Moved models and features into atomistic.

- All features and models were moved to atomistic. Your scripts have to
  be changed to import from `ml4chem.atomistic.features` instead of
  `ml4chem.features` and `ml4chem.atomistic.models` instead of
  `ml4chem.models`.
- Refactored kernelridge and gaussian_process modules.
- Started update of documentation to match publication.

docs/source/data.rst

@@ -11,7 +11,7 @@ We will be adding support to other libraries, soon.
 
 
 ===================
-Data Handler
+Data 
 ===================
 
 .. contents:: :local:
@@ -35,37 +35,3 @@ dictionary with the molecules in ``images.traj`` and the ``targets`` variable
 as a list of energies.
 
 For more information please refer to :mod:`ml4chem.data.handler`.
-
-===================
-Visualization
-===================
-
-We also offer a :mod:`ml4chem.visualization` module to plot interesting
-graphics about your model, features, or even monitor the progress of the loss
-function and error minimization.
-
-Two backends are supported to plot in ML4Chem: Seaborn and Plotly.
-
-An example is shown below::
-
-    from ml4chem.visualization import plot_atomic_features
-    fig = plot_atomic_features("latent_space.db",
-                               method="pca",
-                               dimensions=3,
-                               backend="plotly")
-    fig.write_html("latent_example.html")
-
-This will produce an interactive plot with plotly where dimensionality was
-reduced using PCA, and an html with the name `latent_example.html` is
-created.
-
-.. raw:: html
-   :file: _static/pca_visual.html
-
-To activate plotly in Jupyter or JupyterLab follow the instructions shown in
-`https://plot.ly/python/getting-started/#jupyter-notebook-support <https://plot.ly/python/getting-started/#jupyter-notebook-support>`_
-
-If plotly is not rendering correctly you need to install the jupyter
-extension::
-
-    jupyter labextension install @jupyterlab/plotly-extension

docs/source/index.rst

@@ -25,6 +25,11 @@
 
    models
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Visualization
+
+   visualization
 
 Indices and tables
 ==================

docs/source/ml4chem.atomistic.features.rst

@@ -0,0 +1,62 @@
+ml4chem.atomistic.features package
+==================================
+
+Submodules
+----------
+
+ml4chem.atomistic.features.autoencoders module
+----------------------------------------------
+
+.. automodule:: ml4chem.atomistic.features.autoencoders
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.features.base module
+--------------------------------------
+
+.. automodule:: ml4chem.atomistic.features.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.features.cartesian module
+-------------------------------------------
+
+.. automodule:: ml4chem.atomistic.features.cartesian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.features.coulombmatrix module
+-----------------------------------------------
+
+.. automodule:: ml4chem.atomistic.features.coulombmatrix
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.features.cutoff module
+----------------------------------------
+
+.. automodule:: ml4chem.atomistic.features.cutoff
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.features.gaussian module
+------------------------------------------
+
+.. automodule:: ml4chem.atomistic.features.gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: ml4chem.atomistic.features
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/ml4chem.atomistic.models.rst

@@ -0,0 +1,78 @@
+ml4chem.atomistic.models package
+================================
+
+Submodules
+----------
+
+ml4chem.atomistic.models.autoencoders module
+--------------------------------------------
+
+.. automodule:: ml4chem.atomistic.models.autoencoders
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.models.base module
+------------------------------------
+
+.. automodule:: ml4chem.atomistic.models.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.models.gaussian\_process module
+-------------------------------------------------
+
+.. automodule:: ml4chem.atomistic.models.gaussian_process
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.models.kernelridge module
+-------------------------------------------
+
+.. automodule:: ml4chem.atomistic.models.kernelridge
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.models.loss module
+------------------------------------
+
+.. automodule:: ml4chem.atomistic.models.loss
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.models.merger module
+--------------------------------------
+
+.. automodule:: ml4chem.atomistic.models.merger
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.models.neuralnetwork module
+---------------------------------------------
+
+.. automodule:: ml4chem.atomistic.models.neuralnetwork
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ml4chem.atomistic.models.se3net module
+--------------------------------------
+
+.. automodule:: ml4chem.atomistic.models.se3net
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: ml4chem.atomistic.models
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/ml4chem.atomistic.rst

@@ -0,0 +1,30 @@
+ml4chem.atomistic package
+=========================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    ml4chem.atomistic.features
+    ml4chem.atomistic.models
+
+Submodules
+----------
+
+ml4chem.atomistic.potentials module
+-----------------------------------
+
+.. automodule:: ml4chem.atomistic.potentials
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: ml4chem.atomistic
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/ml4chem.data.rst

@@ -44,14 +44,6 @@ ml4chem.data.utils module
     :undoc-members:
     :show-inheritance:
 
-ml4chem.visualization module
----------------------------------
-
-.. automodule:: ml4chem.visualization
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 
 Module contents
 ---------------

docs/source/ml4chem.features.rst

@@ -1,37 +1,37 @@
-ml4chem.features package
+ml4chem.atomistic.features package
 ========================
 
 Submodules
 ----------
 
-ml4chem.features.autoencoders module
+ml4chem.atomistic.features.autoencoders module
 ------------------------------------
 
-.. automodule:: ml4chem.features.autoencoders
+.. automodule:: ml4chem.atomistic.features.autoencoders
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.features.cartesian module
+ml4chem.atomistic.features.cartesian module
 ---------------------------------
 
-.. automodule:: ml4chem.features.cartesian
+.. automodule:: ml4chem.atomistic.features.cartesian
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.features.cutoff module
+ml4chem.atomistic.features.cutoff module
 ------------------------------
 
-.. automodule:: ml4chem.features.cutoff
+.. automodule:: ml4chem.atomistic.features.cutoff
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.features.gaussian module
+ml4chem.atomistic.features.gaussian module
 --------------------------------
 
-.. automodule:: ml4chem.features.gaussian
+.. automodule:: ml4chem.atomistic.features.gaussian
     :members:
     :undoc-members:
     :show-inheritance:
@@ -40,7 +40,7 @@ ml4chem.features.gaussian module
 Module contents
 ---------------
 
-.. automodule:: ml4chem.features
+.. automodule:: ml4chem.atomistic.features
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/ml4chem.models.rst

@@ -1,69 +1,69 @@
-ml4chem.models package
+ml4chem.atomistic.models package
 ======================
 
 Submodules
 ----------
 
-ml4chem.models.autoencoders module
+ml4chem.atomistic.models.autoencoders module
 ----------------------------------
 
-.. automodule:: ml4chem.models.autoencoders
+.. automodule:: ml4chem.atomistic.models.autoencoders
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.models.gaussian\_process module
+ml4chem.atomistic.models.gaussian\_process module
 ---------------------------------------
 
-.. automodule:: ml4chem.models.gaussian_process
+.. automodule:: ml4chem.atomistic.models.gaussian_process
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.models.kernelridge module
+ml4chem.atomistic.models.kernelridge module
 ---------------------------------
 
-.. automodule:: ml4chem.models.kernelridge
+.. automodule:: ml4chem.atomistic.models.kernelridge
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.models.loss module
+ml4chem.atomistic.models.loss module
 --------------------------
 
-.. automodule:: ml4chem.models.loss
+.. automodule:: ml4chem.atomistic.models.loss
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.models.merger module
+ml4chem.atomistic.models.merger module
 ----------------------------
 
-.. automodule:: ml4chem.models.merger
+.. automodule:: ml4chem.atomistic.models.merger
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.models.neuralnetwork module
+ml4chem.atomistic.models.neuralnetwork module
 -----------------------------------
 
-.. automodule:: ml4chem.models.neuralnetwork
+.. automodule:: ml4chem.atomistic.models.neuralnetwork
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.models.rt module
+ml4chem.atomistic.models.rt module
 ------------------------
 
-.. automodule:: ml4chem.models.rt
+.. automodule:: ml4chem.atomistic.models.rt
     :members:
     :undoc-members:
     :show-inheritance:
 
-ml4chem.models.se3net module
+ml4chem.atomistic.models.se3net module
 ----------------------------
 
-.. automodule:: ml4chem.models.se3net
+.. automodule:: ml4chem.atomistic.models.se3net
     :members:
     :undoc-members:
     :show-inheritance:
@@ -72,7 +72,7 @@ ml4chem.models.se3net module
 Module contents
 ---------------
 
-.. automodule:: ml4chem.models
+.. automodule:: ml4chem.atomistic.models
     :members:
     :undoc-members:
     :show-inheritance: