Merge branch 'main' into release

Author: boulderdaze

.clang-tidy

@@ -23,6 +23,7 @@ Checks: >
   cert-*,
   -cert-err58-cpp,
   -cert-msc51-cpp,
+  performance-*,
 
 WarningsAsErrors: '*'
 

.github/workflows/mac.yml

@@ -44,7 +44,7 @@ jobs:
       matrix:
         compiler:
           - { cpp: g++-14, c: gcc-14}
-          - { cpp: g++-12, c: gcc-12}
+          - { cpp: g++-13, c: gcc-13}
           - { cpp: clang++, c: clang}
         build_type: [Release]
     env:
@@ -54,6 +54,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: maxim-lobanov/setup-xcode@v1
+        with:
+          xcode-version: '16.4'
+
       - name: Run Cmake 
         run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
 

.github/workflows/readme_example.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
       uses: actions/setup-python@v4

.github/workflows/windows.yml

@@ -13,7 +13,7 @@ concurrency:
 
 jobs:
   mingw:
-    runs-on: windows-2019
+    runs-on: windows-latest
     strategy:
       matrix:
         build_type: [Release]
@@ -39,7 +39,7 @@ jobs:
           ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
 
   msvc2022:
-    runs-on: windows-2022
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
@@ -49,24 +49,24 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Run CMake
-      run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -G "Visual Studio 17 2022" -A ${{ matrix.architecture }}
+      run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -A ${{ matrix.architecture }}
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel 10
     - name: Test
       run: cd build ; ctest -j 10 -C ${{ matrix.build_type }} --output-on-failure
 
   clang:
-    runs-on: windows-2019
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
         build_type: [Release]
-        version: [11, 12, 13, 14, 15]
+        version: [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"
       - name: Run CMake
         run: cmake -S . -B build -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -G"MinGW Makefiles"
       - name: Build
@@ -75,7 +75,7 @@ jobs:
         run: cd build ; ctest -j 10 -C ${{ matrix.build_type }} --exclude-regex "test-unicode" --output-on-failure
 
   clang-cl-11:
-    runs-on: windows-2019
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
@@ -85,7 +85,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Run CMake
-        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL
+        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -A ${{ matrix.architecture }} -T ClangCL
       - name: Build
         run: cmake --build build --config ${{ matrix.build_type }} --parallel 10
       - name: Test

CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it as below.
 title: Model Independent Chemistry Module (MICM)
-version: v3.9.0
+version: v3.10.0
 doi: "10.5281/zenodo.10472189"
 authors:
   - family-names: Dawson

CMakeLists.txt

@@ -3,7 +3,7 @@
 cmake_minimum_required(VERSION 3.21)
 
 # project and version must be on the same line so that the docs can extract it
-project(micm VERSION 3.9.0 LANGUAGES CXX)
+project(micm VERSION 3.10.0 LANGUAGES CXX)
 
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Release" CACHE STRING

README.md

@@ -99,7 +99,8 @@ The `k1` and `k2` rate constants are for Arrhenius reactions. See the [MICM docu
 To solve this system save the following code in a file named `foo_chem.cpp`:
 
 ```c++
-#include <micm/process/arrhenius_rate_constant.hpp>
+#include <micm/process/chemical_reaction_builder.hpp>
+#include <micm/process/rate_constant/arrhenius_rate_constant.hpp>
 #include <micm/solver/rosenbrock.hpp>
 #include <micm/solver/solver_builder.hpp>
 
@@ -118,17 +119,19 @@ int main(const int argc, const char *argv[])
 
   System chemical_system{ SystemParameters{ .gas_phase_ = gas_phase } };
 
-  Process r1 = Process::Create()
+  Process r1 = ChemicalReactionBuilder()
                    .SetReactants({ foo })
                    .SetProducts({ Yield(bar, 0.8), Yield(baz, 0.2) })
                    .SetRateConstant(ArrheniusRateConstant({ .A_ = 1.0e-3 }))
-                   .SetPhase(gas_phase);
+                   .SetPhase(gas_phase)
+                   .Build();
 
-  Process r2 = Process::Create()
+  Process r2 = ChemicalReactionBuilder()
                    .SetReactants({ foo, bar })
                    .SetProducts({ Yield(baz, 1) })
                    .SetRateConstant(ArrheniusRateConstant({ .A_ = 1.0e-5, .C_ = 110.0 }))
-                   .SetPhase(gas_phase);
+                   .SetPhase(gas_phase)
+                   .Build();
 
   std::vector<Process> reactions{ r1, r2 };
 
@@ -158,7 +161,7 @@ int main(const int argc, const char *argv[])
 
 To build and run the example using GNU (assuming the default install location):
 ```
-g++ -o foo_chem foo_chem.cpp -I/usr/local/micm-3.9.0/include -std=c++20
+g++ -o foo_chem foo_chem.cpp -I/usr/local/micm-3.10.0/include -std=c++20
 ./foo_chem
 ```
 

docs/source/_static/switcher.json

@@ -1,7 +1,7 @@
 [
   {
-      "name": "v3.9.0 (stable)",
-      "version": "v3.9.0 (stable)",
+      "name": "v3.10.0 (stable)",
+      "version": "v3.10.0 (stable)",
       "url": "https://ncar.github.io/micm"
   },
   {
@@ -49,6 +49,11 @@
     "version": "3.9.0",
     "url": "https://ncar.github.io/micm/versions/3.9.0"
   },
+  {
+    "name": "v3.10.0",
+    "version": "3.10.0",
+    "url": "https://ncar.github.io/micm/versions/3.10.0"
+  },
   {
     "name": "dev",
     "version": "dev",

docs/source/conf.py

@@ -44,6 +44,7 @@
   'sphinx_copybutton',
   'sphinx_design',
   'sphinxcontrib.bibtex',
+  'sphinx.ext.intersphinx'
 ]
 
 bibtex_bibfiles = ['references.bib']
@@ -59,6 +60,13 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
+# -- Link to Intersphinx Mappings ---
+
+intersphinx_mapping = {
+    'musica': ('https://ncar.github.io/musica/', None),
+    'mc': ('https://ncar.github.io/MechanismConfiguration/', None),
+    'mb': ('https://ncar.github.io/music-box/',None)
+}
 
 # -- Options for HTML output -------------------------------------------------
 

docs/source/user_guide/rate_constant_tutorial.rst

@@ -81,9 +81,8 @@ and our reactions, which will be a vector of :cpp:class:`micm::Process` We will
 
         Now that we have a gas phase and our species, we can start building the reactions. Two things to note are that
         stoichiemtric coefficients for reactants are represented by repeating that product as many times as you need.
-        To specify the yield of a product, we've created a typedef :cpp:type:`micm::Yield` 
-        and a function :cpp:func:`micm::Yields` that produces these. Note that we add a conversion for
-        some rate constant parameters to be consistent with the configuration file that expects rate constants
+        To specify the yield of a product, we've created a struct :cpp:type:`micm::Yield`. Note that we add a conversion
+        for some rate constant parameters to be consistent with the configuration file that expects rate constants
         to be in cm^3/molecule/s. (All units will be mks in the next version of the configuration file format.)
 
         .. literalinclude:: ../../../test/tutorial/test_rate_constants_no_user_defined_by_hand.cpp