### Run Example Experiment

Source: https://github.com/numbbo/coco-experiment/blob/main/build/java/README.md

This command runs the example experiment using the compiled JAR and native library, directing results to the 'exdata/' directory.

```bash
java -classpath build/coco.jar -Djava.library.path=build/ ExampleExperiment
```

--------------------------------

### Install coco-experiment using pip

Source: https://github.com/numbbo/coco-experiment/blob/main/build/python/README.md

The recommended way to install the coco-experiment package is by using pip. This command ensures you get the latest version, and it's best practice to do this within a virtual environment.

```bash
pip install -U coco-experiment
```

--------------------------------

### Build Example Experiment with Meson

Source: https://github.com/numbbo/coco-experiment/blob/main/build/c/README.md

Alternatively, use Meson and Ninja to build the example experiment. This method provides another way to compile the C/C++ components.

```bash
meson setup build
meson compile -C build
```

--------------------------------

### Basic CMake Project Setup

Source: https://github.com/numbbo/coco-experiment/blob/main/test/unit-test/CMakeLists.txt

Initializes CMake version and defines the project name, description, and language.

```cmake
cmake_minimum_required(VERSION 3.19)
project(COCOUnitTest
        DESCRIPTION "COCO C unit tests"
        LANGUAGES C)
```

--------------------------------

### Build Example Experiment with CMake

Source: https://github.com/numbbo/coco-experiment/blob/main/build/c/README.md

Use these commands to build the included example experiment using CMake. Ensure you have CMake version 3.19 or greater and a C99-compliant C compiler.

```bash
cmake -B build .
cmake --build build
```

--------------------------------

### Install Cocoex Python Package from Source

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Installs the cocoex Python package locally from its source directory. Uninstall any existing version before installing.

```sh
pip uninstall -y coco-experiment
```

```sh
pip install .
```

--------------------------------

### Install Development Version of Cocoex

Source: https://github.com/numbbo/coco-experiment/blob/main/build/python/DEVELOPMENT.md

Use this command to install the package in development mode from the root directory of the cocoex Python package.

```sh
python -m pip install .
```

--------------------------------

### Install Coco Experiment Python Package

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Installs the coco-experiment Python package from a local build directory. Ensure you uninstall any existing version first.

```sh
python -m pip uninstall -y coco-experiment
```

```sh
python -m pip install ../../build/python/
```

--------------------------------

### CMake Project Configuration

Source: https://github.com/numbbo/coco-experiment/blob/main/build/java/CMakeLists.txt

Sets the minimum CMake version and defines the project name and languages. This is a standard starting point for CMake projects.

```cmake
cmake_minimum_required(VERSION 3.20)

project(COCO LANGUAGES C)
```

--------------------------------

### Install Cocoex Python Package on ARM macOS

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Installs the cocoex Python package from source on an ARM-based macOS system, specifying the architecture.

```sh
arch -arm64 pip install .
```

--------------------------------

### Setup and Run SMS-EMOA in MATLAB

Source: https://github.com/numbbo/coco-experiment/blob/main/examples/bbob-biobj-matlab-smsemoa/README.md

Compiles and runs the SMS-EMOA algorithm and the COCO framework within MATLAB. This is done after the build step.

```matlab
setup
run_smsemoa_on_bbob_biobj
```

--------------------------------

### Install Development Version with Debug Symbols

Source: https://github.com/numbbo/coco-experiment/blob/main/build/python/DEVELOPMENT.md

Install the package with debug symbols enabled for C code assertions. This command should be run from the root directory of the cocoex Python package.

```sh
python -m pip install -e . \
    --no-build-isolation \
    -Csetup-args=-Dbuildtype=debug \
    -Cbuild-dir=build-dbg
```

--------------------------------

### Install Cocoex Python Package with C99 Mode

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Installs the cocoex Python package from source, explicitly enabling C99 mode for the C compiler, which may be necessary on older systems.

```sh
CFLAGS="-std=c99" pip install .
```

--------------------------------

### Test Cocoex Python Package with Pytest

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Installs pytest and runs the package's tests using the pytest framework.

```sh
pip install pytest
```

```sh
python -m pytest test
```

--------------------------------

### Run Regression Tests

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Executes the regression tests using Python scripts. Requires the cocoex Python package to be installed.

```sh
python test_suites.py
```

```sh
python test_loggers.py
```

--------------------------------

### Update Existing Conda Environment

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Installs required development dependencies into an already activated conda environment without creating a new one.

```sh
conda env update --file env.yaml
```

--------------------------------

### Build Classes and Native Library

Source: https://github.com/numbbo/coco-experiment/blob/main/build/java/README.md

Execute this command after configuration to compile the Java classes and the native JNI library.

```bash
cmake --build build
```

--------------------------------

### Configure Build

Source: https://github.com/numbbo/coco-experiment/blob/main/test/integration-test/README.md

Configure the build system using CMake. This command prepares the build environment.

```bash
cmake -B build
```

--------------------------------

### Creating a Static Library

Source: https://github.com/numbbo/coco-experiment/blob/main/test/unit-test/CMakeLists.txt

Builds a static library named 'about_equal' from its source and header files. Includes public directory for headers.

```cmake
add_library(about_equal STATIC about_equal.c about_equal.h)
target_include_directories(about_equal PUBLIC .)
if(MATH_LIBRARY)
    target_link_libraries(about_equal PUBLIC ${MATH_LIBRARY})
endif()
```

--------------------------------

### Fabricate Sources

Source: https://github.com/numbbo/coco-experiment/blob/main/test/integration-test/README.md

Run this command to fabricate the necessary sources for the tests. Ensure you are in the correct directory.

```bash
python ../../../scripts/fabricate
```

--------------------------------

### Run Tests with Valgrind

Source: https://github.com/numbbo/coco-experiment/blob/main/test/unit-test/README.md

Execute the test suite using valgrind to detect potential memory leaks. This command is only available on Linux.

```bash
ctest -T memorycheck --text-dir build
```

--------------------------------

### Change Directory to Unit Tests

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Navigates the file system to the unit tests directory.

```sh
cd test/unit-test
```

--------------------------------

### Build Wheel using build

Source: https://github.com/numbbo/coco-experiment/blob/main/build/python/DEVELOPMENT.md

Build a wheel package using the 'build' tool. Execute this command from the root directory of the cocoex Python package.

```sh
python -m build -w .
```

--------------------------------

### Execute Matlab Experiment

Source: https://github.com/numbbo/coco-experiment/blob/main/build/octave/README.md

Run a Matlab experiment from the system shell. Ensure the experiment file is in the current directory or on the Matlab path.

```shell
matlab exampleexperiment_new_name.m
```

--------------------------------

### Execute Octave Experiment

Source: https://github.com/numbbo/coco-experiment/blob/main/build/octave/README.md

Run an Octave experiment from the system shell. Ensure the experiment file is in the current directory or on the Octave path.

```shell
octave exampleexperiment_new_name.m
```

--------------------------------

### Build Tests with CMake

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Configures and builds the project's tests using CMake. The -B flag creates a build directory if it doesn't exist.

```sh
cmake -B build
```

```sh
cmake --build build
```

--------------------------------

### Configure Build with CMake

Source: https://github.com/numbbo/coco-experiment/blob/main/build/java/README.md

Use this command to configure the build process for the Java and C++ components of the CoCO framework.

```bash
cmake -B build .
```

--------------------------------

### Build sdist Archive using Hatchling

Source: https://github.com/numbbo/coco-experiment/blob/main/build/python/DEVELOPMENT.md

Build a source distribution (sdist tar.gz) using hatchling. Run this command from the root directory of the cocoex Python package.

```sh
python -m hatchling build -t sdist -d dist/
```

--------------------------------

### Execute Matlab/Octave Experiment from Shell

Source: https://github.com/numbbo/coco-experiment/blob/main/build/octave/README.md

Alternatively, execute the experiment directly from the Matlab or Octave interactive shell.

```matlab
example_experiment_new_name
```

--------------------------------

### Build coco-sys Crate

Source: https://github.com/numbbo/coco-experiment/blob/main/build/rust/README.md

Build the coco-sys crate, which provides the low-level system bindings for COCO.

```sh
cargo build -p coco-sys
```

--------------------------------

### Finding Libraries

Source: https://github.com/numbbo/coco-experiment/blob/main/test/unit-test/CMakeLists.txt

Locates system libraries like libm and librt, which may be required for certain functionalities.

```cmake
find_library(LIBM m)
find_library(LIBRT rt)
```

--------------------------------

### Create Conda Environment

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Use this command to create a new conda environment with all necessary dependencies from the env.yaml file.

```sh
conda env create -f env.yaml
```

--------------------------------

### Run Tests (Linux/macOS)

Source: https://github.com/numbbo/coco-experiment/blob/main/test/integration-test/README.md

Execute the tests using ctest on Linux or macOS. This command runs the compiled tests.

```bash
ctest --test-dir build
```

--------------------------------

### Upload Python Packages to PyPI

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Uploads the built Python source package and wheels to the Python Package Index (PyPI) using the twine utility.

```sh
twine upload dist/*
```

--------------------------------

### Build coco-rs Crate

Source: https://github.com/numbbo/coco-experiment/blob/main/build/rust/README.md

Build the main coco-rs crate, which includes the higher-level Rust API.

```sh
cargo build
```

--------------------------------

### Run Tests (Windows)

Source: https://github.com/numbbo/coco-experiment/blob/main/test/integration-test/README.md

Execute the tests using ctest on Windows, specifying the Debug configuration. This command runs the compiled tests.

```bash
ctest --test-dir build -C Debug
```

--------------------------------

### Run Tests with CTest

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Executes the built tests using CTest, specifying the build directory.

```sh
ctest --test-dir build
```

```sh
ctest --test-dir build -C Debug
```

--------------------------------

### Build MATLAB SMS-EMOA Implementation

Source: https://github.com/numbbo/coco-experiment/blob/main/examples/bbob-biobj-matlab-smsemoa/README.md

Builds the MATLAB implementation of SMS-EMOA by updating COCO framework files. This command is executed in the shell before running MATLAB scripts.

```shell
python do.py build-matlab-sms
```

--------------------------------

### MinUnit Test Macro Definition

Source: https://github.com/numbbo/coco-experiment/blob/main/test/unit-test/CMakeLists.txt

Defines a macro to streamline the creation of MinUnit test executables. It adds the executable, links the 'about_equal' library and system libraries, and registers it as a CTest.

```cmake
macro(minunit_test name)  
  add_executable(${name} ${name}.c)
  target_link_libraries(${name} PUBLIC about_equal)
  if (LIBM)
    target_link_libraries(${name} PUBLIC ${LIBM})
  endif()
  if (LIBRT)
    target_link_libraries(${name} PUBLIC ${LIBRT})
  endif()
  add_test(NAME ${name} 
           COMMAND $<TARGET_FILE:${name}> 
           WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
endmacro()
```

--------------------------------

### Tag and Push Git Repository

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Tags a specific commit with a version number and pushes the tag to the remote repository to trigger a release build.

```sh
git tag -a -m 'Version X.Y.Z' vX.Y.Z
```

```sh
git push --tags
```

--------------------------------

### Activate Conda Environment

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Activates the specified conda environment, making its tools and packages available in your current shell session.

```sh
conda activate cocoex
```

--------------------------------

### Rerun Fabricate Script

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Executes the fabricate script to bundle C files and update binding metadata. This should be run after core file changes.

```sh
python ../../scripts/fabricate
```

--------------------------------

### Find Java and JNI Packages

Source: https://github.com/numbbo/coco-experiment/blob/main/build/java/CMakeLists.txt

Locates the required Java and JNI development packages. The 'REQUIRED' keyword ensures the build fails if these packages are not found.

```cmake
find_package(Java REQUIRED)
find_package(JNI REQUIRED)
include(UseJava)
```

--------------------------------

### Add Native Library Target

Source: https://github.com/numbbo/coco-experiment/blob/main/build/java/CMakeLists.txt

Creates a shared native library 'CocoJNI' from C source files. It links this library against the 'coco-native' target and includes JNI directories.

```cmake
add_library(CocoJNI SHARED CocoJNI.c)
target_link_libraries(CocoJNI PRIVATE coco-native)
target_include_directories(CocoJNI PRIVATE ${JNI_INCLUDE_DIRS})
```

--------------------------------

### Tainted Problem Test Executable

Source: https://github.com/numbbo/coco-experiment/blob/main/test/unit-test/CMakeLists.txt

Adds the 'test_tainted_problem' executable, linking it with necessary libraries and registering it as a test with specific arguments and failure properties.

```cmake
add_executable(test_tainted_problem test_tainted_problem.c coco.c)
if (LIBM)
  target_link_libraries(test_tainted_problem PUBLIC ${LIBM})
endif()
if (LIBRT)
  target_link_libraries(test_tainted_problem PUBLIC ${LIBRT})
endif()

add_test(NAME test_tainted-bbob COMMAND $<TARGET_FILE:test_tainted_problem> bbob)
set_property(TEST test_tainted-bbob PROPERTY WILL_FAIL YES)
add_test(NAME test_tainted-bbob-largescale COMMAND $<TARGET_FILE:test_tainted_problem> bbob-largescale)
set_property(TEST test_tainted-bbob-largescale PROPERTY WILL_FAIL YES)
```

--------------------------------

### MinUnit Test Invocations

Source: https://github.com/numbbo/coco-experiment/blob/main/test/unit-test/CMakeLists.txt

Calls the 'minunit_test' macro to define and configure multiple unit tests for various components of the COCO library.

```cmake
minunit_test(test_biobj_utilities)
minunit_test(test_brentq)
minunit_test(test_coco_archive)
minunit_test(test_coco_observer)
minunit_test(test_coco_problem)
minunit_test(test_coco_string)
minunit_test(test_coco_utilities)
minunit_test(test_logger_bbob)
minunit_test(test_logger_biobj)
minunit_test(test_mo_utilities)
```

--------------------------------

### Add Compilation Fix for Older MATLAB/GCC

Source: https://github.com/numbbo/coco-experiment/blob/main/build/octave/README.md

This preprocessor directive may be necessary for C files compiled with gcc in older MATLAB versions (before 2015b). It should be placed before the include of 'mex.h'.

```c
#define char16_t UINT16_T
```

--------------------------------

### Update Conda Environment

Source: https://github.com/numbbo/coco-experiment/blob/main/DEVELOPMENT.md

Use this command to update an existing conda environment with dependencies from env.yaml, pruning any unused packages.

```sh
conda env update -f env.yaml --prune
```

--------------------------------

### Add Java JAR Target

Source: https://github.com/numbbo/coco-experiment/blob/main/build/java/CMakeLists.txt

Defines a Java Archive (JAR) target named 'coco' with specified source files. It also generates native headers for JNI integration.

```cmake
add_jar(coco
  Benchmark.java 
  CocoJNI.java 
  ExampleExperiment.java
  Observer.java
  Problem.java
  Suite.java
  GENERATE_NATIVE_HEADERS coco-native)
```

--------------------------------

### Import cocoex in Python

Source: https://github.com/numbbo/coco-experiment/blob/main/build/python/README.md

When using the coco-experiment package in your Python code, the import name is 'cocoex'. This is similar to how other packages like scikit-learn are structured.

```python
import cocoex
```

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