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dabeledabele
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rename epi namespace and EPI_ macros
rename cmake options and C++ macros from EPI_ to MEMILIO_ remove obsolete references to epidemiology
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Lines changed: 3531 additions & 3531 deletions

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

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Original file line numberDiff line numberDiff line change
@@ -65,7 +65,7 @@ runs:
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exit 1
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fi
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mkdir -p build && cd build
68-
cmake -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DEPI_TEST_COVERAGE=${{ inputs.coverage }} -DEPI_SANITIZE_ADDRESS=${{ inputs.sanitize-addr }} -DEPI_SANITIZE_UNDEFINED=${{ inputs.sanitize-ub }} -DEPI_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} ..
68+
cmake -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitize-addr }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitize-ub }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ 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/windows-build/action.yml‎

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@@ -52,7 +52,7 @@ runs:
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call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" amd64
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)
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cmake --version
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cmake -G "Ninja" -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DEPI_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DHDF5_USE_STATIC_LIBRARIES=ON -DHDF5_DIR="C:\Program Files\HDF_Group\HDF5\1.12.1\share\cmake\hdf5" ..
55+
cmake -G "Ninja" -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DHDF5_USE_STATIC_LIBRARIES=ON -DHDF5_DIR="C:\Program Files\HDF_Group\HDF5\1.12.1\share\cmake\hdf5" ..
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cmake --build . -- -j 4
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- name: Upload built test directory
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uses: actions/upload-artifact@v2

‎cpp/CMakeLists.txt‎

Lines changed: 26 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -2,18 +2,18 @@ cmake_minimum_required(VERSION 3.10)
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project(memilio VERSION 0.1.0)
44

5-
option(EPI_BUILD_TESTS "Build memilio unit tests." ON)
6-
option(EPI_BUILD_EXAMPLES "Build memilio examples." ON)
7-
option(EPI_BUILD_MODELS "Build memilio models." ON)
8-
option(EPI_BUILD_SIMULATIONS "Build memilio unit tests." ON)
9-
option(EPI_USE_BUNDLED_SPDLOG "Use spdlog bundled with epi" ON)
10-
option(EPI_USE_BUNDLED_EIGEN "Use eigen bundled with epi" ON)
11-
option(EPI_USE_BUNDLED_BOOST "Use boost bundled with epi (only for epi-io)" ON)
12-
option(EPI_USE_BUNDLED_JSONCPP "Use jsoncpp bundled with epi (only for epi-io)" ON)
13-
option(EPI_SANITIZE_ADDRESS "Enable address sanitizer." OFF)
14-
option(EPI_SANITIZE_UNDEFINED "Enable undefined behavior sanitizer." OFF)
15-
16-
mark_as_advanced(EPI_USE_BUNDLED_SPDLOG EPI_SANITIZE_ADDRESS EPI_SANITIZE_UNDEFINED)
5+
option(MEMILIO_BUILD_TESTS "Build memilio unit tests." ON)
6+
option(MEMILIO_BUILD_EXAMPLES "Build memilio examples." ON)
7+
option(MEMILIO_BUILD_MODELS "Build memilio models." ON)
8+
option(MEMILIO_BUILD_SIMULATIONS "Build memilio unit tests." ON)
9+
option(MEMILIO_USE_BUNDLED_SPDLOG "Use spdlog bundled with epi" ON)
10+
option(MEMILIO_USE_BUNDLED_EIGEN "Use eigen bundled with epi" ON)
11+
option(MEMILIO_USE_BUNDLED_BOOST "Use boost bundled with epi (only for epi-io)" ON)
12+
option(MEMILIO_USE_BUNDLED_JSONCPP "Use jsoncpp bundled with epi (only for epi-io)" ON)
13+
option(MEMILIO_SANITIZE_ADDRESS "Enable address sanitizer." OFF)
14+
option(MEMILIO_SANITIZE_UNDEFINED "Enable undefined behavior sanitizer." OFF)
15+
16+
mark_as_advanced(MEMILIO_USE_BUNDLED_SPDLOG MEMILIO_SANITIZE_ADDRESS MEMILIO_SANITIZE_UNDEFINED)
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set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
1919
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -22,9 +22,9 @@ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
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# Note: this only works under linux and with make
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# Ninja creates different directory names which do not work together with this scrupt
2424
if(CMAKE_BUILD_TYPE STREQUAL "Debug")
25-
option (EPI_TEST_COVERAGE "Enable GCov coverage analysis (adds a 'coverage' target)" OFF)
26-
mark_as_advanced(EPI_TEST_COVERAGE)
27-
if (EPI_TEST_COVERAGE)
25+
option (MEMILIO_TEST_COVERAGE "Enable GCov coverage analysis (adds a 'coverage' target)" OFF)
26+
mark_as_advanced(MEMILIO_TEST_COVERAGE)
27+
if (MEMILIO_TEST_COVERAGE)
2828
message(STATUS "Coverage enabled")
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include(CodeCoverage)
3030
append_coverage_compiler_flags()
@@ -37,42 +37,42 @@ if(CMAKE_BUILD_TYPE STREQUAL "Debug")
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endif()
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if ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 7))
40-
if(EPI_SANITIZE_ADDRESS)
40+
if(MEMILIO_SANITIZE_ADDRESS)
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string(APPEND CMAKE_CXX_FLAGS_DEBUG " -fsanitize=address")
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string(APPEND CMAKE_LINKER_FLAGS_DEBUG " -fsanitize=address")
43-
endif(EPI_SANITIZE_ADDRESS)
43+
endif(MEMILIO_SANITIZE_ADDRESS)
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45-
if(EPI_SANITIZE_UNDEFINED)
45+
if(MEMILIO_SANITIZE_UNDEFINED)
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string(APPEND CMAKE_CXX_FLAGS_DEBUG " -fsanitize=undefined")
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string(APPEND CMAKE_LINKER_FLAGS_DEBUG " -fsanitize=undefined")
48-
endif(EPI_SANITIZE_UNDEFINED)
48+
endif(MEMILIO_SANITIZE_UNDEFINED)
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50-
if(EPI_SANITIZE_ADDRESS OR EPI_SANITIZE_UNDEFINED)
50+
if(MEMILIO_SANITIZE_ADDRESS OR MEMILIO_SANITIZE_UNDEFINED)
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string(APPEND CMAKE_CXX_FLAGS_DEBUG " -fno-omit-frame-pointer -fno-sanitize-recover=all")
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string(APPEND CMAKE_LINKER_FLAGS_DEBUG " -fno-omit-frame-pointer -fno-sanitize-recover=all")
53-
endif(EPI_SANITIZE_ADDRESS OR EPI_SANITIZE_UNDEFINED)
53+
endif(MEMILIO_SANITIZE_ADDRESS OR MEMILIO_SANITIZE_UNDEFINED)
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endif((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 7))
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5656
include(thirdparty/CMakeLists.txt)
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58-
set(_EPI_CXX_FLAG_ENABLE_WARNING_ERRORS
58+
set(_MEMILIO_CXX_FLAG_ENABLE_WARNING_ERRORS
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"$<$<CXX_COMPILER_ID:GNU>: -Wno-unknown-warning -Wall -Wextra -Werror -Wshadow --pedantic-errors -Wno-deprecated-copy>
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$<$<CXX_COMPILER_ID:CLANG>: -Wno-unknown-warning-option -Wall -Wextra -Werror -Wshadow --pedantic-errors -Wno-deprecated>
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$<$<CXX_COMPILER_ID:MSVC>: /W4 /WX>")
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6363
add_subdirectory(memilio)
64-
if (EPI_BUILD_MODELS)
64+
if (MEMILIO_BUILD_MODELS)
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add_subdirectory(models/abm)
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add_subdirectory(models/secir)
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add_subdirectory(models/seir)
6868
endif()
69-
if (EPI_BUILD_EXAMPLES)
69+
if (MEMILIO_BUILD_EXAMPLES)
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add_subdirectory(examples)
7171
endif()
72-
if (EPI_BUILD_TESTS)
72+
if (MEMILIO_BUILD_TESTS)
7373
add_subdirectory(tests)
7474
endif()
75-
if (EPI_BUILD_SIMULATIONS)
75+
if (MEMILIO_BUILD_SIMULATIONS)
7676
add_subdirectory(simulations)
7777
endif()
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‎cpp/Readme.md‎

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Original file line numberDiff line numberDiff line change
@@ -46,12 +46,12 @@ cmake ..
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```
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4848
Options can be specified with `cmake .. -D<OPTION>=<VALUE>` or by editing the `build/CMakeCache.txt` file after running cmake. The following options are known to the library:
49-
- `EPI_BUILD_TESTS`: build unit tests in the test directory, ON or OFF, default ON.
50-
- `EPI_BUILD_EXAMPLES`: build the example applications in the examples directory, ON or OFF, default ON.
51-
- `EPI_BUILD_MODELS`: build the separate model libraries in the models directory, ON or OFF, default ON.
52-
- `EPI_BUILD_SIMULATIONS`: build the simulation applications in the simulations directory, ON or OFF, default ON.
53-
- `EPI_USE_BUNDLED_SPDLOG/_BOOST/_EIGEN/_JSONCPP`: use the corresponding dependency bundled with this project, ON or OFF, default ON.
54-
- `EPI_SANITIZE_ADDRESS/_UNDEFINED`: compile with specified sanitizers to check correctness, ON or OFF, default OFF.
49+
- `MEMILIO_BUILD_TESTS`: build unit tests in the test directory, ON or OFF, default ON.
50+
- `MEMILIO_BUILD_EXAMPLES`: build the example applications in the examples directory, ON or OFF, default ON.
51+
- `MEMILIO_BUILD_MODELS`: build the separate model libraries in the models directory, ON or OFF, default ON.
52+
- `MEMILIO_BUILD_SIMULATIONS`: build the simulation applications in the simulations directory, ON or OFF, default ON.
53+
- `MEMILIO_USE_BUNDLED_SPDLOG/_BOOST/_EIGEN/_JSONCPP`: use the corresponding dependency bundled with this project, ON or OFF, default ON.
54+
- `MEMILIO_SANITIZE_ADDRESS/_UNDEFINED`: compile with specified sanitizers to check correctness, ON or OFF, default OFF.
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Other important options may need:
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- `CMAKE_BUILD_TYPE`: controls compiler optimizations and diagnostics, Debug, Release, or RelWithDebInfo; not available for Multi-Config CMake Generators like Visual Studio, set the build type in the IDE or when running the compiler.
@@ -60,7 +60,7 @@ Other important options may need:
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To e.g. configure the build without unit tests and with a specific version of HDF5:
6262
```bash
63-
cmake .. -DEPI_BUILD_TESTS=OFF -DHDF5_DIR=/home/xyz/share/hdf5
63+
cmake .. -DMEMILIO_BUILD_TESTS=OFF -DHDF5_DIR=/home/xyz/share/hdf5
6464
```
6565

6666
### Making the library
@@ -88,7 +88,7 @@ Install the project at the location given in the `CMAKE_INSTALL_PREFIX` variable
8888
```bash
8989
cmake --install .
9090
```
91-
This will install the libraries, headers, and executables that were built, i.e. where `EPI_BUILD_<PART>=ON`.
91+
This will install the libraries, headers, and executables that were built, i.e. where `MEMILIO_BUILD_<PART>=ON`.
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### Using the libraries in your project
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‎cpp/examples/CMakeLists.txt‎

Lines changed: 1 addition & 1 deletion
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@@ -1,5 +1,5 @@
11
#configure directory that contains the data files used by examples
2-
file(TO_CMAKE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../../data" EPI_DATA_DIR)
2+
file(TO_CMAKE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../../data" MEMILIO_DATA_DIR)
33
configure_file(data_dir.h.in data_dir.h)
44

55
add_executable(euler_example euler_test.cpp)

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