From 259ad057458e18d1d0758bd9ab9b734ddd219e43 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 12:18:08 +0200
Subject: [PATCH 01/17]  fix build

---
 .github/actions/build-py/action.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 941eded182..fa21926c48 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -19,8 +19,8 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}/
-        /opt/python/cp38-cp38/bin/python setup.py bdist_wheel
-        /opt/python/cp311-cp311/bin/python setup.py bdist_wheel
+        /opt/python/cp38-cp38/bin/python -m build
+        /opt/python/cp311-cp311/bin/python -m build
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel
@@ -35,4 +35,3 @@ runs:
       with:
         name: python-wheels-${{ inputs.package }}
         path: pycode/wheelhouse
-

From 24b3b6a26a20f895d5b02aca574f5ee73cd90075 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 12:28:43 +0200
Subject: [PATCH 02/17] try fix missing pip

---
 .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 fa21926c48..688c306542 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -19,8 +19,8 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}/
-        /opt/python/cp38-cp38/bin/python -m build
-        /opt/python/cp311-cp311/bin/python -m build
+        /opt/python/cp38-cp38/bin/python -m build --no-isolation
+        /opt/python/cp311-cp311/bin/python -m build --no-isolation
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From 3f63ac1d9407d3d3a74c773de80199eeb588b722 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 12:30:37 +0200
Subject: [PATCH 03/17] [tmp] disable non py-build actions

---
 .github/workflows/main.yml | 490 ++++++++++++++++++-------------------
 1 file changed, 245 insertions(+), 245 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9b0c6505ea..6c02ac9616 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -22,240 +22,240 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
-      - uses: pre-commit/action@v3.0.1
+  # pre-commit:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: 3.11
+  #     - 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
@@ -328,28 +328,28 @@ jobs:
           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

From 2011b0554b153d8c8f8975b1b8df041a87c7a367 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 13:35:25 +0200
Subject: [PATCH 04/17] try  ensurepip

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

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index 688c306542..c926d83c4b 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -19,8 +19,10 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}/
-        /opt/python/cp38-cp38/bin/python -m build --no-isolation
-        /opt/python/cp311-cp311/bin/python -m build --no-isolation
+        /opt/python/cp38-cp38/bin/python -m ensurepip --upgrade
+        /opt/python/cp38-cp38/bin/python -m build
+        /opt/python/cp311-cp311/bin/python -m ensurepip --upgrade
+        /opt/python/cp311-cp311/bin/python -m build
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From aa5784f1b8dcf571384087e79c3fa7e177645ac7 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 13:59:46 +0200
Subject: [PATCH 05/17] more args

---
 .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 c926d83c4b..5cc8343d63 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -20,9 +20,9 @@ runs:
       run: |
         cd pycode/memilio-${{ inputs.package }}/
         /opt/python/cp38-cp38/bin/python -m ensurepip --upgrade
-        /opt/python/cp38-cp38/bin/python -m build
+        /opt/python/cp38-cp38/bin/python -m build --no-isolation --installer pip
         /opt/python/cp311-cp311/bin/python -m ensurepip --upgrade
-        /opt/python/cp311-cp311/bin/python -m build
+        /opt/python/cp311-cp311/bin/python -m build --no-isolation --installer pip
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From bfbe5292f436260b84105aae42c40ef92baee27c Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:03:07 +0200
Subject: [PATCH 06/17] args

---
 .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 5cc8343d63..dfc2effc92 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -20,9 +20,9 @@ runs:
       run: |
         cd pycode/memilio-${{ inputs.package }}/
         /opt/python/cp38-cp38/bin/python -m ensurepip --upgrade
-        /opt/python/cp38-cp38/bin/python -m build --no-isolation --installer pip
+        /opt/python/cp38-cp38/bin/python -m build --installer pip
         /opt/python/cp311-cp311/bin/python -m ensurepip --upgrade
-        /opt/python/cp311-cp311/bin/python -m build --no-isolation --installer pip
+        /opt/python/cp311-cp311/bin/python -m build --installer pip
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From 386c0fca65d1ff439dc29253a29b5d2b2f7da32b Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:06:26 +0200
Subject: [PATCH 07/17] install scikit-build manually

---
 .github/actions/build-py/action.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index dfc2effc92..b9b93c70d9 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -19,10 +19,10 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}/
-        /opt/python/cp38-cp38/bin/python -m ensurepip --upgrade
-        /opt/python/cp38-cp38/bin/python -m build --installer pip
-        /opt/python/cp311-cp311/bin/python -m ensurepip --upgrade
-        /opt/python/cp311-cp311/bin/python -m build --installer pip
+        /opt/python/cp38-cp38/bin/python -m pip install scikit-build
+        /opt/python/cp38-cp38/bin/python -m build
+        /opt/python/cp311-cp311/bin/python -m pip install scikit-build
+        /opt/python/cp311-cp311/bin/python -m build
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From fc1f386643de9c709814c266c0bfe2d5b870ef9d Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:09:44 +0200
Subject: [PATCH 08/17] set installer

---
 .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 b9b93c70d9..981771aa17 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -19,10 +19,10 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}/
-        /opt/python/cp38-cp38/bin/python -m pip install scikit-build
-        /opt/python/cp38-cp38/bin/python -m build
+        /opt/python/cp38-cp311/bin/python -m pip install scikit-build
+        /opt/python/cp38-cp38/bin/python -m build --installer pip
         /opt/python/cp311-cp311/bin/python -m pip install scikit-build
-        /opt/python/cp311-cp311/bin/python -m build
+        /opt/python/cp311-cp311/bin/python -m build --installer pip
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From 3e56f5b0d2f16fb25e3f72e2adf3e96db76e2346 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:14:35 +0200
Subject: [PATCH 09/17] fix path

---
 .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 981771aa17..f2dc707410 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -19,7 +19,7 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}/
-        /opt/python/cp38-cp311/bin/python -m pip install scikit-build
+        /opt/python/cp38-cp38/bin/python -m pip install scikit-build
         /opt/python/cp38-cp38/bin/python -m build --installer pip
         /opt/python/cp311-cp311/bin/python -m pip install scikit-build
         /opt/python/cp311-cp311/bin/python -m build --installer pip

From e51ed5468856d36f34af56ce118fa6518cc8f7d0 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:19:52 +0200
Subject: [PATCH 10/17] no isolation

---
 .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 f2dc707410..467cae043f 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -20,9 +20,9 @@ runs:
       run: |
         cd pycode/memilio-${{ inputs.package }}/
         /opt/python/cp38-cp38/bin/python -m pip install scikit-build
-        /opt/python/cp38-cp38/bin/python -m build --installer pip
+        /opt/python/cp38-cp38/bin/python -m build --no-isolation
         /opt/python/cp311-cp311/bin/python -m pip install scikit-build
-        /opt/python/cp311-cp311/bin/python -m build --installer pip
+        /opt/python/cp311-cp311/bin/python -m build --no-isolation
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From 99854ed3fbbd3e2135e6108eddb0f6f41c13968b Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:34:44 +0200
Subject: [PATCH 11/17] cmake

---
 .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 467cae043f..c4362b7622 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -9,7 +9,7 @@ runs:
   steps:    
     - name: Install dependencies
       shell: bash
-      run: yum install ninja-build -qy
+      run: yum install ninja-build cmake -qy
     - name: Make artifact dir
       shell: bash
       run: |

From de23868a1c6da39275ed1b413e65701d607e1ac4 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:40:27 +0200
Subject: [PATCH 12/17] remove cmake dependency listing

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

diff --git a/pycode/memilio-generation/setup.py b/pycode/memilio-generation/setup.py
index 9237035c47..4166b570a3 100644
--- a/pycode/memilio-generation/setup.py
+++ b/pycode/memilio-generation/setup.py
@@ -25,7 +25,7 @@
     description='Part of MEmilio project, automatic generation of model specific python bindings.',
     packages=find_packages(
         where=os.path.dirname(os.path.abspath(__file__))),
-    setup_requires=['cmake'],
+    # setup_requires=['cmake'],
     install_requires=['libclang==18.1.1',
                       'dataclasses', 'dataclasses_json', 'graphviz', 'importlib-resources>=1.1.0; python_version < \'3.9\''],
     extras_require={'dev': []},
diff --git a/pycode/memilio-simulation/setup.py b/pycode/memilio-simulation/setup.py
index b4038394bf..aff8998991 100644
--- a/pycode/memilio-simulation/setup.py
+++ b/pycode/memilio-simulation/setup.py
@@ -21,7 +21,7 @@
     url='https://github.com/SciCompMod/memilio',
     description='Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations.',
     packages=find_packages(where=os.path.dirname(os.path.abspath(__file__))),
-    setup_requires=['cmake'],
+    # setup_requires=['cmake'],
     # need shared libs so there is one shared log level
     cmake_args=['-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON'],
     install_requires=[

From c9d3d78368892fa31b9e616c132063e6125e6127 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:42:22 +0200
Subject: [PATCH 13/17] git?

---
 .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 c4362b7622..f40e88a6ff 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -9,7 +9,7 @@ runs:
   steps:    
     - name: Install dependencies
       shell: bash
-      run: yum install ninja-build cmake -qy
+      run: yum install ninja-build cmake git -qy
     - name: Make artifact dir
       shell: bash
       run: |

From f03d720d38b571fca83615ef376053a7d4573751 Mon Sep 17 00:00:00 2001
From: reneSchm <49305466+reneSchm@users.noreply.github.com>
Date: Tue, 26 Aug 2025 14:47:44 +0200
Subject: [PATCH 14/17] dubious ownership

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

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index f40e88a6ff..6291d00e51 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -18,6 +18,7 @@ runs:
     - name: Build Python Wheels
       shell: bash
       run: |
+        git config --global --add safe.directory $(pwd) # fix to "fatal: detected dubious ownership in repository" 
         cd pycode/memilio-${{ inputs.package }}/
         /opt/python/cp38-cp38/bin/python -m pip install scikit-build
         /opt/python/cp38-cp38/bin/python -m build --no-isolation

From 227ed8c1309d8451aceed8ddbcda2487fbb61105 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 27 Aug 2025 15:00:37 +0200
Subject: [PATCH 15/17] build no SD

---
 .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 6291d00e51..a27a381761 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -21,9 +21,9 @@ runs:
         git config --global --add safe.directory $(pwd) # fix to "fatal: detected dubious ownership in repository" 
         cd pycode/memilio-${{ inputs.package }}/
         /opt/python/cp38-cp38/bin/python -m pip install scikit-build
-        /opt/python/cp38-cp38/bin/python -m build --no-isolation
+        /opt/python/cp38-cp38/bin/python -m build --no-isolation --wheel
         /opt/python/cp311-cp311/bin/python -m pip install scikit-build
-        /opt/python/cp311-cp311/bin/python -m build --no-isolation
+        /opt/python/cp311-cp311/bin/python -m build --no-isolation --wheel
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

From a6a35c59a6bb1d171ff6627e5a58d71339e465c3 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 27 Aug 2025 15:13:50 +0200
Subject: [PATCH 16/17] revert changes

---
 .github/actions/build-py/action.yml |   3 +-
 .github/workflows/main.yml          | 490 ++++++++++++++--------------
 pycode/memilio-generation/setup.py  |   2 +-
 pycode/memilio-simulation/setup.py  |   2 +-
 4 files changed, 248 insertions(+), 249 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index a27a381761..e0a24b22bd 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -9,7 +9,7 @@ runs:
   steps:    
     - name: Install dependencies
       shell: bash
-      run: yum install ninja-build cmake git -qy
+      run: yum install ninja-build -qy
     - name: Make artifact dir
       shell: bash
       run: |
@@ -18,7 +18,6 @@ runs:
     - name: Build Python Wheels
       shell: bash
       run: |
-        git config --global --add safe.directory $(pwd) # fix to "fatal: detected dubious ownership in repository" 
         cd pycode/memilio-${{ inputs.package }}/
         /opt/python/cp38-cp38/bin/python -m pip install scikit-build
         /opt/python/cp38-cp38/bin/python -m build --no-isolation --wheel
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6c02ac9616..9b0c6505ea 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -22,240 +22,240 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  # pre-commit:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - uses: actions/setup-python@v5
-  #       with:
-  #         python-version: 3.11
-  #     - uses: pre-commit/action@v3.0.1
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - 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
@@ -328,28 +328,28 @@ jobs:
           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/pycode/memilio-generation/setup.py b/pycode/memilio-generation/setup.py
index 4166b570a3..9237035c47 100644
--- a/pycode/memilio-generation/setup.py
+++ b/pycode/memilio-generation/setup.py
@@ -25,7 +25,7 @@
     description='Part of MEmilio project, automatic generation of model specific python bindings.',
     packages=find_packages(
         where=os.path.dirname(os.path.abspath(__file__))),
-    # setup_requires=['cmake'],
+    setup_requires=['cmake'],
     install_requires=['libclang==18.1.1',
                       'dataclasses', 'dataclasses_json', 'graphviz', 'importlib-resources>=1.1.0; python_version < \'3.9\''],
     extras_require={'dev': []},
diff --git a/pycode/memilio-simulation/setup.py b/pycode/memilio-simulation/setup.py
index aff8998991..b4038394bf 100644
--- a/pycode/memilio-simulation/setup.py
+++ b/pycode/memilio-simulation/setup.py
@@ -21,7 +21,7 @@
     url='https://github.com/SciCompMod/memilio',
     description='Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations.',
     packages=find_packages(where=os.path.dirname(os.path.abspath(__file__))),
-    # setup_requires=['cmake'],
+    setup_requires=['cmake'],
     # need shared libs so there is one shared log level
     cmake_args=['-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON'],
     install_requires=[

From 341c4424b9b0d2988ab57df917b037385be59352 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 27 Aug 2025 15:17:21 +0200
Subject: [PATCH 17/17] cmake

---
 .github/actions/build-py/action.yml | 2 +-
 pycode/memilio-generation/setup.py  | 1 -
 pycode/memilio-simulation/setup.py  | 1 -
 3 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/actions/build-py/action.yml b/.github/actions/build-py/action.yml
index e0a24b22bd..2cb89fa75d 100644
--- a/.github/actions/build-py/action.yml
+++ b/.github/actions/build-py/action.yml
@@ -9,7 +9,7 @@ runs:
   steps:    
     - name: Install dependencies
       shell: bash
-      run: yum install ninja-build -qy
+      run: yum install ninja-build cmake git -qy
     - name: Make artifact dir
       shell: bash
       run: |
diff --git a/pycode/memilio-generation/setup.py b/pycode/memilio-generation/setup.py
index 9237035c47..2d3370d80e 100644
--- a/pycode/memilio-generation/setup.py
+++ b/pycode/memilio-generation/setup.py
@@ -25,7 +25,6 @@
     description='Part of MEmilio project, automatic generation of model specific python bindings.',
     packages=find_packages(
         where=os.path.dirname(os.path.abspath(__file__))),
-    setup_requires=['cmake'],
     install_requires=['libclang==18.1.1',
                       'dataclasses', 'dataclasses_json', 'graphviz', 'importlib-resources>=1.1.0; python_version < \'3.9\''],
     extras_require={'dev': []},
diff --git a/pycode/memilio-simulation/setup.py b/pycode/memilio-simulation/setup.py
index b4038394bf..037a93df8e 100644
--- a/pycode/memilio-simulation/setup.py
+++ b/pycode/memilio-simulation/setup.py
@@ -21,7 +21,6 @@
     url='https://github.com/SciCompMod/memilio',
     description='Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations.',
     packages=find_packages(where=os.path.dirname(os.path.abspath(__file__))),
-    setup_requires=['cmake'],
     # need shared libs so there is one shared log level
     cmake_args=['-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON'],
     install_requires=[