From 24f1e7c732c3b6300f3c70c7f5d5aa600065cf33 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 23 Feb 2026 08:58:29 +0100
Subject: [PATCH 01/74] building source distribution works

---
 CMakeLists.txt                           | 10 ++++++
 pycode/memilio-simulation/CMakeLists.txt |  9 -----
 pycode/memilio-simulation/pyproject.toml | 39 --------------------
 pyproject.toml                           | 45 +++++++++++++++++++++++-
 4 files changed, 54 insertions(+), 49 deletions(-)
 create mode 100644 CMakeLists.txt
 delete mode 100644 pycode/memilio-simulation/pyproject.toml

diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000000..15b092d12f
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,10 @@
+cmake_minimum_required(VERSION 3.13)
+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)
\ No newline at end of file
diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index f54390d920..94ae9184b0 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -1,9 +1,3 @@
-cmake_minimum_required(VERSION 3.13)
-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)
 
@@ -52,9 +46,6 @@ 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/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
deleted file mode 100644
index d7bc24b90f..0000000000
--- a/pycode/memilio-simulation/pyproject.toml
+++ /dev/null
@@ -1,39 +0,0 @@
-[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 = ">=3.8"
-license = { text = "Apache-2.0" }
-authors = [{ name = "MEmilio Team" }]
-maintainers = [
-  { email = "martin.kuehn@dlr.de" }
-]
-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"
-]
-
-[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.version = ">=3.13"
-cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
-wheel.packages = ["memilio"]
-wheel.install-dir = "memilio/simulation"
-build-dir = "../build/memilio-simulation"
diff --git a/pyproject.toml b/pyproject.toml
index 2f12cc6b19..fec49ef467 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,4 +3,47 @@ max-line-length = 79
 
 [tool.pyright]
 include = ["pycode"]
-exclude = ["pycode/memilio-simulation"]
\ No newline at end of file
+exclude = ["pycode/memilio-simulation"]
+
+[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 = ">=3.8"
+license = { text = "Apache-2.0" }
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "martin.kuehn@dlr.de" }
+]
+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"
+]
+
+[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.version = ">=3.13"
+cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
+wheel.packages = ["memilio"]
+wheel.install-dir = "memilio/simulation"
+build-dir = "../build/memilio-simulation"
+
+[tool.setuptools]
+packages = ["pycode/memilio-simulation"]

From 467748305f3c4177e31f93ef9427f4558724244c Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 23 Feb 2026 14:57:47 +0100
Subject: [PATCH 02/74] try building wheels with ci

---
 .github/workflows/build_wheels.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 .github/workflows/build_wheels.yml

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
new file mode 100644
index 0000000000..a948125dce
--- /dev/null
+++ b/.github/workflows/build_wheels.yml
@@ -0,0 +1,19 @@
+name: Build wheels
+
+on: [pull_request, release]
+
+jobs:
+  build_wheels:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: pypa/cibuildwheel@v2.16
+
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl
\ No newline at end of file

From fe6706c5e9c4a25e363bec1963c27c8c92a18e73 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 23 Feb 2026 15:36:51 +0100
Subject: [PATCH 03/74] [ci skip] try only ubuntu

---
 .github/workflows/build_wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index a948125dce..48e4bccd64 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest]
 
     steps:
       - uses: actions/checkout@v4

From 6b35ba7483365380b8d07a6c2ef0a7e0562cad8c Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 23 Feb 2026 15:38:38 +0100
Subject: [PATCH 04/74] test

---
 .github/workflows/build_wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 48e4bccd64..3c7019f73d 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -1,4 +1,4 @@
-name: Build wheels
+name: Build wheels 
 
 on: [pull_request, release]
 

From 369342fe5af1de461657fba4679444833539bc7b Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 13:36:22 +0100
Subject: [PATCH 05/74] require higher pybind version

---
 .github/workflows/epidata_main.yml | 294 ++++++-------
 .github/workflows/main.yml         | 660 ++++++++++++++---------------
 .github/workflows/message_bot.yml  | 226 +++++-----
 pyproject.toml                     |   1 +
 4 files changed, 591 insertions(+), 590 deletions(-)

diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index 3cd8fea21b..e8e84dd564 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -1,158 +1,158 @@
-name: Epidata-CI
+# name: Epidata-CI
 
-on: 
-  schedule:
-    - cron: "40 1 * * *"
-  push:
-    branches:
-      - 'main'
-    tags:
-      - version-*
-    paths:
-      - '**/memilio-epidata/**'
-      - '.github/**'
-  pull_request:
-    types: [opened, reopened, synchronize, ready_for_review]
-    paths:
-      - '**/memilio-epidata/**'
-      - '.github/**'
-  workflow_dispatch:
+# on: 
+#   schedule:
+#     - cron: "40 1 * * *"
+#   push:
+#     branches:
+#       - 'main'
+#     tags:
+#       - version-*
+#     paths:
+#       - '**/memilio-epidata/**'
+#       - '.github/**'
+#   pull_request:
+#     types: [opened, reopened, synchronize, ready_for_review]
+#     paths:
+#       - '**/memilio-epidata/**'
+#       - '.github/**'
+#   workflow_dispatch:
 
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: 3.12
-    - uses: pre-commit/action@v3.0.1
+# jobs:
+#   pre-commit:
+#     runs-on: ubuntu-latest
+#     steps:
+#     - uses: actions/checkout@v4
+#     - uses: actions/setup-python@v5
+#       with:
+#         python-version: 3.12
+#     - uses: pre-commit/action@v3.0.1
 
-  build-py-epidata:
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: epidata
+#   build-py-epidata:
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: epidata
 
-  build-py-plot:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: plot
+#   build-py-plot:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: plot
 
-  test-py-epidata:
-    needs: build-py-epidata
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with: 
-          version: ${{ matrix.version }}
-          package: epidata
-          coverage: ON
+#   test-py-epidata:
+#     needs: build-py-epidata
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with: 
+#           version: ${{ matrix.version }}
+#           package: epidata
+#           coverage: ON
 
-  test-py-plot:
-    if: github.event.pull_request.draft == false
-    needs: [build-py-plot, build-py-epidata]
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with: 
-          version: ${{ matrix.version }}
-          package: plot
-          coverage: ON 
+#   test-py-plot:
+#     if: github.event.pull_request.draft == false
+#     needs: [build-py-plot, build-py-epidata]
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with: 
+#           version: ${{ matrix.version }}
+#           package: plot
+#           coverage: ON 
 
-  merge-artifacts:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        packages: [epidata, plot]
-    needs: [test-py-plot, test-py-epidata]
-    steps:
-      - name: merge epidata reports
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-py-coverage-reports-${{ matrix.packages }}
-          pattern: test-py-coverage-reports-${{ matrix.packages }}-*
+#   merge-artifacts:
+#     runs-on: ubuntu-latest
+#     strategy:
+#       matrix:
+#         packages: [epidata, plot]
+#     needs: [test-py-plot, test-py-epidata]
+#     steps:
+#       - name: merge epidata reports
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-py-coverage-reports-${{ matrix.packages }}
+#           pattern: test-py-coverage-reports-${{ matrix.packages }}-*
 
-  test-pylint-epidata:
-    needs: build-py-epidata
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-pylint
-        with:
-          package: epidata
+#   test-pylint-epidata:
+#     needs: build-py-epidata
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-pylint
+#         with:
+#           package: epidata
 
-  test-pylint-plot:
-    needs: build-py-plot
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-pylint
-        with:
-          package: plot
+#   test-pylint-plot:
+#     needs: build-py-plot
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-pylint
+#         with:
+#           package: plot
 
-  download-data:
-    needs: build-py-epidata
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - uses: actions/checkout@v4
-      - name: Install dependencies
-        run: |
-          sudo apt-get -qq update
-          sudo apt-get -qq -y install python3-pip gnupg
-          python -m pip install --upgrade pip
-      - name: Download Python Wheels
-        uses: actions/download-artifact@v4
-        with:
-          name: python-wheels-epidata
-          path: pycode/wheelhouse
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-      - name: Install Python Wheels
-        run: |
-          for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
-          for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
-      - name: Download Data
-        run: |
-          mkdir -p data_dl
-          getcasedata -o data_dl --no-progress-indicators
-          getpopuldata -o data_dl --no-progress-indicators
-          getjhdata -o data_dl --no-progress-indicators
-          getdividata -o data_dl --no-progress-indicators
-          getcommutermobility -o data_dl --no-progress-indicators
-          getvaccinationdata -o data_dl --no-progress-indicators
-          gethospitalizationdata -o data_dl --no-progress-indicators
-      - name: Upload Data
-        uses: actions/upload-artifact@v4
-        with:
-          name: data
-          path: |
-            data_dl/*.json
-            data_dl/Germany/*.json
-            data_dl/Spain/*.json
-            data_dl/France/*.json
-            data_dl/Italy*.json
-            data_dl/SouthKorea/*.json
-            data_dl/US/*.json
-            data_dl/China/*.json
-          retention-days: 1
+#   download-data:
+#     needs: build-py-epidata
+#     runs-on: ubuntu-latest
+#     continue-on-error: true
+#     steps:
+#       - uses: actions/checkout@v4
+#       - name: Install dependencies
+#         run: |
+#           sudo apt-get -qq update
+#           sudo apt-get -qq -y install python3-pip gnupg
+#           python -m pip install --upgrade pip
+#       - name: Download Python Wheels
+#         uses: actions/download-artifact@v4
+#         with:
+#           name: python-wheels-epidata
+#           path: pycode/wheelhouse
+#       - name: Set up Python 3.12
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: 3.12
+#       - name: Install Python Wheels
+#         run: |
+#           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
+#           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
+#       - name: Download Data
+#         run: |
+#           mkdir -p data_dl
+#           getcasedata -o data_dl --no-progress-indicators
+#           getpopuldata -o data_dl --no-progress-indicators
+#           getjhdata -o data_dl --no-progress-indicators
+#           getdividata -o data_dl --no-progress-indicators
+#           getcommutermobility -o data_dl --no-progress-indicators
+#           getvaccinationdata -o data_dl --no-progress-indicators
+#           gethospitalizationdata -o data_dl --no-progress-indicators
+#       - name: Upload Data
+#         uses: actions/upload-artifact@v4
+#         with:
+#           name: data
+#           path: |
+#             data_dl/*.json
+#             data_dl/Germany/*.json
+#             data_dl/Spain/*.json
+#             data_dl/France/*.json
+#             data_dl/Italy*.json
+#             data_dl/SouthKorea/*.json
+#             data_dl/US/*.json
+#             data_dl/China/*.json
+#           retention-days: 1
           
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b87795d7bd..4bafd6e343 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,355 +1,355 @@
-name: CI
+# name: CI
 
 
-on:
-  schedule:
-    - cron: "40 2 * * *"
-  push:
-    branches:
-      - "main"
-    tags:
-      - version-*
-    paths-ignore:
-      - "**/memilio-epidata/**"
-  pull_request:
-    types: [opened, reopened, synchronize, ready_for_review]
-    paths-ignore:
-      - "**/memilio-epidata/**"
-  workflow_dispatch:
+# on:
+#   schedule:
+#     - cron: "40 2 * * *"
+#   push:
+#     branches:
+#       - "main"
+#     tags:
+#       - version-*
+#     paths-ignore:
+#       - "**/memilio-epidata/**"
+#   pull_request:
+#     types: [opened, reopened, synchronize, ready_for_review]
+#     paths-ignore:
+#       - "**/memilio-epidata/**"
+#   workflow_dispatch:
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref_name }}-${{ github.event.pull_request.number || github.run_id }}
-  cancel-in-progress: true
+# concurrency:
+#   group: ${{ github.workflow }}-${{ github.ref_name }}-${{ github.event.pull_request.number || github.run_id }}
+#   cancel-in-progress: true
 
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-      - uses: pre-commit/action@v3.0.1
+# jobs:
+#   pre-commit:
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: actions/setup-python@v5
+#         with:
+#           python-version: 3.12
+#       - uses: pre-commit/action@v3.0.1
 
-  build-cpp-gcc_clang:
-    if: github.event.pull_request.draft == false
-    strategy:
-      matrix:
-        compiler: ["gcc", "clang"]
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "ubuntu-latest"
-          - version: "min"
-            os: "ubuntu-22.04"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-build
-        with:
-          compiler: ${{ matrix.compiler }}
-          config: ${{ matrix.config }}
-          version: ${{ matrix.version }}
-          coverage: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }} # `c && t || f` is (usually) equivalent to `c ? t : f`
-          sanitizers: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }}
+#   build-cpp-gcc_clang:
+#     if: github.event.pull_request.draft == false
+#     strategy:
+#       matrix:
+#         compiler: ["gcc", "clang"]
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "ubuntu-latest"
+#           - version: "min"
+#             os: "ubuntu-22.04"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-build
+#         with:
+#           compiler: ${{ matrix.compiler }}
+#           config: ${{ matrix.config }}
+#           version: ${{ matrix.version }}
+#           coverage: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }} # `c && t || f` is (usually) equivalent to `c ? t : f`
+#           sanitizers: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }}
 
-  build-cpp-gcc-no-optional-deps:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-build
-        with:
-          compiler: gcc
-          version: latest
-          config: Release
-          optional-dependencies: OFF
+#   build-cpp-gcc-no-optional-deps:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-build
+#         with:
+#           compiler: gcc
+#           version: latest
+#           config: Release
+#           optional-dependencies: OFF
 
-  build-cpp-gcc-openmp:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-build
-        with:
-          compiler: gcc
-          version: latest
-          config: Release
-          openmp: ON
+#   build-cpp-gcc-openmp:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-build
+#         with:
+#           compiler: gcc
+#           version: latest
+#           config: Release
+#           openmp: ON
 
-  build-cpp-msvc:
-    if: github.event.pull_request.draft == false
-    strategy:
-      matrix:
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "windows-2025"
-          - version: "min"
-            os: "windows-2022"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-build
-        with:
-          config: ${{ matrix.config }}
-          version: ${{ matrix.version }}
+#   build-cpp-msvc:
+#     if: github.event.pull_request.draft == false
+#     strategy:
+#       matrix:
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "windows-2025"
+#           - version: "min"
+#             os: "windows-2022"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-build
+#         with:
+#           config: ${{ matrix.config }}
+#           version: ${{ matrix.version }}
 
-  build-cpp-msvc-no-optional-deps:
-    if: github.event.pull_request.draft == false
-    runs-on: windows-2025
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-build
-        with:
-          config: Release
-          version: latest
-          optional-dependencies: OFF
+#   build-cpp-msvc-no-optional-deps:
+#     if: github.event.pull_request.draft == false
+#     runs-on: windows-2025
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-build
+#         with:
+#           config: Release
+#           version: latest
+#           optional-dependencies: OFF
 
-  test-cpp-gcc_clang:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-gcc_clang
-    strategy:
-      matrix:
-        compiler: ["gcc", "clang"]
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "ubuntu-latest"
-          - version: "min"
-            os: "ubuntu-22.04"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-test
-        with:
-          artifact-pattern: ${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
-          coverage: ${{ (matrix.compiler == 'gcc' && matrix.version == 'latest' && matrix.config == 'Debug') && 'ON' || 'OFF' }}
+#   test-cpp-gcc_clang:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-gcc_clang
+#     strategy:
+#       matrix:
+#         compiler: ["gcc", "clang"]
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "ubuntu-latest"
+#           - version: "min"
+#             os: "ubuntu-22.04"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-test
+#         with:
+#           artifact-pattern: ${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
+#           coverage: ${{ (matrix.compiler == 'gcc' && matrix.version == 'latest' && matrix.config == 'Debug') && 'ON' || 'OFF' }}
  
-  test-cpp-gcc-sbml:
-      if: github.event.pull_request.draft == false
-      needs: build-cpp-gcc_clang
-      runs-on: ubuntu-latest
-      steps:
-        - uses: actions/checkout@v4
-        - uses: ./.github/actions/sbml-test
+#   test-cpp-gcc-sbml:
+#       if: github.event.pull_request.draft == false
+#       needs: build-cpp-gcc_clang
+#       runs-on: ubuntu-latest
+#       steps:
+#         - uses: actions/checkout@v4
+#         - uses: ./.github/actions/sbml-test
 
-  merge-test-artifacts:
-    needs: [test-cpp-gcc_clang, test-cpp-msvc, test-py-surrogatemodel]
-    runs-on: ubuntu-latest
-    steps:
-      - name: merge-coverage-artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-cpp-coverage-reports
-          pattern: test-cpp-coverage-reports-*
-      - name: merge-linux-artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-cpp-linux-report
-          pattern: test-cpp-linux-report-*
-      - name: merge-windows-artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-cpp-win-report
-          pattern: test-cpp-win-report-*
-      - name: merge python reports
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-py-coverage-reports-surrogatemodel
-          pattern: test-py-coverage-reports-surrogatemodel-*
+#   merge-test-artifacts:
+#     needs: [test-cpp-gcc_clang, test-cpp-msvc, test-py-surrogatemodel]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - name: merge-coverage-artifacts
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-cpp-coverage-reports
+#           pattern: test-cpp-coverage-reports-*
+#       - name: merge-linux-artifacts
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-cpp-linux-report
+#           pattern: test-cpp-linux-report-*
+#       - name: merge-windows-artifacts
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-cpp-win-report
+#           pattern: test-cpp-win-report-*
+#       - name: merge python reports
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-py-coverage-reports-surrogatemodel
+#           pattern: test-py-coverage-reports-surrogatemodel-*
 
-  test-cpp-gcc-no-optional-deps:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-gcc-no-optional-deps
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-test
-        with:
-          artifact-pattern: gcc-latest-Release
-          optional-deps: OFF
+#   test-cpp-gcc-no-optional-deps:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-gcc-no-optional-deps
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-test
+#         with:
+#           artifact-pattern: gcc-latest-Release
+#           optional-deps: OFF
 
-  test-cpp-gcc-openmp:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-gcc-openmp
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-    env:
-      OMP_NUM_THREADS: 4
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-test
-        with:
-          artifact-pattern: gcc-latest-Release
-          num-repeat: 10
-          openmp: ON
+#   test-cpp-gcc-openmp:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-gcc-openmp
+#     runs-on: ubuntu-latest
+#     timeout-minutes: 30
+#     env:
+#       OMP_NUM_THREADS: 4
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-test
+#         with:
+#           artifact-pattern: gcc-latest-Release
+#           num-repeat: 10
+#           openmp: ON
 
-  test-cpp-msvc:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-msvc
-    strategy:
-      matrix:
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "windows-2025"
-          - version: "min"
-            os: "windows-2022"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-test
-        with:
-          artifact-pattern: msvc-${{ matrix.version }}-${{ matrix.config }}
+#   test-cpp-msvc:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-msvc
+#     strategy:
+#       matrix:
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "windows-2025"
+#           - version: "min"
+#             os: "windows-2022"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-test
+#         with:
+#           artifact-pattern: msvc-${{ matrix.version }}-${{ matrix.config }}
 
-  test-cpp-msvc-no-optional-deps:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-msvc-no-optional-deps
-    runs-on: windows-2025
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-test
-        with:
-          artifact-pattern: msvc-latest-Release
-          optional-deps: OFF
+#   test-cpp-msvc-no-optional-deps:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-msvc-no-optional-deps
+#     runs-on: windows-2025
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-test
+#         with:
+#           artifact-pattern: msvc-latest-Release
+#           optional-deps: OFF
 
-  run_examples-cpp-gcc_clang:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-gcc_clang
-    strategy:
-      matrix:
-        compiler: ["gcc", "clang"]
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "ubuntu-latest"
-          - version: "min"
-            os: "ubuntu-22.04"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-run_examples
-        with:
-          build-artifact: build-cpp-linux-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
+#   run_examples-cpp-gcc_clang:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-gcc_clang
+#     strategy:
+#       matrix:
+#         compiler: ["gcc", "clang"]
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "ubuntu-latest"
+#           - version: "min"
+#             os: "ubuntu-22.04"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-run_examples
+#         with:
+#           build-artifact: build-cpp-linux-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
 
-  run_examples-cpp-msvc:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-msvc
-    strategy:
-      matrix:
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "windows-2025"
-          - version: "min"
-            os: "windows-2022"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-run_examples
-        with:
-          build-artifact: build-cpp-windows-msvc-${{ matrix.version }}-${{ matrix.config }}
+#   run_examples-cpp-msvc:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-msvc
+#     strategy:
+#       matrix:
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "windows-2025"
+#           - version: "min"
+#             os: "windows-2022"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-run_examples
+#         with:
+#           build-artifact: build-cpp-windows-msvc-${{ matrix.version }}-${{ matrix.config }}
 
-  build-py-generation:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: generation
+#   build-py-generation:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: generation
 
-  build-py-simulation:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: simulation
+#   build-py-simulation:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: simulation
 
-  build-py-surrogatemodel:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: surrogatemodel
+#   build-py-surrogatemodel:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: surrogatemodel
 
-  test-py-generation:
-    if: github.event.pull_request.draft == false
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    needs: build-py-generation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with:
-          package: generation
+#   test-py-generation:
+#     if: github.event.pull_request.draft == false
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     needs: build-py-generation
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with:
+#           package: generation
 
-  test-py-simulation:
-    if: github.event.pull_request.draft == false
-    needs: build-py-simulation
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with:
-          package: simulation
+#   test-py-simulation:
+#     if: github.event.pull_request.draft == false
+#     needs: build-py-simulation
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with:
+#           package: simulation
 
-  test-py-surrogatemodel:
-    if: github.event.pull_request.draft == false
-    needs: [build-py-surrogatemodel, build-py-simulation]
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with:
-          version: ${{ matrix.version }}
-          package: surrogatemodel
-          coverage: ON
+#   test-py-surrogatemodel:
+#     if: github.event.pull_request.draft == false
+#     needs: [build-py-surrogatemodel, build-py-simulation]
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with:
+#           version: ${{ matrix.version }}
+#           package: surrogatemodel
+#           coverage: ON
 
-  codecov:
-    if: github.event.pull_request.draft == false
-    needs: merge-test-artifacts
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Install dependencies
-        run: |
-          sudo apt-get -qq update
-          sudo apt-get -qq -y install git curl
-      - name: Download python coverage report
-        uses: actions/download-artifact@v4
-        with:
-          name: test-py-coverage-reports-surrogatemodel
-      - name: Download cpp coverage report
-        uses: actions/download-artifact@v4
-        with:
-          name: test-cpp-coverage-reports
-      - name: Deploy to codecov.io
-        uses: codecov/codecov-action@v3
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          directory: ./coverage_python
-          files: ./coverage_python/**,./coverage.info
-          verbose: true
+#   codecov:
+#     if: github.event.pull_request.draft == false
+#     needs: merge-test-artifacts
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - name: Install dependencies
+#         run: |
+#           sudo apt-get -qq update
+#           sudo apt-get -qq -y install git curl
+#       - name: Download python coverage report
+#         uses: actions/download-artifact@v4
+#         with:
+#           name: test-py-coverage-reports-surrogatemodel
+#       - name: Download cpp coverage report
+#         uses: actions/download-artifact@v4
+#         with:
+#           name: test-cpp-coverage-reports
+#       - name: Deploy to codecov.io
+#         uses: codecov/codecov-action@v3
+#         with:
+#           token: ${{ secrets.CODECOV_TOKEN }}
+#           directory: ./coverage_python
+#           files: ./coverage_python/**,./coverage.info
+#           verbose: true
diff --git a/.github/workflows/message_bot.yml b/.github/workflows/message_bot.yml
index cd4f322ca1..55fdb1545d 100644
--- a/.github/workflows/message_bot.yml
+++ b/.github/workflows/message_bot.yml
@@ -1,134 +1,134 @@
-# .github/workflows/discussion-monitor.yml
-name: Discussion Monitor
+# # .github/workflows/discussion-monitor.yml
+# name: Discussion Monitor
 
-on:
-  schedule:
-    - cron: '0 9 * * *'
+# on:
+#   schedule:
+#     - cron: '0 9 * * *'
 
 
-jobs:
-  check-discussions:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      discussions: read
-    steps:
-    - name: Check for new discussions
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        MATTERMOST_WEBHOOK_URL: ${{ secrets.MATTERMOST_WEBHOOK_URL }}
-      run: |
-        npm install @octokit/rest
-        cat > check.js << 'EOF'
-        const { Octokit } = require('@octokit/rest');
+# jobs:
+#   check-discussions:
+#     runs-on: ubuntu-latest
+#     permissions:
+#       contents: read
+#       discussions: read
+#     steps:
+#     - name: Check for new discussions
+#       env:
+#         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#         MATTERMOST_WEBHOOK_URL: ${{ secrets.MATTERMOST_WEBHOOK_URL }}
+#       run: |
+#         npm install @octokit/rest
+#         cat > check.js << 'EOF'
+#         const { Octokit } = require('@octokit/rest');
 
-        const octokit = new Octokit({ auth: process.env.GITHUB_TOKEN });
+#         const octokit = new Octokit({ auth: process.env.GITHUB_TOKEN });
 
-        async function check() {
-          const since = new Date();
-          since.setHours(since.getHours() - 25);
+#         async function check() {
+#           const since = new Date();
+#           since.setHours(since.getHours() - 25);
           
-          const [owner, repo] = process.env.GITHUB_REPOSITORY.split('/');
-          console.log(`Checking discussions for ${owner}/${repo}`);
+#           const [owner, repo] = process.env.GITHUB_REPOSITORY.split('/');
+#           console.log(`Checking discussions for ${owner}/${repo}`);
           
-          try {
-            const response = await octokit.graphql(`
-              query { 
-                repository(owner: "${owner}", name: "${repo}") {
-                  discussions(first: 10, orderBy: {field: CREATED_AT, direction: DESC}) {
-                    nodes { 
-                      createdAt
-                      title
-                      url
-                      number
-                      author {
-                        login
-                      }
-                      category {
-                        name
-                        emoji
-                      }
-                    }
-                  }
-                }
-              }
-            `);
+#           try {
+#             const response = await octokit.graphql(`
+#               query { 
+#                 repository(owner: "${owner}", name: "${repo}") {
+#                   discussions(first: 10, orderBy: {field: CREATED_AT, direction: DESC}) {
+#                     nodes { 
+#                       createdAt
+#                       title
+#                       url
+#                       number
+#                       author {
+#                         login
+#                       }
+#                       category {
+#                         name
+#                         emoji
+#                       }
+#                     }
+#                   }
+#                 }
+#               }
+#             `);
             
-            console.log('Full GraphQL response:', JSON.stringify(response, null, 2));
+#             console.log('Full GraphQL response:', JSON.stringify(response, null, 2));
             
-            if (!response || !response.repository) {
-              console.log('Repository not found or discussions not enabled');
-              console.log('Response keys:', Object.keys(response || {}));
-              return;
-            }
+#             if (!response || !response.repository) {
+#               console.log('Repository not found or discussions not enabled');
+#               console.log('Response keys:', Object.keys(response || {}));
+#               return;
+#             }
 
-            if (!response.repository.discussions) {
-              console.log('Discussions not available for this repository');
-              return;
-            }
+#             if (!response.repository.discussions) {
+#               console.log('Discussions not available for this repository');
+#               return;
+#             }
             
-            const newDiscussions = response.repository.discussions.nodes.filter(
-              d => new Date(d.createdAt) > since
-            );
+#             const newDiscussions = response.repository.discussions.nodes.filter(
+#               d => new Date(d.createdAt) > since
+#             );
             
-            console.log(`Found ${newDiscussions.length} new discussions`);
+#             console.log(`Found ${newDiscussions.length} new discussions`);
             
-            if (newDiscussions.length > 0) {
-              let message;
+#             if (newDiscussions.length > 0) {
+#               let message;
               
-              if (newDiscussions.length === 1) {
-                const discussion = newDiscussions[0];
-                message = {
-                  text: `${discussion.category.emoji || '💬'} New Discussion on ${owner}/${repo}
+#               if (newDiscussions.length === 1) {
+#                 const discussion = newDiscussions[0];
+#                 message = {
+#                   text: `${discussion.category.emoji || '💬'} New Discussion on ${owner}/${repo}
 
-        **[${discussion.title}](${discussion.url})**
+#         **[${discussion.title}](${discussion.url})**
 
-        👤 **Author:** ${discussion.author.login}
-        📂 **Category:** ${discussion.category.name}
-        🔢 **Discussion #${discussion.number}**`,
-                  username: "GitHub Discussion Bot",
-                  icon_emoji: ":github:"
-                };
-              } else {
-                const discussionList = newDiscussions.map(d => 
-                  `- ${d.category.emoji || '💬'} **[${d.title}](${d.url})** by ${d.author.login}`
-                ).join('\n');
+#         👤 **Author:** ${discussion.author.login}
+#         📂 **Category:** ${discussion.category.name}
+#         🔢 **Discussion #${discussion.number}**`,
+#                   username: "GitHub Discussion Bot",
+#                   icon_emoji: ":github:"
+#                 };
+#               } else {
+#                 const discussionList = newDiscussions.map(d => 
+#                   `- ${d.category.emoji || '💬'} **[${d.title}](${d.url})** by ${d.author.login}`
+#                 ).join('\n');
                 
-                message = {
-                  text: `🎉 ${newDiscussions.length} New Discussions on ${owner}/${repo}
+#                 message = {
+#                   text: `🎉 ${newDiscussions.length} New Discussions on ${owner}/${repo}
 
-        ${discussionList}
+#         ${discussionList}
 
-        ---
-        *Check out the latest discussions above!*`,
-                  username: "GitHub Discussion Bot",
-                  icon_emoji: ":github:"
-                };
-              }
+#         ---
+#         *Check out the latest discussions above!*`,
+#                   username: "GitHub Discussion Bot",
+#                   icon_emoji: ":github:"
+#                 };
+#               }
               
-              const response = await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
-                method: 'POST',
-                headers: { 'Content-Type': 'application/json' },
-                body: JSON.stringify(message)
-              });
-              console.log('Mattermost notification sent');
-            }
-          } catch (error) {
-            console.error('Error details:', error);
-            if (process.env.MATTERMOST_WEBHOOK_URL) {
-              await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
-                method: 'POST',
-                headers: { 'Content-Type': 'application/json' },
-                body: JSON.stringify({ 
-                  text: '⚠️ **GitHub Discussion Bot Error**\nThere was an error checking discussions. Please check the workflow logs.',
-                  username: "GitHub Discussion Bot",
-                  icon_emoji: ":warning:"
-                })
-              });
-            }
-          }
-        }
+#               const response = await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
+#                 method: 'POST',
+#                 headers: { 'Content-Type': 'application/json' },
+#                 body: JSON.stringify(message)
+#               });
+#               console.log('Mattermost notification sent');
+#             }
+#           } catch (error) {
+#             console.error('Error details:', error);
+#             if (process.env.MATTERMOST_WEBHOOK_URL) {
+#               await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
+#                 method: 'POST',
+#                 headers: { 'Content-Type': 'application/json' },
+#                 body: JSON.stringify({ 
+#                   text: '⚠️ **GitHub Discussion Bot Error**\nThere was an error checking discussions. Please check the workflow logs.',
+#                   username: "GitHub Discussion Bot",
+#                   icon_emoji: ":warning:"
+#                 })
+#               });
+#             }
+#           }
+#         }
 
-        check().catch(console.error);
-        EOF
-        node check.js
+#         check().catch(console.error);
+#         EOF
+#         node check.js
diff --git a/pyproject.toml b/pyproject.toml
index fec49ef467..e9b66a9e66 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,6 +10,7 @@ requires = [
   "scikit-build-core>=0.9.0",
   "setuptools>=68",
   "wheel"
+  "pybind11>=2.11.2"
 ]
 build-backend = "scikit_build_core.build"
 

From c13105fbc38cd9e9de949ce6b17b83f05c591870 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 13:39:51 +0100
Subject: [PATCH 06/74] add comma

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e9b66a9e66..2f298e1118 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ exclude = ["pycode/memilio-simulation"]
 requires = [
   "scikit-build-core>=0.9.0",
   "setuptools>=68",
-  "wheel"
+  "wheel",
   "pybind11>=2.11.2"
 ]
 build-backend = "scikit_build_core.build"

From e25c2184b4ebe7b209d0c51d55db3215d1a9af6a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 14:37:35 +0100
Subject: [PATCH 07/74] skip some pypy versions

---
 pyproject.toml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 2f298e1118..cc1c221201 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -48,3 +48,7 @@ build-dir = "../build/memilio-simulation"
 
 [tool.setuptools]
 packages = ["pycode/memilio-simulation"]
+
+[tool.cibuildwheel]
+# Disable building PyPy 3.8 and 3.9 wheels on all platforms
+skip = ["pp38-*", "pp39-*"]

From 69a5b96a3aaaee6832cd02d7cb59553c166673c6 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 14:57:57 +0100
Subject: [PATCH 08/74] skip all pypy versions

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index cc1c221201..e491bed7aa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,5 +50,5 @@ build-dir = "../build/memilio-simulation"
 packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
-# Disable building PyPy 3.8 and 3.9 wheels on all platforms
-skip = ["pp38-*", "pp39-*"]
+# Disable building PyPy wheels on all platforms
+skip = ["pp*"]

From 73a7fbc453d3d0a3d3964b6277c54648e813b949 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 15:49:51 +0100
Subject: [PATCH 09/74] skip musllinux

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e491bed7aa..d34c2f6c2f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,4 +51,5 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*"]
+skip = ["pp*", "*musllinux*"]
+skip = ["*_i686"] # these work, skip for further testing

From 6ca71df7af474c4c0591e71769861e085879897a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 15:52:09 +0100
Subject: [PATCH 10/74] fix

---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d34c2f6c2f..6358fafdec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,5 +51,4 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*", "*musllinux*"]
-skip = ["*_i686"] # these work, skip for further testing
+skip = ["pp*", "*musllinux*", "*_i686"] # "*_i686" works, skip for now for further testing

From 265a58c9c5d355f3a2df614d6dfbce974d5eb9ae Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 16:16:34 +0100
Subject: [PATCH 11/74] test windows

---
 .github/workflows/build_wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 3c7019f73d..aaa02519cf 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest]
+        os: [windows-latest]
 
     steps:
       - uses: actions/checkout@v4

From 22c73cbcb42b02c710ffb6f0379540a8e2f327b0 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 16:45:36 +0100
Subject: [PATCH 12/74] skip win32

---
 pyproject.toml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6358fafdec..d3eb152a96 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,8 +9,7 @@ exclude = ["pycode/memilio-simulation"]
 requires = [
   "scikit-build-core>=0.9.0",
   "setuptools>=68",
-  "wheel",
-  "pybind11>=2.11.2"
+  "wheel"
 ]
 build-backend = "scikit_build_core.build"
 
@@ -51,4 +50,4 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*", "*musllinux*", "*_i686"] # "*_i686" works, skip for now for further testing
+skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing

From 02edbf2d3bb79a25b6c113d600e4836322175cb0 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 09:20:20 +0100
Subject: [PATCH 13/74] test macos

---
 .github/workflows/build_wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index aaa02519cf..a4ef4c49d9 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows-latest]
+        os: [macos-latest]
 
     steps:
       - uses: actions/checkout@v4

From a1d4085d3e847f9df138cd13bceb37f6e2b81476 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 09:57:00 +0100
Subject: [PATCH 14/74] skip macosx_arm64

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index d3eb152a96..b709e83ee8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,4 +50,4 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
+skip = ["pp*", "*musllinux*", "*_i686", "*-win32", "*-macosx_arm64"] # "*_i686" works, skip for now for further testing

From 59e454a3705dd92875c260d12eade58744c3c2f6 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 11:14:00 +0100
Subject: [PATCH 15/74] test

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b709e83ee8..066f2c4ee4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,4 +50,5 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*", "*musllinux*", "*_i686", "*-win32", "*-macosx_arm64"] # "*_i686" works, skip for now for further testing
+build = ["*-macosx_x86_64", "*-macosx_universal2"]
+skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing

From b4febe3c088d2a4c8b3ef2e1601a8da8da390e7a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 11:19:02 +0100
Subject: [PATCH 16/74] test

---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 066f2c4ee4..254f60d429 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,5 +50,7 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-build = ["*-macosx_x86_64", "*-macosx_universal2"]
+build-verbosity = 3
 skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
+
+

From 6f2ac0a461b302925eabd45b1356d28fc79caccc Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 11:34:05 +0100
Subject: [PATCH 17/74] build sdist in ci

---
 .github/workflows/build_wheels.yml | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index a4ef4c49d9..dcd949973a 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -3,11 +3,25 @@ name: Build wheels
 on: [pull_request, release]
 
 jobs:
+
+  build_sdist: 
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        path: dist/*.tar.gz
+
+
   build_wheels:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest]
+        os: [ubuntu-latest]
 
     steps:
       - uses: actions/checkout@v4

From 4b9ce8df99dd38f83cbebb5defa8781d9d881382 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 12:06:54 +0100
Subject: [PATCH 18/74] add names for artifacts

---
 .github/workflows/build_wheels.yml | 2 ++
 pyproject.toml                     | 3 +--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index dcd949973a..f7711d163d 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -14,6 +14,7 @@ jobs:
 
     - uses: actions/upload-artifact@v4
       with:
+        name: sdist
         path: dist/*.tar.gz
 
 
@@ -30,4 +31,5 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 254f60d429..ec05c47a80 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,8 +49,7 @@ build-dir = "../build/memilio-simulation"
 packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
-# Disable building PyPy wheels on all platforms
-build-verbosity = 3
+# Disable some wheels
 skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
 
 

From 9747c8c3eb7149f7beb0d93b5f52bb7e0568a22f Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 15:32:20 +0100
Subject: [PATCH 19/74] also include other python packages

---
 .github/workflows/build_wheels.yml |  2 +-
 pyproject.toml                     | 34 +++++++++++++++---------------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index f7711d163d..d8ca6d7bec 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -22,7 +22,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, windows_latest]
 
     steps:
       - uses: actions/checkout@v4
diff --git a/pyproject.toml b/pyproject.toml
index ec05c47a80..260a1a979d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,20 +1,5 @@
-[tool.autopep8]
-max-line-length = 79
-
-[tool.pyright]
-include = ["pycode"]
-exclude = ["pycode/memilio-simulation"]
-
-[build-system]
-requires = [
-  "scikit-build-core>=0.9.0",
-  "setuptools>=68",
-  "wheel"
-]
-build-backend = "scikit_build_core.build"
-
 [project]
-name = "memilio-simulation"
+name = "memilio"
 version = "1.0.0"
 description = "Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
@@ -38,6 +23,14 @@ dev = []
 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",
+  "wheel"
+]
+build-backend = "scikit_build_core.build"
+
 [tool.scikit-build]
 cmake.version = ">=3.13"
 cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
@@ -46,10 +39,17 @@ wheel.install-dir = "memilio/simulation"
 build-dir = "../build/memilio-simulation"
 
 [tool.setuptools]
-packages = ["pycode/memilio-simulation"]
+packages = ["pycode/memilio-epidata","pycode/memilio-generation","pycode/memilio-plot","pycode/memilio-simulation","pycode/memilio-surrogatemodel"]
 
 [tool.cibuildwheel]
 # Disable some wheels
 skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
 
+[tool.autopep8]
+max-line-length = 79
+
+[tool.pyright]
+include = ["pycode"]
+exclude = ["pycode/memilio-simulation"]
+
 

From 77bab936db076c3e30819f1f6d992a8bd239455a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 2 Mar 2026 13:18:43 +0100
Subject: [PATCH 20/74] update

---
 pyproject.toml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 260a1a979d..f97d9e91e5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [project]
-name = "memilio"
+name = "memilio-simulation"
 version = "1.0.0"
-description = "Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations."
+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 = { text = "Apache-2.0" }
@@ -39,11 +39,11 @@ wheel.install-dir = "memilio/simulation"
 build-dir = "../build/memilio-simulation"
 
 [tool.setuptools]
-packages = ["pycode/memilio-epidata","pycode/memilio-generation","pycode/memilio-plot","pycode/memilio-simulation","pycode/memilio-surrogatemodel"]
+packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable some wheels
-skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
+skip = ["pp*", "*musllinux*", "*-win32"] 
 
 [tool.autopep8]
 max-line-length = 79

From d5b9b279c1908f336b709ebde42b26babedb3e26 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Thu, 5 Mar 2026 16:59:25 +0100
Subject: [PATCH 21/74] only windows

---
 .github/workflows/build_wheels.yml | 31 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index d8ca6d7bec..fec68b8fcd 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -4,25 +4,11 @@ on: [pull_request, release]
 
 jobs:
 
-  build_sdist: 
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - run: pipx run build --sdist
-
-    - uses: actions/upload-artifact@v4
-      with:
-        name: sdist
-        path: dist/*.tar.gz
-
-
   build_wheels:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows_latest]
+        os: [windows_latest]
 
     steps:
       - uses: actions/checkout@v4
@@ -32,4 +18,17 @@ jobs:
       - uses: actions/upload-artifact@v4
         with:
           name: wheels-${{ matrix.os }}
-          path: ./wheelhouse/*.whl
\ No newline at end of file
+          path: ./wheelhouse/*.whl
+
+  build_sdist: 
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: sdist
+        path: dist/*.tar.gz
\ No newline at end of file

From 6951691cbe2716cc714c747839bc5b5d7455efea Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 6 Mar 2026 11:08:55 +0100
Subject: [PATCH 22/74] fix typo

---
 .github/workflows/build_wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index fec68b8fcd..b007f1fe3f 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows_latest]
+        os: [windows-latest, ubuntu-latest]
 
     steps:
       - uses: actions/checkout@v4

From c8253b1dd390fcdb58ed4df4bdb3c5ffb56041bf Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 11 Mar 2026 14:17:58 +0100
Subject: [PATCH 23/74] test upload

---
 .github/workflows/build_wheels.yml | 26 ++++++++++++++++++++++++--
 pyproject.toml                     |  1 +
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index b007f1fe3f..8908bd320b 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows-latest, ubuntu-latest]
+        os: [ubuntu-latest] # windows-latest
 
     steps:
       - uses: actions/checkout@v4
@@ -31,4 +31,26 @@ jobs:
     - uses: actions/upload-artifact@v4
       with:
         name: sdist
-        path: dist/*.tar.gz
\ No newline at end of file
+        path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    # if: github.event_name == 'release' && github.event.action == 'published'
+    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        # To test uploads to TestPyPI, uncomment the following:
+        with:
+          repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index f97d9e91e5..55db3926fe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,6 +43,7 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable some wheels
+build = [cp38*]
 skip = ["pp*", "*musllinux*", "*-win32"] 
 
 [tool.autopep8]

From 682490bc16a45464b2b1d014e2166061626570f0 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 11 Mar 2026 14:20:29 +0100
Subject: [PATCH 24/74] typo

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 55db3926fe..f275f0b2d5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable some wheels
-build = [cp38*]
+build = ["cp38*"]
 skip = ["pp*", "*musllinux*", "*-win32"] 
 
 [tool.autopep8]

From 47cd7d38316a5b2b9634699631a12f5877e23dfe Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 11 Mar 2026 14:38:22 +0100
Subject: [PATCH 25/74] use token

---
 .github/workflows/build_wheels.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 8908bd320b..0dc10d3f61 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -53,4 +53,6 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@release/v1
         # To test uploads to TestPyPI, uncomment the following:
         with:
+          skip-existing: true
+          password: ${{ secrets.PYPI_TEST_TOKEN }}
           repository-url: https://test.pypi.org/legacy/
\ No newline at end of file

From 2dd392fc785c2c7586b6adbb6346182de19e92f3 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 11 Mar 2026 14:59:06 +0100
Subject: [PATCH 26/74] adapt names, no token

---
 .github/workflows/build_wheels.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 0dc10d3f61..38633bf7af 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -17,7 +17,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: wheels-${{ matrix.os }}
+          name: cibw-wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
 
   build_sdist: 
@@ -30,7 +30,7 @@ jobs:
 
     - uses: actions/upload-artifact@v4
       with:
-        name: sdist
+        name: cibw-sdist
         path: dist/*.tar.gz
 
   upload_pypi:
@@ -54,5 +54,5 @@ jobs:
         # To test uploads to TestPyPI, uncomment the following:
         with:
           skip-existing: true
-          password: ${{ secrets.PYPI_TEST_TOKEN }}
+          # password: ${{ secrets.PYPI_TEST_TOKEN }}
           repository-url: https://test.pypi.org/legacy/
\ No newline at end of file

From 55911ce1a01118d395767f9dd67715d9204714a9 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 11 Mar 2026 16:29:44 +0100
Subject: [PATCH 27/74] try only downloading artifacts

---
 .github/workflows/build_wheels.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 38633bf7af..4f183e3152 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -50,9 +50,9 @@ jobs:
           path: dist
           merge-multiple: true
 
-      - uses: pypa/gh-action-pypi-publish@release/v1
-        # To test uploads to TestPyPI, uncomment the following:
-        with:
-          skip-existing: true
-          # password: ${{ secrets.PYPI_TEST_TOKEN }}
-          repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
+      # - uses: pypa/gh-action-pypi-publish@release/v1
+      #   # To test uploads to TestPyPI, uncomment the following:
+      #   with:
+      #     skip-existing: true
+      #     # password: ${{ secrets.PYPI_TEST_TOKEN }}
+      #     repository-url: https://test.pypi.org/legacy/
\ No newline at end of file

From 0700ae8fc803d507a49f833ae3158b70356c4320 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 11 Mar 2026 17:06:26 +0100
Subject: [PATCH 28/74] try again

---
 .github/workflows/build_wheels.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 4f183e3152..38633bf7af 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -50,9 +50,9 @@ jobs:
           path: dist
           merge-multiple: true
 
-      # - uses: pypa/gh-action-pypi-publish@release/v1
-      #   # To test uploads to TestPyPI, uncomment the following:
-      #   with:
-      #     skip-existing: true
-      #     # password: ${{ secrets.PYPI_TEST_TOKEN }}
-      #     repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        # To test uploads to TestPyPI, uncomment the following:
+        with:
+          skip-existing: true
+          # password: ${{ secrets.PYPI_TEST_TOKEN }}
+          repository-url: https://test.pypi.org/legacy/
\ No newline at end of file

From 881d5e686fc164696a16153d447a780b5b265746 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 11 Mar 2026 17:22:47 +0100
Subject: [PATCH 29/74] try with new version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index f275f0b2d5..11c1c97acb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "memilio-simulation"
-version = "1.0.0"
+version = "1.0.1"
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"

From 58979cd48f6fb8a099596a780c24f22d3f425fee Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 16 Mar 2026 08:22:27 +0100
Subject: [PATCH 30/74] update after merge of main

---
 .github/workflows/build_wheels.yml | 2 +-
 pyproject.toml                     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 38633bf7af..d40ed3b093 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest] # windows-latest
+        os: [ubuntu-latest, windows-latest] # 
 
     steps:
       - uses: actions/checkout@v4
diff --git a/pyproject.toml b/pyproject.toml
index 11c1c97acb..8ce0add29b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "memilio-simulation"
-version = "1.0.1"
+version = "1.0.2"
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"

From 5376644f7ff02b239555454cec652edf3b351d48 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 16 Mar 2026 08:33:57 +0100
Subject: [PATCH 31/74] only ubuntu

---
 .github/workflows/build_wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index d40ed3b093..9999952340 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest] # 
+        os: [ubuntu-latest] # 
 
     steps:
       - uses: actions/checkout@v4

From 8c030078aaf4fcdc739f497aa1f28095570c9e59 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 16 Mar 2026 08:40:24 +0100
Subject: [PATCH 32/74] more cpp versions

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8ce0add29b..79e5d94897 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable some wheels
-build = ["cp38*"]
+# build = ["cp38*"]
 skip = ["pp*", "*musllinux*", "*-win32"] 
 
 [tool.autopep8]

From b1d43b187efc14e71a23a693b7db2b800ef7cd86 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 31 Mar 2026 12:16:19 +0200
Subject: [PATCH 33/74] update path

---
 pyproject.toml | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 79e5d94897..e7797ff745 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,12 +34,9 @@ build-backend = "scikit_build_core.build"
 [tool.scikit-build]
 cmake.version = ">=3.13"
 cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
-wheel.packages = ["memilio"]
+wheel.packages = ["pycode/memilio-simulation/memilio"]
 wheel.install-dir = "memilio/simulation"
-build-dir = "../build/memilio-simulation"
-
-[tool.setuptools]
-packages = ["pycode/memilio-simulation"]
+build-dir = "pycode/build/memilio-simulation"
 
 [tool.cibuildwheel]
 # Disable some wheels
@@ -51,6 +48,4 @@ max-line-length = 79
 
 [tool.pyright]
 include = ["pycode"]
-exclude = ["pycode/memilio-simulation"]
-
-
+exclude = ["pycode/memilio-simulation"]
\ No newline at end of file

From 80b08ce66fb4c6cfcea64527dbbb940247bb7b93 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 31 Mar 2026 12:20:54 +0200
Subject: [PATCH 34/74] update version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e7797ff745..b94026dce2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "memilio-simulation"
-version = "1.0.2"
+version = "1.0.3"
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"

From ed25c02a7baaf130888601c2b1d12f9af57e568e Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 31 Mar 2026 12:27:44 +0200
Subject: [PATCH 35/74] include windows

---
 .github/workflows/build_wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 9999952340..ebb350e730 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest] # 
+        os: [ubuntu-latest, windows-latest]
 
     steps:
       - uses: actions/checkout@v4

From c3af9ce8133459b2ac2fe514eadf4d2f8f56f445 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 31 Mar 2026 12:35:22 +0200
Subject: [PATCH 36/74] update actions for newer node.js version

---
 .github/workflows/build_wheels.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index ebb350e730..e99fbb4a4a 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -11,11 +11,11 @@ jobs:
         os: [ubuntu-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - uses: pypa/cibuildwheel@v2.16
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v6
         with:
           name: cibw-wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl

From 21f9983c2ab575315b0d65ca9fdffa62d8d7d130 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 31 Mar 2026 12:36:36 +0200
Subject: [PATCH 37/74] again

---
 .github/workflows/build_wheels.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index e99fbb4a4a..296574f645 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -24,11 +24,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - run: pipx run build --sdist
 
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v6
       with:
         name: cibw-sdist
         path: dist/*.tar.gz

From eacb371dc92d0372f29a377cfdb019a1f3f109a5 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 1 Apr 2026 13:51:34 +0200
Subject: [PATCH 38/74] try dynamic versioning

---
 .github/workflows/build_wheels.yml | 11 ++++++++---
 pyproject.toml                     |  7 +++++--
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 296574f645..65b6de6401 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -12,6 +12,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v6
 
       - uses: pypa/cibuildwheel@v2.16
 
@@ -25,6 +29,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v5
+      with:
+          fetch-depth: 0
 
     - run: pipx run build --sdist
 
@@ -43,7 +49,7 @@ jobs:
     # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
     # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v5
+      - uses: actions/download-artifact@v8
         with:
           # unpacks all CIBW artifacts into dist/
           pattern: cibw-*
@@ -51,8 +57,7 @@ jobs:
           merge-multiple: true
 
       - uses: pypa/gh-action-pypi-publish@release/v1
-        # To test uploads to TestPyPI, uncomment the following:
         with:
           skip-existing: true
-          # password: ${{ secrets.PYPI_TEST_TOKEN }}
+          # To test uploads to TestPyPI, uncomment the following:
           repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index b94026dce2..b83a7c4ede 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,7 @@
 [project]
 name = "memilio-simulation"
-version = "1.0.3"
+# version = "1.0.3" 
+dynamic = ["version"]
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"
@@ -27,6 +28,7 @@ Team = "https://memilio.readthedocs.io/en/latest/team.html"
 requires = [
   "scikit-build-core>=0.9.0",
   "setuptools>=68",
+  "setuptools-scm>=8",
   "wheel"
 ]
 build-backend = "scikit_build_core.build"
@@ -37,10 +39,11 @@ 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.cibuildwheel]
 # Disable some wheels
-# build = ["cp38*"]
+build = ["cp38*"]
 skip = ["pp*", "*musllinux*", "*-win32"] 
 
 [tool.autopep8]

From c2df5956caeb20baf8f6fbbb57ef1844c68fcad8 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 1 Apr 2026 14:18:45 +0200
Subject: [PATCH 39/74] try again

---
 .github/workflows/build_wheels.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 65b6de6401..10f9cb1a27 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -59,5 +59,6 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           skip-existing: true
+          verbose: true
           # To test uploads to TestPyPI, uncomment the following:
           repository-url: https://test.pypi.org/legacy/
\ No newline at end of file

From bd64248ca3be20c4817cecc86483f90b037449cb Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 1 Apr 2026 14:39:23 +0200
Subject: [PATCH 40/74] no local version

---
 .github/workflows/build_wheels.yml | 2 --
 pyproject.toml                     | 3 +++
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 10f9cb1a27..7dda722fdd 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -15,8 +15,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v6
-
       - uses: pypa/cibuildwheel@v2.16
 
       - uses: actions/upload-artifact@v6
diff --git a/pyproject.toml b/pyproject.toml
index b83a7c4ede..3d6c003e4a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,6 +41,9 @@ 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
 build = ["cp38*"]

From 2a982eba2c9e52f3fc661f89fc534f0e8971dad6 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 1 Apr 2026 15:26:45 +0200
Subject: [PATCH 41/74] general clean up

---
 .github/workflows/build_wheels.yml  |   5 +-
 .github/workflows/epidata_main.yml  | 294 ++++++-------
 .github/workflows/main.yml          | 660 ++++++++++++++--------------
 .github/workflows/message_bot.yml   | 226 +++++-----
 README.md                           |   2 +-
 pycode/memilio-simulation/README.md |   6 +-
 pyproject.toml                      |   2 -
 7 files changed, 595 insertions(+), 600 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 7dda722fdd..1806ab1433 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -43,9 +43,7 @@ jobs:
     environment: pypi
     permissions:
       id-token: write
-    # if: github.event_name == 'release' && github.event.action == 'published'
-    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
-    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+      
     steps:
       - uses: actions/download-artifact@v8
         with:
@@ -57,6 +55,5 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           skip-existing: true
-          verbose: true
           # To test uploads to TestPyPI, uncomment the following:
           repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index e8e84dd564..3cd8fea21b 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -1,158 +1,158 @@
-# name: Epidata-CI
+name: Epidata-CI
 
-# on: 
-#   schedule:
-#     - cron: "40 1 * * *"
-#   push:
-#     branches:
-#       - 'main'
-#     tags:
-#       - version-*
-#     paths:
-#       - '**/memilio-epidata/**'
-#       - '.github/**'
-#   pull_request:
-#     types: [opened, reopened, synchronize, ready_for_review]
-#     paths:
-#       - '**/memilio-epidata/**'
-#       - '.github/**'
-#   workflow_dispatch:
+on: 
+  schedule:
+    - cron: "40 1 * * *"
+  push:
+    branches:
+      - 'main'
+    tags:
+      - version-*
+    paths:
+      - '**/memilio-epidata/**'
+      - '.github/**'
+  pull_request:
+    types: [opened, reopened, synchronize, ready_for_review]
+    paths:
+      - '**/memilio-epidata/**'
+      - '.github/**'
+  workflow_dispatch:
 
-# jobs:
-#   pre-commit:
-#     runs-on: ubuntu-latest
-#     steps:
-#     - uses: actions/checkout@v4
-#     - uses: actions/setup-python@v5
-#       with:
-#         python-version: 3.12
-#     - uses: pre-commit/action@v3.0.1
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - uses: pre-commit/action@v3.0.1
 
-#   build-py-epidata:
-#     runs-on: ubuntu-latest
-#     container: quay.io/pypa/manylinux_2_28_x86_64
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/build-py
-#         with:
-#           package: epidata
+  build-py-epidata:
+    runs-on: ubuntu-latest
+    container: quay.io/pypa/manylinux_2_28_x86_64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/build-py
+        with:
+          package: epidata
 
-#   build-py-plot:
-#     if: github.event.pull_request.draft == false
-#     runs-on: ubuntu-latest
-#     container: quay.io/pypa/manylinux_2_28_x86_64
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/build-py
-#         with:
-#           package: plot
+  build-py-plot:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    container: quay.io/pypa/manylinux_2_28_x86_64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/build-py
+        with:
+          package: plot
 
-#   test-py-epidata:
-#     needs: build-py-epidata
-#     strategy:
-#       matrix: 
-#         version: ["3.8", "3.12"]
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/test-py
-#         with: 
-#           version: ${{ matrix.version }}
-#           package: epidata
-#           coverage: ON
+  test-py-epidata:
+    needs: build-py-epidata
+    strategy:
+      matrix: 
+        version: ["3.8", "3.12"]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/test-py
+        with: 
+          version: ${{ matrix.version }}
+          package: epidata
+          coverage: ON
 
-#   test-py-plot:
-#     if: github.event.pull_request.draft == false
-#     needs: [build-py-plot, build-py-epidata]
-#     strategy:
-#       matrix: 
-#         version: ["3.8", "3.12"]
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/test-py
-#         with: 
-#           version: ${{ matrix.version }}
-#           package: plot
-#           coverage: ON 
+  test-py-plot:
+    if: github.event.pull_request.draft == false
+    needs: [build-py-plot, build-py-epidata]
+    strategy:
+      matrix: 
+        version: ["3.8", "3.12"]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/test-py
+        with: 
+          version: ${{ matrix.version }}
+          package: plot
+          coverage: ON 
 
-#   merge-artifacts:
-#     runs-on: ubuntu-latest
-#     strategy:
-#       matrix:
-#         packages: [epidata, plot]
-#     needs: [test-py-plot, test-py-epidata]
-#     steps:
-#       - name: merge epidata reports
-#         uses: actions/upload-artifact/merge@v4
-#         with:
-#           name: test-py-coverage-reports-${{ matrix.packages }}
-#           pattern: test-py-coverage-reports-${{ matrix.packages }}-*
+  merge-artifacts:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        packages: [epidata, plot]
+    needs: [test-py-plot, test-py-epidata]
+    steps:
+      - name: merge epidata reports
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: test-py-coverage-reports-${{ matrix.packages }}
+          pattern: test-py-coverage-reports-${{ matrix.packages }}-*
 
-#   test-pylint-epidata:
-#     needs: build-py-epidata
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/test-pylint
-#         with:
-#           package: epidata
+  test-pylint-epidata:
+    needs: build-py-epidata
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/test-pylint
+        with:
+          package: epidata
 
-#   test-pylint-plot:
-#     needs: build-py-plot
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/test-pylint
-#         with:
-#           package: plot
+  test-pylint-plot:
+    needs: build-py-plot
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/test-pylint
+        with:
+          package: plot
 
-#   download-data:
-#     needs: build-py-epidata
-#     runs-on: ubuntu-latest
-#     continue-on-error: true
-#     steps:
-#       - uses: actions/checkout@v4
-#       - name: Install dependencies
-#         run: |
-#           sudo apt-get -qq update
-#           sudo apt-get -qq -y install python3-pip gnupg
-#           python -m pip install --upgrade pip
-#       - name: Download Python Wheels
-#         uses: actions/download-artifact@v4
-#         with:
-#           name: python-wheels-epidata
-#           path: pycode/wheelhouse
-#       - name: Set up Python 3.12
-#         uses: actions/setup-python@v5
-#         with:
-#           python-version: 3.12
-#       - name: Install Python Wheels
-#         run: |
-#           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
-#           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
-#       - name: Download Data
-#         run: |
-#           mkdir -p data_dl
-#           getcasedata -o data_dl --no-progress-indicators
-#           getpopuldata -o data_dl --no-progress-indicators
-#           getjhdata -o data_dl --no-progress-indicators
-#           getdividata -o data_dl --no-progress-indicators
-#           getcommutermobility -o data_dl --no-progress-indicators
-#           getvaccinationdata -o data_dl --no-progress-indicators
-#           gethospitalizationdata -o data_dl --no-progress-indicators
-#       - name: Upload Data
-#         uses: actions/upload-artifact@v4
-#         with:
-#           name: data
-#           path: |
-#             data_dl/*.json
-#             data_dl/Germany/*.json
-#             data_dl/Spain/*.json
-#             data_dl/France/*.json
-#             data_dl/Italy*.json
-#             data_dl/SouthKorea/*.json
-#             data_dl/US/*.json
-#             data_dl/China/*.json
-#           retention-days: 1
+  download-data:
+    needs: build-py-epidata
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get -qq update
+          sudo apt-get -qq -y install python3-pip gnupg
+          python -m pip install --upgrade pip
+      - name: Download Python Wheels
+        uses: actions/download-artifact@v4
+        with:
+          name: python-wheels-epidata
+          path: pycode/wheelhouse
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - name: Install Python Wheels
+        run: |
+          for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
+          for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
+      - name: Download Data
+        run: |
+          mkdir -p data_dl
+          getcasedata -o data_dl --no-progress-indicators
+          getpopuldata -o data_dl --no-progress-indicators
+          getjhdata -o data_dl --no-progress-indicators
+          getdividata -o data_dl --no-progress-indicators
+          getcommutermobility -o data_dl --no-progress-indicators
+          getvaccinationdata -o data_dl --no-progress-indicators
+          gethospitalizationdata -o data_dl --no-progress-indicators
+      - name: Upload Data
+        uses: actions/upload-artifact@v4
+        with:
+          name: data
+          path: |
+            data_dl/*.json
+            data_dl/Germany/*.json
+            data_dl/Spain/*.json
+            data_dl/France/*.json
+            data_dl/Italy*.json
+            data_dl/SouthKorea/*.json
+            data_dl/US/*.json
+            data_dl/China/*.json
+          retention-days: 1
           
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4bafd6e343..b87795d7bd 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,355 +1,355 @@
-# name: CI
+name: CI
 
 
-# on:
-#   schedule:
-#     - cron: "40 2 * * *"
-#   push:
-#     branches:
-#       - "main"
-#     tags:
-#       - version-*
-#     paths-ignore:
-#       - "**/memilio-epidata/**"
-#   pull_request:
-#     types: [opened, reopened, synchronize, ready_for_review]
-#     paths-ignore:
-#       - "**/memilio-epidata/**"
-#   workflow_dispatch:
+on:
+  schedule:
+    - cron: "40 2 * * *"
+  push:
+    branches:
+      - "main"
+    tags:
+      - version-*
+    paths-ignore:
+      - "**/memilio-epidata/**"
+  pull_request:
+    types: [opened, reopened, synchronize, ready_for_review]
+    paths-ignore:
+      - "**/memilio-epidata/**"
+  workflow_dispatch:
 
-# concurrency:
-#   group: ${{ github.workflow }}-${{ github.ref_name }}-${{ github.event.pull_request.number || github.run_id }}
-#   cancel-in-progress: true
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref_name }}-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
 
-# jobs:
-#   pre-commit:
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: actions/setup-python@v5
-#         with:
-#           python-version: 3.12
-#       - uses: pre-commit/action@v3.0.1
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - uses: pre-commit/action@v3.0.1
 
-#   build-cpp-gcc_clang:
-#     if: github.event.pull_request.draft == false
-#     strategy:
-#       matrix:
-#         compiler: ["gcc", "clang"]
-#         config: ["Debug", "Release"]
-#         version: ["latest", "min"]
-#         include:
-#           - version: "latest"
-#             os: "ubuntu-latest"
-#           - version: "min"
-#             os: "ubuntu-22.04"
-#     runs-on: ${{ matrix.os }}
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/linux-build
-#         with:
-#           compiler: ${{ matrix.compiler }}
-#           config: ${{ matrix.config }}
-#           version: ${{ matrix.version }}
-#           coverage: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }} # `c && t || f` is (usually) equivalent to `c ? t : f`
-#           sanitizers: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }}
+  build-cpp-gcc_clang:
+    if: github.event.pull_request.draft == false
+    strategy:
+      matrix:
+        compiler: ["gcc", "clang"]
+        config: ["Debug", "Release"]
+        version: ["latest", "min"]
+        include:
+          - version: "latest"
+            os: "ubuntu-latest"
+          - version: "min"
+            os: "ubuntu-22.04"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/linux-build
+        with:
+          compiler: ${{ matrix.compiler }}
+          config: ${{ matrix.config }}
+          version: ${{ matrix.version }}
+          coverage: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }} # `c && t || f` is (usually) equivalent to `c ? t : f`
+          sanitizers: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }}
 
-#   build-cpp-gcc-no-optional-deps:
-#     if: github.event.pull_request.draft == false
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/linux-build
-#         with:
-#           compiler: gcc
-#           version: latest
-#           config: Release
-#           optional-dependencies: OFF
+  build-cpp-gcc-no-optional-deps:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/linux-build
+        with:
+          compiler: gcc
+          version: latest
+          config: Release
+          optional-dependencies: OFF
 
-#   build-cpp-gcc-openmp:
-#     if: github.event.pull_request.draft == false
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/linux-build
-#         with:
-#           compiler: gcc
-#           version: latest
-#           config: Release
-#           openmp: ON
+  build-cpp-gcc-openmp:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/linux-build
+        with:
+          compiler: gcc
+          version: latest
+          config: Release
+          openmp: ON
 
-#   build-cpp-msvc:
-#     if: github.event.pull_request.draft == false
-#     strategy:
-#       matrix:
-#         config: ["Debug", "Release"]
-#         version: ["latest", "min"]
-#         include:
-#           - version: "latest"
-#             os: "windows-2025"
-#           - version: "min"
-#             os: "windows-2022"
-#     runs-on: ${{ matrix.os }}
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/windows-build
-#         with:
-#           config: ${{ matrix.config }}
-#           version: ${{ matrix.version }}
+  build-cpp-msvc:
+    if: github.event.pull_request.draft == false
+    strategy:
+      matrix:
+        config: ["Debug", "Release"]
+        version: ["latest", "min"]
+        include:
+          - version: "latest"
+            os: "windows-2025"
+          - version: "min"
+            os: "windows-2022"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/windows-build
+        with:
+          config: ${{ matrix.config }}
+          version: ${{ matrix.version }}
 
-#   build-cpp-msvc-no-optional-deps:
-#     if: github.event.pull_request.draft == false
-#     runs-on: windows-2025
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/windows-build
-#         with:
-#           config: Release
-#           version: latest
-#           optional-dependencies: OFF
+  build-cpp-msvc-no-optional-deps:
+    if: github.event.pull_request.draft == false
+    runs-on: windows-2025
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/windows-build
+        with:
+          config: Release
+          version: latest
+          optional-dependencies: OFF
 
-#   test-cpp-gcc_clang:
-#     if: github.event.pull_request.draft == false
-#     needs: build-cpp-gcc_clang
-#     strategy:
-#       matrix:
-#         compiler: ["gcc", "clang"]
-#         config: ["Debug", "Release"]
-#         version: ["latest", "min"]
-#         include:
-#           - version: "latest"
-#             os: "ubuntu-latest"
-#           - version: "min"
-#             os: "ubuntu-22.04"
-#     runs-on: ${{ matrix.os }}
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/linux-test
-#         with:
-#           artifact-pattern: ${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
-#           coverage: ${{ (matrix.compiler == 'gcc' && matrix.version == 'latest' && matrix.config == 'Debug') && 'ON' || 'OFF' }}
+  test-cpp-gcc_clang:
+    if: github.event.pull_request.draft == false
+    needs: build-cpp-gcc_clang
+    strategy:
+      matrix:
+        compiler: ["gcc", "clang"]
+        config: ["Debug", "Release"]
+        version: ["latest", "min"]
+        include:
+          - version: "latest"
+            os: "ubuntu-latest"
+          - version: "min"
+            os: "ubuntu-22.04"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/linux-test
+        with:
+          artifact-pattern: ${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
+          coverage: ${{ (matrix.compiler == 'gcc' && matrix.version == 'latest' && matrix.config == 'Debug') && 'ON' || 'OFF' }}
  
-#   test-cpp-gcc-sbml:
-#       if: github.event.pull_request.draft == false
-#       needs: build-cpp-gcc_clang
-#       runs-on: ubuntu-latest
-#       steps:
-#         - uses: actions/checkout@v4
-#         - uses: ./.github/actions/sbml-test
+  test-cpp-gcc-sbml:
+      if: github.event.pull_request.draft == false
+      needs: build-cpp-gcc_clang
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+        - uses: ./.github/actions/sbml-test
 
-#   merge-test-artifacts:
-#     needs: [test-cpp-gcc_clang, test-cpp-msvc, test-py-surrogatemodel]
-#     runs-on: ubuntu-latest
-#     steps:
-#       - name: merge-coverage-artifacts
-#         uses: actions/upload-artifact/merge@v4
-#         with:
-#           name: test-cpp-coverage-reports
-#           pattern: test-cpp-coverage-reports-*
-#       - name: merge-linux-artifacts
-#         uses: actions/upload-artifact/merge@v4
-#         with:
-#           name: test-cpp-linux-report
-#           pattern: test-cpp-linux-report-*
-#       - name: merge-windows-artifacts
-#         uses: actions/upload-artifact/merge@v4
-#         with:
-#           name: test-cpp-win-report
-#           pattern: test-cpp-win-report-*
-#       - name: merge python reports
-#         uses: actions/upload-artifact/merge@v4
-#         with:
-#           name: test-py-coverage-reports-surrogatemodel
-#           pattern: test-py-coverage-reports-surrogatemodel-*
+  merge-test-artifacts:
+    needs: [test-cpp-gcc_clang, test-cpp-msvc, test-py-surrogatemodel]
+    runs-on: ubuntu-latest
+    steps:
+      - name: merge-coverage-artifacts
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: test-cpp-coverage-reports
+          pattern: test-cpp-coverage-reports-*
+      - name: merge-linux-artifacts
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: test-cpp-linux-report
+          pattern: test-cpp-linux-report-*
+      - name: merge-windows-artifacts
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: test-cpp-win-report
+          pattern: test-cpp-win-report-*
+      - name: merge python reports
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: test-py-coverage-reports-surrogatemodel
+          pattern: test-py-coverage-reports-surrogatemodel-*
 
-#   test-cpp-gcc-no-optional-deps:
-#     if: github.event.pull_request.draft == false
-#     needs: build-cpp-gcc-no-optional-deps
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/linux-test
-#         with:
-#           artifact-pattern: gcc-latest-Release
-#           optional-deps: OFF
+  test-cpp-gcc-no-optional-deps:
+    if: github.event.pull_request.draft == false
+    needs: build-cpp-gcc-no-optional-deps
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/linux-test
+        with:
+          artifact-pattern: gcc-latest-Release
+          optional-deps: OFF
 
-#   test-cpp-gcc-openmp:
-#     if: github.event.pull_request.draft == false
-#     needs: build-cpp-gcc-openmp
-#     runs-on: ubuntu-latest
-#     timeout-minutes: 30
-#     env:
-#       OMP_NUM_THREADS: 4
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/linux-test
-#         with:
-#           artifact-pattern: gcc-latest-Release
-#           num-repeat: 10
-#           openmp: ON
+  test-cpp-gcc-openmp:
+    if: github.event.pull_request.draft == false
+    needs: build-cpp-gcc-openmp
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    env:
+      OMP_NUM_THREADS: 4
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/linux-test
+        with:
+          artifact-pattern: gcc-latest-Release
+          num-repeat: 10
+          openmp: ON
 
-#   test-cpp-msvc:
-#     if: github.event.pull_request.draft == false
-#     needs: build-cpp-msvc
-#     strategy:
-#       matrix:
-#         config: ["Debug", "Release"]
-#         version: ["latest", "min"]
-#         include:
-#           - version: "latest"
-#             os: "windows-2025"
-#           - version: "min"
-#             os: "windows-2022"
-#     runs-on: ${{ matrix.os }}
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/windows-test
-#         with:
-#           artifact-pattern: msvc-${{ matrix.version }}-${{ matrix.config }}
+  test-cpp-msvc:
+    if: github.event.pull_request.draft == false
+    needs: build-cpp-msvc
+    strategy:
+      matrix:
+        config: ["Debug", "Release"]
+        version: ["latest", "min"]
+        include:
+          - version: "latest"
+            os: "windows-2025"
+          - version: "min"
+            os: "windows-2022"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/windows-test
+        with:
+          artifact-pattern: msvc-${{ matrix.version }}-${{ matrix.config }}
 
-#   test-cpp-msvc-no-optional-deps:
-#     if: github.event.pull_request.draft == false
-#     needs: build-cpp-msvc-no-optional-deps
-#     runs-on: windows-2025
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/windows-test
-#         with:
-#           artifact-pattern: msvc-latest-Release
-#           optional-deps: OFF
+  test-cpp-msvc-no-optional-deps:
+    if: github.event.pull_request.draft == false
+    needs: build-cpp-msvc-no-optional-deps
+    runs-on: windows-2025
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/windows-test
+        with:
+          artifact-pattern: msvc-latest-Release
+          optional-deps: OFF
 
-#   run_examples-cpp-gcc_clang:
-#     if: github.event.pull_request.draft == false
-#     needs: build-cpp-gcc_clang
-#     strategy:
-#       matrix:
-#         compiler: ["gcc", "clang"]
-#         config: ["Debug", "Release"]
-#         version: ["latest", "min"]
-#         include:
-#           - version: "latest"
-#             os: "ubuntu-latest"
-#           - version: "min"
-#             os: "ubuntu-22.04"
-#     runs-on: ${{ matrix.os }}
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/linux-run_examples
-#         with:
-#           build-artifact: build-cpp-linux-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
+  run_examples-cpp-gcc_clang:
+    if: github.event.pull_request.draft == false
+    needs: build-cpp-gcc_clang
+    strategy:
+      matrix:
+        compiler: ["gcc", "clang"]
+        config: ["Debug", "Release"]
+        version: ["latest", "min"]
+        include:
+          - version: "latest"
+            os: "ubuntu-latest"
+          - version: "min"
+            os: "ubuntu-22.04"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/linux-run_examples
+        with:
+          build-artifact: build-cpp-linux-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
 
-#   run_examples-cpp-msvc:
-#     if: github.event.pull_request.draft == false
-#     needs: build-cpp-msvc
-#     strategy:
-#       matrix:
-#         config: ["Debug", "Release"]
-#         version: ["latest", "min"]
-#         include:
-#           - version: "latest"
-#             os: "windows-2025"
-#           - version: "min"
-#             os: "windows-2022"
-#     runs-on: ${{ matrix.os }}
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/windows-run_examples
-#         with:
-#           build-artifact: build-cpp-windows-msvc-${{ matrix.version }}-${{ matrix.config }}
+  run_examples-cpp-msvc:
+    if: github.event.pull_request.draft == false
+    needs: build-cpp-msvc
+    strategy:
+      matrix:
+        config: ["Debug", "Release"]
+        version: ["latest", "min"]
+        include:
+          - version: "latest"
+            os: "windows-2025"
+          - version: "min"
+            os: "windows-2022"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/windows-run_examples
+        with:
+          build-artifact: build-cpp-windows-msvc-${{ matrix.version }}-${{ matrix.config }}
 
-#   build-py-generation:
-#     if: github.event.pull_request.draft == false
-#     runs-on: ubuntu-latest
-#     container: quay.io/pypa/manylinux_2_28_x86_64
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/build-py
-#         with:
-#           package: generation
+  build-py-generation:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    container: quay.io/pypa/manylinux_2_28_x86_64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/build-py
+        with:
+          package: generation
 
-#   build-py-simulation:
-#     if: github.event.pull_request.draft == false
-#     runs-on: ubuntu-latest
-#     container: quay.io/pypa/manylinux_2_28_x86_64
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/build-py
-#         with:
-#           package: simulation
+  build-py-simulation:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    container: quay.io/pypa/manylinux_2_28_x86_64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/build-py
+        with:
+          package: simulation
 
-#   build-py-surrogatemodel:
-#     if: github.event.pull_request.draft == false
-#     runs-on: ubuntu-latest
-#     container: quay.io/pypa/manylinux_2_28_x86_64
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/build-py
-#         with:
-#           package: surrogatemodel
+  build-py-surrogatemodel:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    container: quay.io/pypa/manylinux_2_28_x86_64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/build-py
+        with:
+          package: surrogatemodel
 
-#   test-py-generation:
-#     if: github.event.pull_request.draft == false
-#     strategy:
-#       matrix: 
-#         version: ["3.8", "3.12"]
-#     needs: build-py-generation
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/test-py
-#         with:
-#           package: generation
+  test-py-generation:
+    if: github.event.pull_request.draft == false
+    strategy:
+      matrix: 
+        version: ["3.8", "3.12"]
+    needs: build-py-generation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/test-py
+        with:
+          package: generation
 
-#   test-py-simulation:
-#     if: github.event.pull_request.draft == false
-#     needs: build-py-simulation
-#     strategy:
-#       matrix: 
-#         version: ["3.8", "3.12"]
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/test-py
-#         with:
-#           package: simulation
+  test-py-simulation:
+    if: github.event.pull_request.draft == false
+    needs: build-py-simulation
+    strategy:
+      matrix: 
+        version: ["3.8", "3.12"]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/test-py
+        with:
+          package: simulation
 
-#   test-py-surrogatemodel:
-#     if: github.event.pull_request.draft == false
-#     needs: [build-py-surrogatemodel, build-py-simulation]
-#     strategy:
-#       matrix: 
-#         version: ["3.8", "3.12"]
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - uses: ./.github/actions/test-py
-#         with:
-#           version: ${{ matrix.version }}
-#           package: surrogatemodel
-#           coverage: ON
+  test-py-surrogatemodel:
+    if: github.event.pull_request.draft == false
+    needs: [build-py-surrogatemodel, build-py-simulation]
+    strategy:
+      matrix: 
+        version: ["3.8", "3.12"]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/test-py
+        with:
+          version: ${{ matrix.version }}
+          package: surrogatemodel
+          coverage: ON
 
-#   codecov:
-#     if: github.event.pull_request.draft == false
-#     needs: merge-test-artifacts
-#     runs-on: ubuntu-latest
-#     steps:
-#       - uses: actions/checkout@v4
-#       - name: Install dependencies
-#         run: |
-#           sudo apt-get -qq update
-#           sudo apt-get -qq -y install git curl
-#       - name: Download python coverage report
-#         uses: actions/download-artifact@v4
-#         with:
-#           name: test-py-coverage-reports-surrogatemodel
-#       - name: Download cpp coverage report
-#         uses: actions/download-artifact@v4
-#         with:
-#           name: test-cpp-coverage-reports
-#       - name: Deploy to codecov.io
-#         uses: codecov/codecov-action@v3
-#         with:
-#           token: ${{ secrets.CODECOV_TOKEN }}
-#           directory: ./coverage_python
-#           files: ./coverage_python/**,./coverage.info
-#           verbose: true
+  codecov:
+    if: github.event.pull_request.draft == false
+    needs: merge-test-artifacts
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get -qq update
+          sudo apt-get -qq -y install git curl
+      - name: Download python coverage report
+        uses: actions/download-artifact@v4
+        with:
+          name: test-py-coverage-reports-surrogatemodel
+      - name: Download cpp coverage report
+        uses: actions/download-artifact@v4
+        with:
+          name: test-cpp-coverage-reports
+      - name: Deploy to codecov.io
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          directory: ./coverage_python
+          files: ./coverage_python/**,./coverage.info
+          verbose: true
diff --git a/.github/workflows/message_bot.yml b/.github/workflows/message_bot.yml
index 55fdb1545d..cd4f322ca1 100644
--- a/.github/workflows/message_bot.yml
+++ b/.github/workflows/message_bot.yml
@@ -1,134 +1,134 @@
-# # .github/workflows/discussion-monitor.yml
-# name: Discussion Monitor
+# .github/workflows/discussion-monitor.yml
+name: Discussion Monitor
 
-# on:
-#   schedule:
-#     - cron: '0 9 * * *'
+on:
+  schedule:
+    - cron: '0 9 * * *'
 
 
-# jobs:
-#   check-discussions:
-#     runs-on: ubuntu-latest
-#     permissions:
-#       contents: read
-#       discussions: read
-#     steps:
-#     - name: Check for new discussions
-#       env:
-#         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-#         MATTERMOST_WEBHOOK_URL: ${{ secrets.MATTERMOST_WEBHOOK_URL }}
-#       run: |
-#         npm install @octokit/rest
-#         cat > check.js << 'EOF'
-#         const { Octokit } = require('@octokit/rest');
+jobs:
+  check-discussions:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      discussions: read
+    steps:
+    - name: Check for new discussions
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        MATTERMOST_WEBHOOK_URL: ${{ secrets.MATTERMOST_WEBHOOK_URL }}
+      run: |
+        npm install @octokit/rest
+        cat > check.js << 'EOF'
+        const { Octokit } = require('@octokit/rest');
 
-#         const octokit = new Octokit({ auth: process.env.GITHUB_TOKEN });
+        const octokit = new Octokit({ auth: process.env.GITHUB_TOKEN });
 
-#         async function check() {
-#           const since = new Date();
-#           since.setHours(since.getHours() - 25);
+        async function check() {
+          const since = new Date();
+          since.setHours(since.getHours() - 25);
           
-#           const [owner, repo] = process.env.GITHUB_REPOSITORY.split('/');
-#           console.log(`Checking discussions for ${owner}/${repo}`);
+          const [owner, repo] = process.env.GITHUB_REPOSITORY.split('/');
+          console.log(`Checking discussions for ${owner}/${repo}`);
           
-#           try {
-#             const response = await octokit.graphql(`
-#               query { 
-#                 repository(owner: "${owner}", name: "${repo}") {
-#                   discussions(first: 10, orderBy: {field: CREATED_AT, direction: DESC}) {
-#                     nodes { 
-#                       createdAt
-#                       title
-#                       url
-#                       number
-#                       author {
-#                         login
-#                       }
-#                       category {
-#                         name
-#                         emoji
-#                       }
-#                     }
-#                   }
-#                 }
-#               }
-#             `);
+          try {
+            const response = await octokit.graphql(`
+              query { 
+                repository(owner: "${owner}", name: "${repo}") {
+                  discussions(first: 10, orderBy: {field: CREATED_AT, direction: DESC}) {
+                    nodes { 
+                      createdAt
+                      title
+                      url
+                      number
+                      author {
+                        login
+                      }
+                      category {
+                        name
+                        emoji
+                      }
+                    }
+                  }
+                }
+              }
+            `);
             
-#             console.log('Full GraphQL response:', JSON.stringify(response, null, 2));
+            console.log('Full GraphQL response:', JSON.stringify(response, null, 2));
             
-#             if (!response || !response.repository) {
-#               console.log('Repository not found or discussions not enabled');
-#               console.log('Response keys:', Object.keys(response || {}));
-#               return;
-#             }
+            if (!response || !response.repository) {
+              console.log('Repository not found or discussions not enabled');
+              console.log('Response keys:', Object.keys(response || {}));
+              return;
+            }
 
-#             if (!response.repository.discussions) {
-#               console.log('Discussions not available for this repository');
-#               return;
-#             }
+            if (!response.repository.discussions) {
+              console.log('Discussions not available for this repository');
+              return;
+            }
             
-#             const newDiscussions = response.repository.discussions.nodes.filter(
-#               d => new Date(d.createdAt) > since
-#             );
+            const newDiscussions = response.repository.discussions.nodes.filter(
+              d => new Date(d.createdAt) > since
+            );
             
-#             console.log(`Found ${newDiscussions.length} new discussions`);
+            console.log(`Found ${newDiscussions.length} new discussions`);
             
-#             if (newDiscussions.length > 0) {
-#               let message;
+            if (newDiscussions.length > 0) {
+              let message;
               
-#               if (newDiscussions.length === 1) {
-#                 const discussion = newDiscussions[0];
-#                 message = {
-#                   text: `${discussion.category.emoji || '💬'} New Discussion on ${owner}/${repo}
+              if (newDiscussions.length === 1) {
+                const discussion = newDiscussions[0];
+                message = {
+                  text: `${discussion.category.emoji || '💬'} New Discussion on ${owner}/${repo}
 
-#         **[${discussion.title}](${discussion.url})**
+        **[${discussion.title}](${discussion.url})**
 
-#         👤 **Author:** ${discussion.author.login}
-#         📂 **Category:** ${discussion.category.name}
-#         🔢 **Discussion #${discussion.number}**`,
-#                   username: "GitHub Discussion Bot",
-#                   icon_emoji: ":github:"
-#                 };
-#               } else {
-#                 const discussionList = newDiscussions.map(d => 
-#                   `- ${d.category.emoji || '💬'} **[${d.title}](${d.url})** by ${d.author.login}`
-#                 ).join('\n');
+        👤 **Author:** ${discussion.author.login}
+        📂 **Category:** ${discussion.category.name}
+        🔢 **Discussion #${discussion.number}**`,
+                  username: "GitHub Discussion Bot",
+                  icon_emoji: ":github:"
+                };
+              } else {
+                const discussionList = newDiscussions.map(d => 
+                  `- ${d.category.emoji || '💬'} **[${d.title}](${d.url})** by ${d.author.login}`
+                ).join('\n');
                 
-#                 message = {
-#                   text: `🎉 ${newDiscussions.length} New Discussions on ${owner}/${repo}
+                message = {
+                  text: `🎉 ${newDiscussions.length} New Discussions on ${owner}/${repo}
 
-#         ${discussionList}
+        ${discussionList}
 
-#         ---
-#         *Check out the latest discussions above!*`,
-#                   username: "GitHub Discussion Bot",
-#                   icon_emoji: ":github:"
-#                 };
-#               }
+        ---
+        *Check out the latest discussions above!*`,
+                  username: "GitHub Discussion Bot",
+                  icon_emoji: ":github:"
+                };
+              }
               
-#               const response = await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
-#                 method: 'POST',
-#                 headers: { 'Content-Type': 'application/json' },
-#                 body: JSON.stringify(message)
-#               });
-#               console.log('Mattermost notification sent');
-#             }
-#           } catch (error) {
-#             console.error('Error details:', error);
-#             if (process.env.MATTERMOST_WEBHOOK_URL) {
-#               await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
-#                 method: 'POST',
-#                 headers: { 'Content-Type': 'application/json' },
-#                 body: JSON.stringify({ 
-#                   text: '⚠️ **GitHub Discussion Bot Error**\nThere was an error checking discussions. Please check the workflow logs.',
-#                   username: "GitHub Discussion Bot",
-#                   icon_emoji: ":warning:"
-#                 })
-#               });
-#             }
-#           }
-#         }
+              const response = await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
+                method: 'POST',
+                headers: { 'Content-Type': 'application/json' },
+                body: JSON.stringify(message)
+              });
+              console.log('Mattermost notification sent');
+            }
+          } catch (error) {
+            console.error('Error details:', error);
+            if (process.env.MATTERMOST_WEBHOOK_URL) {
+              await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
+                method: 'POST',
+                headers: { 'Content-Type': 'application/json' },
+                body: JSON.stringify({ 
+                  text: '⚠️ **GitHub Discussion Bot Error**\nThere was an error checking discussions. Please check the workflow logs.',
+                  username: "GitHub Discussion Bot",
+                  icon_emoji: ":warning:"
+                })
+              });
+            }
+          }
+        }
 
-#         check().catch(console.error);
-#         EOF
-#         node check.js
+        check().catch(console.error);
+        EOF
+        node check.js
diff --git a/README.md b/README.md
index 3e43d6499e..2b94fb33b4 100644
--- 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)
 
 [![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/pycode/memilio-simulation/README.md b/pycode/memilio-simulation/README.md
index 76f0ab82e7..8f23dc82a0 100644
--- 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/pyproject.toml b/pyproject.toml
index 3d6c003e4a..44ef0d806c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,5 @@
 [project]
 name = "memilio-simulation"
-# version = "1.0.3" 
 dynamic = ["version"]
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
@@ -46,7 +45,6 @@ local_scheme = "no-local-version"
 
 [tool.cibuildwheel]
 # Disable some wheels
-build = ["cp38*"]
 skip = ["pp*", "*musllinux*", "*-win32"] 
 
 [tool.autopep8]

From a3e25578dc0ad1ec77076bfed81ba56513f82625 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 1 Apr 2026 17:06:13 +0200
Subject: [PATCH 42/74] update main ci, fix version for now

---
 .github/actions/build-py/action.yml | 13 ++++++++++---
 pyproject.toml                      |  3 ++-
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 757f9f58a0..4df8c2625d 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -13,12 +13,18 @@ runs:
     - 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
@@ -35,7 +41,8 @@ runs:
         fi
         cp -r wheelhouse ..
     - name: Upload Python Wheels
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@v6
       with:
         name: python-wheels-${{ inputs.package }}
         path: pycode/wheelhouse
+
diff --git a/pyproject.toml b/pyproject.toml
index 44ef0d806c..7fb6cdcee1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,7 @@
 [project]
 name = "memilio-simulation"
-dynamic = ["version"]
+version = "2.3.0" 
+# dynamic = ["version"] 
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"

From 5b19727937fe81b66db238bda2d755cb21919c77 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 1 Apr 2026 17:11:08 +0200
Subject: [PATCH 43/74] fix typo in if statement

---
 .github/actions/build-py/action.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 4df8c2625d..950b7119ed 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -13,7 +13,7 @@ runs:
     - name: Make artifact dir
       shell: bash
       run: |
-        if [[ "${{ inputs.package }}" != "simulation" ]; then
+        if [ "${{ inputs.package }}" != "simulation" ]; then
           cd pycode/memilio-${{ inputs.package }}/
         // else stay in root directory
         fi
@@ -21,7 +21,7 @@ runs:
     - name: Build Python Wheels
       shell: bash
       run: |
-        if [[ "${{ inputs.package }}" != "simulation" ]; then
+        if [ "${{ inputs.package }}" != "simulation" ]; then
           cd pycode/memilio-${{ inputs.package }}/
         // else stay in root directory
         fi

From 9f37563d34b0514d13ee53758baba4fb7851579f Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 13:11:58 +0200
Subject: [PATCH 44/74] update ci and link to logo

---
 .github/actions/build-py/action.yml | 10 ++++++----
 README.md                           |  2 +-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 950b7119ed..15dbee19ef 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -21,15 +21,17 @@ runs:
     - name: Build Python Wheels
       shell: bash
       run: |
-        if [ "${{ inputs.package }}" != "simulation" ]; then
-          cd pycode/memilio-${{ inputs.package }}/
-        // else stay in root directory
-        fi
+        # 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 pip install setuptools-scm
         /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/cp312-cp312/bin/python -m pip install scikit-build scikit-build-core
+        /opt/python/cp312-cp312/bin/python -m pip install setuptools-scm
         /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 
diff --git a/README.md b/README.md
index 2b94fb33b4..9105fa1c85 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # MEmilio - a high performance Modular EpideMIcs simuLatIOn software #
 
-![memilio_logo](https://github.com/SciCompMod/memilio/blob/main/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)

From ed9f054eaa6e7b53aedf00523739c2eb41e844ae Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 13:22:58 +0200
Subject: [PATCH 45/74] update paths

---
 .github/actions/build-py/action.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 15dbee19ef..264b02488a 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -14,17 +14,17 @@ runs:
       shell: bash
       run: |
         if [ "${{ inputs.package }}" != "simulation" ]; then
-          cd pycode/memilio-${{ inputs.package }}/
+          cd pycode/memilio-${inputs.package}/
         // else stay in root directory
         fi
         mkdir wheelhouse
     - name: Build Python Wheels
       shell: bash
       run: |
-        # if [ "${{ inputs.package }}" != "simulation" ]; then
-        #   cd pycode/memilio-${{ inputs.package }}/
-        # // else stay in root directory
-        # fi
+        if [ "${{ 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 pip install setuptools-scm

From 15ed20fb32eeb3cb8b3fe3a48c41e33b93ab6cd4 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 13:34:15 +0200
Subject: [PATCH 46/74] again

---
 .github/actions/build-py/action.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 264b02488a..9f4fdb2622 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -14,16 +14,18 @@ runs:
       shell: bash
       run: |
         if [ "${{ inputs.package }}" != "simulation" ]; then
-          cd pycode/memilio-${inputs.package}/
-        // else stay in root directory
+          cd pycode/memilio-${{ inputs.package }}
+        else 
+        // stay in root directory
         fi
         mkdir wheelhouse
     - name: Build Python Wheels
       shell: bash
       run: |
         if [ "${{ inputs.package }}" != "simulation" ]; then
-          cd pycode/memilio-${inputs.package}/
-        // else stay in root directory
+          cd pycode/memilio-${{ 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

From 40108ffac690f97ab40e0f49ce22144d09b3a385 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 13:42:45 +0200
Subject: [PATCH 47/74] update

---
 .github/actions/build-py/action.yml | 5 ++++-
 pyproject.toml                      | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 9f4fdb2622..dd3f401726 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -6,7 +6,10 @@ inputs:
     required: true
 runs:
   using: "composite"
-  steps:    
+  steps:
+    - name: Configure Git safe directory
+      shell: bash 
+      run: git config --global --add safe.directory "${{ github.workspace }}"    
     - name: Install dependencies
       shell: bash
       run: yum install ninja-build cmake git -qy
diff --git a/pyproject.toml b/pyproject.toml
index 7fb6cdcee1..0a3c6dd941 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ 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 = { text = "Apache-2.0" }
+license = { "Apache-2.0" }
 authors = [{ name = "MEmilio Team" }]
 maintainers = [
   { email = "martin.kuehn@dlr.de" }

From 7131d9e1415d80b48d1bbd3e4ad0197137456023 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 13:47:19 +0200
Subject: [PATCH 48/74] again

---
 .github/actions/build-py/action.yml | 2 +-
 pyproject.toml                      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index dd3f401726..79d031b315 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -9,7 +9,7 @@ runs:
   steps:
     - name: Configure Git safe directory
       shell: bash 
-      run: git config --global --add safe.directory "${{ github.workspace }}"    
+      run: git config --global --add safe.directory /__w/memilio/memilio    
     - name: Install dependencies
       shell: bash
       run: yum install ninja-build cmake git -qy
diff --git a/pyproject.toml b/pyproject.toml
index 0a3c6dd941..db8e81c58b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ 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" }
+license = "Apache-2.0" 
 authors = [{ name = "MEmilio Team" }]
 maintainers = [
   { email = "martin.kuehn@dlr.de" }

From 701aa3d53baec4c2e0e8d02c1e38ac6504259457 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 13:57:35 +0200
Subject: [PATCH 49/74] adapt else

---
 .github/actions/build-py/action.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 79d031b315..772dd9cb8c 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -17,9 +17,9 @@ runs:
       shell: bash
       run: |
         if [ "${{ inputs.package }}" != "simulation" ]; then
-          cd pycode/memilio-${{ inputs.package }}
+          cd pycode/memilio-${{ inputs.package }}/
         else 
-        // stay in root directory
+          cd . // stay in root directory
         fi
         mkdir wheelhouse
     - name: Build Python Wheels
@@ -28,7 +28,7 @@ runs:
         if [ "${{ inputs.package }}" != "simulation" ]; then
           cd pycode/memilio-${{ inputs.package }}/
         else
-        // stay in root directory
+          cd . // 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

From 3a79e46389c77a1964efb4ca10e649fcbbe06f99 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 14:01:20 +0200
Subject: [PATCH 50/74] again

---
 .github/actions/build-py/action.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 772dd9cb8c..3c9735f673 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -18,8 +18,7 @@ runs:
       run: |
         if [ "${{ inputs.package }}" != "simulation" ]; then
           cd pycode/memilio-${{ inputs.package }}/
-        else 
-          cd . // stay in root directory
+        # else stay in root directory
         fi
         mkdir wheelhouse
     - name: Build Python Wheels
@@ -27,8 +26,7 @@ runs:
       run: |
         if [ "${{ inputs.package }}" != "simulation" ]; then
           cd pycode/memilio-${{ inputs.package }}/
-        else
-          cd . // stay in root directory
+        # 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

From fd247a1ed700f83d2facfae7ac6767081d684976 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 14:22:35 +0200
Subject: [PATCH 51/74] adapt path for storing wheels

---
 .github/actions/build-py/action.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 3c9735f673..bd6f92e4ad 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -44,7 +44,11 @@ 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@v6
       with:

From 969ec6c09b15844b9da82768a12df48be5db2301 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 15:16:26 +0200
Subject: [PATCH 52/74] try new version to test image

---
 .github/workflows/{build_wheels.yml => pypi.yml} | 4 +++-
 pyproject.toml                                   | 3 ++-
 2 files changed, 5 insertions(+), 2 deletions(-)
 rename .github/workflows/{build_wheels.yml => pypi.yml} (93%)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/pypi.yml
similarity index 93%
rename from .github/workflows/build_wheels.yml
rename to .github/workflows/pypi.yml
index 1806ab1433..7ed54fdfff 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/pypi.yml
@@ -1,5 +1,7 @@
-name: Build wheels 
+name: memilio-simulation PyPI
 
+# on: [release]
+# remove following line before merge: 
 on: [pull_request, release]
 
 jobs:
diff --git a/pyproject.toml b/pyproject.toml
index db8e81c58b..304cbf01c3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,8 @@
 [project]
 name = "memilio-simulation"
-version = "2.3.0" 
 # dynamic = ["version"] 
+# remove following line before merge: 
+version = "2.3.1" 
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"

From 13a1ea220f867057610e538b33edf1200f5406e5 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 16:24:35 +0200
Subject: [PATCH 53/74] prepare for upload to real pypi

---
 .github/workflows/pypi.yml | 8 ++++----
 pyproject.toml             | 4 +---
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index 7ed54fdfff..528a3c8dc4 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -1,8 +1,8 @@
-name: memilio-simulation PyPI
+name: PyPI
 
-# on: [release]
+on: [release]
 # remove following line before merge: 
-on: [pull_request, release]
+# on: [pull_request, release]
 
 jobs:
 
@@ -58,4 +58,4 @@ jobs:
         with:
           skip-existing: true
           # To test uploads to TestPyPI, uncomment the following:
-          repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
+          # repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 304cbf01c3..17045dfdc8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,6 @@
 [project]
 name = "memilio-simulation"
-# dynamic = ["version"] 
-# remove following line before merge: 
-version = "2.3.1" 
+dynamic = ["version"] 
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"

From b12999ba30f6f0f165e2ca7b0721e70f7caaeb41 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 10 Apr 2026 17:02:59 +0200
Subject: [PATCH 54/74] add static version for pr

---
 pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 17045dfdc8..94eb44e596 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,8 @@
 [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"

From d60e0b5c35cb68f47625f2ff623a1cd1b3f12d5a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 09:22:15 +0200
Subject: [PATCH 55/74] fix mpl backend

---
 .github/workflows/epidata_main.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index 3cd8fea21b..3f191f5e47 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -111,6 +111,8 @@ jobs:
     needs: build-py-epidata
     runs-on: ubuntu-latest
     continue-on-error: true
+    env:
+      MPLBACKEND: Agg
     steps:
       - uses: actions/checkout@v4
       - name: Install dependencies

From 39c7dbe9481ee8d4ad29a1cc0b4bb63ee1a69bd9 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 09:48:43 +0200
Subject: [PATCH 56/74] debug pip env

---
 .github/workflows/epidata_main.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index 3f191f5e47..9d3f883282 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -133,6 +133,9 @@ jobs:
         run: |
           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
+      - name: Debug pip environment
+        run: /opt/python/cp312-cp312/bin/python -m pip show matplotlib && \
+             /opt/python/cp312-cp312/bin/python -m pip list | grep -i qt
       - name: Download Data
         run: |
           mkdir -p data_dl

From e8f51a8dd5a59588b825eca6d740668831f81914 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 09:54:34 +0200
Subject: [PATCH 57/74] remove qt bindings

---
 .github/workflows/epidata_main.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index 9d3f883282..db589dea36 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -134,8 +134,10 @@ jobs:
           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
       - name: Debug pip environment
-        run: /opt/python/cp312-cp312/bin/python -m pip show matplotlib && \
-             /opt/python/cp312-cp312/bin/python -m pip list | grep -i qt
+        run: python -m pip show matplotlib && \
+             python -m pip list | grep -i qt
+      - name: Remove Qt bindings
+        run: python -m pip uninstall -y PyQt5 PyQt6 PySide2 PySide6 || true
       - name: Download Data
         run: |
           mkdir -p data_dl

From 0eb295f3c120f16f5f90b80e6f56f07cebf7dd98 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 10:05:17 +0200
Subject: [PATCH 58/74] update

---
 .github/workflows/epidata_main.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index db589dea36..35ef449f52 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -134,10 +134,9 @@ jobs:
           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
       - name: Debug pip environment
-        run: python -m pip show matplotlib && \
-             python -m pip list | grep -i qt
+        run: pip list | grep -i qt
       - name: Remove Qt bindings
-        run: python -m pip uninstall -y PyQt5 PyQt6 PySide2 PySide6 || true
+        run: pip uninstall -y PyQt5 PyQt6 PySide2 PySide6 || true
       - name: Download Data
         run: |
           mkdir -p data_dl

From 4b6c310d5d80e40daf64056dd05162aad127ef42 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 10:09:26 +0200
Subject: [PATCH 59/74] again

---
 .github/workflows/epidata_main.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index 35ef449f52..cac164840a 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -134,9 +134,11 @@ jobs:
           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
       - name: Debug pip environment
-        run: pip list | grep -i qt
+        run: |
+          pip list | grep -i qt
       - name: Remove Qt bindings
-        run: pip uninstall -y PyQt5 PyQt6 PySide2 PySide6 || true
+        run: |
+          pip uninstall -y PyQt5 PyQt6 PyQt6-Qt6 PyQt6_sip || true
       - name: Download Data
         run: |
           mkdir -p data_dl

From 7568f834e3dce845b5b53874af2d2364a0052ffb Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 10:30:34 +0200
Subject: [PATCH 60/74] try again

---
 .github/workflows/epidata_main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index cac164840a..5fc1a104c3 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -142,6 +142,7 @@ jobs:
       - name: Download Data
         run: |
           mkdir -p data_dl
+          python -c "import matplotlib; matplotlib.use('Agg')"
           getcasedata -o data_dl --no-progress-indicators
           getpopuldata -o data_dl --no-progress-indicators
           getjhdata -o data_dl --no-progress-indicators

From b4dd5766e8246f24a712066430bad542848c03d8 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 10:35:45 +0200
Subject: [PATCH 61/74] other version

---
 .github/actions/build-py/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index bd6f92e4ad..686df31e84 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -50,7 +50,7 @@ runs:
           cp -r wheelhouse pycode
         fi 
     - name: Upload Python Wheels
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v4
       with:
         name: python-wheels-${{ inputs.package }}
         path: pycode/wheelhouse

From a37e771e7c105ed51792f7ac05032089aacd6909 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 10:45:54 +0200
Subject: [PATCH 62/74] reset epidata_main and action to previous state

---
 .github/actions/build-py/action.yml | 34 +++++++++++++++--------------
 .github/workflows/epidata_main.yml  |  9 --------
 2 files changed, 18 insertions(+), 25 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 686df31e84..e7ee443571 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -16,25 +16,27 @@ runs:
     - name: Make artifact dir
       shell: bash
       run: |
-        if [ "${{ inputs.package }}" != "simulation" ]; then
-          cd pycode/memilio-${{ inputs.package }}/
-        # else stay in root directory
-        fi
+        # 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-${{ inputs.package }}/
-        # else stay in root directory
-        fi
+        # if [ "${{ inputs.package }}" != "simulation" ]; then
+        #   cd pycode/memilio-${{ inputs.package }}/
+        # # else stay in root directory
+        # fi
+        cd pycode/memilio-${{ inputs.package }}/
         /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 pip install setuptools-scm
+        # /opt/python/cp38-cp38/bin/python -m pip install setuptools-scm
         /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/cp312-cp312/bin/python -m pip install scikit-build scikit-build-core
-        /opt/python/cp312-cp312/bin/python -m pip install setuptools-scm
+        # /opt/python/cp312-cp312/bin/python -m pip install setuptools-scm
         /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" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
@@ -44,14 +46,14 @@ runs:
           # no auditwheel necessary for pure python packages, so only copy the wheels to the same output directory 
           cp dist/*.whl wheelhouse
         fi
-        if [ "${{ inputs.package }}" != "simulation" ]; then
-          cp -r wheelhouse ..
-        else
-          cp -r wheelhouse pycode
-        fi 
+        # if [ "${{ inputs.package }}" != "simulation" ]; then
+        #   cp -r wheelhouse ..
+        # else
+        #   cp -r wheelhouse pycode
+        # fi 
+        cp -r wheelhouse ..
     - name: Upload Python Wheels
       uses: actions/upload-artifact@v4
       with:
         name: python-wheels-${{ inputs.package }}
         path: pycode/wheelhouse
-
diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index 5fc1a104c3..3cd8fea21b 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -111,8 +111,6 @@ jobs:
     needs: build-py-epidata
     runs-on: ubuntu-latest
     continue-on-error: true
-    env:
-      MPLBACKEND: Agg
     steps:
       - uses: actions/checkout@v4
       - name: Install dependencies
@@ -133,16 +131,9 @@ jobs:
         run: |
           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
-      - name: Debug pip environment
-        run: |
-          pip list | grep -i qt
-      - name: Remove Qt bindings
-        run: |
-          pip uninstall -y PyQt5 PyQt6 PyQt6-Qt6 PyQt6_sip || true
       - name: Download Data
         run: |
           mkdir -p data_dl
-          python -c "import matplotlib; matplotlib.use('Agg')"
           getcasedata -o data_dl --no-progress-indicators
           getpopuldata -o data_dl --no-progress-indicators
           getjhdata -o data_dl --no-progress-indicators

From 1acecee951a32e5c64d687554f74eacc4b9bb1d1 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 10:55:29 +0200
Subject: [PATCH 63/74] reintroduce if statements

---
 .github/actions/build-py/action.yml | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index e7ee443571..a29f35eaab 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -25,11 +25,10 @@ runs:
     - name: Build Python Wheels
       shell: bash
       run: |
-        # if [ "${{ inputs.package }}" != "simulation" ]; then
-        #   cd pycode/memilio-${{ inputs.package }}/
-        # # else stay in root directory
-        # fi
-        cd pycode/memilio-${{ inputs.package }}/
+        if [ "${{ inputs.package }}" != "simulation" ]; then
+          cd pycode/memilio-${{ inputs.package }}/
+        # else stay in root directory
+        fi
         /opt/python/cp38-cp38/bin/python -m pip install --upgrade pip setuptools wheel
         /opt/python/cp38-cp38/bin/python -m pip install scikit-build scikit-build-core
         # /opt/python/cp38-cp38/bin/python -m pip install setuptools-scm
@@ -46,12 +45,11 @@ runs:
           # no auditwheel necessary for pure python packages, so only copy the wheels to the same output directory 
           cp dist/*.whl wheelhouse
         fi
-        # if [ "${{ inputs.package }}" != "simulation" ]; then
-        #   cp -r wheelhouse ..
-        # else
-        #   cp -r wheelhouse pycode
-        # fi 
-        cp -r wheelhouse ..
+        if [ "${{ inputs.package }}" != "simulation" ]; then
+          cp -r wheelhouse ..
+        else
+          cp -r wheelhouse pycode
+        fi 
     - name: Upload Python Wheels
       uses: actions/upload-artifact@v4
       with:

From a91d67c5e4c6cafd636e80c37201829c86a46b99 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 11:03:05 +0200
Subject: [PATCH 64/74] install setuptools again

---
 .github/actions/build-py/action.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index a29f35eaab..7d0b9ccf0e 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -31,11 +31,11 @@ runs:
         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 pip install setuptools-scm
+        /opt/python/cp38-cp38/bin/python -m pip install setuptools-scm
         /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/cp312-cp312/bin/python -m pip install scikit-build scikit-build-core
-        # /opt/python/cp312-cp312/bin/python -m pip install setuptools-scm
+        /opt/python/cp312-cp312/bin/python -m pip install setuptools-scm
         /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 

From cf930279ff8024f523558c2dfd4b7c38c2b5aa91 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 11:08:28 +0200
Subject: [PATCH 65/74] install setuptools only for memilio-simulation

---
 .github/actions/build-py/action.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 7d0b9ccf0e..9a4a66ab1d 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -30,13 +30,16 @@ runs:
         # 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 pip install setuptools-scm
+        /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/cp312-cp312/bin/python -m pip install scikit-build scikit-build-core
-        /opt/python/cp312-cp312/bin/python -m pip install setuptools-scm
         /opt/python/cp312-cp312/bin/python -m build --no-isolation --wheel
+        # Install setuptools-scm only for memilio-simulation
+        if [ "${{ inputs.package }}" == "simulation" ]; then
+          /opt/python/cp38-cp38/bin/python -m pip install setuptools-scm
+          /opt/python/cp312-cp312/bin/python -m pip install setuptools-scm
+        fi
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From 7dd3357bd61fa35599f9dc245178d601cdd642a3 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 11:17:35 +0200
Subject: [PATCH 66/74] forgot if statement

---
 .github/actions/build-py/action.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 9a4a66ab1d..f9b9dc6bc2 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -16,11 +16,10 @@ 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-${{ inputs.package }}/
+        if [ "${{ inputs.package }}" != "simulation" ]; then
+          cd pycode/memilio-${{ inputs.package }}/
+        # else stay in root directory
+        fi
         mkdir wheelhouse
     - name: Build Python Wheels
       shell: bash

From 27bb822b69268109154cc29f473081497f52f563 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 13 Apr 2026 11:29:12 +0200
Subject: [PATCH 67/74] fix order

---
 .github/actions/build-py/action.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index f9b9dc6bc2..cec6a7b367 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -29,16 +29,16 @@ runs:
         # 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
-        /opt/python/cp312-cp312/bin/python -m build --no-isolation --wheel
         # 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 
           # includes native dependencies in the wheel

From 37b02339d531c3ea15efe0ecee7c48b212d073e5 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 14 Apr 2026 15:34:58 +0200
Subject: [PATCH 68/74] review suggestions, test changes on test pypi

---
 pyproject.toml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 94eb44e596..d423b845f2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,6 +17,15 @@ dependencies = [
   # 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 :: 3.12",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows"
+]
 
 [project.optional-dependencies]
 dev = []

From 27e4ba77398d40ce8483b007b70d1c38820ec864 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 14 Apr 2026 15:41:39 +0200
Subject: [PATCH 69/74] update workflow according to review

---
 .github/workflows/pypi.yml | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index 528a3c8dc4..47b45d9ce4 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -1,8 +1,11 @@
 name: PyPI
 
-on: [release]
+# on:  
+#   release:  
+#     types:  
+#       - published
 # remove following line before merge: 
-# on: [pull_request, release]
+on: [pull_request, release]
 
 jobs:
 
@@ -13,13 +16,13 @@ jobs:
         os: [ubuntu-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - uses: pypa/cibuildwheel@v2.16
+      - uses: pypa/cibuildwheel@v3.4.1
 
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v4
         with:
           name: cibw-wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
@@ -28,13 +31,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v4
       with:
-          fetch-depth: 0
+        fetch-depth: 0
 
     - run: pipx run build --sdist
 
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v4
       with:
         name: cibw-sdist
         path: dist/*.tar.gz
@@ -47,7 +50,7 @@ jobs:
       id-token: write
       
     steps:
-      - uses: actions/download-artifact@v8
+      - uses: actions/download-artifact@v4
         with:
           # unpacks all CIBW artifacts into dist/
           pattern: cibw-*
@@ -58,4 +61,4 @@ jobs:
         with:
           skip-existing: true
           # To test uploads to TestPyPI, uncomment the following:
-          # repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
+          repository-url: https://test.pypi.org/legacy/
\ No newline at end of file

From 9ab4c4fe45e11f6e7f7546ef73ab2df7533ea4a7 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 15 Apr 2026 11:59:44 +0200
Subject: [PATCH 70/74] update classifiers and readthedocs

---
 docs/source/getting_started.rst | 19 ++++++++++++++-----
 pyproject.toml                  |  4 ++++
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index cd5a521f7e..9b0a0c71b1 100644
--- 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/pyproject.toml b/pyproject.toml
index d423b845f2..64d74ae75d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,11 @@ classifiers = [
     "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"
 ]

From 414b679daf98ab05c49b9b80555d8fd1b3308d5b Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Tue, 21 Apr 2026 08:10:39 +0200
Subject: [PATCH 71/74] extend documentation

---
 docs/source/getting_started.rst     | 45 ++++++++++++++++++++++-------
 docs/source/python/m-simulation.rst | 44 ++++++++++++++++++++++++++--
 pycode/memilio-simulation/README.md | 27 ++++++++++++++---
 3 files changed, 100 insertions(+), 16 deletions(-)

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index 9b0a0c71b1..99adc61b7c 100644
--- a/docs/source/getting_started.rst
+++ b/docs/source/getting_started.rst
@@ -131,13 +131,42 @@ 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:
+Installing ``memilio-simulation``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. code-block:: 
+The simulation package ``memilio-simulation`` provides two installation options depending on your use case:
+
+**Option A.1: Install from PyPI (Recommended - no C++ compiler required)**
+
+If you just want to run simulations with the latest released version, install the pre-built wheel directly from PyPI:
+
+.. code-block:: console
 
    pip install memilio-simulation
 
-For the other packages, you can proceed as follows. 
+This requires no C++ compiler or CMake. Pre-built wheels are provided for Linux and Windows on Python 3.8 to 3.13.
+
+.. note::
+   macOS is currently not supported with pre-built wheels. macOS users can install from source (see Option A.2 below).
+
+**Option A.2: Install from source (for the latest development version or macOS)**
+
+If you need the latest (unreleased) code, want to contribute to the package, or are on macOS, you need to build from source.
+This requires a **C++20 compiler** (e.g. GCC or Clang), **CMake** (>= 3.18), and **Ninja**.
+
+.. code-block:: console
+
+   pip install -e .[dev]
+
+This command must be run from the **root of the MEmilio repository** (the directory containing the top-level ``pyproject.toml``).
+This is necessary because the C++ build requires access to the ``cpp/`` directory.
+Note that this only installs ``memilio-simulation`` and not any other Python packages. The root-level ``pyproject.toml`` belongs exclusively to ``memilio-simulation``.
+
+.. warning::
+   C++ code changes always require re-running ``pip install -e .[dev]`` to recompile.
+
+Installing other Python packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 1.  Navigate to the directory containing our Python code:
 
@@ -145,14 +174,14 @@ For the other packages, you can proceed as follows.
 
        cd pycode
 
-2.  To install the simulation package ``memilio-epidata``, from here you can do:
+2.  To install the ``memilio-epidata`` package for data downloading and handling:
 
     .. code-block:: console
 
        cd memilio-epidata
        pip install -e .
 
-3.  For afterwards installing the ``memilio-surrogatemodel`` package for data downloading and handling, run:
+3.  To install the ``memilio-surrogatemodel`` package for surrogate models:
 
     .. code-block:: console
 
@@ -163,16 +192,12 @@ For the other packages, you can proceed as follows.
 .. tip:: For Contributors: Installing development packages
 
    The ``-e`` flag installs the package in a mode, which links the installation to your local source code folder.
-
-   If you plan to contribute to MEmilio, you can also install all the necessary development dependencies by adding ``[dev]`` to the command:
+   If you plan to contribute to any package, install all development dependencies by adding ``[dev]``:
 
    .. code-block:: console
 
       pip install -e .[dev]
 
-   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.
 
 Option B: Building the C++ core (Advanced)
diff --git a/docs/source/python/m-simulation.rst b/docs/source/python/m-simulation.rst
index fc1d97abe2..b4343b3a14 100644
--- a/docs/source/python/m-simulation.rst
+++ b/docs/source/python/m-simulation.rst
@@ -5,12 +5,52 @@ MEmilio Simulation is a Python interface to the MEmilio C++ library. Using pytho
 
 The package is contained inside the folder `pycode/memilio-simulation <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-simulation>`_.
 
+Installation
+------------
+
+The ``memilio-simulation`` package can be installed in two ways depending on your use case.
+
+**Option 1: Install from PyPI (Recommended - no C++ compiler required)**
+
+Pre-built wheels are provided for Linux and Windows on Python 3.8 to 3.13.
+
+.. code-block:: console
+
+   pip install memilio-simulation
+
+This is the easiest way to get started. No C++ compiler or CMake is needed.
+
+.. note::
+   macOS is currently not supported with pre-built wheels. macOS users must install from source (see Option 2).
+
+**Option 2: Install from source (latest development version, macOS, or contributing)**
+
+If you need the latest unreleased code, want to modify the bindings, or are on macOS, build from source.
+
+Requirements:
+
+* A **C++20 compiler**
+* **CMake** >= 3.18
+* **Ninja** build tool
+* All :doc:`C++ library dependencies <../getting_started>`
+
+Install from the **root of the MEmilio repository** (the directory containing the top-level ``pyproject.toml``):
+
+.. code-block:: console
+
+   pip install -e .[dev]
+
+This is necessary because the C++ build requires access to the ``cpp/`` directory.
+Note that this only installs ``memilio-simulation`` and not any other Python packages.The ``-e`` flag links the installation to your local source code so Python changes are reflected immediately.
+C++ changes require re-running this command to recompile.
+
 Dependencies
 ------------
 
-Required Python packages:
+Required Python packages (installed automatically):
 
-* scikit-build
+* numpy >= 1.22 (not 1.25.*)
+* pandas >= 2.0.0
 
 For a successful build, the development libraries for Python need to be installed, i.e. python3.x-dev. 
 Additionally, as this package builds upon the MEmilio C++ library, 
diff --git a/pycode/memilio-simulation/README.md b/pycode/memilio-simulation/README.md
index 8f23dc82a0..05a6955251 100644
--- a/pycode/memilio-simulation/README.md
+++ b/pycode/memilio-simulation/README.md
@@ -4,17 +4,36 @@ This package contains Python bindings for the MEmilio C++ library. It enables se
 
 ## Installation
 
-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.
+### Option 1: Install from PyPI (Recommended)
 
-To install the package, use the command
+Pre-built wheels are provided for Linux and Windows on Python 3.8 to 3.13.
 
 ```bash
 pip install memilio-simulation
 ```
 
-This builds the C++ library and C++ Python extension module and copies everything required to your site-packages.
+**Note:** macOS is currently not supported with pre-built wheels. macOS users must install from source (see Option 2).
 
-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. 
+### Option 2: Install from source (latest code, macOS, or development)
+
+Use this option if you need the latest unreleased code, want to modify the C++ bindings, or use macOS.
+
+This project is configured via `pyproject.toml`. The following tools must be available on the system:
+
+- A **C++20 compiler**
+- **CMake** >= 3.18
+- **Ninja**
+- All [C++ library dependencies](../../cpp/README.md)
+
+A virtual environment is recommended. Install from the **root of the MEmilio repository** (the directory containing the top-level `pyproject.toml`):
+
+```bash
+pip install -e .[dev]
+```
+
+This is necessary because the C++ build requires access to the `cpp/` directory. Note that this only installs `memilio-simulation` and not any other Python packages.
+
+**Note:** The `-e` flag links the installation to your local source code. Python changes take effect immediately, but C++ changes require re-running this command to recompile.
 
 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:
 

From 1b652a1233c2d5bb6e3de34a6f460ec6a3d8e3ba Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 21 Apr 2026 09:08:57 +0200
Subject: [PATCH 72/74] docu and dont build wheels for python 3.14

---
 docs/source/getting_started.rst     | 7 ++-----
 docs/source/python/m-simulation.rst | 7 ++-----
 pycode/memilio-simulation/README.md | 6 ++----
 pyproject.toml                      | 4 +++-
 4 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index 99adc61b7c..f042e3ee8d 100644
--- a/docs/source/getting_started.rst
+++ b/docs/source/getting_started.rst
@@ -146,12 +146,9 @@ If you just want to run simulations with the latest released version, install th
 
 This requires no C++ compiler or CMake. Pre-built wheels are provided for Linux and Windows on Python 3.8 to 3.13.
 
-.. note::
-   macOS is currently not supported with pre-built wheels. macOS users can install from source (see Option A.2 below).
-
-**Option A.2: Install from source (for the latest development version or macOS)**
+**Option A.2: Install from source (for the latest development version)**
 
-If you need the latest (unreleased) code, want to contribute to the package, or are on macOS, you need to build from source.
+If you need the latest (unreleased) code, or want to contribute to the package, you need to build from source.
 This requires a **C++20 compiler** (e.g. GCC or Clang), **CMake** (>= 3.18), and **Ninja**.
 
 .. code-block:: console
diff --git a/docs/source/python/m-simulation.rst b/docs/source/python/m-simulation.rst
index b4343b3a14..f47a6e0045 100644
--- a/docs/source/python/m-simulation.rst
+++ b/docs/source/python/m-simulation.rst
@@ -20,12 +20,9 @@ Pre-built wheels are provided for Linux and Windows on Python 3.8 to 3.13.
 
 This is the easiest way to get started. No C++ compiler or CMake is needed.
 
-.. note::
-   macOS is currently not supported with pre-built wheels. macOS users must install from source (see Option 2).
+**Option 2: Install from source (latest development version, or contributing)**
 
-**Option 2: Install from source (latest development version, macOS, or contributing)**
-
-If you need the latest unreleased code, want to modify the bindings, or are on macOS, build from source.
+If you need the latest unreleased code, or want to modify the bindings, build from source.
 
 Requirements:
 
diff --git a/pycode/memilio-simulation/README.md b/pycode/memilio-simulation/README.md
index 05a6955251..d521a36e04 100644
--- a/pycode/memilio-simulation/README.md
+++ b/pycode/memilio-simulation/README.md
@@ -12,11 +12,9 @@ Pre-built wheels are provided for Linux and Windows on Python 3.8 to 3.13.
 pip install memilio-simulation
 ```
 
-**Note:** macOS is currently not supported with pre-built wheels. macOS users must install from source (see Option 2).
+### Option 2: Install from source (latest code or development)
 
-### Option 2: Install from source (latest code, macOS, or development)
-
-Use this option if you need the latest unreleased code, want to modify the C++ bindings, or use macOS.
+Use this option if you need the latest unreleased code, or want to modify the C++ bindings.
 
 This project is configured via `pyproject.toml`. The following tools must be available on the system:
 
diff --git a/pyproject.toml b/pyproject.toml
index 64d74ae75d..070131e437 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,4 +1,6 @@
 [project]
+# Note that this file is only installing the memilio-simulation package. For installing the other Python packages, 
+# please go to the respective folder pycode/memilio-* and install from there. 
 name = "memilio-simulation"
 dynamic = ["version"] 
 # remove following line before merge: 
@@ -60,7 +62,7 @@ local_scheme = "no-local-version"
 
 [tool.cibuildwheel]
 # Disable some wheels
-skip = ["pp*", "*musllinux*", "*-win32"] 
+skip = ["pp*", "*musllinux*", "*-win32", "cp314*"] 
 
 [tool.autopep8]
 max-line-length = 79

From 70ba18b54893e0e6da6df66ad02b0d1f65574a09 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 21 Apr 2026 11:18:02 +0200
Subject: [PATCH 73/74] upload to pypi as version 2.3.0

---
 .github/workflows/pypi.yml | 2 +-
 pyproject.toml             | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index 47b45d9ce4..c04e992fae 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -61,4 +61,4 @@ jobs:
         with:
           skip-existing: true
           # To test uploads to TestPyPI, uncomment the following:
-          repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
+          # repository-url: https://test.pypi.org/legacy/
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 070131e437..0a70437463 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,9 +2,9 @@
 # Note that this file is only installing the memilio-simulation package. For installing the other Python packages, 
 # please go to the respective folder pycode/memilio-* and install from there. 
 name = "memilio-simulation"
-dynamic = ["version"] 
+# dynamic = ["version"] 
 # remove following line before merge: 
-# version = "2.3.0"
+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"

From eaf9b945d3acb1185d5226509cf6e7e0787cfe3e Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Tue, 21 Apr 2026 13:27:54 +0200
Subject: [PATCH 74/74] prepare for merge

---
 .github/workflows/pypi.yml | 10 ++++------
 pyproject.toml             |  4 +---
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index c04e992fae..57a2a3a782 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -1,11 +1,9 @@
 name: PyPI
 
-# on:  
-#   release:  
-#     types:  
-#       - published
-# remove following line before merge: 
-on: [pull_request, release]
+on:  
+  release:  
+    types:  
+      - published
 
 jobs:
 
diff --git a/pyproject.toml b/pyproject.toml
index 0a70437463..15fa1202dd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,9 +2,7 @@
 # Note that this file is only installing the memilio-simulation package. For installing the other Python packages, 
 # please go to the respective folder pycode/memilio-* and install from there. 
 name = "memilio-simulation"
-# dynamic = ["version"] 
-# remove following line before merge: 
-version = "2.3.0"
+dynamic = ["version"] 
 description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"