Update the documentation

docs/cpp_api/FeatureCreation.rst

@@ -5,8 +5,8 @@ Feature Creation
 .. toctree::
     :maxdepth: 2
 
-Nodes
------
+Features
+--------
 .. toctree::
     :maxdepth: 3
 

docs/cpp_api/FeatureSpace.rst

 .. _api_feat_space:
 
-Feature Space
-=============
-.. toctree::
-    :maxdepth: 2
-
 FeatureSpace
 ------------
 .. doxygenfile:: FeatureSpace.hpp

docs/cpp_api/Inputs.rst

 .. _api_inputs:
 
-Input Parser
-============
-.. toctree::
-    :maxdepth: 2
-
 InputParser
 -----------
 .. doxygenfile:: InputParser.hpp

docs/cpp_api/math_utils.rst

 .. _api_math_utils:
 
-Math Functions
+Math Utilities
 ==============
 .. toctree::
     :maxdepth: 2
 
-math_funcs
-----------
 .. doxygenfile:: math_funcs.hpp
    :project: SISSO++
 

docs/cpp_api/model.rst

 .. _api_models:
 
-Models
-======
-.. toctree::
-    :maxdepth: 2
 
 Model
 -----

docs/cpp_api/nl_opt.rst

@@ -5,7 +5,5 @@ Non-Linear Parameter Optimization
 .. toctree::
     :maxdepth: 2
 
-NLOptWrapper
-------------
 .. doxygenfile:: NLOptWrapper.hpp
    :project: SISSO++

docs/cpp_api/solvers.rst

 .. _api_solvers:
 
-l0-Regularization Objects
-=========================
-.. toctree::
-    :maxdepth: 2
-
-SISSO_DI
+SISSOSolver
 --------
-.. doxygenfile:: SISSO_DI.hpp
+.. doxygenfile:: SISSOSolver.hpp
    :project: SISSO++
 
 SISSOClassifier

docs/development/CONTRIBUTING.md

 # Contributing Guidelines
 
-When contributing to this repository, please first discuss the change you wish to make via an issue,
-email, or any other method with the maintainers of this repository. This will make life easier for everyone.
+When contributing to this repository, please first discuss the change you wish to make via an issue, email, or any other method with the maintainers of this repository.
+This will make life easier for everyone.
 
 ## Report Issues
 
@@ -17,4 +17,4 @@ Please use the [issue tracker](https://gitlab.com/sissopp-developers/sissopp/-/i
 In order to contribute code to `SISSO++`, please use a merge request (see guidelines of preparing a merge request [here](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)).
 
 - Please _document_ and _test_ your changes. Tests are found in `sissopp/tests` and written with [pytest](https://docs.pytest.org/en/stable/) for the python bindings and [googletest](https://github.com/google/googletest) for the C++ interface.
-- If a new feature is introduced please create a minimal test of the binary file
+- If a new feature is introduced please create a minimal test of the binary file in `exec_tests`

docs/python_api/py_FeatureCreation.rst

@@ -5,8 +5,8 @@ Feature Creation
 .. toctree::
     :maxdepth: 2
 
-Nodes
------
+Features
+--------
 .. toctree::
     :maxdepth: 3
 

docs/python_api/py_FeatureSpace.rst

 .. _py_api_feat_space:
 
-Feature Space
-=============
-.. toctree::
-    :maxdepth: 2
-
 FeatureSpace
 ------------
 .. autoclass:: sissopp.FeatureSpace

docs/python_api/py_Postprocessing.rst

@@ -10,8 +10,7 @@ Postprocessing
     py_post_class
     py_post_load_model
     py_post_cv_check
-    py_post_feat_space_prev
-    py_post_plot_utils
-    py_post_cv_error
     py_post_parity
     py_post_map
+    py_post_plot_utils
+    py_post_feat_space_prev

docs/python_api/py_model.rst

 .. _py_api_models:
 
-Models
-======
-.. toctree::
-    :maxdepth: 2
-
 Model
 -----
+
 .. autoclass:: sissopp.Model
     :special-members: __init__
     :members:
@@ -14,6 +10,9 @@ Model
 
 ModelClassifier
 ---------------
+
+.. currentmodule:: sissopp._sisso
+
 .. autoclass:: sissopp.ModelClassifier
     :special-members: __init__
     :members:
@@ -22,6 +21,9 @@ ModelClassifier
 
 ModelRegressor
 --------------
+
+.. currentmodule:: sissopp._sisso
+
 .. autoclass:: sissopp.ModelRegressor
     :special-members: __init__
     :members:
@@ -30,6 +32,9 @@ ModelRegressor
 
 ModelLogRegressor
 -----------------
+
+.. currentmodule:: sissopp._sisso
+
 .. autoclass:: sissopp.ModelLogRegressor
     :special-members: __init__
     :members:

docs/python_api/py_node.rst

 .. _py_api_node:
 
-Nodes
-=====
-.. toctree::
-    :maxdepth: 2
-
 Node
 ----
 .. autoclass:: sissopp.Node

docs/python_api/py_post_class.rst

@@ -6,3 +6,7 @@ Classification
 .. currentmodule:: sissopp.postprocess.classification
 
 .. autofunction:: update_model_svm
+
+.. currentmodule:: sissopp.postprocess.plot.classification
+
+.. autofunction:: plot_classification

docs/python_api/py_post_cv_check.rst

 .. _py_api_cv_conv
 
 
-Check Cross-Validation Convergence
-----------------------------------
+Cross-Validation Convergence
+----------------------------
 
 .. currentmodule:: sissopp.postprocess.check_cv_convergence
 
 .. autofunction:: jackknife_cv_conv_est
+
+.. currentmodule:: sissopp.postprocess.plot.cv_error_plot
+
+.. autofunction:: plot_validation_rmse
+
+.. autofunction:: plot_errors_dists
+
+.. autofunction:: add_violin
+
+.. autofunction:: add_boxplot
+
+.. autofunction:: add_pointplot

docs/python_api/py_post_cv_error.rst

-.. _py_api_post_cv_err
-
-
-Cross-Validation Visualization
-------------------------------
-
-.. currentmodule:: sissopp.postprocess.cv_error_plot
-
-.. autofunction:: plot_validation_rmse
-.. autofunction:: plot_cv_errors
-.. autofunction:: add_violin
-.. autofunction:: add_boxplot
-.. autofunction:: add_pointplot

docs/python_api/py_post_map.rst

@@ -4,6 +4,6 @@
 Plotting 2D Maps
 ----------------
 
-.. currentmodule:: sissopp.postprocess.maps
+.. currentmodule:: sissopp.postprocess.plot.maps
 
 .. autofunction:: plot_2d_map

docs/python_api/py_post_parity.rst

@@ -3,6 +3,6 @@
 Parity Plots
 ------------
 
-.. currentmodule:: sissopp.postprocess.parity_plot
+.. currentmodule:: sissopp.postprocess.plot.parity_plot
 
 .. autofunction:: plot_model_parity_plot

docs/python_api/py_reading_data_files.rst

@@ -6,6 +6,7 @@ Reading Datafiles
 .. currentmodule:: sissopp.py_interface.import_dataframe
 
 .. autofunction:: read_csv
+.. autofunction:: create_inputs
 .. autofunction:: extract_col
 .. autofunction:: get_unit
 .. autofunction:: strip_units

docs/python_api/py_solvers.rst

 .. _py_api_solvers:
 
-l0-Regularization Objects
-=========================
-.. toctree::
-    :maxdepth: 2
-
-SISSO_DI
---------
-.. autoclass:: sissopp.SISSO_DI
+.. currentmodule:: sissopp._sisso
+
+SISSOSolver
+-----------
+.. autoclass:: SISSOSolver
     :special-members: __init__
     :members:
     :undoc-members:
@@ -15,7 +12,7 @@ SISSO_DI
 
 SISSOClassifier
 ---------------
-.. autoclass:: sissopp.SISSOClassifier
+.. autoclass:: SISSOClassifier
     :special-members: __init__
     :members:
     :undoc-members:
@@ -23,7 +20,7 @@ SISSOClassifier
 
 SISSORegressor
 --------------
-.. autoclass:: sissopp.SISSORegressor
+.. autoclass:: SISSORegressor
     :special-members: __init__
     :members:
     :undoc-members:
@@ -31,7 +28,7 @@ SISSORegressor
 
 SISSOLogRegressor
 -----------------
-.. autoclass:: sissopp.SISSOLogRegressor
+.. autoclass:: SISSOLogRegressor
     :special-members: __init__
     :members:
     :undoc-members: