SciCompMod · annawendler · Feb 23, 2026 · Feb 23, 2026 · Feb 23, 2026 · Feb 23, 2026
diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
@@ -6,24 +6,38 @@ inputs:
     required: true
 runs:
   using: "composite"
-  steps:    
+  steps:
+    - name: Configure Git safe directory
+      shell: bash 
+      run: git config --global --add safe.directory /__w/memilio/memilio    
     - name: Install dependencies
       shell: bash
       run: yum install ninja-build cmake git -qy
     - name: Make artifact dir
       shell: bash
       run: |
-        cd pycode/memilio-${{ inputs.package }}/
+        if [ "${{ inputs.package }}" != "simulation" ]; then
+          cd pycode/memilio-${{ inputs.package }}/
+        # else stay in root directory
+        fi
         mkdir wheelhouse
     - name: Build Python Wheels
       shell: bash
       run: |
-        cd pycode/memilio-${{ inputs.package }}/
+        if [ "${{ inputs.package }}" != "simulation" ]; then
+          cd pycode/memilio-${{ inputs.package }}/
+        # else stay in root directory
+        fi
         /opt/python/cp38-cp38/bin/python -m pip install --upgrade pip setuptools wheel
-        /opt/python/cp38-cp38/bin/python -m pip install scikit-build scikit-build-core
-        /opt/python/cp38-cp38/bin/python -m build --no-isolation --wheel
         /opt/python/cp312-cp312/bin/python -m pip install --upgrade pip setuptools wheel
+        /opt/python/cp38-cp38/bin/python -m pip install scikit-build scikit-build-core 
         /opt/python/cp312-cp312/bin/python -m pip install scikit-build scikit-build-core
+        # Install setuptools-scm only for memilio-simulation
+        if [ "${{ inputs.package }}" == "simulation" ]; then
+          /opt/python/cp38-cp38/bin/python -m pip install setuptools-scm
+          /opt/python/cp312-cp312/bin/python -m pip install setuptools-scm
+        fi
+        /opt/python/cp38-cp38/bin/python -m build --no-isolation --wheel
         /opt/python/cp312-cp312/bin/python -m build --no-isolation --wheel
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
@@ -33,7 +47,11 @@ runs:
           # no auditwheel necessary for pure python packages, so only copy the wheels to the same output directory 
           cp dist/*.whl wheelhouse
         fi
-        cp -r wheelhouse ..
+        if [ "${{ inputs.package }}" != "simulation" ]; then
+          cp -r wheelhouse ..
+        else
+          cp -r wheelhouse pycode
+        fi 
     - name: Upload Python Wheels
       uses: actions/upload-artifact@v4
       with:

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -0,0 +1,64 @@
+name: PyPI
+
+# on:  
+#   release:  
+#     types:  
+#       - published
+# remove following line before merge: 
+on: [pull_request, release]
+
+jobs:
+
+  build_wheels:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: pypa/[email protected]
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist: 
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-sdist
+        path: 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@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - 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/
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,10 @@
+cmake_minimum_required(VERSION 3.14)
+project(memilio-simulation)
+
+set(CMAKE_CXX_STANDARD "20")
+set(CMAKE_CXX_STANDARD_REQUIRED "20")
+
+# add in C++ library
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/cpp ${CMAKE_CURRENT_BINARY_DIR}/cpp EXCLUDE_FROM_ALL)
+
+add_subdirectory(pycode/memilio-simulation)
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # MEmilio - a high performance Modular EpideMIcs simuLatIOn software #
 
-![memilio_logo](docs/memilio-small.png)
+![memilio_logo](https://github.com/SciCompMod/memilio/blob/main/docs/memilio-small.png?raw=true)
 
 [![CI](https://github.com/SciCompMod/memilio/actions/workflows/main.yml/badge.svg)](https://github.com/SciCompMod/memilio/actions/workflows/main.yml)
 [![codecov](https://codecov.io/gh/SciCompMod/memilio/branch/main/graph/badge.svg?token=DVQXIQJHBM)](https://codecov.io/gh/SciCompMod/memilio)

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
@@ -131,25 +131,33 @@ Option A: Installing the Python packages (Recommended for nonexperienced users o
 
 You can run simulations, download data, or create plots, by only installing our Python packages.
 
+If you want to use the simulation package ``memilio-simulation``, you can install it directly via:
+
+.. code-block:: 
+
+   pip install memilio-simulation
+
+For the other packages, you can proceed as follows. 
+
 1.  Navigate to the directory containing our Python code:
 
     .. code-block:: console
 
        cd pycode
 
-2.  To install the simulation package ``memilio-simulation``, from here you can do:
+2.  To install the simulation package ``memilio-epidata``, from here you can do:
 
     .. code-block:: console
 
-       cd memilio-simulation
+       cd memilio-epidata
        pip install -e .
 
-3.  For afterwards installing the ``memilio-epidata`` package for data downloading and handling, run:
+3.  For afterwards installing the ``memilio-surrogatemodel`` package for data downloading and handling, run:
 
     .. code-block:: console
 
        cd ..  # Go back to the pycode directory
-       cd memilio-epidata
+       cd memilio-surrogatemodel
        pip install -e .
 
 .. tip:: For Contributors: Installing development packages
@@ -162,7 +170,8 @@ You can run simulations, download data, or create plots, by only installing our
 
       pip install -e .[dev]
 
-   For regular use, the simple ``pip install -e .`` is sufficient.
+   For regular use, the simple ``pip install -e .`` is sufficient. For development of the ``memilio-simulation`` package, 
+   please also use this command from the root of the MEmilio repository for installation. 
 
 To install other packages, see the items below *Python Interface* in the menu on the left hand side.
 

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
@@ -1,9 +1,3 @@
-cmake_minimum_required(VERSION 3.14)
-project(memilio-python)
-
-set(CMAKE_CXX_STANDARD "20")
-set(CMAKE_CXX_STANDARD_REQUIRED "20")
-
 option(MEMILIO_USE_BUNDLED_PYBIND11 "Use pybind11 bundled with this library." ON)
 mark_as_advanced(MEMILIO_USE_BUNDLED_PYBIND11)
 
@@ -48,9 +42,6 @@ else()
     find_package(pybind11 REQUIRED)
 endif()
 
-# add in C++ library
-add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/../../cpp ${CMAKE_CURRENT_BINARY_DIR}/cpp EXCLUDE_FROM_ALL)
-
 # a list of all "LINKED_LIBRARIES" that are given to add_pymio_module. will contain duplicates
 # used for wheel installation
 set(PYMIO_MEMILIO_LIBS_LIST)

diff --git a/pycode/memilio-simulation/README.md b/pycode/memilio-simulation/README.md
@@ -6,10 +6,10 @@ This package contains Python bindings for the MEmilio C++ library. It enables se
 
 This project is configured via ``pyproject.toml`` and is built with [scikit-build-core](https://scikit-build-core.readthedocs.io). CMake and Ninja must be available on the system. The package uses the [Pybind11 C++ library](https://pybind11.readthedocs.io) to create the bindings.
 
-To install the package, use the command (from the directory containing ``pyproject.toml``)
+To install the package, use the command
 
 ```bash
-pip install .
+pip install memilio-simulation
 ```
 
 This builds the C++ library and C++ Python extension module and copies everything required to your site-packages.
@@ -30,7 +30,7 @@ Alternatively, edit the `CMakeCache.txt` in the directory created by scikit-buil
 
 ## Development
 
-For developement of the cpp bindings use
+For developement of the cpp bindings use the following command from the root of this repository (i.e. the directory containing ``pyproject.toml``)
 
 ```bash
 pip install -e .[dev]

diff --git a/pycode/memilio-simulation/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,67 @@
+[project]
+name = "memilio-simulation"
+dynamic = ["version"] 
+# remove following line before merge: 
+# version = "2.3.0"
+description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
+readme = "README.md"
+requires-python = ">=3.8"
+license = "Apache-2.0" 
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "[email protected]" }
+]
+dependencies = [
+  # smaller numpy versions cause a security issue, 1.25 does not work together with pyfakefs
+  "numpy>=1.22,!=1.25.*",
+  # smaller pandas versions contain a bug that sometimes prevents reading
+  "pandas>=2.0.0"
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows"
+]
+
+[project.optional-dependencies]
+dev = []
+
+[project.urls]
+Homepage = "https://github.com/SciCompMod/memilio"
+Team = "https://memilio.readthedocs.io/en/latest/team.html"
+
+[build-system]
+requires = [
+  "scikit-build-core>=0.9.0",
+  "setuptools>=68",
+  "setuptools-scm>=8",
+  "wheel"
+]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build]
+cmake.version = ">=3.13"
+cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
+wheel.packages = ["pycode/memilio-simulation/memilio"]
+wheel.install-dir = "memilio/simulation"
+build-dir = "pycode/build/memilio-simulation"
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+
+[tool.setuptools_scm]  
+local_scheme = "no-local-version"
+
+[tool.cibuildwheel]
+# Disable some wheels
+skip = ["pp*", "*musllinux*", "*-win32"] 
+
 [tool.autopep8]
 max-line-length = 79