musica 0.9.0__tar.gz → 0.10.0__tar.gz

musica-0.10.0/.github/workflows/close_stale_issues.yml

@@ -0,0 +1,24 @@
+name: 'Close stale issues'
+on:
+  schedule:
+    # Run every day at 7PM UTC
+    - cron: '0 19 * * *'
+jobs:
+  close-stale:
+    permissions:
+      issues: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v9
+        with:
+          stale-issue-message: 'This issue is stale because it has been open 180 days with no activity. Remove stale label or comment or this will be closed in 14 days.'
+          close-issue-message: 'This issue was closed because it has been stalled for 14 days with no activity.'
+          days-before-stale: 180 # Mark as stale after 180 days of inactivity
+          days-before-close: 14  # Close issue if no activity after 14 days of being stale
+          days-before-pr-close: -1
+          # Issues with this label are exempt from being checked if they are stale...
+          exempt-issue-labels: Low Priority
+          # Below are currently defaults, but given in case we decide to change
+          operations-per-run: 30           # This setting specifies the maximum number of operations (such as marking issues as stale or closing them) that the action will perform in a single run
+          stale-issue-label: Stale         # This setting defines the label that will be applied to issues that are considered stale
+          close-issue-reason: not_planned  # This setting specifies the reason that will be given when closing stale issues

musica-0.9.0/.github/workflows/pep8.yml → musica-0.10.0/.github/workflows/format-python.yml

@@ -1,4 +1,4 @@
-name: Pep8
+name: Format python
 
 on:
   push:

{musica-0.9.0 → musica-0.10.0}/.github/workflows/mac.yml

@@ -39,7 +39,6 @@ jobs:
       - run: pip install numpy --user
 
       - name: Run Cmake 
-        if: matrix.compiler.cpp != 'g++-13'
         run: |
             PYTHON_PATH=$(which python)
             cmake -S . -B build \
@@ -49,23 +48,8 @@ jobs:
                 -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
                 -D Python3_EXECUTABLE=$PYTHON_PATH 
 
-      - name: Run Cmake 
-        if: matrix.compiler.cpp == 'g++-13'
-        run: |
-            PYTHON_PATH=$(which python)
-            # for some reason gcc 13 was having issues finding the correct osx sdk
-            # it seems it was a known issue: https://github.com/actions/runner-images/issues/9997
-            # for some reason, passing in an empty string for the osx sysroot fixed the issue
-            cmake -S . -B build \
-                -D CMAKE_CXX_FLAGS=-Wl,-ld_classic \
-                -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                -D MUSICA_GIT_TAG=${{ github.sha }} \
-                -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
-                -D Python3_EXECUTABLE=$PYTHON_PATH \
-                -D CMAKE_OSX_SYSROOT=""
-
       - name: Build
-        run: cmake --build build --verbose --parallel 10
+        run: cmake --build build --verbose
 
       - name: Run tests
         run: |

musica-0.9.0/.github/workflows/pip.yml → musica-0.10.0/.github/workflows/python-tests.yml

@@ -1,4 +1,4 @@
-name: Pip
+name: Python tests
 
 on:
   push:

{musica-0.9.0 → musica-0.10.0}/.github/workflows/release.yml

@@ -1,6 +1,10 @@
 name: Publish Python Package
 
 on:
+  push:
+    branches:
+      - main
+  pull_request:
   workflow_dispatch:
   release:
     types:
@@ -63,6 +67,7 @@ jobs:
   upload_all:
     name: Upload release
     needs: [build_wheels, build_sdist]
+    if: github.event_name == 'release' && github.event.action == 'published'
     runs-on: ubuntu-latest
     environment:
       name: pypi

{musica-0.9.0 → musica-0.10.0}/.github/workflows/ubuntu.yml

@@ -41,24 +41,28 @@ jobs:
           sudo apt-get install -y python3-numpy
 
       - 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=${{ matrix.options.python }}
+                              -D MUSICA_ENABLE_PYTHON_LIBRARY=${{ matrix.options.python }} \
+                              -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
-        if: matrix.compiler.fc != 'gfortran-13' && matrix.options.tuvx != 'ON'
         run: cmake --build build --verbose
+      
+      - name: List the built files
+        run: |
+          cd build
+          ls -l
+          ls -l lib
 
       - 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
@@ -80,7 +84,11 @@ 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=${{ matrix.build_type }} -D MUSICA_GIT_TAG=${{ github.sha }} -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 \
+                              -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --verbose --parallel 1

{musica-0.9.0 → musica-0.10.0}/.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_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+        run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - 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 ${{ matrix.architecture }} -D MUSICA_GIT_TAG=${{ github.sha }} -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 -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
     - 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_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+        run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --parallel
@@ -115,10 +115,60 @@ jobs:
       - run: pip install numpy
 
       - name: Run CMake
-        run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -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 -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --config Debug --parallel
 
       - name: Test
         run: cd build ; ctest -C Debug --output-on-failure --verbose
+
+  fortran:
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        build_type: [Debug, Release]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup MSYS2
+        uses: msys2/setup-msys2@v2
+        with:
+          update: true
+          install: >-
+            base-devel
+            mingw-w64-x86_64-toolchain
+            mingw-w64-x86_64-gcc
+            mingw-w64-x86_64-gcc-fortran
+            mingw-w64-x86_64-cmake
+            mingw-w64-x86_64-netcdf
+            mingw-w64-x86_64-netcdf-fortran
+          msystem: MINGW64
+
+      - name: Add MSYS2 mingw64 to PATH
+        shell: msys2 {0}
+        run: echo "C:/msys64/mingw64/bin" >> $GITHUB_PATH
+
+      - name: Configure with CMake
+        shell: msys2 {0}
+        run: |
+          cmake -S . -B build -G "MinGW Makefiles" \
+                              -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                              -D MUSICA_GIT_TAG=${{ github.sha }} \
+                              -D MUSICA_ENABLE_MICM=ON \
+                              -D MUSICA_ENABLE_TUVX=ON \
+                              -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
+                              -D MUSICA_BUILD_FORTRAN_INTERFACE=ON \
+                              -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+
+      - name: Build the project
+        shell: msys2 {0}
+        run: cmake --build build  --verbose
+
+      - name: Run tests
+        shell: msys2 {0}
+        run: ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
+        working-directory: build

{musica-0.9.0 → musica-0.10.0}/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: 0.9.0
+version: 0.10.0

{musica-0.9.0 → musica-0.10.0}/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 0.9.0)
+project(musica-distribution VERSION 0.10.0)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${CMAKE_MODULE_PATH}/SetDefaults.cmake)
@@ -29,6 +29,7 @@ option(MUSICA_ENABLE_MEMCHECK "Enable memory checking" OFF)
 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)
 
 set(MUSICA_SET_MICM_VECTOR_MATRIX_SIZE "4" CACHE STRING "Set MICM vector-ordered matrix dimension")
 
@@ -45,19 +46,11 @@ if(MUSICA_CREATE_ENVIRONMENT_MODULE)
   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 ${PROJECT_SOURCE_DIR}/fortran)
 set(MUSICA_PROJECT_SRC_DIR ${PROJECT_SOURCE_DIR})
 
 set(musica_compile_definitions "")

musica-0.10.0/PKG-INFO

@@ -0,0 +1,314 @@
+Metadata-Version: 2.2
+Name: musica
+Version: 0.10.0
+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>
+License:                                  Apache License
+                                    Version 2.0, January 2004
+                                 http://www.apache.org/licenses/
+         
+            TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+         
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+         
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+Project-URL: homepage, https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
+Provides-Extra: test
+Requires-Dist: numpy; extra == "test"
+Description-Content-Type: text/markdown
+
+# MUSICA
+[![GitHub Releases](https://img.shields.io/github/release/NCAR/musica.svg)](https://github.com/NCAR/musica/releases)
+[![License](https://img.shields.io/github/license/NCAR/musica.svg)](https://github.com/NCAR/musica/blob/main/LICENSE)
+[![docker](https://github.com/NCAR/musica/actions/workflows/docker.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/docker.yml)
+[![macOS](https://github.com/NCAR/musica/actions/workflows/mac.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/mac.yml)
+[![ubuntu](https://github.com/NCAR/musica/actions/workflows/ubuntu.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/ubuntu.yml)
+[![windows](https://github.com/NCAR/musica/actions/workflows/windows.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/windows.yml)
+[![Python tests](https://github.com/NCAR/musica/actions/workflows/python-tests.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/python-tests.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 is a collection of modeling software, tools, and grids, that
+allow for robust modeling of chemistry in Earth's atmosphere.
+
+At present the project encompasses these components
+- [TUV-x](https://github.com/NCAR/tuv-x)
+    - A photolysis rate calculator 
+
+- [MICM](https://github.com/NCAR/micm)
+    - Model Independent Chemical Module
+
+## Available grids
+
+Pre-made grids for use in MUSICA are available [here](https://wiki.ucar.edu/display/MUSICA/Available+Grids).
+
+# Contributors guide
+Checkout our [software development plan](docs/Software%20Development%20Plan.pdf)
+to see how you can contribute new science to MUSICA software.
+
+## Developer Options
+
+### Specifying dependency versions via paramaterization at configure time
+
+Introduced in [Pull Request #124](https://github.com/NCAR/musica/pull/124), it is possible for developers to specify which versions of various dependencies should be used. These options are currently limited to those dependencies managed via `FetchContent`.  This change allows for more easily testing `musica` against changes committed in different repositories and branches.  The environmental variables introduced are outlined in the following table. 
+
+#### CMake Dependency Variables
+
+| Musica Dependency                                      | Repository                | Branch, Tag or Hash|
+| ------------------------------------------------------ | --------------------------|--------------------|
+| [Google Test](https://github.com/google/googletest.git)| GOOGLETEST_GIT_REPOSITORY | GOOGLETEST_GIT_TAG |
+| [MICM](https://github.com/NCAR/mcim.git)               | MICM_GIT_REPOSITORY       | MICM_GIT_TAG       | 
+| [TUV-X](https://github.com/NCAR/tuv-x.git)             | TUVX_GIT_REPOSITORY       | TUVX_GIT_TAG       |
+| [PyBind11](https://github.com/pybind/pybind11)         | PYBIND11_GIT_REPOSITORY   | PYBIND11_GIT_TAG   |
+
+#### Example Usage
+
+> The following examples assume the working directory is a `build/` directory inside the `musica` source directory.
+
+Specifying a different version of `tuv-x`, to ensure a change won't break anything.
+
+    $ cmake .. \
+        -DTUVX_GIT_REPOSITORY="https://github.com/WardF/tuv-x.git" \
+        -DTUVX_GIT_TAG=test-fix
+
+Specifying a specific version of `tuv-x` by has, but using the official repository.
+
+    $ cmake .. \
+        -DTUVX_GIT_TAG=a6b2c4d8745
+
+
+## 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
+of the MUSICA software. The bibtex entry below can be used to generate a citaiton for this.
+
+```
+@Article { acom.software.musica-vision,
+    author = "Gabriele G. Pfister and Sebastian D. Eastham and Avelino F. Arellano and Bernard Aumont and Kelley C. Barsanti and Mary C. Barth and Andrew Conley and Nicholas A. Davis and Louisa K. Emmons and Jerome D. Fast and Arlene M. Fiore and Benjamin Gaubert and Steve Goldhaber and Claire Granier and Georg A. Grell and Marc Guevara and Daven K. Henze and Alma Hodzic and Xiaohong Liu and Daniel R. Marsh and John J. Orlando and John M. C. Plane and Lorenzo M. Polvani and Karen H. Rosenlof and Allison L. Steiner and Daniel J. Jacob and Guy P. Brasseur",
+    title = "The Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICA)",
+    journal = "Bulletin of the American Meteorological Society",
+    year = "2020",
+    publisher = "American Meteorological Society",
+    address = "Boston MA, USA",
+    volume = "101",
+    number = "10",
+    doi = "10.1175/BAMS-D-19-0331.1",
+    pages= "E1743 - E1760",
+    url = "https://journals.ametsoc.org/view/journals/bams/101/10/bamsD190331.xml"
+}
+```
+
+At present MUSICA is on version zero. MUSICAv0 can be cited using the bibtex entry below.
+MUSICAv0 description and evaluation:
+
+```
+@Article{acom.software.musica,
+    author = {Schwantes, Rebecca H. and Lacey, Forrest G. and Tilmes, Simone and Emmons, Louisa K. and Lauritzen, Peter H. and Walters, Stacy and Callaghan, Patrick and Zarzycki, Colin M. and Barth, Mary C. and Jo, Duseong S. and Bacmeister, Julio T. and Neale, Richard B. and Vitt, Francis and Kluzek, Erik and Roozitalab, Behrooz and Hall, Samuel R. and Ullmann, Kirk and Warneke, Carsten and Peischl, Jeff and Pollack, Ilana B. and Flocke, Frank and Wolfe, Glenn M. and Hanisco, Thomas F. and Keutsch, Frank N. and Kaiser, Jennifer and Bui, Thao Paul V. and Jimenez, Jose L. and Campuzano-Jost, Pedro and Apel, Eric C. and Hornbrook, Rebecca S. and Hills, Alan J. and Yuan, Bin and Wisthaler, Armin},
+    title = {Evaluating the Impact of Chemical Complexity and Horizontal Resolution on Tropospheric Ozone Over the Conterminous US With a Global Variable Resolution Chemistry Model},
+    journal = {Journal of Advances in Modeling Earth Systems},
+    volume = {14},
+    number = {6},
+    pages = {e2021MS002889},
+    doi = {https://doi.org/10.1029/2021MS002889},
+    url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021MS002889},
+    eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021MS002889},
+    year = {2022}
+}
+```

{musica-0.9.0 → musica-0.10.0}/README.md

@@ -5,7 +5,7 @@
 [![macOS](https://github.com/NCAR/musica/actions/workflows/mac.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/mac.yml)
 [![ubuntu](https://github.com/NCAR/musica/actions/workflows/ubuntu.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/ubuntu.yml)
 [![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)
+[![Python tests](https://github.com/NCAR/musica/actions/workflows/python-tests.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/python-tests.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)