Update python library DocStrings

Set up for the python API

src/descriptor_identifier/Model/Model.hpp

@@ -304,6 +304,7 @@ public:
      */
     virtual std::string matlab_expr() const = 0;
 
+    // DocString: model_to_matlab
     /**
      * @brief Convert the model into a Matlab function
      *
@@ -444,6 +445,7 @@ public:
      */
     inline py::list leave_out_inds(){return python_conv_utils::to_list<int>(_leave_out_inds);}
 
+    // DocString: model_eval_arr
     /**
      * @brief Evaluate the model for a new point
      *
@@ -452,6 +454,7 @@ public:
      */
     inline double eval_py(np::ndarray x_in) const {return eval(python_conv_utils::from_ndarray<double>(x_in));}
 
+    // DocString: model_eval_list
     /**
      * @brief Evaluate the model for a new point
      *
@@ -460,14 +463,16 @@ public:
      */
     inline double eval_py(py::list x_in) const {return eval(python_conv_utils::from_list<double>(x_in));}
 
+    // DocString: model_eval_dict
     /**
      * @brief Evaluate the model for a new point
      *
-     * @param x_in_dct Dictionary describing the new point ("feature expr": value)
+     * @param x_in_dct Dictionary describing the new point (\"feature expr\": value)
      * @return The prediction of the model for a given data point
      */
     inline double eval_py(py::dict x_in) const {return eval(python_conv_utils::from_dict<std::string, double>(x_in));}
 
+    // DocString: model_eval_many_arr
     /**
      * @brief Evaluate the model for a set of new points
      *
@@ -476,6 +481,7 @@ public:
      */
     np::ndarray eval_many_py(np::ndarray x_in) const ;
 
+    // DocString: model_eval_many_dict
     /**
      * @brief Evaluate the model for a set of new points
      *

src/descriptor_identifier/Model/ModelClassifier.hpp

@@ -53,7 +53,7 @@ public:
         const std::vector<int> leave_out_inds
     );
 
-    // DocString: model_class_init_str
+    // DocString: model_class_init_train
     /**
      * @brief Construct a model from a training output file
      * @details Reads in all of the data from the output file and recreates the model object
@@ -62,7 +62,7 @@ public:
      */
     ModelClassifier(const std::string train_file);
 
-    // DocString: model_class_init_str_str
+    // DocString: model_class_init_test_train
     /**
      * @brief Construct a model from a training and testing output file
      * @details Reads in all of the data from the output files and recreates the model object
@@ -243,6 +243,7 @@ public:
     }
 
     #ifdef PY_BINDINGS
+    // DocString: model_class_init_new_coefs_list
     /**
      * @brief Construct a new Model with updated coefficient
      * @details Copy a model but update its coefficients
@@ -254,6 +255,7 @@ public:
      */
     ModelClassifier(const ModelClassifier& o, py::list new_coefs, np::ndarray prop_train_est, np::ndarray prop_test_est);
 
+    // DocString: model_class_init_new_coefs_arr
     /**
      * @brief Construct a new Model with updated coefficient
      * @details Copy a model but update its coefficients

src/descriptor_identifier/Model/ModelLogRegressor.hpp

@@ -52,7 +52,7 @@ public:
         const std::vector<int> leave_out_inds
     );
 
-    // DocString: model_log_reg_init_str
+    // DocString: model_log_reg_init_train
     /**
      * @brief Construct a model from a training output file
      * @details Reads in all of the data from the output file and recreates the model object
@@ -61,7 +61,7 @@ public:
      */
     ModelLogRegressor(std::string train_file);
 
-    // DocString: model_log_reg_init_str_str
+    // DocString: model_log_reg_init_test_train
     /**
      * @brief Construct a model from a training and testing output file
      * @details Reads in all of the data from the output files and recreates the model object

src/descriptor_identifier/Model/ModelRegressor.hpp

@@ -51,7 +51,7 @@ public:
         const std::vector<int> leave_out_inds
     );
 
-    // DocString: model_reg_init_str
+    // DocString: model_reg_init_train
     /**
      * @brief Construct a model from a training output file
      * @details Reads in all of the data from the output file and recreates the model object
@@ -60,7 +60,7 @@ public:
      */
     ModelRegressor(const std::string train_file);
 
-    // DocString: model_reg_init_str_str
+    // DocString: model_reg_init_test_train
     /**
      * @brief Construct a model from a training and testing output file
      * @details Reads in all of the data from the output files and recreates the model object

src/descriptor_identifier/SISSO_DI/SISSOClassifier.hpp

@@ -119,6 +119,7 @@ public:
 
     // Python interface functions
     #ifdef PY_BINDINGS
+    // DocString: sisso_class_init_arr
     /**
      * @brief Constructor for the Classifier that takes in python objects (cpp definition in <python/descriptor_identifier/SISSOClassifier.cpp)
      *

src/descriptor_identifier/SISSO_DI/SISSOLogRegressor.hpp

@@ -87,6 +87,7 @@ public:
 
     // Python interface functions
     #ifdef PY_BINDINGS
+    // DocString: sisso_log_reg_init_arr
     /**
      * @brief Constructor for the Regressor that takes in python objects (cpp definition in <python/descriptor_identifier/SISSOLogRegressor.cpp)
      *

src/descriptor_identifier/SISSO_DI/SISSORegressor.hpp

@@ -94,6 +94,8 @@ public:
 
     // Python interface functions
     #ifdef PY_BINDINGS
+
+    // DocString: sisso_reg_init_arr
     /**
      * @brief Constructor for the Regressor that takes in python objects (cpp definition in <python/descriptor_identifier/SISSORegressor.cpp)
      *

src/feature_creation/feature_space/FeatureSpace.hpp

@@ -389,7 +389,6 @@ public:
      * @param allowed_ops list of allowed operators
      * @param allowed_param_ops dictionary of the parameterizable operators and their associated free parameters
      * @param prop The property to be learned (training data)
-     * @param task_sizes The number of samples per task
      * @param project_type The projection operator to use
      * @param max_phi highest rung value for the calculation
      * @param n_sis_select number of features to select during each SIS step
@@ -406,7 +405,6 @@ public:
         py::list allowed_ops,
         py::list allowed_param_ops,
         py::list prop,
-        py::list task_sizes,
         std::string project_type="regression",
         int max_phi=1,
         int n_sis_select=1,
@@ -426,7 +424,6 @@ public:
      * @param phi_0 The initial set of features to combine
      * @param allowed_ops list of allowed operators
      * @param prop The property to be learned (training data)
-     * @param task_sizes The number of samples per task
      * @param project_type The projection operator to use
      * @param max_phi highest rung value for the calculation
      * @param n_sis_select number of features to select during each SIS step
@@ -442,7 +439,6 @@ public:
         py::list allowed_ops,
         py::list allowed_param_ops,
         np::ndarray prop,
-        py::list task_sizes,
         std::string project_type="regression",
         int max_phi=1,
         int n_sis_select=1,
@@ -462,7 +458,6 @@ public:
      * @param phi_0 The initial set of features to combine
      * @param allowed_ops list of allowed operators
      * @param prop The property to be learned (training data)
-     * @param task_sizes The number of samples per task
      * @param project_type The projection operator to use
      * @param max_phi highest rung value for the calculation
      * @param n_sis_select number of features to select during each SIS step
@@ -476,7 +471,6 @@ public:
         py::list phi_0,
         py::list allowed_ops,
         py::list prop,
-        py::list task_sizes,
         std::string project_type="regression",
         int max_phi=1,
         int n_sis_select=1,
@@ -494,7 +488,6 @@ public:
      * @param phi_0 The initial set of features to combine
      * @param allowed_ops list of allowed operators
      * @param prop The property to be learned (training data)
-     * @param task_sizes The number of samples per task
      * @param project_type The projection operator to use
      * @param max_phi highest rung value for the calculation
      * @param n_sis_select number of features to select during each SIS step
@@ -508,7 +501,6 @@ public:
         py::list phi_0,
         py::list allowed_ops,
         np::ndarray prop,
-        py::list task_sizes,
         std::string project_type="regression",
         int max_phi=1,
         int n_sis_select=1,

src/feature_creation/node/FeatureNode.hpp

@@ -74,6 +74,7 @@ public:
         const bool set_val=true
     );
     #ifdef PY_BINDINGS
+    // DocString: feat_node_init_list
     /**
      * @brief Constructs a feature node using numpy arrays (cpp definition in "python/feature_creation/FeatureNode.cpp)
      *
@@ -85,6 +86,7 @@ public:
      */
     FeatureNode(unsigned long int feat_ind, std::string expr, np::ndarray value, np::ndarray test_value, Unit unit);
 
+    // DocString: feat_node_init_arr
     /**
      * @brief Constructs a feature node using Python lists (cpp definition in "python/feature_creation/FeatureNode.cpp)
      *
@@ -143,12 +145,14 @@ public:
      */
     void reset_feats(std::vector<node_ptr>& phi){};
 
+    // DocString: feat_node_x_in_expr
     /**
      * @brief Get the list of feature expressions
      * @return vector storing the expressions for all primary features that show up in feature in the order they appear in the postfix notation
      */
     virtual inline std::vector<std::string> get_x_in_expr_list() const {return std::vector<std::string>(1, _expr);}
 
+    // DocString: feat_node_n_leaves
     /**
      * @brief return the number of leaves in the feature
      *

src/feature_creation/node/ModelNode.hpp

@@ -65,6 +65,7 @@ public:
      */
     ModelNode();
 
+    // DocString: model_node_init
     /**
      * @brief Constructs a feature node
      *
@@ -91,6 +92,7 @@ public:
         const Unit unit
     );
 
+    // DocString: model_node_init_node_ptr
     /**
      * @brief Copy constructor from general node_ptr
      *
@@ -160,7 +162,7 @@ public:
     /**
      * @brief Evaluate the model for a new point
      *
-     * @param x_in_dct Dictionary describing the new point ("feature expr": value)
+     * @param x_in_dct Dictionary describing the new point (\"feature expr\": value)
      * @return The prediction of the model for a given data point
      */
     double eval(std::map<std::string, double> x_in_dct);
@@ -189,12 +191,14 @@ public:
      */
     std::vector<double> eval(std::map<std::string, std::vector<double>> x_in_dct);
 
+    // DocString: model_node_x_in_expr
     /**
      * @brief get the list of feature expressions for each of the leaves
      * @return Vector containing the expression for each leaf in the binary expression tree
      */
     inline std::vector<std::string> get_x_in_expr_list() const {return _x_in_expr_list;}
 
+    // DocString: model_node_n_leaves
     /**
      * @brief return the number of leaves in the feature
      *
@@ -372,6 +376,7 @@ public:
     void update_div_mult_leaves(std::map<std::string, double>& div_mult_leaves, const double fact, double& expected_abs_tot) const;
 
     #ifdef PY_BINDINGS
+    // DocString: model_node_eval_arr
     /**
      * @brief Evaluate the model for a new point
      *
@@ -380,6 +385,7 @@ public:
      */
     inline double eval_py(np::ndarray x_in){return eval(python_conv_utils::from_ndarray<double>(x_in));}
 
+    // DocString: model_node_eval_list
     /**
      * @brief Evaluate the model for a new point
      *
@@ -388,14 +394,16 @@ public:
      */
     inline double eval_py(py::list x_in){return eval(python_conv_utils::from_list<double>(x_in));}
 
+    // DocString: model_node_eval_dict
     /**
      * @brief Evaluate the model for a new point
      *
-     * @param x_in_dct Dictionary describing the new point ("feature expr": value)
+     * @param x_in_dct Dictionary describing the new point (\"feature expr\": value)
      * @return The prediction of the model for a given data point
      */
     inline double eval_py(py::dict x_in){return eval(python_conv_utils::from_dict<std::string, double>(x_in));}
 
+    // DocString: model_node_eval_many_arr
     /**
      * @brief Evaluate the model for a set of new points
      *
@@ -404,6 +412,7 @@ public:
      */
     np::ndarray eval_many_py(np::ndarray x_in);
 
+    // DocString: model_node_eval_many_dict
     /**
      * @brief Evaluate the model for a set of new points
      *

src/feature_creation/node/Node.hpp

@@ -20,7 +20,6 @@
 #include "utils/math_funcs.hpp"
 
 #ifdef PY_BINDINGS
-#include "python/conversion_utils.hpp"
 namespace py = boost::python;
 namespace np = boost::python::numpy;
 #endif
@@ -125,12 +124,14 @@ public:
      */
     virtual void reset_feats(std::vector<std::shared_ptr<Node>>& phi) = 0;
 
+    // DocString: node_x_in_expr
     /**
      * @brief Get the list of feature expressions
      * @return vector storing the expressions for all primary features that show up in feature in the order they appear in the postfix notation
      */
     virtual std::vector<std::string> get_x_in_expr_list() const = 0;
 
+    // DocString: node_n_leaves
     /**
      * @brief return the number of leaves in the feature
      *

src/feature_creation/node/operator_nodes/OperatorNode.hpp

@@ -146,9 +146,9 @@ public:
         return x_in_expr;
     }
 
+    // DocString: op_node_n_leaves
     /**
      * @brief return the number of leaves in the feature
-     * @details [long description]
      *
      * @param cur_n_leaves The current number of primary features that are inside the feature
      * @return total number of leaves of the binary expression tree
@@ -184,24 +184,12 @@ public:
         );
     }
 
-    // DocString: op_node_expr
-    /**
-     * @brief Get the expression for the overall feature (From root node down)
-     */
-    virtual std::string expr() const = 0;
-
     // DocString: node_latex_expr
     /**
      * @brief Get the latexified expression for the overall feature (From root node down)
      */
     virtual std::string get_latex_expr() const = 0;
 
-    // DocString: op_node_unit
-    /**
-     * @brief Get the unit of the feature (combine the units of _feats)
-     */
-    virtual Unit unit() const = 0;
-
     /**
      * @brief Get the training data of the feature
      */

src/feature_creation/node/operator_nodes/allowed_operator_nodes/abs/absolute_value.hpp

@@ -47,6 +47,7 @@ public:
      */
     AbsNode(const node_ptr feat, const unsigned long int feat_ind);
 
+    // DocString: abs_node_init
     /**
      * @brief Constructor
      * @details Constructs the Node from node pointer of the feature to operate on

src/feature_creation/node/operator_nodes/allowed_operator_nodes/abs/parameterized_absolute_value.hpp

@@ -79,6 +79,7 @@ public:
      */
     AbsParamNode(const node_ptr feat, const unsigned long int feat_ind, std::shared_ptr<NLOptimizer> optimizer);
 
+    // DocString: abs_param_node_init
     /**
      * @brief Constructor
      * @details Constructs the Node from node pointer of the feature to operate on

src/feature_creation/node/operator_nodes/allowed_operator_nodes/abs_diff/absolute_difference.hpp

@@ -51,6 +51,7 @@ public:
      */
     AbsDiffNode(const node_ptr feat_1, const node_ptr feat_2, const unsigned long int feat_ind);
 
+    // DocString: abs_diff_node_init
     /**
      * @brief Constructor
      * @details Constructs the Node from node pointer of the features to operate on

src/feature_creation/node/operator_nodes/allowed_operator_nodes/abs_diff/parameterized_absolute_difference.hpp

@@ -80,6 +80,7 @@ public:
      */
     AbsDiffParamNode(const node_ptr feat_1, const node_ptr feat_2, const unsigned long int feat_ind, std::shared_ptr<NLOptimizer> optimizer);
 
+    // DocString: abs_diff_param_node_init
     /**
      * @brief Constructor
      * @details Constructs the Node from node pointer of the feature to operate on

src/feature_creation/node/operator_nodes/allowed_operator_nodes/add/add.hpp

@@ -48,6 +48,7 @@ public:
      */
     AddNode(const node_ptr feat_1, const node_ptr feat_2, const unsigned long int feat_ind);
 
+    // DocString: add_node_init
     /**
      * @brief Constructor
      * @details Constructs the Node from node pointer of the features to operate on

src/feature_creation/node/operator_nodes/allowed_operator_nodes/add/parameterized_add.hpp

@@ -82,6 +82,7 @@ public:
      */
     AddParamNode(const node_ptr feat_1, const node_ptr feat_2, const unsigned long int feat_ind, std::shared_ptr<NLOptimizer> optimizer);
 
+    // DocString: add_param_node_init
     /**
      * @brief Constructor
      * @details Constructs the Node from node pointer of the feature to operate on

src/feature_creation/node/operator_nodes/allowed_operator_nodes/cb/cube.hpp

@@ -47,6 +47,7 @@ public:
      */
     CbNode(const node_ptr feat, const unsigned long int feat_ind);
 
+    // DocString: cb_node_init
     /**
      * @brief Constructor
      * @details Constructs the Node from node pointer of the feature to operate on

src/feature_creation/node/operator_nodes/allowed_operator_nodes/cb/parameterized_cube.hpp

@@ -79,6 +79,7 @@ public:
      */
     CbParamNode(const node_ptr feat, const unsigned long int feat_ind, std::shared_ptr<NLOptimizer> optimizer);
 
+    // DocString: cb_param_node_init
     /**
      * @brief Constructor
      * @details Constructs the Node from node pointer of the feature to operate on