Move build files into pycode/memilio-simulation and update actions

.github/actions/build-py/action.yml

@@ -16,29 +16,22 @@ runs:
     - name: Make artifact dir
       shell: bash
       run: |
-        if [ "${{ inputs.package }}" != "simulation" ]; then
-          cd pycode/memilio-${{ inputs.package }}/
-        # else stay in root directory
-        fi
+        cd pycode/memilio-${{ inputs.package }}/
         mkdir wheelhouse
     - name: Build Python Wheels
       shell: bash
       run: |
-        if [ "${{ inputs.package }}" != "simulation" ]; then
-          cd pycode/memilio-${{ inputs.package }}/
-        # else stay in root directory
-        fi
-        /opt/python/cp39-cp39/bin/python -m pip install --upgrade pip setuptools wheel
-        /opt/python/cp313-cp313/bin/python -m pip install --upgrade pip setuptools wheel
-        /opt/python/cp39-cp39/bin/python -m pip install scikit-build scikit-build-core 
-        /opt/python/cp313-cp313/bin/python -m pip install scikit-build scikit-build-core
-        # Install setuptools-scm only for memilio-simulation
-        if [ "${{ inputs.package }}" == "simulation" ]; then
-          /opt/python/cp39-cp39/bin/python -m pip install setuptools-scm
-          /opt/python/cp313-cp313/bin/python -m pip install setuptools-scm
-        fi
-        /opt/python/cp39-cp39/bin/python -m build --no-isolation --wheel
-        /opt/python/cp313-cp313/bin/python -m build --no-isolation --wheel
+        cd pycode/memilio-${{ inputs.package }}/
+        # install dependencies and build wheels with specified python versions
+        for python_cmd in /opt/python/cp39-cp39/bin/python /opt/python/cp313-cp313/bin/python
+        do
+          $python_cmd -m pip install --upgrade pip setuptools wheel
+          $python_cmd -m pip install scikit-build scikit-build-core
+          if [ "${{ inputs.package }}" == "simulation" ]
+            then $python_cmd -m pip install setuptools-scm
+          fi
+          $python_cmd -m build --no-isolation --wheel
+        done    
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel
@@ -47,11 +40,7 @@ runs:
           # no auditwheel necessary for pure python packages, so only copy the wheels to the same output directory 
           cp dist/*.whl wheelhouse
         fi
-        if [ "${{ inputs.package }}" != "simulation" ]; then
-          cp -r wheelhouse ..
-        else
-          cp -r wheelhouse pycode
-        fi 
+        cp -r wheelhouse ..
     - name: Upload Python Wheels
       uses: actions/upload-artifact@v7
       with:

.github/workflows/pypi.yml

@@ -1,52 +1,66 @@
 name: PyPI
 
-on:  
-  release:  
-    types:  
+on:
+  release:
+    types:
       - published
+  ### Uncomment the "push:" together with the "repository-url:" field of action pypa/gh-action-pypi-publish
+  ### to make a test release. Building this is rather expensive so do not merge this uncommented!
+  #push:
+  ### @Reviewer: MAKE SURE THE LINE ABOVE IS COMMENTED OUT BEFORE MERGE! ###
 
 jobs:
 
   build_wheels:
-    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-2025-vs2026]
+        os: [ubuntu-latest, windows-2025-vs2026, macos-26]
+    runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v6
+      - name: "Checkout"
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - uses: pypa/cibuildwheel@v3.4.1
+      - name: "Build Wheels"
+        uses: pypa/cibuildwheel@v3.4.1
+        with:
+          package-dir: pycode/memilio-simulation
 
-      - uses: actions/upload-artifact@v7
+      - name: "Upload Artifacts"
+        uses: actions/upload-artifact@v7
         with:
           name: cibw-wheels-${{ matrix.os }}
-          path: ./wheelhouse/*.whl
+          path: wheelhouse/*.whl
 
-  build_sdist: 
+  build_sdist:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v6
+    - name: "Checkout"
+      uses: actions/checkout@v6
       with:
         fetch-depth: 0
 
-    - run: pipx run build --sdist
+    - name: "Build Source Distribution"
+      run:  |
+        cd pycode/memilio-simulation
+        pipx run build --sdist
 
-    - uses: actions/upload-artifact@v7
+    - name: "Upload Artifacts"
+      uses: actions/upload-artifact@v7
       with:
         name: cibw-sdist
-        path: dist/*.tar.gz
+        path: pycode/memilio-simulation/dist/*.tar.gz
 
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     environment: pypi
     permissions:
       id-token: write
-      
+
     steps:
       - uses: actions/download-artifact@v7
         with:
@@ -58,5 +72,5 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           skip-existing: true
-          # To test uploads to TestPyPI, uncomment the following:
-          # repository-url: https://test.pypi.org/legacy/
+          ### To test uploads to TestPyPI in a PR, uncomment the following, as well as the "push:" line at the top:
+          #repository-url: https://test.pypi.org/legacy/

cpp/CMakeLists.txt

@@ -156,7 +156,7 @@ elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
         "-Wno-unknown-warning-option;-Wno-deprecated;-Wno-gnu-zero-variadic-macro-arguments;")
 endif()
 
-# woyrkarounds for compiler bugs or overzealous optimization/analysis
+# workarounds for compiler bugs or overzealous optimization/analysis
 if(CMAKE_BUILD_TYPE STREQUAL "Release" OR CMAKE_BUILD_TYPE STREQUAL "RELEASE")
     if(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
         string(APPEND MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS

cpp/README.md

@@ -52,7 +52,6 @@ Options can be specified with `cmake .. -D<OPTION>=<VALUE>` or by editing the `b
 - `MEMILIO_BUILD_TESTS`: build unit tests in the test directory, ON or OFF, default ON.
 - `MEMILIO_BUILD_EXAMPLES`: build the example applications in the examples directory, ON or OFF, default ON.
 - `MEMILIO_BUILD_MODELS`: build the separate model libraries in the models directory, ON or OFF, default ON.
-- `MEMILIO_BUILD_SIMULATIONS`: build the simulation applications in the simulations directory, ON or OFF, default ON.
 - `MEMILIO_USE_BUNDLED_SPDLOG/_BOOST/_EIGEN/_JSONCPP`: use the corresponding dependency bundled with this project, ON or OFF, default ON.
 - `MEMILIO_BUILD_BENCHMARKS`: build the benchmarks for this project, ON or OFF, default OFF.
 - `MEMILIO_SANITIZE_ADDRESS/_UNDEFINED`: compile with specified sanitizers to check correctness, ON or OFF, default OFF.

docs/source/cpp/cpp_makros_preprocessing.rst

@@ -1,5 +1,5 @@
 Configuration macros
--------------------
+--------------------
 
 MEmilio provides several compile-time configuration options through CMake that control which features and dependencies are available during compilation. These configurations are defined as preprocessor macros and can be used to conditionally compile code sections based on available libraries and enabled features.
 The following macros are automatically defined by CMake during the build process based on the availability of dependencies and build options:
@@ -22,7 +22,7 @@ The following macros are automatically defined by CMake during the build process
      - Defined when profiling support is enabled. Activates performance monitoring and timing instrumentation throughout the codebase.
 
 Usage in Code
-^^^^^^^^^^^^^^
+^^^^^^^^^^^^^
 
 These macros are used with preprocessor conditionals to enable or disable specific functionality. You should use these macros to ensure that your code can compile and run correctly depending on the available libraries and features. 
 When using these macros, you should always consider fallbacks or alternative implementations when a feature is not available. This ensures that your code remains robust and can handle cases where optional dependencies are not present.

docs/source/cpp/glct.rst

@@ -56,6 +56,7 @@ The initial conditions of the model are represented by a class ``LctPopulations`
 
 
 .. _Nonpharmaceutical Interventions GLCT:
+
 Nonpharmaceutical interventions
 -------------------------------
 

docs/source/cpp/ide.rst

@@ -81,6 +81,7 @@ start time of the simulation.
 
 
 .. _Nonpharmaceutical Interventions IDE:
+
 Nonpharmaceutical interventions
 -------------------------------
 
@@ -150,7 +151,3 @@ List of models
 
     models/isecir
     models/iseir
-
-
-
-