Feature/fictive species

.github/build_dependencies.sh

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+#!/bin/bash
+pushd ${RUNNER_TEMP}
+
+curl -fsSLO "https://github.com/HDFGroup/hdf5/releases/download/hdf5_${HDF5_VERSION}/hdf5-${HDF5_VERSION}.tar.gz"
+tar -xzf hdf5-${HDF5_VERSION}.tar.gz
+mkdir -p hdf5-${HDF5_VERSION}/build
+pushd hdf5-${HDF5_VERSION}/build
+
+cmake -G "$GENERATOR" \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX="${HDF5_DIR}" \
+    -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON \
+    -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON \
+    -DHDF5_BUILD_EXAMPLES:BOOL=OFF \
+    -DHDF5_BUILD_TOOLS:BOOL=OFF \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ \
+    -DZLIB_PACKAGE_NAME:STRING=zlib \
+    -DZLIB_TGZ_NAME:STRING=zlib-${ZLIB_VERSION}.tar.gz \
+    -DZLIB_TGZ_ORIGPATH:STRING=https://github.com/madler/zlib/releases/download/v${ZLIB_VERSION} \
+    -DZLIB_USE_LOCALCONTENT:BOOL=OFF \
+    -DLIBAEC_PACKAGE_NAME:STRING=libaec \
+    -DLIBAEC_TGZ_NAME:STRING=libaec-${LIBAEC_VERSION}.tar.gz \
+    -DLIBAEC_TGZ_ORIGPATH:STRING=https://github.com/MathisRosenhauer/libaec/releases/download/v${LIBAEC_VERSION} \
+    -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF \
+    -DHDF_PACKAGE_NAMESPACE:STRING=ct_ \
+    ..
+
+cmake --build . --target install --config Release
+popd
+
+curl -fsSLO https://github.com/BlueBrain/HighFive/archive/refs/tags/v${HIGHFIVE_VERSION}.tar.gz
+tar -xzf v${HIGHFIVE_VERSION}.tar.gz
+mkdir -p HighFive-${HIGHFIVE_VERSION}/build
+pushd HighFive-${HIGHFIVE_VERSION}/build
+
+cmake -G "$GENERATOR" \
+    -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DHDF5_ROOT="${HDF5_DIR}" \
+    -DCMAKE_INSTALL_PREFIX="${HIGHFIVE_DIR}" \
+    -DHIGHFIVE_USE_BOOST:BOOL=OFF \
+    -DHIGHFIVE_UNIT_TESTS:BOOL=OFF \
+    -DHIGHFIVE_EXAMPLES:BOOL=OFF \
+    -DHIGHFIVE_BUILD_DOCS:BOOL=OFF \
+    ..
+
+cmake --build . --target install --config Release
+popd
+
+curl -fsSLO https://github.com/LLNL/sundials/releases/download/v${SUNDIALS_VERSION}/sundials-${SUNDIALS_VERSION}.tar.gz
+tar -xzf sundials-${SUNDIALS_VERSION}.tar.gz
+mkdir -p sundials-${SUNDIALS_VERSION}/build
+pushd sundials-${SUNDIALS_VERSION}/build
+
+cmake -G "$GENERATOR" \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX="${SUNDIALS_DIR}" \
+    -DEXAMPLES_INSTALL=OFF \
+    -DEXAMPLES_ENABLE_C=OFF \
+    -DBUILD_ARKODE=OFF \
+    -DBUILD_CVODE=OFF \
+    -DBUILD_IDA=OFF \
+    -DBUILD_KINSOL=OFF \
+    -DBUILD_CPODES=OFF \
+    -DBUILD_FORTRAN_MODULE_INTERFACE=OFF \
+    "${SUNDIALS_BUILD_OPTIONS[@]}" \
+    ..
+
+cmake --build . --target install --config Release
+popd
+
+curl -fsSLO https://github.com/jbeder/yaml-cpp/archive/refs/tags/${YAML_CPP_VERSION}.tar.gz
+tar -xzf ${YAML_CPP_VERSION}.tar.gz
+mkdir -p yaml-cpp-${YAML_CPP_VERSION}/build
+pushd yaml-cpp-${YAML_CPP_VERSION}/build
+cmake -G "$GENERATOR" \
+    -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
+    -DCMAKE_INSTALL_PREFIX="${YAML_CPP_DIR}" \
+    -DCMAKE_BUILD_TYPE:STRING=Release \
+    -DCMAKE_INSTALL_LIBDIR:STRING=lib \
+    -DYAML_CPP_FORMAT_SOURCE:BOOL=OFF \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DBUILD_SHARED_LIBS:BOOL=ON \
+    ..
+
+cmake --build . --target install --config Release
+popd

.github/cibw_before_all_macos.sh

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+#!/bin/bash
+# Adapted from h5py. Licensed under the BSD 3-Clause license.
+# Copyright (c) 2008 Andrew Collette and contributors
+# All rights reserved.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+
+# 1. Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+
+# 2. Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the
+#    distribution.
+
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from
+#    this software without specific prior written permission.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+set -eo pipefail # Option pour que le script exit si une erreur est détecté dans l'un des pipeline 
+set +x # set -x correspond au mode debug qui permet de print les commende avant de les exécuter, set -x permet d'éviter ça (utile pour éviter que les token github apparaissent dans les log) 
+
+function setup_github_env {
+    echo "HDF5_ROOT=${HDF5_DIR}" | tee -a $GITHUB_ENV
+    echo "HighFive_ROOT=${HIGHFIVE_DIR}" | tee -a $GITHUB_ENV
+    echo "SUNDIALS_ROOT=${SUNDIALS_DIR}" | tee -a $GITHUB_ENV
+    echo "MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}" | tee -a $GITHUB_ENV
+    echo "DYLD_FALLBACK_LIBRARY_PATH=${HDF5_DIR}/lib:${YAML_CPP_DIR}/lib" | tee -a $GITHUB_ENV
+    echo "yaml-cpp_ROOT=${YAML_CPP_DIR}" | tee -a $GITHUB_ENV
+}
+
+# Check if the current script ($0) is called with the correct option ($1) which should correspond to the project path 
+if [[ "$1" == "" ]] ; then
+    echo "Usage: $0 <PROJECT_PATH>"
+    exit 1
+fi
+
+PROJECT_PATH="$1"
+ARCH=$(uname -m) # Récupère l'architecture du système (arm64 / x86_64 ...)
+GENERATOR="Ninja"
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
+source "${SCRIPT_DIR}/dependencies.sh"
+
+HDF5_DIR="${PROJECT_PATH}/cache/hdf5/${HDF5_VERSION}-${ARCH}"
+HIGHFIVE_DIR="${PROJECT_PATH}/cache/highfive/${HIGHFIVE_VERSION}-${ARCH}"
+SUNDIALS_DIR="${PROJECT_PATH}/cache/sundials/${SUNDIALS_VERSION}-${ARCH}"
+SUNDIALS_BUILD_OPTIONS=(
+    "-DENABLE_LAPACK=ON"
+    "-DBLA_VENDOR=Apple"
+    "-DSUNDIALS_LAPACK_CASE=LOWER"
+    "-DSUNDIALS_LAPACK_UNDERSCORES=NONE"
+)
+YAML_CPP_DIR="${PROJECT_PATH}/cache/yaml-cpp/${YAML_CPP_VERSION}-${ARCH}"
+
+# When compiling HDF5, we should use the minimum across all Python versions for a given
+# arch, for versions see for example a more updated version of the following:
+# https://github.com/pypa/cibuildwheel/blob/9c75ea15c2f31a77e6043b80b1b7081372319d85/cibuildwheel/macos.py#L302-L315
+if [[ "${ARCH}" == "arm64" ]]; then
+    export MACOSX_DEPLOYMENT_TARGET="11.0"
+else
+    # This is the minimum version for Cantera
+    export MACOSX_DEPLOYMENT_TARGET="10.15"
+fi
+
+lib_name=libhdf5.dylib
+inc_name=highfive.hpp
+
+if [ -f ${HDF5_DIR}/lib/${lib_name} ] && [ -f ${HIGHFIVE_DIR}/include/highfive/${inc_name} ]; then
+    echo "using cached build"
+    setup_github_env
+    exit 0
+else
+    echo "building dependencies"
+fi
+
+brew uninstall cmake
+
+brew install ninja cmake --formula
+
+source "${SCRIPT_DIR}/build_dependencies.sh" # Build here hdf5, highFive, sundials, yaml_cpp
+
+setup_github_env

.github/dependencies.sh

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+export HDF5_VERSION="1.14.5"
+export LIBAEC_VERSION="1.1.3"
+export ZLIB_VERSION="1.3.1"
+export HIGHFIVE_VERSION="2.10.0"
+export SUNDIALS_VERSION="7.1.1"
+export YAML_CPP_VERSION="0.8.0"