musica 0.12.0__tar.gz → 0.12.2__tar.gz

{musica-0.12.0 → musica-0.12.2}/.dockerignore

@@ -17,4 +17,4 @@
 !pyproject.toml
 !LICENSE
 !README.md
-!wheelhouse
+!tutorials

{musica-0.12.0 → musica-0.12.2}/.github/workflows/docker.yml

@@ -26,7 +26,6 @@ jobs:
           - Dockerfile.openmp
           - Dockerfile.mpi
           - Dockerfile.mpi_openmp
-          - Dockerfile.python
           - Dockerfile.nvhpc
           - Dockerfile.coverage
         build_type: [Release, Debug]

musica-0.12.0/.github/workflows/clang_format.yml → musica-0.12.2/.github/workflows/format.yml

@@ -1,4 +1,4 @@
-name: Clang-Format
+name: Format Code with Clang-Format and autopep8
 
 on:
   push:
@@ -8,7 +8,7 @@ on:
 
 jobs:
   format:
-    name: Run Clang-Format
+    name: Run Formatting
     runs-on: ubuntu-latest
 
     steps:
@@ -21,10 +21,17 @@ jobs:
           ref: ${{ github.head_ref }}
           token: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: autopep8
+        uses: peter-evans/autopep8@v2
+        with:
+          args: --recursive --in-place --aggressive --aggressive --max-line-length 120 .
+
       - name: Run clang-format
         run: |
           find include -type f \( -name '*.hpp' -or -name '*.h' \) -exec clang-format -i --style=file --verbose {} +
           find src -type f \( -name '*.cpp' -or -name '*.c' \) -exec clang-format -i --style=file --verbose {} +
+          find musica -type f \( -name '*.cpp' -or -name '*.c' \) -exec clang-format -i --style=file --verbose {} +
+          find musica -type f \( -name '*.hpp' -or -name '*.h' \) -exec clang-format -i --style=file --verbose {} +
 
       - name: Check for changes
         id: check-changes
@@ -37,7 +44,7 @@ jobs:
         run: |
           git config --global user.name "GitHub Actions"
           git config --global user.email "actions@github.com"
-          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+          git commit -am "Auto-format code using Clang-Format and autopep8" || echo "No changes to commit"
 
       - name: Push changes to main-formatting branch
         if: steps.check-changes.outcome != 'success'
@@ -48,7 +55,7 @@ jobs:
         uses: peter-evans/create-pull-request@v6
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          commit-message: "Auto-format code using Clang-Format"
+          commit-message: "Auto-format code using Clang-Format and autopep8"
           title: "Auto-format code changes"
-          body: "This is an automated pull request to apply code formatting using Clang-Format."
+          body: "This is an automated pull request to apply code formatting using Clang-Format and autopep8."
           branch: main-formatting

{musica-0.12.0 → musica-0.12.2}/.github/workflows/gh_pages.yml

@@ -1,11 +1,8 @@
 # Build and deploy documentation to GitHub Pages
 name: GitHub Pages
 
-on:
+on: 
   push:
-    branches:
-      - main
-      - release
   pull_request:
   workflow_dispatch:
 
@@ -15,14 +12,7 @@ env:
 jobs:
   build-and-deploy:
     name: Build and deploy to gh-pages
-    runs-on: ubuntu-24.04
-    strategy:
-      matrix:
-        gcc-version: [13]
-    env:
-      CXX: g++-${{ matrix.gcc-version }}
-      CC: gcc-${{ matrix.gcc-version }}
-      FC: gfortran-${{ matrix.gcc-version }}
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
@@ -94,7 +84,8 @@ jobs:
       # _gh-pages/branch/$brname (transforming '/' into '--')
       - name: Build and copy documentation (branch)
         if: |
-          contains(github.event_name, 'push') &&
+          (contains(github.event_name, 'push') ||
+          contains(github.event_name, 'pull_request')) &&
           !contains(github.ref, env.DEFAULT_BRANCH)
         run: |
           set -x
@@ -102,10 +93,16 @@ jobs:
           id=$(docker create musica)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id
-          brname="${{github.ref}}"
-          brname="${brname##refs/heads/}"
+          # Determine branch name for deployment directory
+          if [ "${{ github.event_name }}" = "pull_request" ]; then
+            brname="${{ github.head_ref }}"
+          else
+            brname="${{ github.ref }}"
+            brname="${brname##refs/heads/}"
+          fi
           brdir=${brname//\//--}   # replace '/' with '--'
           rm -rf   _gh-pages/branch/${brdir}
+          mkdir -p _gh-pages/branch/${brdir}
           rsync -a tmpdocs/ _gh-pages/branch/${brdir}
 
       # Go through each branch in _gh-pages/branch/, if it's not a
@@ -156,4 +153,4 @@ jobs:
               repo: context.repo.repo,
               issue_number: context.payload.pull_request.number,
               body: commentBody
-            });
+            });

{musica-0.12.0 → musica-0.12.2}/.github/workflows/mac.yml

@@ -18,11 +18,9 @@ jobs:
     strategy:
       matrix:
         compiler:
-          - { 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}
+          - { cpp: clang++, c: clang, fc: gfortran-14}
         build_type: [Release]
     env:
       CC: ${{ matrix.compiler.c }}
@@ -32,6 +30,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: maxim-lobanov/setup-xcode@v1
+        with:
+          xcode-version: '16.4'
+
       - name: Install dependencies
         run: brew install netcdf netcdf-fortran
 

{musica-0.12.0 → musica-0.12.2}/.github/workflows/python-tests.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [windows-latest, macos-13, ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         # python versions: https://devguide.python.org/versions/
 
     runs-on: ${{ matrix.platform }}
@@ -23,6 +23,17 @@ jobs:
       with:
         submodules: true
 
+    - name: Install dependencies
+      if: matrix.platform == 'ubuntu-latest'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libnetcdf-dev netcdf-bin libnetcdff-dev liblapack-dev
+    
+    - name: Install dependencies
+      if: matrix.platform == 'macos-13'
+      run: |
+        brew install netcdf netcdf-fortran lapack
+
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
@@ -32,6 +43,8 @@ jobs:
 
     - name: Build and install
       run: pip install --verbose .[test]
+      env:
+        FC: gfortran-14
 
     - name: Test
-      run: pytest
+      run: pytest -s

{musica-0.12.0 → musica-0.12.2}/.github/workflows/python-wheels.yml

@@ -36,8 +36,32 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.12"]
+        include:
+          # Linux builds (supports cross-compilation via QEMU)
+          - os: ubuntu-latest
+            python-version: "3.13"
+            cibw_archs: "x86_64 i686"
+          
+          - os: ubuntu-24.04-arm
+            python-version: "3.13"
+            cibw_archs: "aarch64"
+
+          # Windows builds (separate runners needed for different archs)
+          - os: windows-latest
+            python-version: "3.13"
+            cibw_archs: "AMD64 x86 ARM64"
+          
+          # macOS Intel
+          - os: macos-13  # Intel runner
+            python-version: "3.13"
+            cibw_archs: "x86_64"
+            fc: gfortran-15
+          
+          # macOS Apple Silicon
+          - os: macos-latest  # ARM64 runner
+            python-version: "3.13"
+            cibw_archs: "arm64"
+            fc: gfortran-15
 
     steps:
     - uses: actions/checkout@v4
@@ -47,21 +71,24 @@ jobs:
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+  
+    - name: CI Build Wheels
+      if: ${{ matrix.fc != '' }}
+      uses: pypa/cibuildwheel@v3.1.3
+      env:
+        CIBW_ARCHS: ${{ matrix.cibw_archs }}
+        FC: ${{ matrix.fc }}
 
     - name: CI Build Wheels
-      uses: pypa/cibuildwheel@v2.17
+      if: ${{ matrix.fc == '' }}
+      uses: pypa/cibuildwheel@v3.1.3
       env:
-        CIBW_ENVIRONMENT_PASS_LINUX: CIBW_ARCHS
-        CIBW_ENVIRONMENT_LINUX: >
-          CUDA_PATH=/usr/local/cuda
-          PATH=/usr/local/cuda/bin:$PATH
-          LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
-          BUILD_GPU=1
+        CIBW_ARCHS: ${{ matrix.cibw_archs }}
 
     - name: Upload wheels
       uses: actions/upload-artifact@v4
       with:
-        name: cibw-wheels-${{ matrix.os }}-py${{ matrix.python-version }}
+        name: cibw-wheels-${{ matrix.os }}-${{ matrix.cibw_archs }}-py${{ matrix.python-version }}
         path: wheelhouse/*.whl
 
   upload_all:
@@ -87,4 +114,4 @@ jobs:
         merge-multiple: true
 
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@release/v1

{musica-0.12.0 → musica-0.12.2}/.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: 
-          - {micm: ON, tuvx: OFF, python: ON}
-          - {micm: OFF, tuvx: ON, python: OFF}
+          - {micm: ON, tuvx: OFF, carma: OFF, python: ON}
+          - {micm: OFF, tuvx: ON, carma: OFF, python: OFF}
         build_type: [Release]
     env:
       CC: ${{ matrix.compiler.c }}
@@ -46,6 +46,7 @@ jobs:
                               -D MUSICA_GIT_TAG=${{ github.sha }} \
                               -D MUSICA_ENABLE_MICM=${{ matrix.options.micm }} \
                               -D MUSICA_ENABLE_TUVX=${{ matrix.options.tuvx }} \
+                              -D MUSICA_ENABLE_CARMA=${{ matrix.options.carma }} \
                               -D MUSICA_ENABLE_PYTHON_LIBRARY=${{ matrix.options.python }} \
                               -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 

{musica-0.12.0 → musica-0.12.2}/.github/workflows/windows.yml

@@ -28,7 +28,7 @@ jobs:
           static: 0
 
       - name: Run Cmake 
-        run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --parallel
@@ -57,7 +57,7 @@ jobs:
         architecture: x86
 
     - name: Run CMake
-      run: cmake -S . -B build -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
+      run: cmake -S . -B build -A ${{ matrix.architecture }} -D MUSICA_GIT_TAG=${{ github.sha }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel
@@ -79,7 +79,7 @@ jobs:
         run: curl -fsSL -o LLVM${{ 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"
 
       - 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=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --parallel
@@ -105,7 +105,7 @@ jobs:
           architecture: x86
 
       - name: Run CMake
-        run: cmake -S . -B build -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
+        run: cmake -S . -B build -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --config Debug --parallel
@@ -119,7 +119,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        build_type: [Debug, Release]
+        # for some reason the debug build fails with an error in the python library
+        # something about the usage of mechanism configuration and variants causes missing type information
+        # This commit for mechanism configuration works: 903150064277e024b0afcfc879df419e1cefc87b
+        # This one doesn't: a3ef728c69f619f80c272d634bc2a17ca5ab4de9
+        build_type: [Release]
 
     steps:
       - name: Checkout code
@@ -137,12 +141,17 @@ jobs:
             mingw-w64-x86_64-cmake
             mingw-w64-x86_64-netcdf
             mingw-w64-x86_64-netcdf-fortran
+            mingw-w64-x86_64-lapack
           msystem: MINGW64
 
       - name: Add MSYS2 mingw64 to PATH
         shell: msys2 {0}
         run: echo "C:/msys64/mingw64/bin" >> $GITHUB_PATH
 
+      - name: Clean build directory
+        shell: msys2 {0}
+        run: rm -rf build
+
       - name: Configure with CMake
         shell: msys2 {0}
         run: |
@@ -151,6 +160,7 @@ jobs:
                               -D MUSICA_GIT_TAG=${{ github.sha }} \
                               -D MUSICA_ENABLE_MICM=ON \
                               -D MUSICA_ENABLE_TUVX=ON \
+                              -D MUSICA_ENABLE_CARMA=ON \
                               -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
                               -D MUSICA_BUILD_FORTRAN_INTERFACE=ON \
                               -D CMAKE_POLICY_VERSION_MINIMUM=3.5

{musica-0.12.0 → musica-0.12.2}/.gitignore

@@ -16,3 +16,8 @@ musica.egg-info
 **/*__pycache__*
 **/*.pyc
 wheelhouse
+
+error.json
+
+.ipynb_checkpoints
+configs/tuvx/output/

{musica-0.12.0 → musica-0.12.2}/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: 0.12.0
+version: 0.12.2

{musica-0.12.0 → musica-0.12.2}/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 0.12.0)
+project(musica-distribution VERSION 0.12.2)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${PROJECT_SOURCE_DIR}/cmake/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_CARMA "Enable CARMA" 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)
@@ -40,6 +41,9 @@ set(MUSICA_SET_MICM_DEFAULT_VECTOR_SIZE "4" CACHE STRING "Set MICM vector-ordere
 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)
 
+cmake_dependent_option(
+  MUSICA_ONLY_PYTHON "Build only the Python bindings. This option is used when building Python wheels primarily" OFF "MUSICA_ENABLE_PYTHON_LIBRARY" OFF)
+
 ################################################################################
 # Projet wide setup variables 
 set(MUSICA_INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_INCLUDEDIR})
@@ -92,7 +96,7 @@ endif()
 # since sources are collected so that python libraries can target them directly,
 # we need to know if we are targeting Fortran before we collect the sources
 # otherwise cmake freaks out, and I don't know why, but this fixes it
-if(MUSICA_ENABLE_TUVX)
+if(MUSICA_ENABLE_TUVX OR MUSICA_ENABLE_CARMA)
     enable_language(Fortran)
 endif()
 

{musica-0.12.0 → musica-0.12.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: musica
-Version: 0.12.0
+Version: 0.12.2
 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>
@@ -207,13 +207,25 @@ License:                                  Apache License
             limitations under the License.
          
 Project-URL: homepage, https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
+Requires-Python: >=3.9
 Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: xarray>=2022.3.0
+Requires-Dist: ussa1976>=v0.3.4
 Provides-Extra: test
 Requires-Dist: numpy; extra == "test"
 Requires-Dist: pytest; extra == "test"
+Requires-Dist: matplotlib; extra == "test"
 Provides-Extra: gpu
 Requires-Dist: nvidia-cublas-cu12; extra == "gpu"
 Requires-Dist: nvidia-cuda-runtime-cu12; extra == "gpu"
+Provides-Extra: tutorial
+Requires-Dist: pandas; extra == "tutorial"
+Requires-Dist: matplotlib; extra == "tutorial"
+Requires-Dist: numpy; extra == "tutorial"
+Requires-Dist: scipy; extra == "tutorial"
+Requires-Dist: seaborn; extra == "tutorial"
+Requires-Dist: dask[distributed]; extra == "tutorial"
+Requires-Dist: dask-jobqueue; extra == "tutorial"
 Description-Content-Type: text/markdown
 
 # MUSICA
@@ -228,6 +240,8 @@ Description-Content-Type: text/markdown
 [![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)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NCAR/musica/HEAD?filepath=tutorials)
+
 
 Multi-Scale Infrastructure for Chemistry and Aerosols
 
@@ -241,6 +255,9 @@ At present the project encompasses these core components
 - [MICM](https://github.com/NCAR/micm)
     - Model Independent Chemical Module
 
+- [CARMA](https://github.com/ESCOMP/CARMA)
+    - Community Aerosol and Radiation Model for Atmospheres (integration in development)
+
 - [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration)
     - The standardized format to describe atmospheric chemistry
 
@@ -257,6 +274,27 @@ MUSICA is installable via pip for Python or CMake for C++.
 pip install musica
 ```
 
+If you would like GPU support, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then you can specify the gpu install option for MUSICA. Note that GPU support has only been tested on linux.
+
+```
+pip install --upgrade setuptools pip wheel
+pip install nvidia-pyindex
+pip install musica[gpu]
+```
+
+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 .
+```
+
 ## CMake
 ```
 $ git clone https://github.com/NCAR/musica.git
@@ -270,7 +308,7 @@ $ make install
 
 # Using the MUSICA Python API
 MUSICA makes its chemical mechanism analysis and visualization available through a Python API. The following example works through solving a simple chemistry system. Please refer to the [official documentation](https://ncar.github.io/musica/index.html) for further tutorials and examples.
-```
+```python
 # --- Import Musica ---
 import musica
 import musica.mechanism_configuration as mc
@@ -305,7 +343,6 @@ pressure=101000.0
 state = solver.create_state()
 state.set_concentrations({"A": 1.0, "B": 3.0, "C": 5.0})
 state.set_conditions(temperature, pressure)
-initial_pressure = state.get_conditions()['air_density'][0] # store for visualization and output
 
 # --- 6. Time parameters ---
 time_step = 4  # stepping
@@ -368,7 +405,7 @@ Introduced in [Pull Request #124](https://github.com/NCAR/musica/pull/124), it i
 | 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       | 
+| [MICM](https://github.com/NCAR/micm.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   |
 | [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration.git) | MECH_CONFIG_GIT_REPOSITORY | MECH_CONFIG_GIT_TAG |
@@ -388,41 +425,6 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
     $ cmake .. \
         -DTUVX_GIT_TAG=a6b2c4d8745
 
-
-### Python build
-Musica has python bindings. If you want to install the python package, you may `pip install musica`.
-
-#### PyPi
-If you only want to use the CPU components, 
-
-```
-pip install musica
-```
-
-Note that GPU support has only been tested on linux. If you have an NVIDIA GPU and would like to take 
-advantage of our GPU solver, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then install musica with our gpu option.
-
-```
-pip install --upgrade setuptools pip wheel
-pip install nvidia-pyindex
-pip install musica[gpu]
-```
-
-#### Local build
-
-Musica has python bindings. 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 .
-```
-
 # Contributing
 
 We welcome contributions from the community! Please see our [Contributing Guide](CONTRIBUTING.md) for information on how to get involved.

{musica-0.12.0 → musica-0.12.2}/README.md

@@ -10,6 +10,8 @@
 [![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)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NCAR/musica/HEAD?filepath=tutorials)
+
 
 Multi-Scale Infrastructure for Chemistry and Aerosols
 
@@ -23,6 +25,9 @@ At present the project encompasses these core components
 - [MICM](https://github.com/NCAR/micm)
     - Model Independent Chemical Module
 
+- [CARMA](https://github.com/ESCOMP/CARMA)
+    - Community Aerosol and Radiation Model for Atmospheres (integration in development)
+
 - [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration)
     - The standardized format to describe atmospheric chemistry
 
@@ -39,6 +44,27 @@ MUSICA is installable via pip for Python or CMake for C++.
 pip install musica
 ```
 
+If you would like GPU support, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then you can specify the gpu install option for MUSICA. Note that GPU support has only been tested on linux.
+
+```
+pip install --upgrade setuptools pip wheel
+pip install nvidia-pyindex
+pip install musica[gpu]
+```
+
+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 .
+```
+
 ## CMake
 ```
 $ git clone https://github.com/NCAR/musica.git
@@ -52,7 +78,7 @@ $ make install
 
 # Using the MUSICA Python API
 MUSICA makes its chemical mechanism analysis and visualization available through a Python API. The following example works through solving a simple chemistry system. Please refer to the [official documentation](https://ncar.github.io/musica/index.html) for further tutorials and examples.
-```
+```python
 # --- Import Musica ---
 import musica
 import musica.mechanism_configuration as mc
@@ -87,7 +113,6 @@ pressure=101000.0
 state = solver.create_state()
 state.set_concentrations({"A": 1.0, "B": 3.0, "C": 5.0})
 state.set_conditions(temperature, pressure)
-initial_pressure = state.get_conditions()['air_density'][0] # store for visualization and output
 
 # --- 6. Time parameters ---
 time_step = 4  # stepping
@@ -150,7 +175,7 @@ Introduced in [Pull Request #124](https://github.com/NCAR/musica/pull/124), it i
 | 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       | 
+| [MICM](https://github.com/NCAR/micm.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   |
 | [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration.git) | MECH_CONFIG_GIT_REPOSITORY | MECH_CONFIG_GIT_TAG |
@@ -170,41 +195,6 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
     $ cmake .. \
         -DTUVX_GIT_TAG=a6b2c4d8745
 
-
-### Python build
-Musica has python bindings. If you want to install the python package, you may `pip install musica`.
-
-#### PyPi
-If you only want to use the CPU components, 
-
-```
-pip install musica
-```
-
-Note that GPU support has only been tested on linux. If you have an NVIDIA GPU and would like to take 
-advantage of our GPU solver, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then install musica with our gpu option.
-
-```
-pip install --upgrade setuptools pip wheel
-pip install nvidia-pyindex
-pip install musica[gpu]
-```
-
-#### Local build
-
-Musica has python bindings. 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 .
-```
-
 # Contributing
 
 We welcome contributions from the community! Please see our [Contributing Guide](CONTRIBUTING.md) for information on how to get involved.