From 61508d193ec752951b0994ede3745023dffa1e85 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Thu, 6 Nov 2025 09:21:19 +0100
Subject: [PATCH 01/19] first try

---
 .github/actions/build-py/action.yml           |   6 +-
 .github/actions/test-pylint/action.yml        |   6 +-
 docs/source/python/m-epidata.rst              |   2 +-
 docs/source/python/m-generation.rst           |   2 +-
 docs/source/python/python_packages.rst        |  10 +-
 pycode/memilio-epidata/README.rst             |   8 +-
 pycode/memilio-epidata/pyproject.toml         |  61 +++++++++
 pycode/memilio-epidata/setup.py               | 117 ------------------
 pycode/memilio-epidata/tools/run_pylint.py    |  51 ++++++++
 pycode/memilio-generation/README.md           |   4 +-
 .../memilio/generation/scanner_config.py      |   2 +-
 pycode/memilio-generation/pyproject.toml      |  40 ++++++
 pycode/memilio-generation/setup.py            |  35 ------
 pycode/memilio-plot/README.md                 |   6 +-
 pycode/memilio-plot/pyproject.toml            |  47 +++++++
 pycode/memilio-plot/setup.py                  |  97 ---------------
 pycode/memilio-plot/tools/run_pylint.py       |  51 ++++++++
 pycode/memilio-simulation/README.md           |  14 +--
 pycode/memilio-simulation/pyproject.toml      |  35 ++++++
 pycode/memilio-simulation/setup.py            |  38 ------
 .../tools/generate_stubs.py                   |  41 +++---
 pycode/memilio-surrogatemodel/README.md       |   4 +-
 pycode/memilio-surrogatemodel/pyproject.toml  |  37 ++++++
 pycode/memilio-surrogatemodel/setup.py        |  30 -----
 24 files changed, 381 insertions(+), 363 deletions(-)
 create mode 100644 pycode/memilio-epidata/pyproject.toml
 delete mode 100644 pycode/memilio-epidata/setup.py
 create mode 100644 pycode/memilio-epidata/tools/run_pylint.py
 create mode 100644 pycode/memilio-generation/pyproject.toml
 delete mode 100644 pycode/memilio-generation/setup.py
 create mode 100644 pycode/memilio-plot/pyproject.toml
 delete mode 100644 pycode/memilio-plot/setup.py
 create mode 100644 pycode/memilio-plot/tools/run_pylint.py
 create mode 100644 pycode/memilio-simulation/pyproject.toml
 delete mode 100644 pycode/memilio-simulation/setup.py
 create mode 100644 pycode/memilio-surrogatemodel/pyproject.toml
 delete mode 100644 pycode/memilio-surrogatemodel/setup.py

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 2cb89fa75d..e0632831b3 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -19,9 +19,11 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}/
-        /opt/python/cp38-cp38/bin/python -m pip install scikit-build
+        /opt/python/cp38-cp38/bin/python -m pip install --upgrade pip setuptools wheel
+        /opt/python/cp38-cp38/bin/python -m pip install scikit-build scikit-build-core
         /opt/python/cp38-cp38/bin/python -m build --no-isolation --wheel
-        /opt/python/cp311-cp311/bin/python -m pip install scikit-build
+        /opt/python/cp311-cp311/bin/python -m pip install --upgrade pip setuptools wheel
+        /opt/python/cp311-cp311/bin/python -m pip install scikit-build scikit-build-core
         /opt/python/cp311-cp311/bin/python -m build --no-isolation --wheel
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
diff --git a/.github/actions/test-pylint/action.yml b/.github/actions/test-pylint/action.yml
index 9f9f50bc2c..12af19357c 100644
--- a/.github/actions/test-pylint/action.yml
+++ b/.github/actions/test-pylint/action.yml
@@ -28,7 +28,11 @@ runs:
       run: |
         cd pycode/memilio-${{ inputs.package }}
         mkdir -p build_pylint
-        python setup.py pylint
+        if [ -f tools/run_pylint.py ]; then
+          python tools/run_pylint.py
+        else
+          python -m pylint --rcfile=../pylintrc --load-plugins=pylint_json2html --output-format=jsonextended memilio/ > build_pylint/pylint_extended.json || true
+        fi
         pylint-json2html -f jsonextended -o build_pylint/pylint.html < build_pylint/pylint_extended.json
     - name: Upload Pylint Report
       uses: actions/upload-artifact@v4
diff --git a/docs/source/python/m-epidata.rst b/docs/source/python/m-epidata.rst
index c908e339c9..8c306d90c7 100644
--- a/docs/source/python/m-epidata.rst
+++ b/docs/source/python/m-epidata.rst
@@ -85,7 +85,7 @@ When you start creating a new script:
 
 When you add a new script
 
-- Add an executable to the setup.py in "pycode/memilio-epidata".
+- Add a console script entry to the ``pycode/memilio-epidata/pyproject.toml`` file.
 - Add it to the cli_dict in getDataIntoPandasDataFrame.py.
     - Add a meaningful key for the new script.
     - for the dict value add a list in the form [comment to print when script is started, list of used parser arguments (optional)].
diff --git a/docs/source/python/m-generation.rst b/docs/source/python/m-generation.rst
index 858edd92d4..bcabac83f1 100644
--- a/docs/source/python/m-generation.rst
+++ b/docs/source/python/m-generation.rst
@@ -30,7 +30,7 @@ For a successful build, the development libraries for Python need to be installe
 .. warning::
     Generation currently requires specifically version ``18.1.1`` of `libclang.so`, since the function ``create_ast`` in `ast.py <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-generation/memilio/generation/ast.py>`_ generates the abstract syntax tree using `clang-18`. Different versions may lead to unsupported abstractions.
 
-    If you want to try a different version, set your `libclang` version under ``install_requires`` in the `setup.py <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-generation/setup.py>`_ and change the clang command in ``create_ast`` in `ast.py <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-generation/memilio/generation/ast.py>`_.
+    If you want to try a different version, set your `libclang` version under ``dependencies`` in the `pyproject.toml <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-generation/pyproject.toml>`_ and change the clang command in ``create_ast`` in `ast.py <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-generation/memilio/generation/ast.py>`_.
 
 Usage
 -----
diff --git a/docs/source/python/python_packages.rst b/docs/source/python/python_packages.rst
index e9c703a429..daa5ed893d 100644
--- a/docs/source/python/python_packages.rst
+++ b/docs/source/python/python_packages.rst
@@ -111,9 +111,9 @@ Please see the individual package documentation for more details on the function
 Installation
 ------------
 
-Each package provides a `setup.py` script that installs the package and its dependencies. 
+Each package provides a ``pyproject.toml`` that installs the package and its dependencies with pip.
 The dependencies of the individual packages are denoted in their documentation.
-The installation can be run with the following command (from the directory containing the `setup.py`)
+The installation can be run with the following command (from the directory containing the ``pyproject.toml`` file)
 
 .. code-block:: console 
     
@@ -171,9 +171,11 @@ Run pylint with the commands in the package folder
 
 .. code-block:: console
 
-    python setup.py pylint
+    python tools/run_pylint.py
     pylint-json2html -f jsonextended -o build_pylint/pylint.html < build_pylint/pylint_extended.json
 
+Packages without the helper script can run pylint directly, for example ``python -m pylint memilio``.
+
 Pylint report for actual master:
 
-`Pylint Report <https://dlr-sc.github.io/memilio/pylint/>`_
\ No newline at end of file
+`Pylint Report <https://dlr-sc.github.io/memilio/pylint/>`_
diff --git a/pycode/memilio-epidata/README.rst b/pycode/memilio-epidata/README.rst
index be21a21a89..69a9a692e3 100644
--- a/pycode/memilio-epidata/README.rst
+++ b/pycode/memilio-epidata/README.rst
@@ -23,9 +23,9 @@ A more detailed description of the sources can be found in the `epidata subfolde
 Installation
 ------------
 
-Use the provided ``setup.py`` script to install the package and its dependencies.
+This project uses ``pyproject.toml`` to install the package and its dependencies.
 
-To install the package, use (from the directory that contains ``setup.py``)
+To install the package, run (from the directory that contains ``pyproject.toml``)
 
 .. code:: sh
 
@@ -116,7 +116,7 @@ Run pylint with the commands
 
 .. code:: sh
 
-    python setup.py pylint
+    python tools/run_pylint.py
     pylint-json2html -f jsonextended -o build_pylint/pylint.html < build_pylint/pylint_extended.json
 
 Pylint report for actual master:
@@ -163,7 +163,7 @@ When you start creating a new script:
 
 When you add a new script
 
-- add a executable to the setup.py in "pycode/memilio-epidata"
+- add a script entry to ``pyproject.toml`` in "pycode/memilio-epidata"
 - add it to the cli_dict in getDataIntoPandasDataFrame.py
     - add a meaningfull key for the new script
     - as the value add a list in the form [comment to print when script is started, list of used parser arguments (optional)]
diff --git a/pycode/memilio-epidata/pyproject.toml b/pycode/memilio-epidata/pyproject.toml
new file mode 100644
index 0000000000..a50a151244
--- /dev/null
+++ b/pycode/memilio-epidata/pyproject.toml
@@ -0,0 +1,61 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "memilio-epidata"
+version = "1.0.0"
+description = "Part of MEmilio project, reads epidemiological data from different official and unofficial sources."
+readme = "README.rst"
+requires-python = ">=3.9"
+license = { text = "Apache-2.0" }
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "martin.kuehn@dlr.de" }
+]
+urls = { 
+  Homepage = "https://github.com/SciCompMod/memilio",
+  Team = "https://memilio.readthedocs.io/en/latest/team.html"
+}
+dependencies = [
+  "pandas>=2.0.0",
+  "pyarrow",
+  "matplotlib",
+  "tables",
+  "numpy>=1.22,<1.25",
+  "openpyxl",
+  "xlrd",
+  "xlsxwriter",
+  "requests",
+  "pyxlsb",
+  "wget",
+  "twill==3.1",
+  "PyQt6-sip<13.9",
+  "PyQt6",
+  "python-calamine",
+  "python-magic-bin; sys_platform == 'win32'",
+  "python-magic; sys_platform != 'win32'"
+]
+
+[project.optional-dependencies]
+dev = [
+  "pyfakefs>=4.6,<5.3.3",
+  "coverage>=7.0.1",
+  "pylint>=2.13.0,<2.16",
+  "pylint_json2html==0.4.0"
+]
+
+[project.scripts]
+getcasedata = "memilio.epidata.getCaseData:main"
+getpopuldata = "memilio.epidata.getPopulationData:main"
+getjhdata = "memilio.epidata.getJHData:main"
+getdividata = "memilio.epidata.getDIVIData:main"
+getsimdata = "memilio.epidata.getSimulationData:main"
+cleandata = "memilio.epidata.cleanData:main"
+getcommutermobility = "memilio.epidata.getCommuterMobility:main"
+getvaccinationdata = "memilio.epidata.getVaccinationData:main"
+gethospitalizationdata = "memilio.epidata.getHospitalizationData:main"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["memilio*"]
diff --git a/pycode/memilio-epidata/setup.py b/pycode/memilio-epidata/setup.py
deleted file mode 100644
index 3d6616cd40..0000000000
--- a/pycode/memilio-epidata/setup.py
+++ /dev/null
@@ -1,117 +0,0 @@
-import os
-import subprocess
-import sys
-
-from setuptools import Command, find_packages, setup
-
-__version__ = '1.0.0'
-
-
-class PylintCommand(Command):
-    """Custom command to run pylint and get a report as html."""
-    description = "Runs pylint and outputs the report as html."
-    user_options = []
-
-    def initialize_options(self):
-        """ """
-        from pylint.reporters.json_reporter import JSONReporter
-        from pylint.reporters.text import ParseableTextReporter, TextReporter
-        from pylint_json2html import JsonExtendedReporter
-
-        self.lint_modules = ["memilio/"]
-        self.out_format = "extendedjson"
-
-        self.REPORTERS = {
-            "parseable": (ParseableTextReporter, "build_pylint/pylint_parseable.txt"),
-            "text": (TextReporter, "build_pylint/pylint.txt"),
-            "json": (JSONReporter, "build_pylint/pylint.json"),
-            "extendedjson": (JsonExtendedReporter, "build_pylint/pylint_extended.json")
-        }
-
-    def finalize_options(self):
-        """ """
-        self.reporter, self.out_file = self.REPORTERS.get(
-            self.out_format)  # , self.REPORTERS.get("parseable"))
-
-    def run(self):
-        """ """
-        os.makedirs("build_pylint", exist_ok=True)
-
-        # Run pylint
-        from pylint import lint
-        with open(self.out_file, "w", encoding="utf-8") as report_file:
-            options = ["--rcfile=../pylintrc", *self.lint_modules]
-
-            lint.Run(options, reporter=self.reporter(
-                report_file), do_exit=False)
-
-
-# Python-magic needs DLLs for libmagic. They have to be installed only on windows.
-if sys.platform == 'win32':
-    pymagic = 'python-magic-bin'
-else:
-    pymagic = 'python-magic'
-
-setup(
-    name='memilio-epidata',
-    version=__version__,
-    author='DLR-SC',
-    author_email='daniel.abele@dlr.de',
-    maintainer_email='martin.kuehn@dlr.de',
-    url='https://github.com/SciCompMod/memilio',
-    description='Part of MEmilio project, reads epidemiological data from different official and unofficial sources.',
-    entry_points={
-        'console_scripts': [
-            'getcasedata=memilio.epidata.getCaseData:main',
-            'getpopuldata=memilio.epidata.getPopulationData:main',
-            'getjhdata = memilio.epidata.getJHData:main',
-            'getdividata = memilio.epidata.getDIVIData:main',
-            'getsimdata = memilio.epidata.getSimulationData:main',
-            'cleandata = memilio.epidata.cleanData:main',
-            'getcommutermobility = memilio.epidata.getCommuterMobility:main',
-            'getvaccinationdata = memilio.epidata.getVaccinationData:main',
-            'gethospitalizationdata = memilio.epidata.getHospitalizationData:main'
-        ],
-    },
-    packages=find_packages(where=os.path.dirname(os.path.abspath(__file__))),
-    long_description='',
-    test_suite='memilio.epidata_test',
-    install_requires=[
-        # pandas 2.0 is minimum for CoW
-        'pandas>=2.0.0',
-        # FutureWarning of pandas that pyarrow will be required in a future release
-        'pyarrow',
-        'matplotlib',
-        'tables',
-        # smaller numpy versions cause a security issue, 1.25 breaks testing with pyfakefs
-        'numpy>=1.22,<1.25',
-        'openpyxl',
-        'xlrd',
-        'xlsxwriter',
-        'requests',
-        'pyxlsb',
-        'wget',
-        'twill==3.1',
-        # set PyQt6-sip version as the one pulled by PyQt6 in Epidata-CI (using manylinux_2_28_x86_64) req. python 3.9
-        'PyQt6-sip<13.9',
-        'PyQt6',
-        'python-calamine',
-        pymagic
-    ],
-    extras_require={
-        'dev': [
-            # first support of python 3.11 4.6
-            # 5.3.4 has conflicts with openpyxl
-            # 5.3.3 broken
-            'pyfakefs>=4.6,<5.3.3',
-            # coverage 7.0.0 can't find .whl files and breaks CI
-            'coverage>=7.0.1',
-            # pylint 2.16 creates problem with wrapt package version
-            'pylint>=2.13.0,<2.16',
-            'pylint_json2html==0.4.0',
-        ],
-    },
-    cmdclass={
-        'pylint': PylintCommand
-    },
-)
diff --git a/pycode/memilio-epidata/tools/run_pylint.py b/pycode/memilio-epidata/tools/run_pylint.py
new file mode 100644
index 0000000000..2f9b4b7c2c
--- /dev/null
+++ b/pycode/memilio-epidata/tools/run_pylint.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+"""Generate Pylint reports in jsonextended format for the epidata package."""
+
+from __future__ import annotations
+
+import subprocess
+import sys
+from pathlib import Path
+
+
+def main() -> int:
+    project_dir = Path(__file__).resolve().parent.parent
+    repo_root = project_dir.parent
+    build_dir = project_dir / "build_pylint"
+    build_dir.mkdir(exist_ok=True)
+    output_file = build_dir / "pylint_extended.json"
+
+    cmd = [
+        sys.executable,
+        "-m",
+        "pylint",
+        "--rcfile",
+        str(repo_root / "pylintrc"),
+        "--load-plugins",
+        "pylint_json2html",
+        "--output-format=jsonextended",
+        "memilio/",
+    ]
+
+    with output_file.open("w", encoding="utf-8") as stream:
+        result = subprocess.run(
+            cmd,
+            cwd=project_dir,
+            stdout=stream,
+            stderr=subprocess.PIPE,
+            text=True,
+            check=False,
+        )
+
+    if result.stderr:
+        sys.stderr.write(result.stderr)
+
+    if result.returncode:
+        sys.stderr.write(
+            "pylint reported issues; see build_pylint/pylint_extended.json for details.\n"
+        )
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/pycode/memilio-generation/README.md b/pycode/memilio-generation/README.md
index 31ae30a0c2..b8ebedb7e0 100644
--- a/pycode/memilio-generation/README.md
+++ b/pycode/memilio-generation/README.md
@@ -13,7 +13,7 @@ The package uses the [Clang C++ library](https://clang.llvm.org/) and the [LibCl
 
 ## Installation
 
-Use the provided `setup.py` script to build and install the package. To install the package, use the command (from the directory containing `setup.py`)
+Use the provided `pyproject.toml` file to build and install the package. To install the package, use the command (from the directory containing `pyproject.toml`)
 
 ```bash
 pip install -e .[dev]
@@ -51,4 +51,4 @@ When implementing new model features you can follow these steps:
 - Adjust the substitution dictionaries in the [Generator class](./memilio/generation/generator.py).
 - Write new/Adjust script in the [tool folder](./memilio/tools/) for the model and try to run.
 - Add new strings in the [Default dict](/pycode/memilio-generation/memilio/generation/default_generation_dict.py)
-- Update [tests](./memilio/generation_test/).
\ No newline at end of file
+- Update [tests](./memilio/generation_test/).
diff --git a/pycode/memilio-generation/memilio/generation/scanner_config.py b/pycode/memilio-generation/memilio/generation/scanner_config.py
index a4fb482133..a52a31244b 100644
--- a/pycode/memilio-generation/memilio/generation/scanner_config.py
+++ b/pycode/memilio-generation/memilio/generation/scanner_config.py
@@ -39,7 +39,7 @@ class ScannerConfig:
         path_database: Path to the folder of the compile_commands.json
         namespace: C++ namespace of the model class
         python_module_name: Individual name for binded python module
-        python_generation_module_path: Path to the setup.py of the generation module
+        python_generation_module_path: Path to the ``pyproject.toml`` of the generation module
         skbuild_path_to_database: Path to compile_commands.json
         target_folder: Target folder for generated files
         optional: List with optional arguments
diff --git a/pycode/memilio-generation/pyproject.toml b/pycode/memilio-generation/pyproject.toml
new file mode 100644
index 0000000000..2652447295
--- /dev/null
+++ b/pycode/memilio-generation/pyproject.toml
@@ -0,0 +1,40 @@
+[build-system]
+requires = [
+  "scikit-build-core>=0.9.0",
+  "setuptools>=68",
+  "wheel"
+]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "memilio-generation"
+version = "0.1.0"
+description = "Part of MEmilio project, automatic generation of model specific python bindings."
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "Apache-2.0" }
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "martin.kuehn@dlr.de" }
+]
+urls = { 
+  Homepage = "https://github.com/SciCompMod/memilio",
+  Team = "https://memilio.readthedocs.io/en/latest/team.html"
+}
+dependencies = [
+  "libclang==18.1.1",
+  "dataclasses",
+  "dataclasses_json",
+  "graphviz",
+  "importlib-resources>=1.1.0; python_version < '3.9'"
+]
+
+[project.optional-dependencies]
+dev = []
+
+[tool.scikit-build]
+cmake.minimum-version = "3.13"
+wheel.packages = ["memilio"]
+
+[tool.scikit-build.package-data]
+"memilio.generation" = ["tools/*.json"]
diff --git a/pycode/memilio-generation/setup.py b/pycode/memilio-generation/setup.py
deleted file mode 100644
index 2d3370d80e..0000000000
--- a/pycode/memilio-generation/setup.py
+++ /dev/null
@@ -1,35 +0,0 @@
-import os
-import subprocess
-import sys
-
-from setuptools import find_packages, setup
-
-try:
-    from skbuild import setup
-except ImportError:
-    print('scikit-build is required to build from source.')
-    print('Installation:  python -m pip install scikit-build')
-    subprocess.check_call(
-        [sys.executable, "-m", "pip", "install", "scikit-build"])
-    from skbuild import setup
-
-__version__ = '0.1.0'
-
-setup(
-    name='memilio-generation',
-    version=__version__,
-    author='DLR-SC',
-    author_email='maximilian.betz@dlr.de',
-    maintainer_email='martin.kuehn@dlr.de',
-    url='https://github.com/SciCompMod/memilio',
-    description='Part of MEmilio project, automatic generation of model specific python bindings.',
-    packages=find_packages(
-        where=os.path.dirname(os.path.abspath(__file__))),
-    install_requires=['libclang==18.1.1',
-                      'dataclasses', 'dataclasses_json', 'graphviz', 'importlib-resources>=1.1.0; python_version < \'3.9\''],
-    extras_require={'dev': []},
-    long_description='',
-    test_suite='memilio.generation_test',
-    package_data={'memilio.generation': [
-        '../../_skbuild/*/cmake-build/compile_commands.json', '../tools/config.json']},
-)
diff --git a/pycode/memilio-plot/README.md b/pycode/memilio-plot/README.md
index 014b8a8221..97d0d06a42 100644
--- a/pycode/memilio-plot/README.md
+++ b/pycode/memilio-plot/README.md
@@ -23,9 +23,9 @@ by other packages of the MEmilio software.
 Installation
 ------------
 
-Use the provided ``setup.py`` script to install the package and its dependencies.
+This project uses ``pyproject.toml`` to install the package and its dependencies.
 
-To install the package, use (from the directory that contains ``setup.py``)
+To install the package, use pip (from the directory that contains ``pyproject.toml``)
 
 .. code:: sh
 
@@ -104,7 +104,7 @@ Run pylint with the commands
 
 .. code:: sh
 
-    python setup.py pylint
+    python tools/run_pylint.py
     pylint-json2html -f jsonextended -o build_pylint/pylint.html < build_pylint/pylint_extended.json
 
 Pylint report for actual master:
diff --git a/pycode/memilio-plot/pyproject.toml b/pycode/memilio-plot/pyproject.toml
new file mode 100644
index 0000000000..0149b86a02
--- /dev/null
+++ b/pycode/memilio-plot/pyproject.toml
@@ -0,0 +1,47 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "memilio-plot"
+version = "1.0.0"
+description = "Part of MEmilio project, plots data to maps or visualizes simulation curves."
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "Apache-2.0" }
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "martin.kuehn@dlr.de" }
+]
+urls = { 
+  Homepage = "https://github.com/SciCompMod/memilio",
+  Team = "https://memilio.readthedocs.io/en/latest/team.html"
+}
+dependencies = [
+  "pandas>=1.2.2",
+  "matplotlib",
+  "numpy>=1.22,<1.25",
+  "openpyxl",
+  "xlrd",
+  "requests",
+  "pyxlsb",
+  "wget",
+  "folium",
+  "mapclassify",
+  "geopandas",
+  "h5py",
+  "imageio",
+  "datetime"
+]
+
+[project.optional-dependencies]
+dev = [
+  "pyfakefs>=4.6",
+  "coverage>=7.0.1",
+  "pylint>=2.13.0,<2.16",
+  "pylint_json2html==0.4.0"
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["memilio*"]
diff --git a/pycode/memilio-plot/setup.py b/pycode/memilio-plot/setup.py
deleted file mode 100644
index 9c6a85908a..0000000000
--- a/pycode/memilio-plot/setup.py
+++ /dev/null
@@ -1,97 +0,0 @@
-import os
-import subprocess
-import sys
-
-from setuptools import Command, find_packages, setup
-
-__version__ = '1.0.0'
-
-
-class PylintCommand(Command):
-    """Custom command to run pylint and get a report as html."""
-    description = "Runs pylint and outputs the report as html."
-    user_options = []
-
-    def initialize_options(self):
-        """ """
-        from pylint.reporters.json_reporter import JSONReporter
-        from pylint.reporters.text import ParseableTextReporter, TextReporter
-        from pylint_json2html import JsonExtendedReporter
-
-        self.lint_modules = ["memilio/"]
-        self.out_format = "extendedjson"
-
-        self.REPORTERS = {
-            "parseable": (ParseableTextReporter, "build_pylint/pylint_parseable.txt"),
-            "text": (TextReporter, "build_pylint/pylint.txt"),
-            "json": (JSONReporter, "build_pylint/pylint.json"),
-            "extendedjson": (JsonExtendedReporter, "build_pylint/pylint_extended.json")
-        }
-
-    def finalize_options(self):
-        """ """
-        self.reporter, self.out_file = self.REPORTERS.get(
-            self.out_format)  # , self.REPORTERS.get("parseable"))
-
-    def run(self):
-        """ """
-        os.makedirs("build_pylint", exist_ok=True)
-
-        # Run pylint
-        from pylint import lint
-        with open(self.out_file, "w", encoding="utf-8") as report_file:
-            options = ["--rcfile=../pylintrc", *self.lint_modules]
-
-            lint.Run(options, reporter=self.reporter(
-                report_file), do_exit=False)
-
-
-setup(
-    name='memilio-plot',
-    version=__version__,
-    author='DLR-SC',
-    author_email='martin.kuehn@dlr.de',
-    maintainer_email='martin.kuehn@dlr.de',
-    url='https://github.com/SciCompMod/memilio',
-    description='Part of MEmilio project, plots data to maps or visualizes simulation curves.',
-    entry_points={
-        'console_scripts': [
-        ],
-    },
-    packages=find_packages(where=os.path.dirname(os.path.abspath(__file__))),
-    long_description='',
-    test_suite='memilio.plot_test',
-    install_requires=[
-        # smaller pandas versions contain a bug that sometimes prevents reading
-        # some excel files (e.g. population or mobility data)
-        'pandas>=1.2.2',
-        'matplotlib',
-        # smaller numpy versions cause a security issue, 1.25 breaks testing with pyfakefs
-        'numpy>=1.22,<1.25',
-        'openpyxl',
-        'xlrd',
-        'requests',
-        'pyxlsb',
-        'wget',
-        'folium',
-        'matplotlib',
-        'mapclassify',
-        'geopandas',
-        'h5py',
-        'imageio',
-        'datetime'
-    ],
-    extras_require={
-        'dev': [
-            # first support of python 3.11
-            'pyfakefs>=4.6',
-            'coverage>=7.0.1',
-            # pylint 2.16 creates problem with wrapt package version
-            'pylint>=2.13.0,<2.16',
-            'pylint_json2html==0.4.0',
-        ],
-    },
-    cmdclass={
-        'pylint': PylintCommand
-    },
-)
diff --git a/pycode/memilio-plot/tools/run_pylint.py b/pycode/memilio-plot/tools/run_pylint.py
new file mode 100644
index 0000000000..035473cf6e
--- /dev/null
+++ b/pycode/memilio-plot/tools/run_pylint.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+"""Generate Pylint reports in jsonextended format for the plot package."""
+
+from __future__ import annotations
+
+import subprocess
+import sys
+from pathlib import Path
+
+
+def main() -> int:
+    project_dir = Path(__file__).resolve().parent.parent
+    repo_root = project_dir.parent
+    build_dir = project_dir / "build_pylint"
+    build_dir.mkdir(exist_ok=True)
+    output_file = build_dir / "pylint_extended.json"
+
+    cmd = [
+        sys.executable,
+        "-m",
+        "pylint",
+        "--rcfile",
+        str(repo_root / "pylintrc"),
+        "--load-plugins",
+        "pylint_json2html",
+        "--output-format=jsonextended",
+        "memilio/",
+    ]
+
+    with output_file.open("w", encoding="utf-8") as stream:
+        result = subprocess.run(
+            cmd,
+            cwd=project_dir,
+            stdout=stream,
+            stderr=subprocess.PIPE,
+            text=True,
+            check=False,
+        )
+
+    if result.stderr:
+        sys.stderr.write(result.stderr)
+
+    if result.returncode:
+        sys.stderr.write(
+            "pylint reported issues; see build_pylint/pylint_extended.json for details.\n"
+        )
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/pycode/memilio-simulation/README.md b/pycode/memilio-simulation/README.md
index b2de287d6b..1bf8c03fbe 100644
--- a/pycode/memilio-simulation/README.md
+++ b/pycode/memilio-simulation/README.md
@@ -4,9 +4,9 @@ This package contains Python bindings for the MEmilio C++ library. It enables se
 
 ## Installation
 
-Use the provided `setup.py` script to build the bindings and install the package. The script requires CMake and the Scikit-Build packages. Both are installed by the script if not available on the system. The package uses the [Pybind11 C++ library](https://pybind11.readthedocs.io) to create the bindings.
+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 `setup.py`)
+To install the package, use the command (from the directory containing ``pyproject.toml``)
 
 ```bash
 pip install .
@@ -16,17 +16,17 @@ This builds the C++ library and C++ Python extension module and copies everythin
 
 All the requirements of the [C++ library](../../cpp/README.md) must be met in order to build and use the python bindings. A virtual environment is recommended. 
 
-CMake is executed internally by the `setup.py` script. All the options provided by the CMake configuration of the C++ library are available when building the Python extension as well. Additionally, the CMake configuration for the bindings provide the following CMake options:
+CMake is executed internally by scikit-build-core. All the options provided by the CMake configuration of the C++ library are available when building the Python extension as well. Additionally, the CMake configuration for the bindings provide the following CMake options:
 
 - MEMILIO_USE_BUNDLED_PYBIND11: ON or OFF, default ON. If ON, downloads Pybind11 automatically from a repository during CMake configuration. If OFF, Pybind11 needs to be installed on the system.
 
-When building the bindings, CMake options can be set by appending them to the install command, e.g.
+When building the bindings, CMake options can be forwarded with configuration settings, e.g.
 
 ```bash
-python setup.py install -- -DCMAKE_BUILD_TYPE=Debug -DMEMILIO_USE_BUNDLED_PYBIND11=OFF
+pip install . --config-settings=cmake.args="-DCMAKE_BUILD_TYPE=Debug" --config-settings=cmake.args="-DMEMILIO_USE_BUNDLED_PYBIND11=OFF"
 ```
 
-Alternatively, the `CMakeCache.txt` in the directory created by Scikit-Build can be edited to set the options.
+Alternatively, edit the `CMakeCache.txt` in the directory created by scikit-build-core.
 
 ## Development
 
@@ -38,8 +38,6 @@ pip install -e .[dev]
 
 This command allows you to work on the code without having to reinstall the package after a change. Note that this only works for changes to Python code. If C++ code is modified, the install command has to be repeated every time. The command also installs all additional dependencies required for development and maintenance. 
 
-For development, it may be easier to use the alternative command `python setup.py <build|install|develop>` which provides better configuration and observation of the C++ build process.
-
 The [bindings](memilio/simulation/bindings/) folder contains all the C++ code to expose the MEmilio library to Python and follows its structure, expect for the models that are bundled in a subfolder.
 
 In order to add a new model, the following steps need to be taken:
diff --git a/pycode/memilio-simulation/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
new file mode 100644
index 0000000000..f149b26108
--- /dev/null
+++ b/pycode/memilio-simulation/pyproject.toml
@@ -0,0 +1,35 @@
+[build-system]
+requires = [
+  "scikit-build-core>=0.9.0",
+  "setuptools>=68",
+  "wheel"
+]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "memilio-simulation"
+version = "1.0.0"
+description = "Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations."
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "Apache-2.0" }
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "martin.kuehn@dlr.de" }
+]
+urls = { 
+  Homepage = "https://github.com/SciCompMod/memilio",
+  Team = "https://memilio.readthedocs.io/en/latest/team.html"
+}
+dependencies = []
+
+[project.optional-dependencies]
+dev = [
+  "numpy>=1.22,<1.25",
+  "pandas>=2.0.0"
+]
+
+[tool.scikit-build]
+cmake.minimum-version = "3.13"
+cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
+wheel.packages = ["memilio"]
diff --git a/pycode/memilio-simulation/setup.py b/pycode/memilio-simulation/setup.py
deleted file mode 100644
index 037a93df8e..0000000000
--- a/pycode/memilio-simulation/setup.py
+++ /dev/null
@@ -1,38 +0,0 @@
-import os
-import subprocess
-import sys
-
-from setuptools import find_packages, setup
-
-try:
-    from skbuild import setup
-except ImportError:
-    print('scikit-build is required to build from source.')
-    print('Installation:  python -m pip install scikit-build')
-    subprocess.check_call(
-        [sys.executable, "-m", "pip", "install", "scikit-build"])
-    from skbuild import setup
-
-__version__ = '1.0.0'
-
-setup(
-    name='memilio-simulation', version=__version__, author='DLR-SC',
-    author_email='daniel.abele@dlr.de', maintainer_email='Martin.Kuehn@DLR.de',
-    url='https://github.com/SciCompMod/memilio',
-    description='Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations.',
-    packages=find_packages(where=os.path.dirname(os.path.abspath(__file__))),
-    # need shared libs so there is one shared log level
-    cmake_args=['-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON'],
-    install_requires=[
-    ],
-    extras_require={
-        'dev': [
-            # smaller numpy versions cause a security issue, 1.25 breaks testing with pyfakefs
-            'numpy>=1.22,<1.25',
-            # smaller pandas versions contain a bug that sometimes prevents reading
-            # some excel files (e.g. population or mobility data)
-            'pandas>=2.0.0',
-        ],
-    },
-    long_description='', test_suite='memilio.simulation_test',
-)
diff --git a/pycode/memilio-simulation/tools/generate_stubs.py b/pycode/memilio-simulation/tools/generate_stubs.py
index 6ac97d1d88..c22782a08c 100644
--- a/pycode/memilio-simulation/tools/generate_stubs.py
+++ b/pycode/memilio-simulation/tools/generate_stubs.py
@@ -17,23 +17,29 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #############################################################################
+import importlib.util
 import os
+import shutil
 import subprocess
 import sys
-import importlib.util
-import shutil
 
-setup_content_protected_module = f"""
-from setuptools import setup, find_packages
-
-setup(
-    name='memilio-stubs',
-    version='0.1',
-    packages=['memilio-stubs'],
-    package_data={{
-        'memilio-stubs': ['simulation/*.pyi'],
-    }},
-)
+pyproject_content_protected_module = """[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "memilio-stubs"
+version = "0.1"
+description = "Stubs for the memilio.simulation package."
+requires-python = ">=3.8"
+dependencies = []
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["memilio-stubs"]
+
+[tool.setuptools.package-data]
+"memilio-stubs" = ["simulation/*.pyi"]
 """
 
 # Define if the generated stubs of mypy should be configured
@@ -71,7 +77,8 @@
     # memilio-stubs/simulation module needs same structure as memilio/simulation
     # test --include-docstrings, --doc-dir PATH for better docs
     subprocess.check_call(
-        ['stubgen', '--include-docstrings', '-o', package_dir, '-p', 'memilio.simulation'])
+        ['stubgen', '--include-docstrings', '-o', package_dir, '-p',
+         'memilio.simulation'])
 
     # TODO:
     #   - fix numpy.float64[m, 1] to
@@ -163,8 +170,8 @@
     shutil.move(os.path.join(package_dir, "memilio"),
                 os.path.join(package_dir, "memilio-stubs"))
 
-    # create setup.py and install package
-    with open(os.path.join(package_dir, "setup.py"), "w") as setup_file:
-        setup_file.write(setup_content_protected_module)
+    # create pyproject.toml and install package
+    with open(os.path.join(package_dir, "pyproject.toml"), "w", encoding="utf-8") as pyproject_file:
+        pyproject_file.write(pyproject_content_protected_module)
     subprocess.check_call(
         [python_interpreter, '-m', 'pip', 'install', package_dir])
diff --git a/pycode/memilio-surrogatemodel/README.md b/pycode/memilio-surrogatemodel/README.md
index c1ac0ef10e..951469e853 100644
--- a/pycode/memilio-surrogatemodel/README.md
+++ b/pycode/memilio-surrogatemodel/README.md
@@ -4,8 +4,8 @@ This package contains machine learning based surrogate models that make predicti
  
 ## Installation
 
-Use the provided `setup.py` script install the package. 
-To install the package, use the command (from the directory containing `setup.py`)
+Use the provided `pyproject.toml` file to install the package. 
+To install the package, use the command (from the directory containing `pyproject.toml`)
 
 ```bash
 pip install .
diff --git a/pycode/memilio-surrogatemodel/pyproject.toml b/pycode/memilio-surrogatemodel/pyproject.toml
new file mode 100644
index 0000000000..a2ad6b1a2f
--- /dev/null
+++ b/pycode/memilio-surrogatemodel/pyproject.toml
@@ -0,0 +1,37 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "memilio-surrogatemodel"
+version = "1.0.0"
+description = "Part of MEmilio project, implementation of surrogate models for the existing models in MEmilio."
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "Apache-2.0" }
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "martin.kuehn@dlr.de" }
+]
+urls = { 
+  Homepage = "https://github.com/SciCompMod/memilio",
+  Team = "https://memilio.readthedocs.io/en/latest/team.html"
+}
+dependencies = [
+  "pandas>=1.2.2",
+  "progress",
+  "numpy>=1.22,<1.25",
+  "tensorflow",
+  "matplotlib",
+  "scikit-learn"
+]
+
+[project.optional-dependencies]
+dev = [
+  "pyfakefs>=4.6",
+  "coverage>=7.0.1"
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["memilio*"]
diff --git a/pycode/memilio-surrogatemodel/setup.py b/pycode/memilio-surrogatemodel/setup.py
deleted file mode 100644
index cbd176f47e..0000000000
--- a/pycode/memilio-surrogatemodel/setup.py
+++ /dev/null
@@ -1,30 +0,0 @@
-import os
-
-from setuptools import find_packages, setup
-
-__version__ = '1.0.0'
-
-setup(
-    name='memilio-surrogatemodel', version=__version__, author='DLR-SC',
-    author_email='henrik.zunker@dlr.de',
-    maintainer_email='martin.kuehn@dlr.de',
-    url='https://github.com/SciCompMod/memilio',
-    description='Part of MEmilio project, implementation of surrogate models for the existing models in MEmilio.',
-    packages=find_packages(
-        where=os.path.dirname(os.path.abspath(__file__))),
-    install_requires=[
-        # smaller pandas versions contain a bug that sometimes prevents reading
-        # some excel files (e.g. population or mobility data)
-        'pandas>=1.2.2',
-        'progress',
-        # smaller numpy versions cause a security issue, 1.25 breaks testing with pyfakefs
-        'numpy>=1.22,<1.25',
-        'tensorflow',
-        'matplotlib',
-        'scikit-learn', ],
-    extras_require={'dev': [
-        # first support of python 3.11
-        'pyfakefs>=4.6',
-        'coverage>=7.0.1',
-    ], },
-    long_description='', test_suite='memilio.surrogatemodel_test',)

From b521b94452b0eca4f992059562c6a78bebe7f45e Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Thu, 6 Nov 2025 09:39:04 +0100
Subject: [PATCH 02/19] move urls and reset rtd build

---
 .readthedocs.yaml                            |  2 +-
 pycode/memilio-epidata/pyproject.toml        |  8 ++++----
 pycode/memilio-generation/pyproject.toml     | 10 +++++-----
 pycode/memilio-plot/pyproject.toml           |  8 ++++----
 pycode/memilio-simulation/pyproject.toml     |  8 ++++----
 pycode/memilio-surrogatemodel/pyproject.toml |  8 ++++----
 6 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 859c882a57..3f637630d7 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -11,7 +11,7 @@ build:
   jobs:
     install:
       - pip install --exists-action=w --no-cache-dir -r docs/requirements-build.txt
-      - pip install --exists-action=w --no-cache-dir -r docs/requirements.txt --no-build-isolation
+      - pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
 
 sphinx:
   configuration: docs/source/conf.py
diff --git a/pycode/memilio-epidata/pyproject.toml b/pycode/memilio-epidata/pyproject.toml
index a50a151244..414c05b954 100644
--- a/pycode/memilio-epidata/pyproject.toml
+++ b/pycode/memilio-epidata/pyproject.toml
@@ -13,10 +13,6 @@ authors = [{ name = "MEmilio Team" }]
 maintainers = [
   { email = "martin.kuehn@dlr.de" }
 ]
-urls = { 
-  Homepage = "https://github.com/SciCompMod/memilio",
-  Team = "https://memilio.readthedocs.io/en/latest/team.html"
-}
 dependencies = [
   "pandas>=2.0.0",
   "pyarrow",
@@ -56,6 +52,10 @@ getcommutermobility = "memilio.epidata.getCommuterMobility:main"
 getvaccinationdata = "memilio.epidata.getVaccinationData:main"
 gethospitalizationdata = "memilio.epidata.getHospitalizationData:main"
 
+[project.urls]
+Homepage = "https://github.com/SciCompMod/memilio"
+Team = "https://memilio.readthedocs.io/en/latest/team.html"
+
 [tool.setuptools.packages.find]
 where = ["."]
 include = ["memilio*"]
diff --git a/pycode/memilio-generation/pyproject.toml b/pycode/memilio-generation/pyproject.toml
index 2652447295..c75bc01497 100644
--- a/pycode/memilio-generation/pyproject.toml
+++ b/pycode/memilio-generation/pyproject.toml
@@ -17,10 +17,6 @@ authors = [{ name = "MEmilio Team" }]
 maintainers = [
   { email = "martin.kuehn@dlr.de" }
 ]
-urls = { 
-  Homepage = "https://github.com/SciCompMod/memilio",
-  Team = "https://memilio.readthedocs.io/en/latest/team.html"
-}
 dependencies = [
   "libclang==18.1.1",
   "dataclasses",
@@ -32,9 +28,13 @@ dependencies = [
 [project.optional-dependencies]
 dev = []
 
+[project.urls]
+Homepage = "https://github.com/SciCompMod/memilio"
+Team = "https://memilio.readthedocs.io/en/latest/team.html"
+
 [tool.scikit-build]
 cmake.minimum-version = "3.13"
 wheel.packages = ["memilio"]
 
 [tool.scikit-build.package-data]
-"memilio.generation" = ["tools/*.json"]
+"memilio.generation" = ["tools/*.json", "tools/*.txt", "tools/README.md"]
diff --git a/pycode/memilio-plot/pyproject.toml b/pycode/memilio-plot/pyproject.toml
index 0149b86a02..56531fd8b3 100644
--- a/pycode/memilio-plot/pyproject.toml
+++ b/pycode/memilio-plot/pyproject.toml
@@ -13,10 +13,6 @@ authors = [{ name = "MEmilio Team" }]
 maintainers = [
   { email = "martin.kuehn@dlr.de" }
 ]
-urls = { 
-  Homepage = "https://github.com/SciCompMod/memilio",
-  Team = "https://memilio.readthedocs.io/en/latest/team.html"
-}
 dependencies = [
   "pandas>=1.2.2",
   "matplotlib",
@@ -42,6 +38,10 @@ dev = [
   "pylint_json2html==0.4.0"
 ]
 
+[project.urls]
+Homepage = "https://github.com/SciCompMod/memilio"
+Team = "https://memilio.readthedocs.io/en/latest/team.html"
+
 [tool.setuptools.packages.find]
 where = ["."]
 include = ["memilio*"]
diff --git a/pycode/memilio-simulation/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
index f149b26108..8e934fe806 100644
--- a/pycode/memilio-simulation/pyproject.toml
+++ b/pycode/memilio-simulation/pyproject.toml
@@ -17,10 +17,6 @@ authors = [{ name = "MEmilio Team" }]
 maintainers = [
   { email = "martin.kuehn@dlr.de" }
 ]
-urls = { 
-  Homepage = "https://github.com/SciCompMod/memilio",
-  Team = "https://memilio.readthedocs.io/en/latest/team.html"
-}
 dependencies = []
 
 [project.optional-dependencies]
@@ -29,6 +25,10 @@ dev = [
   "pandas>=2.0.0"
 ]
 
+[project.urls]
+Homepage = "https://github.com/SciCompMod/memilio"
+Team = "https://memilio.readthedocs.io/en/latest/team.html"
+
 [tool.scikit-build]
 cmake.minimum-version = "3.13"
 cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
diff --git a/pycode/memilio-surrogatemodel/pyproject.toml b/pycode/memilio-surrogatemodel/pyproject.toml
index a2ad6b1a2f..377127cbe5 100644
--- a/pycode/memilio-surrogatemodel/pyproject.toml
+++ b/pycode/memilio-surrogatemodel/pyproject.toml
@@ -13,10 +13,6 @@ authors = [{ name = "MEmilio Team" }]
 maintainers = [
   { email = "martin.kuehn@dlr.de" }
 ]
-urls = { 
-  Homepage = "https://github.com/SciCompMod/memilio",
-  Team = "https://memilio.readthedocs.io/en/latest/team.html"
-}
 dependencies = [
   "pandas>=1.2.2",
   "progress",
@@ -32,6 +28,10 @@ dev = [
   "coverage>=7.0.1"
 ]
 
+[project.urls]
+Homepage = "https://github.com/SciCompMod/memilio"
+Team = "https://memilio.readthedocs.io/en/latest/team.html"
+
 [tool.setuptools.packages.find]
 where = ["."]
 include = ["memilio*"]

From ca1b6128d66f550ed0c07a04565e5bda35f3a8a6 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Thu, 6 Nov 2025 09:45:40 +0100
Subject: [PATCH 03/19] allow py 3.8

---
 pycode/memilio-epidata/pyproject.toml        | 2 +-
 pycode/memilio-generation/pyproject.toml     | 2 +-
 pycode/memilio-plot/pyproject.toml           | 2 +-
 pycode/memilio-simulation/pyproject.toml     | 2 +-
 pycode/memilio-surrogatemodel/pyproject.toml | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/pycode/memilio-epidata/pyproject.toml b/pycode/memilio-epidata/pyproject.toml
index 414c05b954..b282267810 100644
--- a/pycode/memilio-epidata/pyproject.toml
+++ b/pycode/memilio-epidata/pyproject.toml
@@ -7,7 +7,7 @@ name = "memilio-epidata"
 version = "1.0.0"
 description = "Part of MEmilio project, reads epidemiological data from different official and unofficial sources."
 readme = "README.rst"
-requires-python = ">=3.9"
+requires-python = ">=3.8"
 license = { text = "Apache-2.0" }
 authors = [{ name = "MEmilio Team" }]
 maintainers = [
diff --git a/pycode/memilio-generation/pyproject.toml b/pycode/memilio-generation/pyproject.toml
index c75bc01497..02ef9c257c 100644
--- a/pycode/memilio-generation/pyproject.toml
+++ b/pycode/memilio-generation/pyproject.toml
@@ -11,7 +11,7 @@ name = "memilio-generation"
 version = "0.1.0"
 description = "Part of MEmilio project, automatic generation of model specific python bindings."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.8"
 license = { text = "Apache-2.0" }
 authors = [{ name = "MEmilio Team" }]
 maintainers = [
diff --git a/pycode/memilio-plot/pyproject.toml b/pycode/memilio-plot/pyproject.toml
index 56531fd8b3..aab85cbb6a 100644
--- a/pycode/memilio-plot/pyproject.toml
+++ b/pycode/memilio-plot/pyproject.toml
@@ -7,7 +7,7 @@ name = "memilio-plot"
 version = "1.0.0"
 description = "Part of MEmilio project, plots data to maps or visualizes simulation curves."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.8"
 license = { text = "Apache-2.0" }
 authors = [{ name = "MEmilio Team" }]
 maintainers = [
diff --git a/pycode/memilio-simulation/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
index 8e934fe806..d091d221e1 100644
--- a/pycode/memilio-simulation/pyproject.toml
+++ b/pycode/memilio-simulation/pyproject.toml
@@ -11,7 +11,7 @@ name = "memilio-simulation"
 version = "1.0.0"
 description = "Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.8"
 license = { text = "Apache-2.0" }
 authors = [{ name = "MEmilio Team" }]
 maintainers = [
diff --git a/pycode/memilio-surrogatemodel/pyproject.toml b/pycode/memilio-surrogatemodel/pyproject.toml
index 377127cbe5..706f45993d 100644
--- a/pycode/memilio-surrogatemodel/pyproject.toml
+++ b/pycode/memilio-surrogatemodel/pyproject.toml
@@ -7,7 +7,7 @@ name = "memilio-surrogatemodel"
 version = "1.0.0"
 description = "Part of MEmilio project, implementation of surrogate models for the existing models in MEmilio."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.8"
 license = { text = "Apache-2.0" }
 authors = [{ name = "MEmilio Team" }]
 maintainers = [

From f7aef7fb5a2939e3138854a38e585d5f5e51ac7a Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Thu, 6 Nov 2025 09:56:26 +0100
Subject: [PATCH 04/19] fix py version for pylint test

---
 .github/actions/test-pylint/action.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/actions/test-pylint/action.yml b/.github/actions/test-pylint/action.yml
index 12af19357c..021e3a0471 100644
--- a/.github/actions/test-pylint/action.yml
+++ b/.github/actions/test-pylint/action.yml
@@ -13,6 +13,10 @@ runs:
         sudo apt-get -qq update
         sudo apt-get -qq -y install python3-pip gnupg
         python -m pip install --upgrade pip
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
     - name: Download Python Wheels
       uses: actions/download-artifact@v4
       with:

From c70c86f3292db9f0c7ab2c2d99d5b3b0cfdd78f1 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Thu, 6 Nov 2025 10:02:46 +0100
Subject: [PATCH 05/19] wrong syntax to fix cmake version

---
 pycode/memilio-generation/pyproject.toml | 7 +++++--
 pycode/memilio-simulation/pyproject.toml | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/pycode/memilio-generation/pyproject.toml b/pycode/memilio-generation/pyproject.toml
index 02ef9c257c..523fe2a44a 100644
--- a/pycode/memilio-generation/pyproject.toml
+++ b/pycode/memilio-generation/pyproject.toml
@@ -33,8 +33,11 @@ Homepage = "https://github.com/SciCompMod/memilio"
 Team = "https://memilio.readthedocs.io/en/latest/team.html"
 
 [tool.scikit-build]
-cmake.minimum-version = "3.13"
+cmake.version = "3.13"
 wheel.packages = ["memilio"]
 
-[tool.scikit-build.package-data]
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
 "memilio.generation" = ["tools/*.json", "tools/*.txt", "tools/README.md"]
diff --git a/pycode/memilio-simulation/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
index d091d221e1..b355da1a34 100644
--- a/pycode/memilio-simulation/pyproject.toml
+++ b/pycode/memilio-simulation/pyproject.toml
@@ -30,6 +30,6 @@ Homepage = "https://github.com/SciCompMod/memilio"
 Team = "https://memilio.readthedocs.io/en/latest/team.html"
 
 [tool.scikit-build]
-cmake.minimum-version = "3.13"
+cmake.version = "3.13"
 cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
 wheel.packages = ["memilio"]

From 09cc12c9d105e18f5fd4146c2d6b2794450e927e Mon Sep 17 00:00:00 2001
From: Henrik Zunker <henrik.zunker@dlr.de>
Date: Tue, 11 Nov 2025 09:02:30 +0100
Subject: [PATCH 06/19] .

---
 pycode/memilio-generation/pyproject.toml | 2 +-
 pycode/memilio-simulation/pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pycode/memilio-generation/pyproject.toml b/pycode/memilio-generation/pyproject.toml
index 523fe2a44a..12cb7ed1e0 100644
--- a/pycode/memilio-generation/pyproject.toml
+++ b/pycode/memilio-generation/pyproject.toml
@@ -33,7 +33,7 @@ Homepage = "https://github.com/SciCompMod/memilio"
 Team = "https://memilio.readthedocs.io/en/latest/team.html"
 
 [tool.scikit-build]
-cmake.version = "3.13"
+cmake.version = ">=3.13"
 wheel.packages = ["memilio"]
 
 [tool.setuptools]
diff --git a/pycode/memilio-simulation/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
index b355da1a34..e82574f361 100644
--- a/pycode/memilio-simulation/pyproject.toml
+++ b/pycode/memilio-simulation/pyproject.toml
@@ -30,6 +30,6 @@ Homepage = "https://github.com/SciCompMod/memilio"
 Team = "https://memilio.readthedocs.io/en/latest/team.html"
 
 [tool.scikit-build]
-cmake.version = "3.13"
+cmake.version = ">=3.13"
 cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
 wheel.packages = ["memilio"]

From 40668e7368749916cd7485cf7c61a8df9cd0ab63 Mon Sep 17 00:00:00 2001
From: Henrik Zunker <henrik.zunker@dlr.de>
Date: Tue, 11 Nov 2025 10:57:56 +0100
Subject: [PATCH 07/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 15c186b68f..3370a43d1b 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -100,3 +100,20 @@ add_pymio_module(_simulation_omseirs4
     LINKED_LIBRARIES memilio ode_mseirs4
     SOURCES memilio/simulation/bindings/models/omseirs4.cpp
 )
+
+# Install shared libraries for auditwheel to bundle them into the wheel
+if(BUILD_SHARED_LIBS)
+    if(TARGET jsoncpp_lib)
+        install(TARGETS jsoncpp_lib
+            LIBRARY DESTINATION memilio/simulation
+            RUNTIME DESTINATION memilio/simulation
+        )
+    endif()
+
+    if(TARGET memilio)
+        install(TARGETS memilio
+            LIBRARY DESTINATION memilio/simulation
+            RUNTIME DESTINATION memilio/simulation
+        )
+    endif()
+endif()

From 64609bc8ca674ce7fa4a9d194fa30b5579a265d8 Mon Sep 17 00:00:00 2001
From: Henrik Zunker <henrik.zunker@dlr.de>
Date: Tue, 11 Nov 2025 11:42:28 +0100
Subject: [PATCH 08/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 3370a43d1b..ad7ff8412c 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -103,17 +103,13 @@ add_pymio_module(_simulation_omseirs4
 
 # Install shared libraries for auditwheel to bundle them into the wheel
 if(BUILD_SHARED_LIBS)
-    if(TARGET jsoncpp_lib)
-        install(TARGETS jsoncpp_lib
-            LIBRARY DESTINATION memilio/simulation
-            RUNTIME DESTINATION memilio/simulation
-        )
-    endif()
-
-    if(TARGET memilio)
-        install(TARGETS memilio
-            LIBRARY DESTINATION memilio/simulation
-            RUNTIME DESTINATION memilio/simulation
-        )
-    endif()
+    install(DIRECTORY ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/
+        DESTINATION memilio/simulation
+        FILES_MATCHING PATTERN "*.so*"
+        PATTERN "*.dylib*"
+    )
+    install(DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/
+        DESTINATION memilio/simulation
+        FILES_MATCHING PATTERN "*.dll"
+    )
 endif()

From 36c6fd46ee9533b61edf447d0ddd0bfad7146473 Mon Sep 17 00:00:00 2001
From: Henrik Zunker <henrik.zunker@dlr.de>
Date: Tue, 11 Nov 2025 12:04:11 +0100
Subject: [PATCH 09/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index ad7ff8412c..4a71ee0752 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -103,13 +103,8 @@ add_pymio_module(_simulation_omseirs4
 
 # Install shared libraries for auditwheel to bundle them into the wheel
 if(BUILD_SHARED_LIBS)
-    install(DIRECTORY ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/
-        DESTINATION memilio/simulation
-        FILES_MATCHING PATTERN "*.so*"
-        PATTERN "*.dylib*"
-    )
-    install(DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/
-        DESTINATION memilio/simulation
-        FILES_MATCHING PATTERN "*.dll"
+    install(TARGETS jsoncpp_lib memilio
+        LIBRARY DESTINATION memilio/simulation
+        RUNTIME DESTINATION memilio/simulation
     )
 endif()

From 0f1470cafcef36c75606f3277615df426261c9e5 Mon Sep 17 00:00:00 2001
From: Henrik Zunker <henrik.zunker@dlr.de>
Date: Tue, 11 Nov 2025 12:40:36 +0100
Subject: [PATCH 10/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 8 --------
 pycode/memilio-simulation/pyproject.toml | 1 +
 2 files changed, 1 insertion(+), 8 deletions(-)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 4a71ee0752..15c186b68f 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -100,11 +100,3 @@ add_pymio_module(_simulation_omseirs4
     LINKED_LIBRARIES memilio ode_mseirs4
     SOURCES memilio/simulation/bindings/models/omseirs4.cpp
 )
-
-# Install shared libraries for auditwheel to bundle them into the wheel
-if(BUILD_SHARED_LIBS)
-    install(TARGETS jsoncpp_lib memilio
-        LIBRARY DESTINATION memilio/simulation
-        RUNTIME DESTINATION memilio/simulation
-    )
-endif()
diff --git a/pycode/memilio-simulation/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
index e82574f361..3a7d07285e 100644
--- a/pycode/memilio-simulation/pyproject.toml
+++ b/pycode/memilio-simulation/pyproject.toml
@@ -33,3 +33,4 @@ Team = "https://memilio.readthedocs.io/en/latest/team.html"
 cmake.version = ">=3.13"
 cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
 wheel.packages = ["memilio"]
+wheel.install-dir = "memilio/simulation"

From b6037d7886ce66ba6057bce16d15c6d0393f95a4 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 12 Nov 2025 08:42:26 +0100
Subject: [PATCH 11/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 31 ++++++++++++++++++++++--
 1 file changed, 29 insertions(+), 2 deletions(-)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 15c186b68f..443e236836 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -13,7 +13,12 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 set(CMAKE_PDB_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
-set(CMAKE_INSTALL_RPATH "${CMAKE_BINARY_DIR}/lib" "${CMAKE_BINARY_DIR}/bin")
+set(CMAKE_INSTALL_RPATH
+    "$ORIGIN"
+    "$ORIGIN/lib"
+    "${CMAKE_BINARY_DIR}/lib"
+    "${CMAKE_BINARY_DIR}/bin"
+)
 
 if(MEMILIO_USE_BUNDLED_PYBIND11)
     # Fetch pybind11
@@ -45,7 +50,11 @@ function(add_pymio_module target_name)
     pybind11_add_module(${target_name} MODULE ${PYBIND11_MODULE_SOURCES})
     target_link_libraries(${target_name} PRIVATE ${PYBIND11_MODULE_LINKED_LIBRARIES})
     target_include_directories(${target_name} PRIVATE memilio/simulation/bindings)
-    install(TARGETS ${target_name} LIBRARY DESTINATION memilio/simulation)
+    install(TARGETS ${target_name}
+        LIBRARY DESTINATION .
+        ARCHIVE DESTINATION .
+        RUNTIME DESTINATION .
+    )
 endfunction()
 
 # build python extensions
@@ -100,3 +109,21 @@ add_pymio_module(_simulation_omseirs4
     LINKED_LIBRARIES memilio ode_mseirs4
     SOURCES memilio/simulation/bindings/models/omseirs4.cpp
 )
+
+set(MEMILIO_SIMULATION_LIBS
+    memilio
+    abm
+    ode_sir
+    ode_seir
+    ode_secir
+    ode_secirvvs
+    sde_sir
+    sde_sirs
+    ode_mseirs4
+)
+
+install(TARGETS ${MEMILIO_SIMULATION_LIBS}
+    LIBRARY DESTINATION lib
+    ARCHIVE DESTINATION lib
+    RUNTIME DESTINATION lib
+)

From be760d56253878fb86c4c7b677494b7ac5aed219 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 12 Nov 2025 16:07:28 +0100
Subject: [PATCH 12/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 443e236836..912b4a9a09 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -127,3 +127,21 @@ install(TARGETS ${MEMILIO_SIMULATION_LIBS}
     ARCHIVE DESTINATION lib
     RUNTIME DESTINATION lib
 )
+
+# If jsoncpp was built as part of the bundled third-party dependencies, make sure its
+# libraries are installed into the wheel as well so auditwheel can bundle them.
+set(MEMILIO_JSONCPP_LIBS)
+if(TARGET jsoncpp_lib)
+    list(APPEND MEMILIO_JSONCPP_LIBS jsoncpp_lib)
+endif()
+if(TARGET jsoncpp_static)
+    list(APPEND MEMILIO_JSONCPP_LIBS jsoncpp_static)
+endif()
+
+if(MEMILIO_JSONCPP_LIBS)
+    install(TARGETS ${MEMILIO_JSONCPP_LIBS}
+        LIBRARY DESTINATION lib
+        ARCHIVE DESTINATION lib
+        RUNTIME DESTINATION lib
+    )
+endif()

From 36f10d9f152e53e24c7168ec5e28ad86e14df105 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 12 Nov 2025 16:24:12 +0100
Subject: [PATCH 13/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 912b4a9a09..8644823004 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -130,16 +130,8 @@ install(TARGETS ${MEMILIO_SIMULATION_LIBS}
 
 # If jsoncpp was built as part of the bundled third-party dependencies, make sure its
 # libraries are installed into the wheel as well so auditwheel can bundle them.
-set(MEMILIO_JSONCPP_LIBS)
 if(TARGET jsoncpp_lib)
-    list(APPEND MEMILIO_JSONCPP_LIBS jsoncpp_lib)
-endif()
-if(TARGET jsoncpp_static)
-    list(APPEND MEMILIO_JSONCPP_LIBS jsoncpp_static)
-endif()
-
-if(MEMILIO_JSONCPP_LIBS)
-    install(TARGETS ${MEMILIO_JSONCPP_LIBS}
+    install(TARGETS jsoncpp_lib
         LIBRARY DESTINATION lib
         ARCHIVE DESTINATION lib
         RUNTIME DESTINATION lib

From 2cf81c2c5e3be289831a0e803df98d94a9b46b8d Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 12 Nov 2025 16:38:53 +0100
Subject: [PATCH 14/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 8644823004..e9f72a5b81 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -137,3 +137,11 @@ if(TARGET jsoncpp_lib)
         RUNTIME DESTINATION lib
     )
 endif()
+
+if(TARGET spdlog)
+    install(TARGETS spdlog
+        LIBRARY DESTINATION lib
+        ARCHIVE DESTINATION lib
+        RUNTIME DESTINATION lib
+    )
+endif()

From 5eb7aef5f493f15fef2877f3fa3e87e710595992 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 12 Nov 2025 17:28:20 +0100
Subject: [PATCH 15/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index e9f72a5b81..66592688af 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -50,6 +50,9 @@ function(add_pymio_module target_name)
     pybind11_add_module(${target_name} MODULE ${PYBIND11_MODULE_SOURCES})
     target_link_libraries(${target_name} PRIVATE ${PYBIND11_MODULE_LINKED_LIBRARIES})
     target_include_directories(${target_name} PRIVATE memilio/simulation/bindings)
+    set_target_properties(${target_name} PROPERTIES
+        INSTALL_RPATH "\\$ORIGIN;\\$ORIGIN/lib"
+    )
     install(TARGETS ${target_name}
         LIBRARY DESTINATION .
         ARCHIVE DESTINATION .
@@ -122,6 +125,14 @@ set(MEMILIO_SIMULATION_LIBS
     ode_mseirs4
 )
 
+foreach(target_name IN LISTS MEMILIO_SIMULATION_LIBS)
+    if(TARGET ${target_name})
+        set_target_properties(${target_name} PROPERTIES
+            INSTALL_RPATH "\\$ORIGIN"
+        )
+    endif()
+endforeach()
+
 install(TARGETS ${MEMILIO_SIMULATION_LIBS}
     LIBRARY DESTINATION lib
     ARCHIVE DESTINATION lib
@@ -131,6 +142,9 @@ install(TARGETS ${MEMILIO_SIMULATION_LIBS}
 # If jsoncpp was built as part of the bundled third-party dependencies, make sure its
 # libraries are installed into the wheel as well so auditwheel can bundle them.
 if(TARGET jsoncpp_lib)
+    set_target_properties(jsoncpp_lib PROPERTIES
+        INSTALL_RPATH "\\$ORIGIN"
+    )
     install(TARGETS jsoncpp_lib
         LIBRARY DESTINATION lib
         ARCHIVE DESTINATION lib
@@ -139,6 +153,9 @@ if(TARGET jsoncpp_lib)
 endif()
 
 if(TARGET spdlog)
+    set_target_properties(spdlog PROPERTIES
+        INSTALL_RPATH "\\$ORIGIN"
+    )
     install(TARGETS spdlog
         LIBRARY DESTINATION lib
         ARCHIVE DESTINATION lib

From 928ee52bd4e754397c8a96d7a31a8dfd1cb134e5 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 12 Nov 2025 17:50:03 +0100
Subject: [PATCH 16/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 34 +++++++++++++++++-------
 1 file changed, 25 insertions(+), 9 deletions(-)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 66592688af..c72cfcd049 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -140,15 +140,24 @@ install(TARGETS ${MEMILIO_SIMULATION_LIBS}
 )
 
 # If jsoncpp was built as part of the bundled third-party dependencies, make sure its
-# libraries are installed into the wheel as well so auditwheel can bundle them.
+# shared library is copied into the wheel with the exact SONAME the runtime loader will
+# request. Wheels do not preserve symlinks, so install real copies for every relevant
+# name.
 if(TARGET jsoncpp_lib)
     set_target_properties(jsoncpp_lib PROPERTIES
         INSTALL_RPATH "\\$ORIGIN"
     )
-    install(TARGETS jsoncpp_lib
-        LIBRARY DESTINATION lib
-        ARCHIVE DESTINATION lib
-        RUNTIME DESTINATION lib
+    set(JSONCPP_LIB_FILE $<TARGET_FILE:jsoncpp_lib>)
+    install(FILES ${JSONCPP_LIB_FILE}
+        DESTINATION lib
+    )
+    install(FILES ${JSONCPP_LIB_FILE}
+        DESTINATION lib
+        RENAME libjsoncpp.so.26
+    )
+    install(FILES ${JSONCPP_LIB_FILE}
+        DESTINATION lib
+        RENAME libjsoncpp.so
     )
 endif()
 
@@ -156,9 +165,16 @@ if(TARGET spdlog)
     set_target_properties(spdlog PROPERTIES
         INSTALL_RPATH "\\$ORIGIN"
     )
-    install(TARGETS spdlog
-        LIBRARY DESTINATION lib
-        ARCHIVE DESTINATION lib
-        RUNTIME DESTINATION lib
+    set(SPDLOG_LIB_FILE $<TARGET_FILE:spdlog>)
+    install(FILES ${SPDLOG_LIB_FILE}
+        DESTINATION lib
+    )
+    install(FILES ${SPDLOG_LIB_FILE}
+        DESTINATION lib
+        RENAME libspdlog.so.1.15
+    )
+    install(FILES ${SPDLOG_LIB_FILE}
+        DESTINATION lib
+        RENAME libspdlog.so
     )
 endif()

From 301ec91e93f4541ac864602edd6f00a39c5dcf86 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Thu, 13 Nov 2025 12:36:43 +0100
Subject: [PATCH 17/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index c72cfcd049..128fbb618d 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -20,6 +20,9 @@ set(CMAKE_INSTALL_RPATH
     "${CMAKE_BINARY_DIR}/bin"
 )
 
+# Bundled JsonCpp must be linked statically so the wheel stays self-contained.
+set(MEMILIO_PREFER_STATIC_JSONCPP ON CACHE BOOL "" FORCE)
+
 if(MEMILIO_USE_BUNDLED_PYBIND11)
     # Fetch pybind11
     include(FetchContent)

From 152b9f6af2d38cc1b837199984dfcf7eed489b67 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Thu, 13 Nov 2025 14:25:05 +0100
Subject: [PATCH 18/19] .

---
 pycode/memilio-simulation/CMakeLists.txt | 34 +++++++++++++-----------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index 128fbb618d..2267a59db6 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -22,6 +22,7 @@ set(CMAKE_INSTALL_RPATH
 
 # Bundled JsonCpp must be linked statically so the wheel stays self-contained.
 set(MEMILIO_PREFER_STATIC_JSONCPP ON CACHE BOOL "" FORCE)
+set(MEMILIO_PREFER_STATIC_SPDLOG ON CACHE BOOL "" FORCE)
 
 if(MEMILIO_USE_BUNDLED_PYBIND11)
     # Fetch pybind11
@@ -165,19 +166,22 @@ if(TARGET jsoncpp_lib)
 endif()
 
 if(TARGET spdlog)
-    set_target_properties(spdlog PROPERTIES
-        INSTALL_RPATH "\\$ORIGIN"
-    )
-    set(SPDLOG_LIB_FILE $<TARGET_FILE:spdlog>)
-    install(FILES ${SPDLOG_LIB_FILE}
-        DESTINATION lib
-    )
-    install(FILES ${SPDLOG_LIB_FILE}
-        DESTINATION lib
-        RENAME libspdlog.so.1.15
-    )
-    install(FILES ${SPDLOG_LIB_FILE}
-        DESTINATION lib
-        RENAME libspdlog.so
-    )
+    get_target_property(_SPDLOG_LIB_TYPE spdlog TYPE)
+    if(_SPDLOG_LIB_TYPE STREQUAL "SHARED_LIBRARY")
+        set_target_properties(spdlog PROPERTIES
+            INSTALL_RPATH "\\$ORIGIN"
+        )
+        set(SPDLOG_LIB_FILE $<TARGET_FILE:spdlog>)
+        install(FILES ${SPDLOG_LIB_FILE}
+            DESTINATION lib
+        )
+        install(FILES ${SPDLOG_LIB_FILE}
+            DESTINATION lib
+            RENAME libspdlog.so.1.15
+        )
+        install(FILES ${SPDLOG_LIB_FILE}
+            DESTINATION lib
+            RENAME libspdlog.so
+        )
+    endif()
 endif()

From 1b183a3212f25d07a4c416135dcebcb2e6a5967b Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Thu, 13 Nov 2025 15:32:23 +0100
Subject: [PATCH 19/19] ..

---
 cpp/thirdparty/CMakeLists.txt | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/cpp/thirdparty/CMakeLists.txt b/cpp/thirdparty/CMakeLists.txt
index 1fc70bfdc3..68d9904ac0 100644
--- a/cpp/thirdparty/CMakeLists.txt
+++ b/cpp/thirdparty/CMakeLists.txt
@@ -37,7 +37,22 @@ if(MEMILIO_USE_BUNDLED_SPDLOG)
 
     if(NOT spdlog_POPULATED)
         FetchContent_Populate(spdlog)
+
+        # Even when the rest builds shared libraries, we sometimes
+        # prefer to keep spdlog static (e.g. for Python wheels where we don't want
+        # an extra shared dependency). Temporarily override BUILD_SHARED_LIBS while
+        # configuring spdlog to force a static build in that case.
+        if(MEMILIO_PREFER_STATIC_SPDLOG)
+            set(_MEMILIO_PREV_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
+            set(BUILD_SHARED_LIBS OFF)
+        endif()
+
         add_subdirectory(${spdlog_SOURCE_DIR} ${spdlog_BINARY_DIR} EXCLUDE_FROM_ALL)
+
+        if(MEMILIO_PREFER_STATIC_SPDLOG)
+            set(BUILD_SHARED_LIBS ${_MEMILIO_PREV_BUILD_SHARED_LIBS})
+            unset(_MEMILIO_PREV_BUILD_SHARED_LIBS)
+        endif()
     endif()
 
 else()
@@ -198,6 +213,7 @@ else()
 endif()
 
 find_package(sbml ${MEMILIO_SBML_VERSION} CONFIG)
+
 if(sbml_FOUND)
     set(MEMILIO_HAS_SBML ON)
     message(STATUS "Found libSBML: ${libsbml_INCLUDE_DIRS}")