Commit 7d215bee authored by Thomas Purcell's avatar Thomas Purcell
Browse files

Update file docstrings for C++ header files and standardize path names

parent 63884b07
...@@ -3,7 +3,7 @@ ...@@ -3,7 +3,7 @@
* *
* A dictionary representation of the domain for a features (key = domain, value = power) * A dictionary representation of the domain for a features (key = domain, value = power)
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
......
#include <descriptor_identifier/Model/ModelLogRegressorFitC.hpp> #include <descriptor_identifier/model/ModelLogRegressorFitC.hpp>
ModelLogRegressorFitC::ModelLogRegressorFitC(Unit prop_unit, std::vector<double> prop_train, std::vector<double> prop_test, std::vector<model_node_ptr> feats, std::vector<int> task_sizes_train, std::vector<int> task_sizes_test, bool fix_intercept) : ModelLogRegressorFitC::ModelLogRegressorFitC(Unit prop_unit, std::vector<double> prop_train, std::vector<double> prop_test, std::vector<model_node_ptr> feats, std::vector<int> task_sizes_train, std::vector<int> task_sizes_test, bool fix_intercept) :
ModelLogRegressor(prop_unit, prop_train, prop_test, feats, task_sizes_train, task_sizes_test, fix_intercept), ModelLogRegressor(prop_unit, prop_train, prop_test, feats, task_sizes_train, task_sizes_test, fix_intercept),
......
...@@ -4,13 +4,14 @@ ...@@ -4,13 +4,14 @@
* Creates a ModelLogRegressorFitC generated from SISSO and the corresponding output file. * Creates a ModelLogRegressorFitC generated from SISSO and the corresponding output file.
* It also has functionality to read in an output file to regenerate the model. * It also has functionality to read in an output file to regenerate the model.
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef MODEL_LOG_REGRESSOR_FIT_C #ifndef MODEL_LOG_REGRESSOR_FIT_C
#define MODEL_LOG_REGRESSOR_FIT_C #define MODEL_LOG_REGRESSOR_FIT_C
#include <descriptor_identifier/Model/ModelLogRegressor.hpp> #include <descriptor_identifier/model/ModelLogRegressor.hpp>
#include <nl_opt/NLOptWrapper.hpp> #include <nl_opt/NLOptWrapper.hpp>
#ifdef PY_BINDINGS #ifdef PY_BINDINGS
namespace np = boost::python::numpy; namespace np = boost::python::numpy;
......
#include <descriptor_identifier/SISSO_DI/SISSOLogRegressorFitC.hpp> #include <descriptor_identifier/solver/SISSOLogRegressorFitC.hpp>
SISSOLogRegressorFitC::SISSOLogRegressorFitC( SISSOLogRegressorFitC::SISSOLogRegressorFitC(
std::shared_ptr<FeatureSpace> feat_space, std::shared_ptr<FeatureSpace> feat_space,
......
...@@ -3,14 +3,15 @@ ...@@ -3,14 +3,15 @@
* *
* Takes in a feature space and performs SISSO on it while storing the selected features in _models * Takes in a feature space and performs SISSO on it while storing the selected features in _models
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef SISSO_LOG_REGRESSOR_FIT_C #ifndef SISSO_LOG_REGRESSOR_FIT_C
#define SISSO_LOG_REGRESSOR_FIT_C #define SISSO_LOG_REGRESSOR_FIT_C
#include <descriptor_identifier/Model/ModelLogRegressorFitC.hpp> #include <descriptor_identifier/model/ModelLogRegressorFitC.hpp>
#include <descriptor_identifier/SISSO_DI/SISSOLogRegressor.hpp> #include <descriptor_identifier/solver/SISSOLogRegressor.hpp>
#ifdef PY_BINDINGS #ifdef PY_BINDINGS
namespace np = boost::python::numpy; namespace np = boost::python::numpy;
...@@ -146,7 +147,7 @@ public: ...@@ -146,7 +147,7 @@ public:
// DocString: sisso_log_reg_models_py // DocString: sisso_log_reg_models_py
/** /**
* @brief The selected models (cpp definition in <python/descriptor_identifier/SISSO_DI.cpp) * @brief The selected models (cpp definition in <python/descriptor_identifier/SISSOSolver.cpp)
* @return models as a python list * @return models as a python list
*/ */
py::list models_py(); py::list models_py();
......
...@@ -11,12 +11,14 @@ ...@@ -11,12 +11,14 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file classification/ConvexHull1D.hpp /** @file classification/ConvexHull1D.hpp
* @brief A set of functions to create convex hulls, and compare overlap/distance * @brief Defines a class that calculates the 1D Convex Hull overlap of a vector with property labels
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef CONVEX_UTILS #ifndef CONVEX_UTILS
#define CONVEX_UTILS #define CONVEX_UTILS
......
...@@ -11,10 +11,11 @@ ...@@ -11,10 +11,11 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file classification/LPWrapper.hpp /** @file classification/LPWrapper.hpp
* @brief A class used to wrap Coin-Clp into a single class * @brief A class used to wrap the Coin-Clp Simplex Library, and facilitate its use with SISSO++
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
......
...@@ -11,6 +11,7 @@ ...@@ -11,6 +11,7 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
#include "classification/SVMWrapper.hpp" #include "classification/SVMWrapper.hpp"
SVMWrapper::SVMWrapper(const int n_class, const int n_dim, const int n_samp, const double* prop) : SVMWrapper::SVMWrapper(const int n_class, const int n_dim, const int n_samp, const double* prop) :
......
...@@ -11,10 +11,11 @@ ...@@ -11,10 +11,11 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file classification/SVMWrapper.hpp /** @file classification/SVMWrapper.hpp
* @brief A class used to wrap libsvm in more C++ oriented data structure * @brief A class used to wrap libsvm in more C++ oriented data structure
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
......
...@@ -11,12 +11,14 @@ ...@@ -11,12 +11,14 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file classification/prop_sorted_d_mat.hpp
* @brief Central storage area for a sorted descriptor matrix based on the task/class of a sample
* @author Thomas A. R. Purcell (tpurcell) /** @file classification/prop_sorted_d_mat.hpp
* @brief Central storage area for a sorted descriptor matrix based on the task/class of a sample
*
* @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef PROP_SORTED_D_MAT #ifndef PROP_SORTED_D_MAT
#define PROP_SORTED_D_MAT #define PROP_SORTED_D_MAT
......
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
#include "descriptor_identifier/Model/Model.hpp" #include "descriptor_identifier/model/Model.hpp"
Model::Model( Model::Model(
const std::string prop_label, const std::string prop_label,
......
...@@ -11,15 +11,14 @@ ...@@ -11,15 +11,14 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file descriptor_identifier/Model/Model.hpp
* @brief Object to store the models generated form SISSO /** @file descriptor_identifier/model/Model.hpp
* * @brief Defines the base class of the output Models for SISSO
* Creates a Model generated from SISSO and the corresponding output file.
* It also has functionality to read in an output file to regenerate the model.
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef MODEL #ifndef MODEL
#define MODEL #define MODEL
......
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
#include "descriptor_identifier/Model/ModelClassifier.hpp" #include "descriptor_identifier/model/ModelClassifier.hpp"
ModelClassifier::ModelClassifier( ModelClassifier::ModelClassifier(
const std::string prop_label, const std::string prop_label,
......
...@@ -11,19 +11,18 @@ ...@@ -11,19 +11,18 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file descriptor_identifier/ModelClassifier/ModelClassifier.hpp
* @brief Object to store the models generated form SISSO /** @file descriptor_identifier/model/ModelClassifier.hpp
* * @brief Defines a class for the output models from solving a classification problem
* Creates a ModelClassifier generated from SISSO and the corresponding output file.
* It also has functionality to read in an output file to regenerate the model.
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef MODEL_CLASSIFIER #ifndef MODEL_CLASSIFIER
#define MODEL_CLASSIFIER #define MODEL_CLASSIFIER
#include "descriptor_identifier/Model/Model.hpp" #include "descriptor_identifier/model/Model.hpp"
#ifdef PY_BINDINGS #ifdef PY_BINDINGS
namespace np = boost::python::numpy; namespace np = boost::python::numpy;
......
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
#include "descriptor_identifier/Model/ModelLogRegressor.hpp" #include "descriptor_identifier/model/ModelLogRegressor.hpp"
ModelLogRegressor::ModelLogRegressor() ModelLogRegressor::ModelLogRegressor()
{} {}
......
...@@ -11,19 +11,18 @@ ...@@ -11,19 +11,18 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file descriptor_identifier/ModelLogRegressor/ModelLogRegressor.hpp
* @brief Object to store the models generated form SISSO /** @file descriptor_identifier/model/ModelLogRegressor.hpp
* * @brief Defines a class for the output models from solving a log regression problem
* Creates a ModelLogRegressor generated from SISSO and the corresponding output file.
* It also has functionality to read in an output file to regenerate the model.
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef MODEL_LOG_REGRESSOR #ifndef MODEL_LOG_REGRESSOR
#define MODEL_LOG_REGRESSOR #define MODEL_LOG_REGRESSOR
#include "descriptor_identifier/Model/ModelRegressor.hpp" #include "descriptor_identifier/model/ModelRegressor.hpp"
#ifdef PY_BINDINGS #ifdef PY_BINDINGS
namespace np = boost::python::numpy; namespace np = boost::python::numpy;
......
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
#include "descriptor_identifier/Model/ModelRegressor.hpp" #include "descriptor_identifier/model/ModelRegressor.hpp"
ModelRegressor::ModelRegressor() ModelRegressor::ModelRegressor()
{} {}
......
...@@ -11,19 +11,18 @@ ...@@ -11,19 +11,18 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file descriptor_identifier/ModelRegressor/ModelRegressor.hpp
* @brief Object to store the models generated form SISSO /** @file descriptor_identifier/model/ModelRegressor.hpp
* * @brief Defines a class for the output models from solving a regression problem
* Creates a ModelRegressor generated from SISSO and the corresponding output file.
* It also has functionality to read in an output file to regenerate the model.
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef MODEL_REGRESSOR #ifndef MODEL_REGRESSOR
#define MODEL_REGRESSOR #define MODEL_REGRESSOR
#include "descriptor_identifier/Model/Model.hpp" #include "descriptor_identifier/model/Model.hpp"
#ifdef PY_BINDINGS #ifdef PY_BINDINGS
namespace np = boost::python::numpy; namespace np = boost::python::numpy;
......
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
#include "descriptor_identifier/SISSO_DI/SISSOClassifier.hpp" #include "descriptor_identifier/solver/SISSOClassifier.hpp"
SISSOClassifier::SISSOClassifier( SISSOClassifier::SISSOClassifier(
const std::shared_ptr<FeatureSpace> feat_space, const std::shared_ptr<FeatureSpace> feat_space,
...@@ -26,7 +26,7 @@ SISSOClassifier::SISSOClassifier( ...@@ -26,7 +26,7 @@ SISSOClassifier::SISSOClassifier(
const int n_residual, const int n_residual,
const int n_models_store const int n_models_store
): ):
SISSO_DI( SISSOSolver(
"classification", "classification",
feat_space, feat_space,
prop_label, prop_label,
......
...@@ -11,21 +11,21 @@ ...@@ -11,21 +11,21 @@
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and // See the License for the specific language governing permissions and
// limitations under the License. // limitations under the License.
/** @file descriptor_identifier/SISSOClassifier.hpp /** @file descriptor_identifier/SISSOClassifier.hpp
* @brief Perform SISSO on a previously generated Feature Space * @brief Define a class for solving classification problems with SISSO
*
* Takes in a feature space and performs SISSO on it while storing the selected features in _models
* *
* @author Thomas A. R. Purcell (tpurcell) * @author Thomas A. R. Purcell (tpurcell90)
* @bug No known bugs. * @bug No known bugs.
*/ */
#ifndef SISSO_CLASSIFIER #ifndef SISSO_CLASSIFIER
#define SISSO_CLASSIFIER #define SISSO_CLASSIFIER
#include <coin/ClpSimplex.hpp> #include <coin/ClpSimplex.hpp>
#include "classification/prop_sorted_d_mat.hpp" #include "classification/prop_sorted_d_mat.hpp"
#include "descriptor_identifier/Model/ModelClassifier.hpp" #include "descriptor_identifier/model/ModelClassifier.hpp"
#include "descriptor_identifier/SISSO_DI/SISSO_DI.hpp" #include "descriptor_identifier/solver/SISSOSolver.hpp"
#include "utils/vector_utils.hpp" #include "utils/vector_utils.hpp"
#ifdef PY_BINDINGS #ifdef PY_BINDINGS
...@@ -38,7 +38,7 @@ ...@@ -38,7 +38,7 @@
* @brief SISSO Classifier class, performs the SISSO algorithm and stores all selected models * @brief SISSO Classifier class, performs the SISSO algorithm and stores all selected models
* *
*/ */
class SISSOClassifier: public SISSO_DI class SISSOClassifier: public SISSOSolver
{ {
protected: protected:
std::vector<std::vector<ModelClassifier>> _models; //!< List of models std::vector<std::vector<ModelClassifier>> _models; //!< List of models
......
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