Docs auto

README.rst

+.. |pipeline| image:: https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/pipeline.svg
+    :alt: Pipeline status
+
 .. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
     :target: http://www.gnu.org/licenses/gpl-3.0
     :alt: License: GPL v3
 
-.. |pipeline| image:: https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/pipeline.svg
-    :alt: Pipeline status
-
 |pipeline|
 
 .. image:: https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/coverage.svg
@@ -20,13 +20,8 @@ This project aims to be an easy-to-use solution to run a prior benchmark on a da
 Getting Started
 ---------------
 
-Prerequisites (will be automatically installed)
-<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
 SuMMIT has been designed and uses continuous integration for Linux platforms (ubuntu 18.04), but we try to keep it as compatible as possible with Mac and Windows.
 
-Last tests on each platform :
-
 +----------+-------------------+
 | Platform | Last positive test|
 +==========+===================+
@@ -38,11 +33,14 @@ Last tests on each platform :
 +----------+-------------------+
 
 
+Prerequisites
+<<<<<<<<<<<<<
+
 To be able to use this project, you'll need :
 
 * `Python 3 <https://docs.python.org/3/>`_
 
-And the following python modules :
+And the following python modules will be automatically installed  :
 
 * `numpy <http://www.numpy.org/>`_, `scipy <https://scipy.org/>`_,
 * `matplotlib <http://matplotlib.org/>`_ - Used to plot results,
@@ -82,6 +80,7 @@ To run the test suite of SuMMIT, run :
     cd path/to/summit
     pytest
 
+The coverage report is automatically generated and stored in the ``htmlcov/`` directory
 
 Running on simulated data
 <<<<<<<<<<<<<<<<<<<<<<<<<

docs/source/api.rst

 API Documentation
 =================
 
-Multiview dataset management module
------------------------------------
 
-.. automodule:: summit.multiview_platform.utils.dataset
-   :members:
-   :inherited-members:
+
+.. toctree::
+    :maxdepth: 3
+
+    api_files/dataset
+    autoapi/summit/multiview_platform/monoview_classifiers/index
+    autoapi/summit/multiview_platform/multiview_classifiers/index
+
+

docs/source/api_files/dataset.rst

+Multiview dataset management module
+-----------------------------------
+
+.. automodule:: summit.multiview_platform.utils.dataset
+   :members:
+   :inherited-members:
\ No newline at end of file

docs/source/conf.py

@@ -54,11 +54,20 @@ extensions = ['sphinx.ext.autodoc',
 #              'sphinx.ext.ifconfig',
 #              'sphinx.ext.viewcode',
 #              'sphinx.ext.githubpages',
-               'sphinx.ext.napoleon',]
-
+               'sphinx.ext.napoleon',
+                'autoapi.extension'
+              ]
 
+autoapi_type = 'python'
+autoapi_dirs = [os.path.join(repo_path, "summit", "multiview_platform", "monoview_classifiers", ""),
+                os.path.join(repo_path, "summit", "multiview_platform", "multiview_classifiers", "")]
+autoapi_options = ["members", "show-module-summary", 'undoc-members']
+autoapi_ignore = ["*additions*"]
+autoapi_keep_files = False
+auto_api_add_toctree_entry = False
+autoapi_template_dir = os.path.join(repo_path, "docs", "source", "templates_autoapi")
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ['_templates', 'templates_autoapi']
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
@@ -193,6 +202,9 @@ rst_prolog = """
 .. role:: yaml(code)
     :language: yaml
     
+.. role:: mod(code)
+    :language: python
+    
 .. |platf| replace:: SuMMIT
 
 .. |HP| replace:: hyper-parameter

docs/source/index.rst

@@ -12,12 +12,19 @@ This documentation consists in a short read me, with instructions to install and
     All the content labelled WIP is Work In Progress
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 2
 
    tutorials/index
+
+.. toctree::
+   :maxdepth: 3
+
    api
 
 
+Read me
+=========
+
 .. include:: readme_link.rst
 
 

docs/source/templates_autoapi/python/module.rst

+{% if not obj.display %}
+:orphan:
+
+{% endif %}
+:mod:`{{ obj.name }}`
+======={{ "=" * obj.name|length }}
+
+.. py:module:: {{obj.name}}
+
+{% if obj.docstring %}
+.. autoapi-nested-parse::
+
+   {{ obj.docstring|prepare_docstring|indent(3) }}
+
+{% endif %}
+
+{% block subpackages %}
+{% set visible_subpackages = obj.subpackages|selectattr("display")|list %}
+{% if visible_subpackages %}
+Subpackages
+-----------
+
+.. toctree::
+   :titlesonly:
+   :maxdepth: 3
+
+{% for subpackage in visible_subpackages %}
+   {{ subpackage.short_name }}/index.rst
+
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% block submodules %}
+{% set visible_submodules = obj.submodules|selectattr("display")|list %}
+{% if visible_submodules %}
+Submodules
+----------
+
+.. toctree::
+   :titlesonly:
+   :maxdepth: 1
+
+{% for submodule in visible_submodules %}
+   {{ submodule.short_name }}/index.rst
+
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% block content %}
+{% if obj.all is not none %}
+{% set visible_children = obj.children|selectattr("short_name", "in", obj.all)|list %}
+{% elif obj.type is equalto("package") %}
+{% set visible_children = obj.children|selectattr("display")|list %}
+{% else %}
+{% set visible_children = obj.children|selectattr("display")|rejectattr("imported")|list %}
+{% endif %}
+{% if visible_children %}
+{{ obj.short_name }}
+{{ "-" * obj.short_name|length }}
+
+{% set visible_classes = visible_children|selectattr("type", "equalto", "class")|list %}
+{% set visible_functions = visible_children|selectattr("type", "equalto", "function")|list %}
+{% if "show-module-summary" in autoapi_options and (visible_classes or visible_functions) %}
+{% block classes %}
+{% if visible_classes %}
+
+Classes
+~~~~~~~
+
+.. autoapisummary::
+
+{% for klass in visible_classes %}
+   {{ klass.id }}
+
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+
+{% block functions %}
+{% if visible_functions %}
+Functions
+~~~~~~~~~
+
+.. autoapisummary::
+
+{% for function in visible_functions %}
+   {{ function.id }}
+
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% endif %}
+{% for obj_item in visible_children %}
+{{ obj_item.rendered|indent(0) }}
+{% endfor %}
+{% endif %}
+{% endblock %}

docs/source/templates_autoapi/python/package.rst

+{% if not obj.display %}
+:orphan:
+
+{% endif %}
+:mod:`{{ obj.name }}`
+======={{ "=" * obj.name|length }}
+
+.. py:module:: {{obj.name}}
+
+{% if obj.docstring %}
+.. autoapi-nested-parse::
+
+   {{ obj.docstring|prepare_docstring|indent(3) }}
+
+{% endif %}
+
+{% block subpackages %}
+{% set visible_subpackages = obj.subpackages|selectattr("display")|list %}
+{% if visible_subpackages %}
+Subpackages
+-----------
+
+.. toctree::
+   :titlesonly:
+   :maxdepth: 3
+
+{% for subpackage in visible_subpackages %}
+   {{ subpackage.short_name }}/index.rst
+
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% block submodules %}
+{% set visible_submodules = obj.submodules|selectattr("display")|list %}
+{% if visible_submodules %}
+{% if obj.short_name is equalto("monoview_classifiers") %}
+Available monoview classifiers
+------------------------------
+{% elif obj.short_name is equalto("multiview_classifiers") %}
+Available multiview classifiers
+-------------------------------
+{% endif %}
+
+.. toctree::
+   :titlesonly:
+   :maxdepth: 1
+
+{% for submodule in visible_submodules %}
+   {{ submodule.short_name }}/index.rst
+
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% block content %}
+{% if obj.all is not none %}
+{% set visible_children = obj.children|selectattr("short_name", "in", obj.all)|list %}
+{% elif obj.type is equalto("package") %}
+{% set visible_children = obj.children|selectattr("display")|list %}
+{% else %}
+{% set visible_children = obj.children|selectattr("display")|rejectattr("imported")|list %}
+{% endif %}
+{% if visible_children %}
+{{ obj.short_name }}
+{{ "-" * obj.short_name|length }}
+
+{% set visible_classes = visible_children|selectattr("type", "equalto", "class")|list %}
+{% set visible_functions = visible_children|selectattr("type", "equalto", "function")|list %}
+{% if "show-module-summary" in autoapi_options and (visible_classes or visible_functions) %}
+{% block classes %}
+{% if visible_classes %}
+
+Classes
+~~~~~~~
+
+.. autoapisummary::
+
+{% for klass in visible_classes %}
+   {{ klass.id }}
+
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+
+{% block functions %}
+{% if visible_functions %}
+Functions
+~~~~~~~~~
+
+.. autoapisummary::
+
+{% for function in visible_functions %}
+   {{ function.id }}
+
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% endif %}
+{% for obj_item in visible_children %}
+{{ obj_item.rendered|indent(0) }}
+{% endfor %}
+{% endif %}
+{% endblock %}

docs/source/tutorials/hps_theory.rst

+:orphan:
 ============================
 Hyper-parameter 101
 ============================

setup.py

@@ -58,7 +58,7 @@ def setup_package():
     install_requires=requirements,
     extras_requires={
             'dev': ['pytest', 'pytest-cov'],
-            'doc': ['sphinx', 'numpydoc', 'docutils']},
+            'doc': ['sphinx', 'numpydoc', 'docutils', 'sphinx-autoapi']},
 
     # Il est d'usage de mettre quelques metadata à propos de sa lib
     # Pour que les robots puissent facilement la classer.

summit/multiview_platform/monoview_classifiers/adaboost.py

+""" Ada"""
 import os
 import time
 

summit/multiview_platform/utils/dataset.py

@@ -75,7 +75,7 @@ class Dataset():
 
     def to_numpy_array(self, sample_indices=None, view_indices=None):
         """
-        To concatenate the needed views in one big numpy array while saving the
+        Concatenates the needed views in one big numpy array while saving the
         limits of each view in a list, to be able to retrieve them later.
 
         Parameters
@@ -192,15 +192,6 @@ class RAMDataset(Dataset):
         return self.view_names[view_idx]
 
     def init_attrs(self):
-        """
-        Used to init the two attributes that are modified when self.dataset
-        changes
-
-        Returns
-        -------
-
-        """
-
         self.nb_view = len(self.views)
         self.view_dict = dict((view_ind, self.view_names[view_ind])
                               for view_ind in range(self.nb_view))
@@ -239,10 +230,6 @@ class RAMDataset(Dataset):
                 pass
 
     def get_nb_class(self, sample_indices=None):
-        """
-        Gets the number of class of the dataset
-
-        """
         sample_indices = self.init_sample_indices(sample_indices)
         return len(np.unique(self.labels[sample_indices]))
 
@@ -277,9 +264,9 @@ class RAMDataset(Dataset):
 
 class HDF5Dataset(Dataset):
     """
-    Class of Dataset
+    Dataset class
 
-    This class is used to encapsulate the multiview dataset while keeping it stored on the disk instead of in RAM.
+    This is used to encapsulate the multiview dataset while keeping it stored on the disk instead of in RAM.
 
 
     Parameters
@@ -311,7 +298,7 @@ class HDF5Dataset(Dataset):
         The name for each unique value of the labels given in labels.
 
     is_temp : bool
-        Used if a temporary dataset has to be used by the benchmark.
+        Used if a temporary dataset has to be stored by the benchmark.
 
     Attributes
     ----------
@@ -327,7 +314,7 @@ class HDF5Dataset(Dataset):
 
     """
 
-    # The following methods use hdf5
+    # The following methods use h5py
 
     def __init__(self, views=None, labels=None, are_sparse=False,
                  file_name="dataset.hdf5", view_names=None, path="",
@@ -379,7 +366,7 @@ class HDF5Dataset(Dataset):
                                    for i in range(labels.shape[0])]
 
     def get_v(self, view_index, sample_indices=None):
-        r""" Extract the view and returns a numpy.ndarray containing the description
+        """ Extract the view and returns a numpy.ndarray containing the description
         of the samples specified in sample_indices
 
         Parameters
@@ -452,14 +439,14 @@ class HDF5Dataset(Dataset):
 
         Returns
         -------
-
+            int
         """
         return self.dataset["Metadata"].attrs["datasetLength"]
 
     def get_view_dict(self):
         """
-        Returns the dictionary with view indices as keys and their corresponding
-        names as values
+        Returns the dictionary containing view indices as keys and their
+        corresponding names as values
         """
         view_dict = {}
         for view_index in range(self.nb_view):
@@ -481,7 +468,8 @@ class HDF5Dataset(Dataset):
 
         Returns
         -------
-
+            list
+            seleted labels' names
         """
         selected_labels = self.get_labels(sample_indices)
         if decode:
@@ -609,11 +597,6 @@ class HDF5Dataset(Dataset):
 
     def add_gaussian_noise(self, random_state, path,
                            noise_std=0.15):
-        """In this function, we add a guaussian noise centered in 0 with specified
-        std to each view, according to it's range (the noise will be
-        mutliplied by this range) and we crop the noisy signal according to the
-        view's attributes limits.
-        This is done by creating a new dataset, to keep clean data."""
         noisy_dataset = h5py.File(path + self.get_name() + "_noised.hdf5", "w")
         self.dataset.copy("Metadata", noisy_dataset)
         self.dataset.copy("Labels", noisy_dataset)
@@ -643,7 +626,7 @@ class HDF5Dataset(Dataset):
     # The following methods are hdf5 free
 
     def get_name(self):
-        """Ony works if there are not multiple dots in the files name"""
+        """Gets the name of the dataset hdf5 file"""
         return os.path.split(self.dataset.filename)[-1].split('.')[0]