diff --git a/README.rst b/README.rst
index ddbdfd4664c129ade129d31d212664834cec32d9..650b3a2c3618d29c306073533f51f15446307a8c 100644
--- a/README.rst
+++ b/README.rst
@@ -1,10 +1,10 @@
+.. |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
<<<<<<<<<<<<<<<<<<<<<<<<<
diff --git a/docs/source/api.rst b/docs/source/api.rst
index 6999ad11ec276454994f380661ec50d7dbf488f6..185c395b5f3dbe5288d495b113ad73a5d98ca374 100644
--- a/docs/source/api.rst
+++ b/docs/source/api.rst
@@ -1,9 +1,13 @@
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
+
+
diff --git a/docs/source/api_files/dataset.rst b/docs/source/api_files/dataset.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a41cca087bfe81079182d4f74b0e9384e793e978
--- /dev/null
+++ b/docs/source/api_files/dataset.rst
@@ -0,0 +1,6 @@
+Multiview dataset management module
+-----------------------------------
+
+.. automodule:: summit.multiview_platform.utils.dataset
+ :members:
+ :inherited-members:
\ No newline at end of file
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 2875ddb1eb61cf4673effe8a312191fba11c3419..82190952429ff520f90ed83a7cadfc63faf7d6d1 100644
--- a/docs/source/conf.py
+++ b/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:
@@ -190,9 +199,12 @@ rst_prolog = """
.. role:: python(code)
:language: python
-.. role :: yaml(code)
+.. role:: yaml(code)
:language: yaml
+.. role:: mod(code)
+ :language: python
+
.. |platf| replace:: SuMMIT
.. |HP| replace:: hyper-parameter
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 1151c1cfac10eedc4922cc3ec8deb9bf82cd622f..285ab422dfb4fb7ec285e0e5a42621cc24ab3963 100644
--- a/docs/source/index.rst
+++ b/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
diff --git a/docs/source/templates_autoapi/python/module.rst b/docs/source/templates_autoapi/python/module.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f682d9a29a2062613707bbdf52fc3d3041f66959
--- /dev/null
+++ b/docs/source/templates_autoapi/python/module.rst
@@ -0,0 +1,105 @@
+{% 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 %}
diff --git a/docs/source/templates_autoapi/python/package.rst b/docs/source/templates_autoapi/python/package.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6e70183d2e2cd4143df2194b9725a1c9c0efaa74
--- /dev/null
+++ b/docs/source/templates_autoapi/python/package.rst
@@ -0,0 +1,110 @@
+{% 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 %}
diff --git a/docs/source/tutorials/hps_theory.rst b/docs/source/tutorials/hps_theory.rst
index ae819bcff773f3da14b45e188f599c67c771f2f6..13e1a3685ccc76701414e61b63401623d8d93b2f 100644
--- a/docs/source/tutorials/hps_theory.rst
+++ b/docs/source/tutorials/hps_theory.rst
@@ -1,3 +1,4 @@
+:orphan:
============================
Hyper-parameter 101
============================
diff --git a/docs/source/tutorials/images/example_0/zoom_plotly.gif b/docs/source/tutorials/images/example_0/zoom_plotly.gif
new file mode 100644
index 0000000000000000000000000000000000000000..5be247545c014ba5ce79583e1dcdc4ad7bbc5c5c
Binary files /dev/null and b/docs/source/tutorials/images/example_0/zoom_plotly.gif differ
diff --git a/setup.py b/setup.py
index 407b77d6439567da51a63e5af5c13ad9c014b8ef..773e677c18ede85726486aa79976482c39bfcdee 100644
--- a/setup.py
+++ b/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.
diff --git a/summit/multiview_platform/monoview_classifiers/adaboost.py b/summit/multiview_platform/monoview_classifiers/adaboost.py
index 5bd49ef47fcf6541e021257fa7942e6a7dab3ca5..605041556c5b0f488d0c1474a45fa031e57792e9 100644
--- a/summit/multiview_platform/monoview_classifiers/adaboost.py
+++ b/summit/multiview_platform/monoview_classifiers/adaboost.py
@@ -1,3 +1,4 @@
+""" Ada"""
import os
import time
diff --git a/summit/multiview_platform/utils/dataset.py b/summit/multiview_platform/utils/dataset.py
index 953bcb16cabf747cc95f9f50d761dd14d023027f..25c396fa8fcb84fcb0e4e7152bd266fb824f7c77 100644
--- a/summit/multiview_platform/utils/dataset.py
+++ b/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]