musica 0.11.1.2__tar.gz → 0.11.1.4__tar.gz

{musica-0.11.1.2 → musica-0.11.1.4}/.dockerignore

@@ -17,3 +17,4 @@
 !pyproject.toml
 !LICENSE
 !README.md
+!wheelhouse

{musica-0.11.1.2 → musica-0.11.1.4}/.github/workflows/windows.yml

@@ -13,7 +13,7 @@ concurrency:
 
 jobs:
   mingw:
-    runs-on: windows-2019
+    runs-on: windows-latest
     strategy:
       matrix:
         architecture: [x64]
@@ -25,9 +25,6 @@ jobs:
         with:
           platform: ${{ matrix.architecture }}
           version: 12.2.0 # https://github.com/egor-tensin/setup-mingw/issues/14
-      
-      - uses: actions/setup-python@v5
-      - 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 -D CMAKE_POLICY_VERSION_MINIMUM=3.5
@@ -40,8 +37,8 @@ jobs:
           cd build
           ctest -C Debug --rerun-failed --output-on-failure . --verbose
 
-  msvc2022:
-    runs-on: windows-2022
+  msvc:
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
@@ -58,10 +55,8 @@ jobs:
         python-version: '3.x'
         architecture: x86
 
-    - 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 -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_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel
@@ -70,11 +65,11 @@ jobs:
       run: cd build ; ctest -C ${{ matrix.build_type }} --output-on-failure  --verbose
 
   clang:
-    runs-on: windows-2019
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
-        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]
+        version: [18.1.0, 19.1.0, 20.1.0]
 
     steps:
       - uses: actions/checkout@v4
@@ -82,9 +77,6 @@ jobs:
       - name: Install Clang
         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
-
       - 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
 
@@ -95,7 +87,7 @@ jobs:
         run: cd build ; ctest -C Debug --output-on-failure  --verbose
 
   clang-cl-11:
-    runs-on: windows-2019
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
@@ -111,11 +103,8 @@ jobs:
           python-version: '3.x'
           architecture: x86
 
-      - uses: actions/setup-python@v5
-      - 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 -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_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --config Debug --parallel

{musica-0.11.1.2 → musica-0.11.1.4}/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 0.11.1.2)
+project(musica-distribution VERSION 0.11.1.4)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${PROJECT_SOURCE_DIR}/cmake/SetDefaults.cmake)
@@ -89,6 +89,13 @@ if(MUSICA_BUILD_C_CXX_INTERFACE)
   endif()
 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)
+    enable_language(Fortran)
+endif()
+
 # Add flags when using the ClangCL toolset
 if(CMAKE_GENERATOR_TOOLSET STREQUAL "ClangCL")
   list(APPEND musica_compile_definitions MUSICA_USING_CLANGCL)

{musica-0.11.1.2 → musica-0.11.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: musica
-Version: 0.11.1.2
+Version: 0.11.1.4
 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>
@@ -240,7 +240,110 @@ At present the project encompasses these components
 - [MICM](https://github.com/NCAR/micm)
     - Model Independent Chemical Module
 
-## Available grids
+# Installation
+MUSICA is installable via pip for Python or CMake for C++. 
+
+## Pip
+```
+pip install musica
+```
+## CMake
+```
+$ git clone https://github.com/NCAR/musica.git
+$ cd musica
+$ mkdir build
+$ cd build
+$ ccmake ..
+$ make
+$ 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.
+```
+# --- Import Musica ---
+import musica
+import musica.mechanism_configuration as mc
+
+# --- 1. Define the chemical system of interest ---
+A = mc.Species(name="A")
+B = mc.Species(name="B")
+C = mc.Species(name="C")
+species = [A, B, C]
+gas = mc.Phase(name="gas", species=species)
+
+# --- 2. Define a mechanism of interest ---
+# Through Musica, several different mechanisms can be explored to define reaction rates. Here, we use the Arrhenius equation as a simple example.
+
+r1 = mc.Arrhenius(name="A->B", A=4.0e-3, C=50, reactants=[A], products=[B], gas_phase=gas)
+r2 = mc.Arrhenius(name="B->C", A=1.2e-4, B=2.5, C=75, D=50, E=0.5, reactants=[B], products=[C], gas_phase=gas)
+
+mechanism = mc.Mechanism(name="musica_example", species=species, phases=[gas], reactions=[r1, r2])
+
+# --- 3. Create MICM solver ---
+# A solver must be initialized with either a configuration file or a mechanism:
+
+solver = musica.MICM(mechanism=mechanism, solver_type=musica.SolverType.rosenbrock_standard_order)
+
+# --- 4. Define environmental conditions ---
+temperature=300.0
+pressure=101000.0
+
+# --- 5. Create and initialize State ---
+# In the model, conditions represent the starting environment for the reactions and are assigned by modifying the state.
+
+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
+sim_length = 20  # total simulation time
+
+# --- (Optional) 7. Save initial state (t=0) for output visualization ---
+initial_row = {"time.s": 0.0, "ENV.temperature.K": temperature, "ENV.pressure.Pa": pressure, "ENV.air number density.mol m-3": state.get_conditions()['air_density'][0]}
+initial_row.update({f"CONC.{k}.mol m-3": v[0] for k, v in state.get_concentrations().items()})
+
+# --- 8. Solve through time loop only ---
+# The following loop simply solves the model per each time step:
+
+curr_time = time_step
+while curr_time <= sim_length:
+    solver.solve(state, time_step)
+    concentrations = state.get_concentrations()
+    curr_time += time_step
+
+# --- 9. Solve and create DataFrame ---
+# It is likely more useful to solve at each time step and store the associated data:
+import pandas as pd
+
+output_data = [] # prepare to store output per time step
+output_data.append(initial_row) # save t=0 data
+
+curr_time = time_step
+while curr_time <= sim_length:
+    solver.solve(state, time_step)
+    row = {
+        "time.s": curr_time,
+        "ENV.temperature.K": state.get_conditions()['temperature'][0],
+        "ENV.pressure.Pa": state.get_conditions()['pressure'][0],
+        "ENV.air number density.mol m-3": state.get_conditions()['air_density'][0]
+    }
+    row.update({f"CONC.{k}.mol m-3": v[0] for k, v in state.get_concentrations().items()})
+    output_data.append(row)
+    curr_time += time_step
+
+df = pd.DataFrame(output_data)
+print(df)
+
+# --- 10. Visualize Specific Results ---
+import matplotlib.pyplot as plt
+
+df.plot(x='time.s', y=['CONC.A.mol m-3', 'CONC.B.mol m-3', 'CONC.C.mol m-3'], title='Concentration over time', ylabel='Concentration (mol m-3)', xlabel='Time (s)')
+plt.show()
+```
+# Available grids
 
 Pre-made grids for use in MUSICA are available [here](https://wiki.ucar.edu/display/MUSICA/Available+Grids).
 
@@ -282,7 +385,25 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
 ### Python build
 Musica has python bindings. If you want to install the python package, you may `pip install musica`.
 
-To build the package locally,
+#### 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 .

{musica-0.11.1.2 → musica-0.11.1.4}/README.md

@@ -23,7 +23,110 @@ At present the project encompasses these components
 - [MICM](https://github.com/NCAR/micm)
     - Model Independent Chemical Module
 
-## Available grids
+# Installation
+MUSICA is installable via pip for Python or CMake for C++. 
+
+## Pip
+```
+pip install musica
+```
+## CMake
+```
+$ git clone https://github.com/NCAR/musica.git
+$ cd musica
+$ mkdir build
+$ cd build
+$ ccmake ..
+$ make
+$ 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.
+```
+# --- Import Musica ---
+import musica
+import musica.mechanism_configuration as mc
+
+# --- 1. Define the chemical system of interest ---
+A = mc.Species(name="A")
+B = mc.Species(name="B")
+C = mc.Species(name="C")
+species = [A, B, C]
+gas = mc.Phase(name="gas", species=species)
+
+# --- 2. Define a mechanism of interest ---
+# Through Musica, several different mechanisms can be explored to define reaction rates. Here, we use the Arrhenius equation as a simple example.
+
+r1 = mc.Arrhenius(name="A->B", A=4.0e-3, C=50, reactants=[A], products=[B], gas_phase=gas)
+r2 = mc.Arrhenius(name="B->C", A=1.2e-4, B=2.5, C=75, D=50, E=0.5, reactants=[B], products=[C], gas_phase=gas)
+
+mechanism = mc.Mechanism(name="musica_example", species=species, phases=[gas], reactions=[r1, r2])
+
+# --- 3. Create MICM solver ---
+# A solver must be initialized with either a configuration file or a mechanism:
+
+solver = musica.MICM(mechanism=mechanism, solver_type=musica.SolverType.rosenbrock_standard_order)
+
+# --- 4. Define environmental conditions ---
+temperature=300.0
+pressure=101000.0
+
+# --- 5. Create and initialize State ---
+# In the model, conditions represent the starting environment for the reactions and are assigned by modifying the state.
+
+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
+sim_length = 20  # total simulation time
+
+# --- (Optional) 7. Save initial state (t=0) for output visualization ---
+initial_row = {"time.s": 0.0, "ENV.temperature.K": temperature, "ENV.pressure.Pa": pressure, "ENV.air number density.mol m-3": state.get_conditions()['air_density'][0]}
+initial_row.update({f"CONC.{k}.mol m-3": v[0] for k, v in state.get_concentrations().items()})
+
+# --- 8. Solve through time loop only ---
+# The following loop simply solves the model per each time step:
+
+curr_time = time_step
+while curr_time <= sim_length:
+    solver.solve(state, time_step)
+    concentrations = state.get_concentrations()
+    curr_time += time_step
+
+# --- 9. Solve and create DataFrame ---
+# It is likely more useful to solve at each time step and store the associated data:
+import pandas as pd
+
+output_data = [] # prepare to store output per time step
+output_data.append(initial_row) # save t=0 data
+
+curr_time = time_step
+while curr_time <= sim_length:
+    solver.solve(state, time_step)
+    row = {
+        "time.s": curr_time,
+        "ENV.temperature.K": state.get_conditions()['temperature'][0],
+        "ENV.pressure.Pa": state.get_conditions()['pressure'][0],
+        "ENV.air number density.mol m-3": state.get_conditions()['air_density'][0]
+    }
+    row.update({f"CONC.{k}.mol m-3": v[0] for k, v in state.get_concentrations().items()})
+    output_data.append(row)
+    curr_time += time_step
+
+df = pd.DataFrame(output_data)
+print(df)
+
+# --- 10. Visualize Specific Results ---
+import matplotlib.pyplot as plt
+
+df.plot(x='time.s', y=['CONC.A.mol m-3', 'CONC.B.mol m-3', 'CONC.C.mol m-3'], title='Concentration over time', ylabel='Concentration (mol m-3)', xlabel='Time (s)')
+plt.show()
+```
+# Available grids
 
 Pre-made grids for use in MUSICA are available [here](https://wiki.ucar.edu/display/MUSICA/Available+Grids).
 
@@ -65,7 +168,25 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
 ### Python build
 Musica has python bindings. If you want to install the python package, you may `pip install musica`.
 
-To build the package locally,
+#### 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 .

musica-0.11.1.4/cmake/setup_musica_target.cmake

@@ -0,0 +1,63 @@
+function(musica_setup_target target)
+  cmake_parse_arguments(ARG "" "MODE" "" ${ARGN})
+
+  if (MUSICA_ENABLE_PYTHON_LIBRARY OR MUSICA_ENABLE_PIC)
+    set_target_properties(${target_name} PROPERTIES POSITION_INDEPENDENT_CODE ON)
+  endif()
+
+  target_include_directories(${target}
+    PUBLIC
+      $<BUILD_INTERFACE:${MUSICA_PROJECT_SRC_DIR}/include>
+      $<INSTALL_INTERFACE:${MUSICA_INSTALL_INCLUDE_DIR}>
+  )
+
+  target_compile_features(${target} PUBLIC cxx_std_20)
+
+  target_link_libraries(${target}
+    PUBLIC
+      musica::mechanism_configuration
+  )
+
+  if (MUSICA_ENABLE_MPI)
+    list(APPEND musica_compile_definitions MUSICA_USE_MPI)
+  endif()
+
+  if (MUSICA_ENABLE_OPENMP)
+    list(APPEND musica_compile_definitions MUSICA_USE_OPENMP)
+  endif()
+
+  if (MUSICA_ENABLE_MICM) 
+    list(APPEND musica_compile_definitions MUSICA_USE_MICM)
+    target_link_libraries(${target}
+      PUBLIC
+        musica::micm
+    )
+
+    if(ARG_MODE STREQUAL "GPU")
+      set_target_properties(micm_cuda PROPERTIES POSITION_INDEPENDENT_CODE ON)
+      list(APPEND musica_compile_definitions MUSICA_ENABLE_CUDA)
+      target_link_libraries(${target} PUBLIC musica::micm_cuda)
+    endif()
+  endif()
+
+  if (MUSICA_ENABLE_TUVX)
+    target_sources(${target}
+      PRIVATE
+        $<TARGET_OBJECTS:tuvx_object>
+    )
+    target_link_libraries(${target}
+      PUBLIC
+        tuvx_object
+    )
+    target_include_directories(${target}
+      PUBLIC
+        $<BUILD_INTERFACE:${MUSICA_MOD_DIR}>
+        $<INSTALL_INTERFACE:${MUSICA_INSTALL_INCLUDE_DIR}>
+    )
+  endif()
+
+  target_compile_definitions(${target} PUBLIC ${musica_compile_definitions})
+
+  silence_warnings(${target})
+endfunction()
+

{musica-0.11.1.2 → musica-0.11.1.4}/configs/v1/chapman/config.json

@@ -1,6 +1,6 @@
 {
   "version": "1.0.0",
-  "name": "Full Configuration",
+  "name": "Chapman",
   "species": [
     {
       "name": "M",

{musica-0.11.1.2 → musica-0.11.1.4}/docker/Dockerfile.python

@@ -1,5 +1,8 @@
 FROM fedora:latest
 
+ARG MUSICA_GIT_TAG=main
+ARG BUILD_TYPE=Release
+
 RUN dnf -y update \
     && dnf -y install \
         cmake \

musica-0.11.1.4/docker/Dockerfile.wheel

@@ -0,0 +1,22 @@
+# To use this file, you will need to have built the wheel first.
+# You can do this by running cibuildwheel with the appropriate environment variables set, 
+# which can be done after installing cibuildwheel.
+# CIBW_ARCHS=x86_64 CIBW_PLATFORM=linux CIBW_ENVIRONMENT="CUDA_PATH=/usr/local/cuda PATH=/usr/local/cuda/bin:\$PATH LD_LIBRARY_PATH=/usr/local/cuda/lib64:\$LD_LIBRARY_PATH" cibuildwheel --output-dir wheelhouse > log.txt 2>&1
+
+# This wheel specifically checks if the python 3.12 x86_64 python wheel can be installed
+# and imported correctly.
+
+FROM --platform=linux/amd64 python:3.12-slim
+
+COPY wheelhouse/ wheelhouse/
+
+RUN apt update && \
+    apt install -y \
+      binutils
+
+RUN pip install --upgrade pip
+
+# note that you will need to update the version number here to match the one you built
+RUN pip install "musica[gpu] @ file:/wheelhouse/musica-0.11.1.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
+
+CMD ["python", "-c", "import musica; print(musica.__version__)"]

{musica-0.11.1.2 → musica-0.11.1.4}/fortran/test/fetch_content_integration/test_micm_api.F90

@@ -71,7 +71,7 @@ contains
     integer                               :: O2_index, O_index, O1D_index, O3_index
     integer                               :: jO2_index, jO3a_index, jO3b_index
     
-    config_path = "configs/chapman"
+    config_path = "configs/v0/chapman"
     solver_type = RosenbrockStandardOrder
     num_grid_cells = 1
     time_step = 200
@@ -170,7 +170,7 @@ contains
     ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
     deallocate(micm)
     deallocate(state)
-    micm => micm_t( "configs/invalid", solver_type, error )
+    micm => micm_t( "configs/v0/invalid", solver_type, error )
     ASSERT( error%is_error( MUSICA_ERROR_CATEGORY_PARSING, MUSICA_PARSE_INVALID_CONFIG_FILE ) )
     ASSERT( .not. associated( micm ) )
 
@@ -357,7 +357,7 @@ contains
     real(real64), parameter :: test_accuracy = 5.0e-3
     integer                 :: max_grid_cells
 
-    micm => micm_t( "configs/analytical", Rosenbrock, error )
+    micm => micm_t( "configs/v0/analytical", Rosenbrock, error )
     ASSERT( error%is_success() )
     max_grid_cells = micm%get_maximum_number_of_grid_cells( )
     ASSERT_GT( max_grid_cells, 0 )
@@ -378,7 +378,7 @@ contains
     real(real64), parameter :: test_accuracy = 5.0e-3
     integer                 :: max_grid_cells
 
-    micm => micm_t( "configs/analytical", RosenbrockStandardOrder, error )
+    micm => micm_t( "configs/v0/analytical", RosenbrockStandardOrder, error )
     ASSERT( error%is_success() )
     max_grid_cells = micm%get_maximum_number_of_grid_cells( )
     ASSERT_GT( max_grid_cells, 1e8 )
@@ -399,7 +399,7 @@ contains
     real(real64), parameter :: test_accuracy = 0.1
     integer                 :: max_grid_cells
 
-    micm => micm_t( "configs/analytical", BackwardEuler, error )
+    micm => micm_t( "configs/v0/analytical", BackwardEuler, error )
     ASSERT( error%is_success() )
     max_grid_cells = micm%get_maximum_number_of_grid_cells( )
     ASSERT_GT( max_grid_cells, 0 )
@@ -420,7 +420,7 @@ contains
     real(real64), parameter :: test_accuracy = 0.1
     integer                 :: max_grid_cells
 
-    micm => micm_t( "configs/analytical", BackwardEulerStandardOrder, error )
+    micm => micm_t( "configs/v0/analytical", BackwardEulerStandardOrder, error )
     ASSERT( error%is_success() )
     max_grid_cells = micm%get_maximum_number_of_grid_cells( )
     ASSERT_GT( max_grid_cells, 1e8 )
@@ -451,7 +451,7 @@ contains
       return
     end if
 
-    micm => micm_t( "configs/analytical", CudaRosenbrock, error )
+    micm => micm_t( "configs/v0/analytical", CudaRosenbrock, error )
     ASSERT( error%is_success() )
     max_grid_cells = micm%get_maximum_number_of_grid_cells( )
     ASSERT_GT( max_grid_cells, 0 )
@@ -581,7 +581,7 @@ contains
     ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
     deallocate( micm )
     deallocate( state )
-    micm => micm_t( "configs/invalid", solver_type, error )
+    micm => micm_t( "configs/v0/invalid", solver_type, error )
     ASSERT( error%is_error( MUSICA_ERROR_CATEGORY_PARSING, MUSICA_PARSE_INVALID_CONFIG_FILE ) )
     ASSERT( .not. associated( micm ) )
 

{musica-0.11.1.2 → musica-0.11.1.4}/fortran/test/fetch_content_integration/test_micm_box_model.F90

@@ -31,7 +31,7 @@ contains
     type(state_t), pointer  :: state
     integer                 :: i
 
-    config_path = "configs/analytical"
+    config_path = "configs/v0/analytical"
     solver_type = RosenbrockStandardOrder
     num_grid_cells = 1
 
@@ -84,7 +84,7 @@ contains
     type(state_t), pointer  :: state
     integer                 :: i
 
-    config_path = "configs/analytical"
+    config_path = "configs/v0/analytical"
     solver_type = RosenbrockStandardOrder
     num_grid_cells = 1
 

musica-0.11.1.4/musica/CMakeLists.txt

@@ -0,0 +1,42 @@
+################################################################################
+# Python Extension Modules
+
+#include(setup_muisca_target)
+
+# Define the list of Python extension module targets
+set(PY_MODULES _musica)
+
+set(
+  MUSICA_PYTHON_SOURCES 
+    binding_common.cpp
+    cuda.cpp 
+    mechanism_configuration.cpp 
+    musica.cpp 
+
+    ${MUSICA_SOURCES}
+)
+
+pybind11_add_module(_musica cpu_binding.cpp ${MUSICA_PYTHON_SOURCES})
+musica_setup_target(_musica MODE CPU)
+
+if (NOT ${MUSICA_GPU_TYPE} STREQUAL "None")
+  pybind11_add_module(_musica_gpu gpu_binding.cpp ${MUSICA_PYTHON_SOURCES}) 
+  musica_setup_target(_musica_gpu MODE GPU)
+  list(APPEND PY_MODULES _musica_gpu)
+endif()
+
+foreach(lib ${PY_MODULES})
+  if (APPLE)
+    set_target_properties(${lib} PROPERTIES
+      INSTALL_RPATH "@loader_path"
+      BUILD_WITH_INSTALL_RPATH TRUE
+    )
+  elseif(UNIX)
+    set_target_properties(${lib} PROPERTIES
+      INSTALL_RPATH "$ORIGIN"
+      BUILD_WITH_INSTALL_RPATH TRUE
+    )
+  endif()
+
+  install(TARGETS ${lib} LIBRARY DESTINATION musica)
+endforeach()