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refactor(serif): fixed typos and updated names to reflect 4DSSE->SERiF

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This commit is contained in:
Emily Boudreaux
2025-06-12 09:04:03 -04:00
parent 620f3d495c
commit 2eca802d01
9 changed files with 302 additions and 308 deletions
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4
meson.build
View File

@@ -18,7 +18,7 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# *********************************************************************** #
project('4DSSE', 'cpp', version: '0.0.1a', default_options: ['cpp_std=c++23'], meson_version: '>=1.6.0')
project('SERiF', 'cpp', version: '0.0.1a', default_options: ['cpp_std=c++23'], meson_version: '>=1.6.0')
# Add default visibility for all C++ targets
add_project_arguments('-fvisibility=default', language: 'cpp')
@@ -32,7 +32,7 @@ endif
if mode == 1
data_dir = meson.project_source_root() + '/assets/dynamic'
else
data_dir = get_option('prefix') + '/' + get_option('datadir') + '/4DSSE'
data_dir = get_option('prefix') + '/' + get_option('datadir') + '/SERiF'
endif
# Pass the DATA_DIR definition to the compiler

64
mk
View File

@@ -26,7 +26,7 @@ Options:
You can use these flags in any order. Flags not passed will get default values.
Examples:
For an end user who wants a seemless experience 4DSSE:
For an end user who wants a seamless experience 4DSSE:
./mk --user
For developers who want to modify the source:
./mk
@@ -83,7 +83,7 @@ if [[ ! -d "$LOGDIR" ]]; then
echo -e "${BLUE}[Info] Creating log directory...${NC}"
mkdir "$LOGDIR"
else
echo -e "${MAGENTA}[Succsess] Log directory already exists. Skipping...${NC}"
echo -e "${MAGENTA}[Success] Log directory already exists. Skipping...${NC}"
fi
LOGFILE="${LOGDIR}/4DSSE-install-log.txt"
@@ -112,7 +112,7 @@ if ! command -v clang &> /dev/null && ! command -v gcc &> /dev/null; then
log "${YELLOW}[Info] Please install Clang or GCC and try again.${NC}"
exit 1
else
log "${MAGENTA}[Succsess] Clang or GCC is installed. Continuing...${NC}"
log "${MAGENTA}[Success] Clang or GCC is installed. Continuing...${NC}"
fi
# --- Check if MESON is installed ---
@@ -137,7 +137,7 @@ if ! command -v meson &> /dev/null; then
log "${YELLOW}[Info] Please install pip and try again.${NC}"
exit 1
else
log "${MAGENTA}[Succsess] pip is installed. Continuing...${NC}"
log "${MAGENTA}[Success] pip is installed. Continuing...${NC}"
fi
# check if python3 is installed
@@ -147,7 +147,7 @@ if ! command -v meson &> /dev/null; then
log "${YELLOW}[INFO] If you have python3 installed, please add it to your PATH.${NC}"
exit 1
else
log "${MAGENTA}[Succsess] python3 is installed. Continuing...${NC}"
log "${MAGENTA}[Success] python3 is installed. Continuing...${NC}"
fi
# Check if the venv ~/.4DSSE_env exists
@@ -155,9 +155,9 @@ if ! command -v meson &> /dev/null; then
log "${BLUE}[Info] Creating virtual environment...${NC}"
python3 -m venv "$HOME/.4DSSE_env"
source "$HOME/.4DSSE_env/bin/activate"
log "${GREEN}[Succsess] Virtual environment created.${NC}"
log "${GREEN}[Success] Virtual environment created.${NC}"
else
log "${MAGENTA}[Succsess] Virtual environment already exists. Skipping...${NC}"
log "${MAGENTA}[Success] Virtual environment already exists. Skipping...${NC}"
fi
# install meson
@@ -170,14 +170,14 @@ if ! command -v meson &> /dev/null; then
log "${YELLOW}[Info] Please manually install Meson and try again.${NC}"
exit 1
else
log "${GREEN}[Succsess] Meson installed.${NC}"
log "${GREEN}[Success] Meson installed.${NC}"
fi
else
log "${YELLOW}[Info] Please install Meson and try again.${NC}"
exit 1
fi
else
log "${MAGENTA}[Succsess] Meson is installed. Continuing...${NC}"
log "${MAGENTA}[Success] Meson is installed. Continuing...${NC}"
fi
# --- Check if NINJA is installed ---
@@ -203,7 +203,7 @@ if ! command -v ninja &> /dev/null; then
log "${YELLOW}[Info] Please install pip and try again.${NC}"
exit 1
else
log "${MAGENTA}[Succsess] pip is installed. Continuing...${NC}"
log "${MAGENTA}[Success] pip is installed. Continuing...${NC}"
fi
# check if python3 is installed
@@ -213,7 +213,7 @@ if ! command -v ninja &> /dev/null; then
log "${YELLOW}[INFO] If you have python3 installed, please add it to your PATH.${NC}"
exit 1
else
log "${MAGENTA}[Succsess] python3 is installed. Continuing...${NC}"
log "${MAGENTA}[Success] python3 is installed. Continuing...${NC}"
fi
# Check if the venv ~/.4DSSE_env exists
@@ -221,9 +221,9 @@ if ! command -v ninja &> /dev/null; then
log "${BLUE}[Info] Creating virtual environment...${NC}"
python3 -m venv "$HOME/.4DSSE_env"
source "$HOME/.4DSSE_env/bin/activate"
log "${GREEN}[Succsess] Virtual environment created.${NC}"
log "${GREEN}[Success] Virtual environment created.${NC}"
else
log "${MAGENTA}[Succsess] Virtual environment already exists. Skipping...${NC}"
log "${MAGENTA}[Success] Virtual environment already exists. Skipping...${NC}"
fi
# install ninja
@@ -236,14 +236,14 @@ if ! command -v ninja &> /dev/null; then
log "${YELLOW}[Info] Please manually install Ninja and try again.${NC}"
exit 1
else
log "${GREEN}[Succsess] Ninja installed.${NC}"
log "${GREEN}[Success] Ninja installed.${NC}"
fi
else
log "${YELLOW}[Info] Please install Ninja and try again.${NC}"
exit 1
fi
else
log "${MAGENTA}[Succsess] Ninja is installed. Continuing...${NC}"
log "${MAGENTA}[Success] Ninja is installed. Continuing...${NC}"
fi
# --- Check if CMake is installed ---
@@ -269,7 +269,7 @@ if ! command -v cmake &> /dev/null; then
log "${YELLOW}[Info] Please install pip and try again.${NC}"
exit 1
else
log "${MAGENTA}[Succsess] pip is installed. Continuing...${NC}"
log "${MAGENTA}[Success] pip is installed. Continuing...${NC}"
fi
# check if python3 is installed
@@ -279,7 +279,7 @@ if ! command -v cmake &> /dev/null; then
log "${YELLOW}[INFO] If you have python3 installed, please add it to your PATH.${NC}"
exit 1
else
log "${MAGENTA}[Succsess] python3 is installed. Continuing...${NC}"
log "${MAGENTA}[Success] python3 is installed. Continuing...${NC}"
fi
# Check if the venv ~/.4DSSE_env exists
@@ -287,9 +287,9 @@ if ! command -v cmake &> /dev/null; then
log "${BLUE}[Info] Creating virtual environment...${NC}"
python3 -m venv "$HOME/.4DSSE_env"
source "$HOME/.4DSSE_env/bin/activate"
log "${GREEN}[Succsess] Virtual environment created.${NC}"
log "${GREEN}[Success] Virtual environment created.${NC}"
else
log "${MAGENTA}[Succsess] Virtual environment already exists. Skipping...${NC}"
log "${MAGENTA}[Success] Virtual environment already exists. Skipping...${NC}"
fi
# install cmake
@@ -302,11 +302,11 @@ if ! command -v cmake &> /dev/null; then
log "${YELLOW}[Info] Please manually install CMake and try again.${NC}"
exit 1
else
log "${GREEN}[Succsess] CMake installed.${NC}"
log "${GREEN}[Success] CMake installed.${NC}"
fi
fi
else
log "${MAGENTA}[Succsess] CMake is installed. Continuing...${NC}"
log "${MAGENTA}[Success] CMake is installed. Continuing...${NC}"
fi
# --- Build 4DSSE ---
@@ -327,7 +327,7 @@ fi
log "${BLUE}[Info] Checking Boost status...${NC}"
# if the following script exists with anything other than a 0 status the script will exit
if [[ -f ./build-config/boost/.boost_installed ]]; then
log "${MAGENTA}[Succsess] Boost already installed. Skipping...${NC}"
log "${MAGENTA}[Success] Boost already installed. Skipping...${NC}"
else
log "${BLUE}[Info] Installing Boost...${NC}"
if ! ./build-config/boost/install.sh; then
@@ -335,7 +335,7 @@ else
exit 1
else
touch ./build-config/boost/.boost_installed
log "${GREEN}[Succsess] Boost check passed.${NC}"
log "${GREEN}[Success] Boost check passed.${NC}"
fi
fi
@@ -343,7 +343,7 @@ fi
log "${BLUE}[Info] Checking MPI status...${NC}"
# if the following script exists with anything other than a 0 status the script will exit
if [[ -f ./build-config/mpi/.mpi_installed ]]; then
log "${MAGENTA}[Succsess] MPI already installed. Skipping...${NC}"
log "${MAGENTA}[Success] MPI already installed. Skipping...${NC}"
else
log "${BLUE}[Info] Installing MPI...${NC}"
if ! ./build-config/mpi/install.sh; then
@@ -351,7 +351,7 @@ else
exit 1
else
touch ./build-config/mpi/.mpi_installed
log "${GREEN}[Succsess] MPI check passed.${NC}"
log "${GREEN}[Success] MPI check passed.${NC}"
fi
fi
@@ -369,7 +369,7 @@ if [[ -f $buildDir/.last_build_flags ]]; then
lastUserFlag=$(grep -Eo 'userFlag=[0-9]+' $buildDir/.last_build_flags | cut -d'=' -f2)
lastTestsFlag=$(grep -Eo 'testsFlag=[0-9]+' $buildDir/.last_build_flags | cut -d'=' -f2)
if [[ $lastUserFlag -eq $userFlag && $lastTestsFlag -eq $testsFlag ]]; then
log "${MAGENTA}[Succsess] Last build flags match current build flags. Skipping configuration...${NC}"
log "${MAGENTA}[Success] Last build flags match current build flags. Skipping configuration...${NC}"
doReconfigure=0
else
log "${YELLOW}[Info] Last build flags do not match current build flags. Reconfiguring...${NC}"
@@ -384,7 +384,7 @@ fi
if [[ $doReconfigure -eq 1 ]]; then
log "${BLUE}[Info] Configuring build directory...${NC}"
if [ -f "$buildDir/build.ninja" ]; then
log "${MAGENTA}[Succsess] Build directory already configured. Skipping...${NC}"
log "${MAGENTA}[Success] Build directory already configured. Skipping...${NC}"
else
if [[ $userFlag -eq 1 ]]; then
meson setup "$buildDir" -Duser_mode=true --buildtype=release
@@ -395,7 +395,7 @@ if [[ $doReconfigure -eq 1 ]]; then
meson setup "$buildDir" --buildtype=debug -Dbuild_tests=false
fi
fi
log "${GREEN}[Succsess] Build directory configured successfully.${NC}"
log "${GREEN}[Success] Build directory configured successfully.${NC}"
fi
log "${BLUE}[Info] Caching last build flags...${NC}"
@@ -411,7 +411,7 @@ if [[ $doReconfigure -eq 1 ]]; then
echo "testsFlag=0" >> $buildDir/.last_build_flags
fi
log "${GREEN}[Succsess] Last build flags cached.${NC}"
log "${GREEN}[Success] Last build flags cached.${NC}"
fi
log "${BLUE}[Info] Building 4DSSE...${NC}"
@@ -429,10 +429,10 @@ if [[ $runTestsFlag -eq 1 ]]; then
fi
if [[ $userFlag -eq 1 ]]; then
log "${GREEN}[Succsess] 4DSSE built and installed successfully.${NC}"
log "${GREEN}[Success] 4DSSE built and installed successfully.${NC}"
else
log "${GREEN}[Succsess] 4DSSE built successfully.${NC}"
log "${GREEN}[Success] 4DSSE built successfully.${NC}"
fi
log "${GREEN}[Succsess] 4DSSE mk script complete.${NC}"
log "${GREEN}[Success] 4DSSE mk script complete.${NC}"

10
src/config/private/config.cpp
View File

@@ -29,8 +29,7 @@
#include "config.h"
namespace serif {
namespace config {
namespace serif::config {
Config::Config() {}
@@ -90,8 +89,8 @@ bool Config::has(const std::string &key) {
void recurse_keys(const YAML::Node& node, std::vector<std::string>& keyList, const std::string& path = "") {
if (node.IsMap()) {
for (const auto& it : node) {
std::string key = it.first.as<std::string>();
std::string new_path = path.empty() ? key : path + ":" + key;
auto key = it.first.as<std::string>();
auto new_path = path.empty() ? key : path + ":" + key;
recurse_keys(it.second, keyList, new_path);
}
} else {
@@ -107,5 +106,4 @@ std::vector<std::string> Config::keys() const {
return keyList;
}
} // namespace config
} // namespace serif
}

9
src/config/public/config.h
View File

@@ -32,11 +32,11 @@
#include "yaml-cpp/yaml.h"
// -- Forward Def of Resource manager to let it act as a friend of Config --
namespace serif { namespace resource { class ResourceManager; } } // Forward declaration
namespace serif::resource { class ResourceManager; }
class configTestPrivateAccessor; // Forward declaration for test utility
namespace serif {
namespace config {
namespace serif::config {
/**
* @class Config
@@ -242,5 +242,4 @@ public:
friend class serif::resource::ResourceManager; // Adjusted friend declaration
};
} // namespace config
} // namespace serif
}

12
src/eos/private/helm.cpp
View File

@@ -41,12 +41,16 @@
#include "config.h"
#include "quill/LogMacros.h"
namespace serif::constant {
class Constants;
}
using namespace std;
// interpolating polynomila function definitions
namespace serif::eos::helmholtz {
double** heap_allocate_contiguous_2D_memory(int rows, int cols) {
double **array = new double*[rows];
auto array = new double*[rows];
array[0] = new double[rows * cols];
for (int i = 1; i < rows; i++) {
@@ -124,13 +128,13 @@ namespace serif::eos::helmholtz {
// this function reads in the HELM table and stores in the above arrays
std::unique_ptr<HELMTable> read_helm_table(const std::string filename) {
serif::config::Config& config = serif::config::Config::getInstance();
std::string logFile = config.get<std::string>("EOS:Helm:LogFile", "log");
auto logFile = config.get<std::string>("EOS:Helm:LogFile", "log");
serif::probe::LogManager& logManager = serif::probe::LogManager::getInstance();
quill::Logger* logger = logManager.getLogger(logFile);
LOG_INFO(logger, "read_helm_table : Reading HELM table from file {}", filename);
// Make a unique pointer to the HELMTable
std::unique_ptr<serif::eos::helmholtz::HELMTable> table = std::make_unique<serif::eos::helmholtz::HELMTable>();
auto table = std::make_unique<serif::eos::helmholtz::HELMTable>();
string data;
int i, j;
@@ -235,7 +239,7 @@ namespace serif::eos::helmholtz {
***/
serif::eos::helmholtz::EOS get_helm_EOS(serif::eos::helmholtz::EOSInput &q, const serif::eos::helmholtz::HELMTable &table) {
serif::config::Config& config = serif::config::Config::getInstance();
std::string logFile = config.get<std::string>("EOS:Helm:LogFile", "log");
auto logFile = config.get<std::string>("EOS:Helm:LogFile", "log");
serif::probe::LogManager& logManager = serif::probe::LogManager::getInstance();
quill::Logger* logger = logManager.getLogger(logFile);

13
src/polytrope/utils/private/integrators.cpp
View File

@@ -25,9 +25,7 @@
#include "config.h"
#include <string>
namespace serif {
namespace polytrope {
namespace polyMFEMUtils {
namespace serif::polytrope::polyMFEMUtils {
NonlinearPowerIntegrator::NonlinearPowerIntegrator(const double n) :
m_polytropicIndex(n),
m_epsilon(serif::config::Config::getInstance().get<double>("Poly:Solver:Epsilon", 1.0e-8)) {
@@ -50,7 +48,7 @@ namespace polyMFEMUtils {
mfem::Vector &elvect) {
const mfem::IntegrationRule *ir = &mfem::IntRules.Get(el.GetGeomType(), 2 * el.GetOrder() + 3);
int dof = el.GetDof();
const int dof = el.GetDof();
elvect.SetSize(dof);
elvect = 0.0;
@@ -71,9 +69,6 @@ namespace polyMFEMUtils {
double u_nl;
Trans.Transform(ip, physCoord);
const double r = physCoord.Norml2();
std::ofstream outFile("r.dat", std::ios::app);
outFile << r << '\n';
outFile.close();
if (r > m_regularizationRadius) {
if (u_val < m_epsilon) {
u_nl = fmod(u_val, m_polytropicIndex, m_epsilon);
@@ -141,6 +136,4 @@ namespace polyMFEMUtils {
}
}
} // namespace polyMFEMUtils
} // namespace polytrope
} // namespace serif
}

4
src/resource/private/resourceManager.cpp
View File

@@ -38,7 +38,7 @@ namespace serif::resource {
ResourceManager::ResourceManager() {
const std::string defaultDataDir = TOSTRING(DATA_DIR);
m_dataDir = m_config.get<std::string>("Data:Dir", defaultDataDir);
// -- Get the index file path using filesytem to make it a system safe path
// -- Get the index file path using filesystem to make it a system safe path
const std::string indexFilePath = m_dataDir + "/index.yaml";
// TODO Add checks to make sure data dir exists and index.yaml exists
const std::filesystem::path indexFile(indexFilePath);
@@ -50,7 +50,7 @@ namespace serif::resource {
}
std::vector<std::string> ResourceManager::getAvaliableResources() const {
std::vector<std::string> ResourceManager::getAvailableResources() const {
const std::vector<std::string> resources = m_resourceConfig.keys();
return resources;
}

4
src/resource/public/resourceManager.h
View File

@@ -87,10 +87,10 @@ namespace serif::resource {
* Example usage:
* @code
* ResourceManager& manager = ResourceManager::getInstance();
* std::vector<std::string> resources = manager.getAvaliableResources();
* std::vector<std::string> resources = manager.getAvailableResources();
* @endcode
*/
std::vector<std::string> getAvaliableResources() const;
std::vector<std::string> getAvailableResources() const;
/**
* @brief Gets a resource by name.

2
tests/resource/resourceManagerTest.cpp
View File

@@ -35,7 +35,7 @@ TEST_F(resourceManagerTest, constructor) {
TEST_F(resourceManagerTest, getAvaliableResources) {
serif::config::Config::getInstance().loadConfig(TEST_CONFIG);
serif::resource::ResourceManager& rm = serif::resource::ResourceManager::getInstance();
std::vector<std::string> resources = rm.getAvaliableResources();
std::vector<std::string> resources = rm.getAvailableResources();
std::set<std::string> expected = {"eos:helm", "mesh:sphere"};
std::set<std::string> actual(resources.begin(), resources.end());
EXPECT_EQ(expected, actual);