kyle Shores <kshores@ucar.edu>, Montek Thind <mthind@ucar.edu>
 Maintainer-Email: ACOM MUSICA Developers <musica-support@ucar.edu>
@@ -209,6 +209,10 @@ License:                                  Apache License
 Project-URL: homepage, https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
 Provides-Extra: test
 Requires-Dist: numpy; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: gpu
+Requires-Dist: nvidia-cublas-cu12; extra == "gpu"
+Requires-Dist: nvidia-cuda-runtime-cu12; extra == "gpu"
 Description-Content-Type: text/markdown
 
 # MUSICA
@@ -222,6 +226,7 @@ Description-Content-Type: text/markdown
 [![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)
+[![codecov](https://codecov.io/gh/NCAR/musica/branch/main/graph/badge.svg)](https://codecov.io/gh/NCAR/musica)
 
 Multi-Scale Infrastructure for Chemistry and Aerosols
 
@@ -274,6 +279,22 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
         -DTUVX_GIT_TAG=a6b2c4d8745
 
 
+### Python build
+Musica has python bindings. If you want to install the python package, you may `pip install musica`.
+
+To build the package locally,
+
+```
+pip install -e .
+```
+
+If you have an NVIDIA GPU and cuda installed, you can enable a build of musica with GPU support by setting the environment 
+variable `BUILD_GPU`.
+
+```
+BUILD_GPU=1 pip install -e .
+```
+
 ## Citing MUSICA
 
 MUSICA can be cited in at least two ways. The first is to cite [the paper](https://doi.org/10.1175/BAMS-D-19-0331.1) that defines the vision

{musica-0.10.1 → musica-0.11.1.1}/README.md

@@ -9,6 +9,7 @@
 [![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)
+[![codecov](https://codecov.io/gh/NCAR/musica/branch/main/graph/badge.svg)](https://codecov.io/gh/NCAR/musica)
 
 Multi-Scale Infrastructure for Chemistry and Aerosols
 
@@ -61,6 +62,22 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
         -DTUVX_GIT_TAG=a6b2c4d8745
 
 
+### Python build
+Musica has python bindings. If you want to install the python package, you may `pip install musica`.
+
+To build the package locally,
+
+```
+pip install -e .
+```
+
+If you have an NVIDIA GPU and cuda installed, you can enable a build of musica with GPU support by setting the environment 
+variable `BUILD_GPU`.
+
+```
+BUILD_GPU=1 pip install -e .
+```
+
 ## Citing MUSICA
 
 MUSICA can be cited in at least two ways. The first is to cite [the paper](https://doi.org/10.1175/BAMS-D-19-0331.1) that defines the vision