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Merge branch 'main' into parallel-processing
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‎.github/actions/linux-build/action.yml‎

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@@ -40,7 +40,7 @@ runs:
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sudo apt-get -qq update
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sudo apt-get -qq -y install lcov ccache
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if [[ "${{ inputs.optional-dependencies }}" == "ON" ]]; then
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sudo apt-get -qq -y install libhdf5-dev
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sudo apt-get -qq -y install libhdf5-dev
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fi
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if [[ "${{ inputs.compiler }}" == "gcc" ]]; then
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if [[ "${{ inputs.version }}" == "min" ]]; then
@@ -97,7 +97,7 @@ runs:
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exit 1
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fi
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mkdir -p build && cd build
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cmake -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_BUILD_TYPE=${{ 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=${{ inputs.openmp }} ..
100+
cmake -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_BUILD_TYPE=${{ 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.optional-dependencies }} ..
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make -j4
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- name: create build dir archive
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shell: bash

‎.github/actions/linux-test/action.yml‎

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@@ -27,7 +27,10 @@ runs:
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shell: bash
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run: |
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sudo apt-get -qq update
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sudo apt-get -qq -y install libhdf5-10* wget gnupg lcov
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sudo apt-get -qq -y install wget gnupg lcov
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if [[ "${{ inputs.optional-deps }}" == "ON" ]]; then
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sudo apt-get -qq -y install libhdf5-10*
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fi
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sudo apt-get -qq update
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- name: Download built test directory
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uses: actions/download-artifact@v4

‎.github/actions/sbml-test/action.yaml‎

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@@ -38,7 +38,7 @@ runs:
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shell: bash
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run: |
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cd cpp/build
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cmake -DCMAKE_BUILD_TYPE=Release -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
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cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
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cmake --build . -j 4
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- name: Run SBML importer
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shell: bash
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shell: bash
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run: |
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cd cpp/build
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cmake -DCMAKE_BUILD_TYPE=Release -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
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cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
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cmake --build . -j 4

‎.github/pull_request_template.md‎

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@@ -18,19 +18,19 @@ Please check our [git workflow](https://memilio.readthedocs.io/en/latest/develop
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### Checks by code author
2020

21-
- [ ] Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
22-
- [ ] New code adheres to [coding guidelines](https://memilio.readthedocs.io/en/latest/development.html#coding-guidelines)
23-
- [ ] No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
24-
- [ ] Tests are added for new functionality and a local test run was successful (with and without OpenMP)
25-
- [ ] Appropriate **documentation within the code** (Doxygen) for new functionality has been added in the code
26-
- [ ] Appropriate **external documentation** (ReadTheDocs) for new functionality has been added to the online documentation
27-
- [ ] Proper attention to licenses, especially no new third-party software with conflicting license has been added
21+
- [ ] Every addressed issue is linked (use the "Closes #ISSUE" keyword below).
22+
- [ ] New code adheres to [coding guidelines](https://memilio.readthedocs.io/en/latest/development.html#coding-guidelines).
23+
- [ ] No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.).
24+
- [ ] Tests are added for new functionality and a local test run was successful (with and without OpenMP).
25+
- [ ] Appropriate **documentation within the code** (Doxygen) for new functionality has been added in the code.
26+
- [ ] Appropriate **external documentation** (ReadTheDocs) for new functionality has been added to the online documentation and checked in the preview.
27+
- [ ] Proper attention to licenses, especially no new third-party software with conflicting license has been added.
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- [ ] (For ABM development) Checked [benchmark results](https://memilio.readthedocs.io/en/latest/development.html#agent-based-model-development) and ran and posted a local test above from before and after development to ensure performance is monitored.
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### Checks by code reviewer(s)
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32-
- [ ] Corresponding issue(s) is/are linked and addressed
33-
- [ ] Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
34-
- [ ] Appropriate **unit tests** have been added, CI passes, code coverage and performance is acceptable (did not decrease)
35-
- [ ] No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
32+
- [ ] Corresponding issue(s) is/are linked and addressed.
33+
- [ ] Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.).
34+
- [ ] Appropriate **unit tests** have been added, CI passes, code coverage and performance is acceptable (did not decrease).
35+
- [ ] No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.).
3636
- [ ] On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the **briefly-list-the-changes** above (best case) or the separate commit messages (worst case).

‎.gitignore‎

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@@ -282,6 +282,7 @@ docs/html
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docs/xml
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docs/source/api
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docs/source/generated
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docs/source/cppapi
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# VS Code
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.vscode/

‎.gitmodules‎

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[submodule "docs/doxygen-awesome-css"]
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path = docs/doxygen-awesome-css
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url = https://github.com/jothepro/doxygen-awesome-css.git

‎cpp/CMakeLists.txt‎

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@@ -9,7 +9,6 @@ option(MEMILIO_BUILD_TESTS "Build memilio unit tests." ON)
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option(MEMILIO_BUILD_EXAMPLES "Build memilio examples." ON)
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option(MEMILIO_BUILD_MODELS "Build memilio models." ON)
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option(MEMILIO_BUILD_BENCHMARKS "Build memilio benchmarks with google benchmark." OFF)
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option(MEMILIO_BUILD_SBML_MODELS "Build the SBML importer and imported models." ON)
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option(MEMILIO_USE_BUNDLED_SPDLOG "Use spdlog bundled with epi" ON)
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option(MEMILIO_USE_BUNDLED_EIGEN "Use eigen bundled with epi" ON)
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option(MEMILIO_USE_BUNDLED_BOOST "Use boost bundled with epi (only for epi-io)" ON)
@@ -20,6 +19,8 @@ option(MEMILIO_BUILD_SHARED_LIBS "Build memilio as a shared library." ON)
2019
option(MEMILIO_BUILD_STATIC_LIBS "Build memilio as a static library." ON)
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option(MEMILIO_ENABLE_MPI "Build memilio with MPI." OFF)
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option(MEMILIO_ENABLE_OPENMP "Enable Multithreading with OpenMP." OFF)
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option(MEMILIO_ENABLE_HDF5 "Build memilio with HDF5 IO support." ON)
23+
option(MEMILIO_ENABLE_SBML "Build memilio with the SBML importer and imported models." OFF)
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option(MEMILIO_ENABLE_WARNINGS "Build memilio with warnings." ON)
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option(MEMILIO_ENABLE_WARNINGS_AS_ERRORS "Build memilio with warnings as errors." ON)
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option(MEMILIO_ENABLE_IPOPT "Enable numerical optimization with Ipopt, requires a Fortran compiler." OFF)
@@ -210,7 +211,7 @@ if(MEMILIO_BUILD_BENCHMARKS)
210211
add_subdirectory(benchmarks)
211212
endif()
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213-
if(MEMILIO_BUILD_SBML_MODELS)
214+
if(MEMILIO_ENABLE_SBML)
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add_subdirectory(sbml_model_generation)
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endif()
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‎cpp/README.md‎

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@@ -53,12 +53,13 @@ Options can be specified with `cmake .. -D<OPTION>=<VALUE>` or by editing the `b
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- `MEMILIO_BUILD_EXAMPLES`: build the example applications in the examples directory, ON or OFF, default ON.
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- `MEMILIO_BUILD_MODELS`: build the separate model libraries in the models directory, ON or OFF, default ON.
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- `MEMILIO_BUILD_SIMULATIONS`: build the simulation applications in the simulations directory, ON or OFF, default ON.
56-
- `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.
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- `MEMILIO_USE_BUNDLED_SPDLOG/_BOOST/_EIGEN/_JSONCPP`: use the corresponding dependency bundled with this project, ON or OFF, default ON.
5857
- `MEMILIO_BUILD_BENCHMARKS`: build the benchmarks for this project, ON or OFF, default OFF.
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- `MEMILIO_SANITIZE_ADDRESS/_UNDEFINED`: compile with specified sanitizers to check correctness, ON or OFF, default OFF.
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- `MEMILIO_ENABLE_OPENMP`: compile MEmilio with multithreading using OpenMP, ON or OFF, default OFF.
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- `MEMILIO_ENABLE_MPI`: compile MEmilio with distributed memory parallelization using MPI. ON or OFF, default OFF. Requires an MPI implementation to be installed on the system.
61+
- `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.
62+
- `MEMILIO_ENABLE_SBML`: build the SBML importer and imported models, i.e. everythin in the folder `sbml_model_generation`, ON or OFF, default OFF.
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- `MEMILIO_ENABLE_WARNINGS`: enable compilation warnings (beyond those enabled in the compiler by default). ON or OFF, default ON.
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- `MEMILIO_ENABLE_WARNINGS_AS_ERRORS`: compilation warnings are treated as compilation errors. ON or OFF, default ON.
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- `MEMILIO_ENABLE_PROFILING`: compile with runtime profiling support. ON or OFF, default OFF. See [here](benchmarks/profiling.md) for information.

‎cpp/benchmarks/secir_ageres_setups.h‎

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@@ -30,7 +30,7 @@ namespace mio
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{
3131
namespace benchmark
3232
{
33-
namespace detail
33+
namespace details
3434
{
3535
/**
3636
* @brief Helper function to create a secir model with consistent setup for use in benchmarking.
@@ -89,7 +89,7 @@ mio::osecir::Model<ScalarType> make_model(int num)
8989

9090
return model;
9191
}
92-
} // namespace detail
92+
} // namespace details
9393

9494
namespace model
9595
{
@@ -98,7 +98,7 @@ namespace model
9898
*/
9999
mio::osecir::Model<ScalarType> SecirAgeres(size_t num_agegroups)
100100
{
101-
mio::osecir::Model<ScalarType> model = mio::benchmark::detail::make_model(num_agegroups);
101+
mio::osecir::Model<ScalarType> model = mio::benchmark::details::make_model(num_agegroups);
102102

103103
auto nb_groups = model.parameters.get_num_groups();
104104
ScalarType cont_freq = 10, fact = 1.0 / (ScalarType)(size_t)nb_groups;
@@ -117,7 +117,7 @@ mio::osecir::Model<ScalarType> SecirAgeres(size_t num_agegroups)
117117
*/
118118
mio::osecir::Model<ScalarType> SecirAgeresDampings(size_t num_agegroups)
119119
{
120-
mio::osecir::Model<ScalarType> model = mio::benchmark::detail::make_model(num_agegroups);
120+
mio::osecir::Model<ScalarType> model = mio::benchmark::details::make_model(num_agegroups);
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122122
auto nb_groups = model.parameters.get_num_groups();
123123
ScalarType cont_freq = 10, fact = 1.0 / (ScalarType)(size_t)nb_groups;
@@ -145,7 +145,7 @@ mio::osecir::Model<ScalarType> SecirAgeresDampings(size_t num_agegroups)
145145
*/
146146
mio::osecir::Model<ScalarType> SecirAgeresAbsurdDampings(size_t num_agegroups)
147147
{
148-
mio::osecir::Model<ScalarType> model = mio::benchmark::detail::make_model(num_agegroups);
148+
mio::osecir::Model<ScalarType> model = mio::benchmark::details::make_model(num_agegroups);
149149

150150
auto nb_groups = model.parameters.get_num_groups();
151151
ScalarType cont_freq = 10, fact = 1.0 / (ScalarType)(size_t)nb_groups;

‎cpp/memilio/ad/ad.h‎

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2727
#include <cmath>
2828
#include <limits>
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30+
namespace ad
31+
{
32+
namespace internal
33+
{
34+
35+
/**
36+
* @brief Format AD types (like ad::gt1s<double>::type) using their value for logging with spdlog.
37+
*
38+
* If derivative information is needed as well, use `ad::derivative(...)` or define a `fmt::formatter<...>`.
39+
*/
40+
template <class FP, class DataHandler>
41+
const FP& format_as(const active_type<FP, DataHandler>& ad_type)
42+
{
43+
// Note: the format_as function needs to be in the same namespace as the value it takes
44+
return value(ad_type);
45+
}
46+
47+
} // namespace internal
48+
} // namespace ad
49+
3050
// Allow std::numeric_limits to work with AD types.
3151
template <class FP, class DataHandler>
3252
struct std::numeric_limits<ad::internal::active_type<FP, DataHandler>> : public numeric_limits<FP> {

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