1429 move example output to example_results

.github/actions/build-py/action.yml

@@ -28,17 +28,17 @@ runs:
           cd pycode/memilio-${{ inputs.package }}/
         # else stay in root directory
         fi
-        /opt/python/cp38-cp38/bin/python -m pip install --upgrade pip setuptools wheel
-        /opt/python/cp312-cp312/bin/python -m pip install --upgrade pip setuptools wheel
-        /opt/python/cp38-cp38/bin/python -m pip install scikit-build scikit-build-core 
-        /opt/python/cp312-cp312/bin/python -m pip install scikit-build scikit-build-core
+        /opt/python/cp39-cp39/bin/python -m pip install --upgrade pip setuptools wheel
+        /opt/python/cp314-cp314/bin/python -m pip install --upgrade pip setuptools wheel
+        /opt/python/cp39-cp39/bin/python -m pip install scikit-build scikit-build-core 
+        /opt/python/cp314-cp314/bin/python -m pip install scikit-build scikit-build-core
         # Install setuptools-scm only for memilio-simulation
         if [ "${{ 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
+          /opt/python/cp39-cp39/bin/python -m pip install setuptools-scm
+          /opt/python/cp314-cp314/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
+        /opt/python/cp39-cp39/bin/python -m build --no-isolation --wheel
+        /opt/python/cp314-cp314/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

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

@@ -38,7 +38,7 @@ runs:
       shell: bash
       run: |
         cd cpp/build
-        cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
+        cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_BUILD_TESTS=OFF -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
         cmake --build . -j 4
     - name: Run SBML importer
       shell: bash
@@ -49,5 +49,5 @@ runs:
       shell: bash
       run: |
         cd cpp/build
-        cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
+        cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_BUILD_TESTS=OFF -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
         cmake --build . -j 4

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

@@ -7,7 +7,7 @@ inputs:
   version:
     description: "Python version to use for the test."
     required: false
-    default: "3.8"
+    default: "3.9"
   coverage:
     description: "Generate coverage report from running the tests, ON or OFF, default OFF."
     required: false

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

@@ -13,12 +13,12 @@ runs:
         sudo apt-get -qq update
         sudo apt-get -qq -y install python3-pip gnupg
         python -m pip install --upgrade pip
-    # Pylint runs against the prebuilt wheels in pycode/wheelhouse/*cp312*.
+    # Pylint runs against the prebuilt wheels in pycode/wheelhouse/*cp314*.
     # So, use current latest supported Python version.
-    - name: Set up Python 3.12
+    - name: Set up Python 3.13
       uses: actions/setup-python@v6
       with:
-        python-version: "3.12"
+        python-version: "3.13"
     - name: Download Python Wheels
       uses: actions/download-artifact@v7
       with:
@@ -28,7 +28,7 @@ runs:
       shell: bash
       run: |
         shopt -s nullglob
-        for pkg in pycode/wheelhouse/*cp312*.whl; do python -m pip install "$pkg"; done # packages that contain native extensions are version specific
+        for pkg in pycode/wheelhouse/*cp314*.whl; do python -m pip install "$pkg"; done # packages that contain native extensions are version specific
         for pkg in pycode/wheelhouse/*py3*.whl; do python -m pip install "$pkg"; done # pure python packages are not version specific
         python -m pip install --upgrade-strategy only-if-needed --prefer-binary --find-links pycode/wheelhouse "memilio-${{ inputs.package }}[dev]"
     - name: Run pylint

.github/workflows/epidata_main.yml

@@ -25,7 +25,7 @@ jobs:
     - uses: actions/checkout@v6
     - uses: actions/setup-python@v6
       with:
-        python-version: 3.12
+        python-version: 3.13
     - uses: pre-commit/action@v3.0.1
 
   build-py-epidata:
@@ -51,7 +51,7 @@ jobs:
     needs: build-py-epidata
     strategy:
       matrix: 
-        version: ["3.8", "3.12"]
+        version: ["3.9", "3.13"]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
@@ -66,7 +66,7 @@ jobs:
     needs: [build-py-plot, build-py-epidata]
     strategy:
       matrix: 
-        version: ["3.8", "3.12"]
+        version: ["3.9", "3.13"]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
@@ -123,13 +123,13 @@ jobs:
         with:
           name: python-wheels-epidata
           path: pycode/wheelhouse
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@v6
         with:
-          python-version: 3.12
+          python-version: 3.13
       - 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/*cp314*.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: |

.github/workflows/main.yml

@@ -28,7 +28,7 @@ jobs:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
         with:
-          python-version: 3.12
+          python-version: 3.13
       - uses: pre-commit/action@v3.0.1
 
   build-cpp-gcc_clang:
@@ -339,7 +339,7 @@ jobs:
     if: github.event.pull_request.draft == false
     strategy:
       matrix: 
-        version: ["3.8", "3.12"]
+        version: ["3.9", "3.13"]
     needs: build-py-generation
     runs-on: ubuntu-latest
     steps:
@@ -353,7 +353,7 @@ jobs:
     needs: build-py-simulation
     strategy:
       matrix: 
-        version: ["3.8", "3.12"]
+        version: ["3.9", "3.13"]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
@@ -366,7 +366,7 @@ jobs:
     needs: [build-py-surrogatemodel, build-py-simulation]
     strategy:
       matrix: 
-        version: ["3.8", "3.12"]
+        version: ["3.9", "3.13"]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6

.pre-commit-config.yaml

@@ -1,15 +1,15 @@
 exclude: ^(docs|cpp)/
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v6.0.0
   hooks:
     -   id: check-merge-conflict
     -   id: check-yaml
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.2.2
+  rev: v3.21.2
   hooks:
     - id: pyupgrade
-      args: [--py37-plus]
+      args: [--py39-plus]
 - repo: https://github.com/hhatto/autopep8
   rev: v2.3.2
   hooks:

cpp/CMakeLists.txt

@@ -28,7 +28,21 @@ option(MEMILIO_ENABLE_IPOPT "Enable numerical optimization with Ipopt, requires
 option(MEMILIO_ENABLE_PROFILING "Enable runtime performance profiling of memilio." OFF)
 option(MEMILIO_ENABLE_LIKWID_MARKER "Enable performance measuring with likwid markers." OFF)
 
-mark_as_advanced(MEMILIO_USE_BUNDLED_SPDLOG MEMILIO_SANITIZE_ADDRESS MEMILIO_SANITIZE_UNDEFINED)
+cmake_path(CONVERT "${PROJECT_SOURCE_DIR}/.." TO_CMAKE_PATH_LIST PROJECT_ROOT_NORMALIZED NORMALIZE)
+set(MEMILIO_BASE_DIR "${PROJECT_ROOT_NORMALIZED}" CACHE PATH
+    "Path to the MEmilio project root, used for file I/O. Accessed via mio::base_dir().")
+set(MEMILIO_DATA_DIR "${PROJECT_ROOT_NORMALIZED}/data" CACHE PATH
+    "Path to the MEmilio data directory. Accessed via mio::data_dir().")
+
+mark_as_advanced(
+    MEMILIO_USE_BUNDLED_SPDLOG
+    MEMILIO_SANITIZE_ADDRESS
+    MEMILIO_SANITIZE_UNDEFINED
+    MEMILIO_BUILD_SHARED_LIBS
+    MEMILIO_BUILD_STATIC_LIBS
+    MEMILIO_BASE_DIR
+    MEMILIO_DATA_DIR
+    )
 
 # try to treat AppleClang as Clang, but warn about missing support
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
@@ -77,9 +91,6 @@ set(CMAKE_PDB_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
 set(CMAKE_INSTALL_RPATH "${CMAKE_BINARY_DIR}/lib" "${CMAKE_BINARY_DIR}/bin")
 
-# sets MEMILIO_BASE_DIR to the directory containing cpp (i.e., the root of the git repo)
-cmake_path(CONVERT "${PROJECT_SOURCE_DIR}/.." TO_CMAKE_PATH_LIST MEMILIO_BASE_DIR NORMALIZE)
-
 # code coverage analysis
 # Note: this only works under linux and with make
 # Ninja creates different directory names which do not work together with this scrupt

cpp/README.md

@@ -28,7 +28,7 @@ The following table lists the dependencies that are used. Most of them are requi
 
 | Library | Version  | Required | Bundled               | Notes |
 |---------|----------|----------|-----------------------|-------|
-| spdlog  | 1.15.0   | Yes      | Yes (git repo)        | https://github.com/gabime/spdlog |
+| spdlog  | 1.17.0   | Yes      | Yes (git repo)        | https://github.com/gabime/spdlog |
 | Eigen   | 3.4.0    | Yes      | Yes (git repo)        | http://gitlab.com/libeigen/eigen |
 | Boost   | 1.84.0   | Yes      | Yes (git repo)        | https://github.com/boostorg/boost |
 | JsonCpp | 1.9.6    | No       | Yes (git repo)        | https://github.com/open-source-parsers/jsoncpp |

cpp/benchmarks/flow_simulation_ode_secirvvs.cpp

@@ -21,11 +21,11 @@
 #include "benchmarks/flow_simulation_ode_secirvvs.h"
 #include "memilio/compartments/flow_simulation.h"
 #include "memilio/compartments/simulation.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 #include "ode_secirvvs/model.h"
 #include <string>
 
-const std::string config_path = mio::base_dir() + "cpp/benchmarks/simulation.config";
+const std::string config_path = (mio::base_dir() / "cpp/benchmarks/simulation.config").string();
 
 // simulation without flows (not in Model definition and not calculated by Simulation)
 void flowless_sim(::benchmark::State& state)

cpp/benchmarks/flow_simulation_ode_seir.cpp

@@ -20,12 +20,12 @@
 #include "benchmarks/simulation.h"
 #include "memilio/compartments/flow_simulation.h"
 #include "memilio/compartments/simulation.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 #include "ode_seir/model.h"
 
 #include <string>
 
-const std::string config_path = mio::base_dir() + "cpp/benchmarks/simulation.config";
+const std::string config_path = (mio::base_dir() / "cpp/benchmarks/simulation.config").string();
 
 namespace mio
 {

cpp/benchmarks/graph_simulation.cpp

@@ -22,11 +22,11 @@
 #include "memilio/compartments/simulation.h"
 #include "memilio/math/adapt_rk.h"
 #include "memilio/mobility/metapopulation_mobility_instant.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 #include "ode_secirvvs/model.h"
 #include <string>
 
-const std::string config_path = mio::base_dir() + "cpp/benchmarks/graph_simulation.config";
+const std::string config_path = (mio::base_dir() / "cpp/benchmarks/graph_simulation.config").string();
 
 mio::osecirvvs::Model<ScalarType> create_model(size_t num_agegroups, const ScalarType tmax)
 {

cpp/benchmarks/integrator_step.cpp

@@ -22,7 +22,7 @@
 
 #include "memilio/math/adapt_rk.h"
 #include "memilio/math/stepper_wrapper.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 
 template <class Integrator>
 void integrator_step(::benchmark::State& state)
@@ -33,8 +33,8 @@ void integrator_step(::benchmark::State& state)
     // with "num_agegroups" agegroups, and taking "yt" as the state of the simulation at "t_init"
     // NOTE: yt must have #agegroups * #compartments entries
     // benchmark setup
-    auto cfg =
-        mio::benchmark::IntegratorStepConfig::initialize(mio::base_dir() + "cpp/benchmarks/integrator_step.config");
+    auto cfg = mio::benchmark::IntegratorStepConfig::initialize(
+        (mio::base_dir() / "cpp/benchmarks/integrator_step.config").string());
     //auto cfg = mio::benchmark::IntegratorStepConfig::initialize();
     auto model = mio::benchmark::model::SecirAgeres(cfg.num_agegroups);
     // set deriv function and integrator

cpp/benchmarks/simulation.cpp

@@ -22,15 +22,16 @@
 
 #include "memilio/math/adapt_rk.h"
 #include "memilio/math/stepper_wrapper.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 
 template <class Integrator>
 void simulation(::benchmark::State& state)
 {
     // suppress non-critical messages
     mio::set_log_level(mio::LogLevel::critical);
     // setup benchmark parameters
-    auto cfg = mio::benchmark::SimulationConfig::initialize(mio::base_dir() + "cpp/benchmarks/simulation.config");
+    auto cfg =
+        mio::benchmark::SimulationConfig::initialize((mio::base_dir() / "cpp/benchmarks/simulation.config").string());
     //auto cfg = mio::benchmark::SimulationConfig::initialize(10);
     auto model = mio::benchmark::model::SecirAgeres(cfg.num_agegroups);
 

cpp/examples/CMakeLists.txt

@@ -1,7 +1,3 @@
-# configure directory that contains the data files used by examples
-file(TO_CMAKE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../../data" MEMILIO_DATA_DIR)
-configure_file(data_dir.h.in data_dir.h)
-
 add_executable(euler_example euler_test.cpp)
 target_link_libraries(euler_example PRIVATE memilio)
 target_compile_options(euler_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
@@ -18,17 +14,17 @@ add_executable(adapt_rk_example adapt_rk_test.cpp)
 target_link_libraries(adapt_rk_example PRIVATE memilio)
 target_compile_options(adapt_rk_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
 
-add_executable(ode_seir_example ode_seir.cpp)
-target_link_libraries(ode_seir_example PRIVATE memilio ode_seir)
-target_compile_options(ode_seir_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
-
-add_executable(ode_seirdb_example ode_seirdb.cpp)
-target_link_libraries(ode_seirdb_example PRIVATE memilio ode_seirdb)
-target_compile_options(ode_seirdb_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
-
-add_executable(ode_seir_ageres_example ode_seir_ageres.cpp)
-target_link_libraries(ode_seir_ageres_example PRIVATE memilio ode_seir)
-target_compile_options(ode_seir_ageres_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+add_executable(ode_seir_example ode_seir.cpp)
+target_link_libraries(ode_seir_example PRIVATE memilio ode_seir)
+target_compile_options(ode_seir_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+
+add_executable(ode_seirdb_example ode_seirdb.cpp)
+target_link_libraries(ode_seirdb_example PRIVATE memilio ode_seirdb)
+target_compile_options(ode_seirdb_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+
+add_executable(ode_seir_ageres_example ode_seir_ageres.cpp)
+target_link_libraries(ode_seir_ageres_example PRIVATE memilio ode_seir)
+target_compile_options(ode_seir_ageres_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
 
 add_executable(ode_sir_example ode_sir.cpp)
 target_link_libraries(ode_sir_example PRIVATE memilio ode_sir)

cpp/examples/abm_history_object.cpp

@@ -22,8 +22,10 @@
 #include "abm/simulation.h"
 #include "abm/model.h"
 #include "abm/location_type.h"
+#include "memilio/io/io.h"
 #include "memilio/utils/abstract_parameter_distribution.h"
 #include "memilio/io/history.h"
+#include "memilio/io/directories.h"
 #include "memilio/utils/parameter_distributions.h"
 
 #include <fstream>
@@ -43,7 +45,8 @@ void write_log_to_file(const T& history)
     auto loc_id      = std::get<1>(logg);
     auto time_points = std::get<0>(logg);
     std::string input;
-    std::ofstream myfile("test_output.txt");
+    std::ofstream myfile(mio::create_directories_or_exit(mio::example_results_dir("abm_history_object")) /
+                         "test_output.txt");
     myfile << "Locations as numbers:\n";
     for (auto&& id : loc_id[0]) {
         myfile << convert_loc_id_to_string(id) << "\n";

cpp/examples/abm_minimal.cpp

@@ -21,6 +21,7 @@
 #include "abm/lockdown_rules.h"
 #include "abm/model.h"
 #include "abm/common_abm_loggers.h"
+#include "memilio/io/directories.h"
 
 #include <fstream>
 
@@ -161,14 +162,12 @@ int main()
     // Run the simulation until tmax with the history object.
     sim.advance(tmax, historyTimeSeries);
 
-    // The results are written into the file "abm_minimal.txt" as a table with 9 columns.
-    // The first column is Time. The other columns correspond to the number of people with a certain infection state at this Time:
-    // Time = Time in days, S = Susceptible, E = Exposed, I_NS = InfectedNoSymptoms, I_Sy = InfectedSymptoms, I_Sev = InfectedSevere,
-    // I_Crit = InfectedCritical, R = Recovered, D = Dead
-    std::ofstream outfile("abm_minimal.txt");
+    // Write results to a file. Also print the filepath to make it easier to find
+    auto outpath = mio::create_directories_or_exit(mio::example_results_dir("abm_minimal")) / "history.txt";
+    std::ofstream outfile(outpath);
     std::get<0>(historyTimeSeries.get_log())
         .print_table(outfile, {"S", "E", "I_NS", "I_Sy", "I_Sev", "I_Crit", "R", "D"}, 7, 4);
-    std::cout << "Results written to abm_minimal.txt" << std::endl;
+    std::cout << "Results written to " << outpath << std::endl;
 
     return 0;
 }