From 0e739363165aaf87cc6119ba02825b8a68eafde5 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 4 Mar 2026 10:31:35 +0100
Subject: [PATCH 1/2] add MEMILIO_USE_HDF5 option. New CI runs

---
 .github/actions/linux-build/action.yml | 15 ++++++++++-----
 .github/actions/linux-test/action.yml  | 16 ++++++++++++----
 .github/workflows/main.yml             | 23 +++++++++++++++++++++++
 cpp/README.md                          |  1 +
 cpp/thirdparty/CMakeLists.txt          | 14 +++++++++-----
 docs/source/cpp/installation.rst       |  2 ++
 6 files changed, 57 insertions(+), 14 deletions(-)

diff --git a/.github/actions/linux-build/action.yml b/.github/actions/linux-build/action.yml
index 027647f126..603587b53b 100644
--- a/.github/actions/linux-build/action.yml
+++ b/.github/actions/linux-build/action.yml
@@ -31,6 +31,10 @@ inputs:
     description: "Enable Multithreading with OpenMP (ON or OFF, default OFF). If ON, adds `-omp` to the name of the artifact."
     required: false
     default: "OFF"
+  hdf5:
+    description: "Build with HDF5 (ON or OFF, default ON). If OFF, adds `-nohdf5` to the artifact name. If no optional dependencies are built, HDF5 is also not built, even if this option is set to ON."
+    required: false
+    default: "ON"
 runs:
   using: "composite"
   steps:
@@ -38,10 +42,11 @@ runs:
       shell: bash
       run: |
         sudo apt-get -qq update
-        sudo apt-get -qq -y install lcov ccache
-        if [[ "${{ inputs.optional-dependencies }}" == "ON" ]]; then
-          sudo apt-get -qq -y install libhdf5-dev 
+        HDF5_PACKAGES=""
+        if [[ "${{ inputs.optional-dependencies }}" == "ON" && "${{ inputs.hdf5 }}" == "ON" ]]; then
+          HDF5_PACKAGES="libhdf5-dev"
         fi
+        sudo apt-get -qq -y install lcov ccache $HDF5_PACKAGES
         if [[ "${{ inputs.compiler }}" == "gcc" ]]; then
           if [[ "${{ inputs.version }}" == "min" ]]; then
             sudo apt-get -qq -y install gcc-11
@@ -97,7 +102,7 @@ runs:
           exit 1
         fi
         mkdir -p build && cd build
-        cmake -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_ENABLE_IPOPT=ON -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitizers }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitizers }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DMEMILIO_ENABLE_OPENMP=${{ inputs.openmp }} ..
+        cmake -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_ENABLE_IPOPT=ON -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitizers }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitizers }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DMEMILIO_ENABLE_OPENMP=${{ inputs.openmp }} -DMEMILIO_USE_HDF5=${{ inputs.hdf5 }} ..
         make -j4
     - name: create build dir archive
       shell: bash
@@ -108,6 +113,6 @@ runs:
       uses: actions/upload-artifact@v4
       with:
         #artifacts in one pipeline must have a different name, so options must add a suffix to the artifact name if different values are used in the same pipeline
-        name: build-cpp-linux-${{ inputs.compiler }}-${{ inputs.version }}-${{ inputs.config }}${{ inputs.optional-dependencies == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}
+        name: build-cpp-linux-${{ inputs.compiler }}-${{ inputs.version }}-${{ inputs.config }}${{ inputs.optional-dependencies == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}${{ inputs.hdf5 == 'OFF' && '-nohdf5' || ''}}
         path: cpp/build.tar.gz
         retention-days: 1
diff --git a/.github/actions/linux-test/action.yml b/.github/actions/linux-test/action.yml
index 2ae4d5c860..dcfdac3d49 100644
--- a/.github/actions/linux-test/action.yml
+++ b/.github/actions/linux-test/action.yml
@@ -20,6 +20,10 @@ inputs:
     description: "Enabled Multithreading with OpenMP (ON or OFF, default OFF). If ON, adds `-omp` to the name of the artifact."
     required: false
     default: "OFF"
+  hdf5:
+    description: "Build with HDF5 (ON or OFF, default ON). If OFF, adds `-nohdf5` to the artifact name. If no optional dependencies are built, HDF5 is also not built, even if this option is set to ON."
+    required: false
+    default: "ON"
 runs:
   using: "composite"
   steps:
@@ -27,12 +31,16 @@ runs:
       shell: bash
       run: |
         sudo apt-get -qq update
-        sudo apt-get -qq -y install libhdf5-10* wget gnupg lcov
+        HDF5_PACKAGES=""
+        if [[ "${{ inputs.optional-deps }}" == "ON" && "${{ inputs.hdf5 }}" == "ON" ]]; then
+          HDF5_PACKAGES="libhdf5-10*"
+        fi
+        sudo apt-get -qq -y install wget gnupg lcov $HDF5_PACKAGES
         sudo apt-get -qq update
     - name: Download built test directory
       uses: actions/download-artifact@v4
       with:
-        name: build-cpp-linux-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}
+        name: build-cpp-linux-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}${{ inputs.hdf5 == 'OFF' && '-nohdf5' || ''}}
         path: cpp
     - name: extract build archive
       shell: bash
@@ -58,14 +66,14 @@ runs:
     - name: Upload test report
       uses: actions/upload-artifact@v4
       with:
-        name: test-cpp-linux-report-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}
+        name: test-cpp-linux-report-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}${{ inputs.hdf5 == 'OFF' && '-nohdf5' || ''}}
         path: cpp/build/bin/report.xml
         if-no-files-found: error
         retention-days: 1
     - name: Upload coverage reports
       uses: actions/upload-artifact@v4
       with:
-        name: test-cpp-coverage-reports-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}
+        name: test-cpp-coverage-reports-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}${{ inputs.hdf5 == 'OFF' && '-nohdf5' || ''}}
         path: |
           cpp/build/coverage.info
           cpp/build/coverage
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b87795d7bd..783e710206 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -66,6 +66,18 @@ jobs:
           config: Release
           optional-dependencies: OFF
 
+  build-cpp-gcc-no-hdf5:
+    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
+          hdf5: OFF
+
   build-cpp-gcc-openmp:
     if: github.event.pull_request.draft == false
     runs-on: ubuntu-latest
@@ -162,6 +174,17 @@ jobs:
           name: test-py-coverage-reports-surrogatemodel
           pattern: test-py-coverage-reports-surrogatemodel-*
 
+  test-cpp-gcc-no-hdf5:
+    if: github.event.pull_request.draft == false
+    needs: build-cpp-gcc-no-hdf5
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/linux-test
+        with:
+          artifact-pattern: gcc-latest-Release
+          hdf5: OFF
+
   test-cpp-gcc-no-optional-deps:
     if: github.event.pull_request.draft == false
     needs: build-cpp-gcc-no-optional-deps
diff --git a/cpp/README.md b/cpp/README.md
index 4039380ffa..746fe8002c 100644
--- a/cpp/README.md
+++ b/cpp/README.md
@@ -55,6 +55,7 @@ Options can be specified with `cmake .. -D<OPTION>=<VALUE>` or by editing the `b
 - `MEMILIO_BUILD_SIMULATIONS`: build the simulation applications in the simulations directory, ON or OFF, default ON.
 - `MEMILIO_BUILD_SBML_MODELS`: build the SBML importer and imported models, i.e. everythin in the folder `sbml_model_generation`, ON or OFF, default ON.
 - `MEMILIO_USE_BUNDLED_SPDLOG/_BOOST/_EIGEN/_JSONCPP`: use the corresponding dependency bundled with this project, ON or OFF, default ON.
+- `MEMILIO_USE_HDF5`: build MEmilio with HDF5 IO support, ON or OFF, default ON. If OFF, HDF5 is not searched for and features like `save_result`/`read_result` are disabled.
 - `MEMILIO_BUILD_BENCHMARKS`: build the benchmarks for this project, ON or OFF, default OFF.
 - `MEMILIO_SANITIZE_ADDRESS/_UNDEFINED`: compile with specified sanitizers to check correctness, ON or OFF, default OFF.
 - `MEMILIO_ENABLE_OPENMP`: compile MEmilio with multithreading using OpenMP, ON or OFF, default OFF.
diff --git a/cpp/thirdparty/CMakeLists.txt b/cpp/thirdparty/CMakeLists.txt
index 46ec58ef92..37ce91e06f 100644
--- a/cpp/thirdparty/CMakeLists.txt
+++ b/cpp/thirdparty/CMakeLists.txt
@@ -145,12 +145,16 @@ else()
 endif()
 
 # ## HDF5
-find_package(HDF5 COMPONENTS C)
+option(MEMILIO_USE_HDF5 "Build memilio with HDF5." ON)
 
-if(HDF5_FOUND)
-    set(MEMILIO_HAS_HDF5 ON)
-else()
-    message(WARNING "HDF5 was not found. Memilio will be built without some IO features. Install HDF5 Libraries and set the HDF5_DIR cmake variable to the directory containing the hdf5-config.cmake file to build with HDF5.")
+if(MEMILIO_USE_HDF5)
+    find_package(HDF5 COMPONENTS C)
+
+    if(HDF5_FOUND)
+        set(MEMILIO_HAS_HDF5 ON)
+    else()
+        message(WARNING "HDF5 was not found. Memilio will be built without some IO features. Install HDF5 Libraries and set the HDF5_DIR cmake variable to the directory containing the hdf5-config.cmake file to build with HDF5.")
+    endif()
 endif()
 
 # ## JSONCPP
diff --git a/docs/source/cpp/installation.rst b/docs/source/cpp/installation.rst
index 9e0bfebea6..2b83334b70 100644
--- a/docs/source/cpp/installation.rst
+++ b/docs/source/cpp/installation.rst
@@ -148,6 +148,8 @@ Additional options can be specified by appending one or more ``-D<OPTION>=<VALUE
       - Build the SBML importer and imported models, i.e. everything in the folder ``sbml_model_generation``, ON or OFF, default ON. You may need to set ``sbml_DIR``
     * - ``MEMILIO_USE_BUNDLED_SPDLOG/_BOOST/_EIGEN/_JSONCPP``:
       - Use the corresponding dependency bundled with this project, ON or OFF, default ON.
+    * - ``MEMILIO_USE_HDF5``
+      - Build MEmilio with HDF5 IO support, ON or OFF, default ON. If OFF, HDF5 is not searched for and features like ``save_result``/``read_result`` are disabled.
     * - ``MEMILIO_BUILD_BENCHMARKS``
       - Build the benchmarks for this project, ON or OFF, default OFF.
     * - ``MEMILIO_SANITIZE_ADDRESS/_UNDEFINED``

From 14f00161d0afcf9e0f365f141ac0f50934154c75 Mon Sep 17 00:00:00 2001
From: HenrZu <69154294+HenrZu@users.noreply.github.com>
Date: Wed, 4 Mar 2026 16:13:35 +0100
Subject: [PATCH 2/2] rename option + move to cpp cmakelist

---
 .github/actions/linux-build/action.yml | 2 +-
 cpp/CMakeLists.txt                     | 1 +
 cpp/README.md                          | 2 +-
 cpp/thirdparty/CMakeLists.txt          | 4 +---
 docs/source/cpp/installation.rst       | 2 +-
 5 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/actions/linux-build/action.yml b/.github/actions/linux-build/action.yml
index 603587b53b..8279dc0266 100644
--- a/.github/actions/linux-build/action.yml
+++ b/.github/actions/linux-build/action.yml
@@ -102,7 +102,7 @@ runs:
           exit 1
         fi
         mkdir -p build && cd build
-        cmake -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_ENABLE_IPOPT=ON -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitizers }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitizers }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DMEMILIO_ENABLE_OPENMP=${{ inputs.openmp }} -DMEMILIO_USE_HDF5=${{ inputs.hdf5 }} ..
+        cmake -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_ENABLE_IPOPT=ON -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitizers }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitizers }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DMEMILIO_ENABLE_OPENMP=${{ inputs.openmp }} -DMEMILIO_ENABLE_HDF5=${{ inputs.hdf5 }} ..
         make -j4
     - name: create build dir archive
       shell: bash
diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
index b771d041be..72eb58e8d0 100644
--- a/cpp/CMakeLists.txt
+++ b/cpp/CMakeLists.txt
@@ -20,6 +20,7 @@ option(MEMILIO_BUILD_SHARED_LIBS "Build memilio as a shared library." ON)
 option(MEMILIO_BUILD_STATIC_LIBS "Build memilio as a static library." ON)
 option(MEMILIO_ENABLE_MPI "Build memilio with MPI." OFF)
 option(MEMILIO_ENABLE_OPENMP "Enable Multithreading with OpenMP." OFF)
+option(MEMILIO_ENABLE_HDF5 "Build memilio with HDF5 IO support." ON)
 option(MEMILIO_ENABLE_WARNINGS "Build memilio with warnings." ON)
 option(MEMILIO_ENABLE_WARNINGS_AS_ERRORS "Build memilio with warnings as errors." ON)
 option(MEMILIO_ENABLE_IPOPT "Enable numerical optimization with Ipopt, requires a Fortran compiler." OFF)
diff --git a/cpp/README.md b/cpp/README.md
index 746fe8002c..e6de6b0b93 100644
--- a/cpp/README.md
+++ b/cpp/README.md
@@ -55,7 +55,7 @@ Options can be specified with `cmake .. -D<OPTION>=<VALUE>` or by editing the `b
 - `MEMILIO_BUILD_SIMULATIONS`: build the simulation applications in the simulations directory, ON or OFF, default ON.
 - `MEMILIO_BUILD_SBML_MODELS`: build the SBML importer and imported models, i.e. everythin in the folder `sbml_model_generation`, ON or OFF, default ON.
 - `MEMILIO_USE_BUNDLED_SPDLOG/_BOOST/_EIGEN/_JSONCPP`: use the corresponding dependency bundled with this project, ON or OFF, default ON.
-- `MEMILIO_USE_HDF5`: build MEmilio with HDF5 IO support, ON or OFF, default ON. If OFF, HDF5 is not searched for and features like `save_result`/`read_result` are disabled.
+- `MEMILIO_ENABLE_HDF5`: build MEmilio with HDF5 IO support, ON or OFF, default ON. If OFF, HDF5 is not searched for and features like `save_result`/`read_result` are disabled.
 - `MEMILIO_BUILD_BENCHMARKS`: build the benchmarks for this project, ON or OFF, default OFF.
 - `MEMILIO_SANITIZE_ADDRESS/_UNDEFINED`: compile with specified sanitizers to check correctness, ON or OFF, default OFF.
 - `MEMILIO_ENABLE_OPENMP`: compile MEmilio with multithreading using OpenMP, ON or OFF, default OFF.
diff --git a/cpp/thirdparty/CMakeLists.txt b/cpp/thirdparty/CMakeLists.txt
index 37ce91e06f..80921bd065 100644
--- a/cpp/thirdparty/CMakeLists.txt
+++ b/cpp/thirdparty/CMakeLists.txt
@@ -145,9 +145,7 @@ else()
 endif()
 
 # ## HDF5
-option(MEMILIO_USE_HDF5 "Build memilio with HDF5." ON)
-
-if(MEMILIO_USE_HDF5)
+if(MEMILIO_ENABLE_HDF5)
     find_package(HDF5 COMPONENTS C)
 
     if(HDF5_FOUND)
diff --git a/docs/source/cpp/installation.rst b/docs/source/cpp/installation.rst
index 2b83334b70..1f6fffc18f 100644
--- a/docs/source/cpp/installation.rst
+++ b/docs/source/cpp/installation.rst
@@ -148,7 +148,7 @@ Additional options can be specified by appending one or more ``-D<OPTION>=<VALUE
       - Build the SBML importer and imported models, i.e. everything in the folder ``sbml_model_generation``, ON or OFF, default ON. You may need to set ``sbml_DIR``
     * - ``MEMILIO_USE_BUNDLED_SPDLOG/_BOOST/_EIGEN/_JSONCPP``:
       - Use the corresponding dependency bundled with this project, ON or OFF, default ON.
-    * - ``MEMILIO_USE_HDF5``
+    * - ``MEMILIO_ENABLE_HDF5``
       - Build MEmilio with HDF5 IO support, ON or OFF, default ON. If OFF, HDF5 is not searched for and features like ``save_result``/``read_result`` are disabled.
     * - ``MEMILIO_BUILD_BENCHMARKS``
       - Build the benchmarks for this project, ON or OFF, default OFF.