Reworking'

README.md

-[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)
-[![Build Status](https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/pipeline.svg)](https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/pipeline.svg)
-[![Coverage Report](https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/coverage.svg)](http://baptiste.bauvin.pages.lis-lab.fr/summit/coverage/index.html)
-# Supervised MultiModal Integration Tool's Readme
-
-This project aims to be an easy-to-use solution to run a prior benchmark on a dataset and evaluate mono- & multi-view algorithms capacity to classify it correctly.
-
-## Getting Started
-
-### Prerequisites (will be automatically installed)
-
-To be able to use this project, you'll need :
-
-* [Python 3.6](https://docs.python.org/3/) 
-
-And the following python modules :
-
-* [numpy](http://www.numpy.org/), [scipy](https://scipy.org/),
-* [matplotlib](http://matplotlib.org/) - Used to plot results,
-* [sklearn](http://scikit-learn.org/stable/) - Used for the monoview classifiers,
-* [joblib](https://pypi.python.org/pypi/joblib) - Used to compute on multiple threads,
-* [h5py](https://www.h5py.org) - Used to generate HDF5 datasets on hard drive and use them to spare RAM,
-* [pickle](https://docs.python.org/3/library/pickle.html) - Used to store some results,
-* [pandas](https://pandas.pydata.org/) - Used to manipulate data efficiently,
-* [six](https://pypi.org/project/six/) - 
-* [m2r](https://pypi.org/project/m2r/) - Used to generate documentation from the readme,
-* [docutils](https://pypi.org/project/docutils/) - Used to generate documentation,
-* [pyyaml](https://pypi.org/project/PyYAML/) - Used to read the config files,
-* [plotly](https://plot.ly/) - Used to generate interactive HTML visuals,
-* [tabulate](https://pypi.org/project/tabulate/) - Used to generated the confusion matrix.
-
-
-### Installing
-
-Once you cloned the project from the [gitlab repository](https://gitlab.lis-lab.fr/baptiste.bauvin/summit/), you just have to use :  
-
-```
-cd path/to/summit/
-pip install -e .
-```
-In the `summit` directory to install SuMMIT and its dependencies.
-
-### Running the tests
-
-To run the test suite of SuMMIT, run :
-```
-cd path/to/summit
-pytest
-```
-
-### Running on simulated data
-
-In order to run it you'll need to try on **simulated** data with the command
-```python 
-from multiview_platform.execute import execute
-execute("example 1")
-```
-This will run the first example. 
-
-For more information about the examples, see the [documentation](http://baptiste.bauvin.pages.lis-lab.fr/summit/).
-Results will be stored in the results directory of the installation path : 
-`path/to/summit/multiview_platform/examples/results`.
-
-The documentation proposes a detailed interpretation of the results through [6 tutorials](http://baptiste.bauvin.pages.lis-lab.fr/summit/). 
-
-### Discovering the arguments
-
-All the arguments of the platform are stored in a YAML config file. Some config files are given as examples. 
-The file stored in `summit/config_files/config.yml` is documented and it is highly recommended
-to read it carefully before playing around with the parameters.   
-
-You can create your own configuration file. In order to run the platform with it, run : 
-```python
-from summit.execute import execute
-execute(config_path="/absolute/path/to/your/config/file")
-```
-
-For further information about classifier-specific arguments, see the [documentation](http://baptiste.bauvin.pages.lis-lab.fr/summit/). 
- 
-
-### Dataset compatibility
-
-
-In order to start a benchmark on your own dataset, you need to format it so SuMMIT can use it. To do so, a [python script](https://gitlab.lis-lab.fr/baptiste.bauvin/summit/-/blob/master/format_dataset.py) is provided.
-
-For more information, see [Example 6](http://baptiste.bauvin.pages.lis-lab.fr/summit/tutorials/example4.html)
-
-### Running on your dataset 
-
-Once you have formatted your dataset, to run SuMMIT on it you need to modify the config file as  
-```yaml
-name: ["your_file_name"]
-*
-pathf: "path/to/your/dataset"
-```
-This will run a full benchmark on your dataset using all available views and labels.
- 
-It is highly recommended to follow the documentation's [tutorials](http://baptiste.bauvin.pages.lis-lab.fr/summit/tutorials/index.html) to learn the use of each parameter. 
- 
-
-## Author
-
-* **Baptiste BAUVIN**
-* **Dominique BENIELLI**
-* **Alexis PROD'HOMME**
-

README.rst

+.. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0
+    :alt: License: GPL v3
+
+.. image:: https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/pipeline.svg
+    :alt: Pipeline status
+
+.. image:: https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/coverage.svg
+    :target: http://baptiste.bauvin.pages.lis-lab.fr/summit/coverage/index.html
+    :alt: Coverage
+
+
+Supervised MultiModal Integration Tool's Readme
+===============================================
+
+This project aims to be an easy-to-use solution to run a prior benchmark on a dataset and evaluate mono- & multi-view algorithms capacity to classify it correctly.
+
+Getting Started
+---------------
+
+Prerequisites (will be automatically installed)
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+To be able to use this project, you'll need :
+
+* `Python 3.6 <https://docs.python.org/3/>`_
+
+And the following python modules :
+
+* `numpy <http://www.numpy.org/>`_, `scipy <https://scipy.org/>`_,
+* `matplotlib <http://matplotlib.org/>`_ - Used to plot results,
+* `sklearn <http://scikit-learn.org/stable/>`_ - Used for the monoview classifiers,
+* `joblib <https://pypi.python.org/pypi/joblib>`_ - Used to compute on multiple threads,
+* `h5py <https://www.h5py.org>`_ - Used to generate HDF5 datasets on hard drive and use them to spare RAM,
+* `pickle <https://docs.python.org/3/library/pickle.html>`_ - Used to store some results,
+* `pandas <https://pandas.pydata.org/>`_ - Used to manipulate data efficiently,
+* `six <https://pypi.org/project/six/>`_ -
+* `m2r <https://pypi.org/project/m2r/>`_ - Used to generate documentation from the readme,
+* `docutils <https://pypi.org/project/docutils/>`_ - Used to generate documentation,
+* `pyyaml <https://pypi.org/project/PyYAML/>`_ - Used to read the config files,
+* `plotly <https://plot.ly/>`_ - Used to generate interactive HTML visuals,
+* `tabulate <https://pypi.org/project/tabulate/>`_ - Used to generated the confusion matrix.
+
+
+Installing
+<<<<<<<<<<
+
+Once you cloned the project from the `gitlab repository <https://gitlab.lis-lab.fr/baptiste.bauvin/summit/>`_, you just have to use :
+
+.. code:: bash
+
+    cd path/to/summit/
+    pip install -e .
+
+
+In the `summit` directory to install SuMMIT and its dependencies.
+
+Running the tests
+<<<<<<<<<<<<<<<<<
+
+To run the test suite of SuMMIT, run :
+
+.. code:: bash
+
+    cd path/to/summit
+    pytest
+
+
+Running on simulated data
+<<<<<<<<<<<<<<<<<<<<<<<<<
+
+For your first go with SuMMIT, you can run it on simulated data with
+
+.. code:: bash
+
+    python
+    >>> from summit.execute import execute
+    >>> execute("example 1")
+
+This will run the benchmark of `documentation's Example 1 <http://baptiste.bauvin.pages.lis-lab.fr/summit/tutorials/example1.html>`_.
+
+For more information about the examples, see the `documentation <http://baptiste.bauvin.pages.lis-lab.fr/summit/>`_.
+Results will, by default, be stored in the results directory of the installation path :
+``path/to/summit/multiview_platform/examples/results``.
+
+The documentation proposes a detailed interpretation of the results and arguments of SuMMIT through `6 tutorials <http://baptiste.bauvin.pages.lis-lab.fr/summit/>`_.
+
+Dataset compatibility
+<<<<<<<<<<<<<<<<<<<<<
+
+In order to start a benchmark on your own dataset, you need to format it so SuMMIT can use it. To do so, a `python script <https://gitlab.lis-lab.fr/baptiste.bauvin/summit/-/blob/master/format_dataset.py>`_ is provided.
+
+For more information, see `Example 5 <http://baptiste.bauvin.pages.lis-lab.fr/summit/tutorials/example5.html>`_
+
+Running on your dataset
++++++++++++++++++++++++
+
+Once you have formatted your dataset, to run SuMMIT on it you need to modify the config file as
+
+.. code:: yaml
+
+    name: ["your_file_name"]
+    pathf: "path/to/your/dataset"
+
+
+It is however highly recommended to follow the documentation's `tutorials <http://baptiste.bauvin.pages.lis-lab.fr/summit/tutorials/index.html>`_ to learn the use of each parameter.
+ 
+
+## Author
+
+* **Baptiste BAUVIN**
+* **Dominique BENIELLI**
+* **Alexis PROD'HOMME**
+

docs/source/analyzeresult.rst

-Result analysis module
-======================
-
-.. automodule:: summit.multiview_platform.result_analysis
-   :members:

docs/source/api.rst

-Multiview Platform
-==================
+API Documentation
+=================
 
-.. toctree::
-   :maxdepth: 3
-   :caption: Contents:
+Multiview dataset management module
+-----------------------------------
 
-   execution
-   monomultidoc
-   analyzeresult
+.. automodule:: summit.multiview_platform.utils.dataset
+   :members:
+   :inherited-members:

docs/source/conf.py

@@ -199,8 +199,8 @@ rst_prolog = """
 """
 
 
-extlinks = {'base_source': ('https://gitlab.lis-lab.fr/baptiste.bauvin/summit/-/tree/master/', "base_source"),
-            'base_doc': ('http://baptiste.bauvin.pages.lis-lab.fr/summit/', 'base_doc')}
+extlinks = {'base_source': ('https://gitlab.lis-lab.fr/baptiste.bauvin/summit/-/tree/master/%s', "_"),
+            'base_doc': ('http://baptiste.bauvin.pages.lis-lab.fr/summit/%s', '_')}
 
 
 

docs/source/execution.rst

-Welcome to the exection documentation
-=====================================
-
-.. automodule:: summit.execute
-   :members:
-

docs/source/index.rst

@@ -15,12 +15,12 @@ This documentation consists in a short read me, with instructions to install and
    :maxdepth: 1
 
    tutorials/index
-   references/multiview_platform
+   api
+   readme_link
 
 .. examples
 
 
-
 Indices and tables
 ==================
 

docs/source/modules.rst

-summit
-======
-
-.. toctree::
-   :maxdepth: 4
-
-   summit

docs/source/readme_link.rst

-
-<../../README.md>
+.. include:: ../../README.rst

docs/source/references/monomulti/exec_classif.rst

-Classification execution module
-===============================
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.exec_classif
-   :members:
-   :inherited-members:

docs/source/references/monomulti/metrics.rst

-Metrics framework
-=================
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.metrics.framework
-   :members:
-   :inherited-members:

docs/source/references/monomulti/multiview_classifiers/classifiers.rst

-Classifiers
-===========
-
-.. autosummary::
-   :toctree: DIRNAME
-
-    multiview_platform.mono_multi_view_classifiers.monoview_classifiers
-

docs/source/references/monomulti/multiview_classifiers/diversity_fusion.rst

-Diversity Fusion Classifiers
-============================
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview.additions.diversity_utils
-   :members:

docs/source/references/monomulti/utils/execution.rst

-Utils execution module
-======================
-
-.. automodule:: multiview_platform.MonoMultiViewClassifiers.utils.execution
-:members:
-       :inherited-members:
\ No newline at end of file

docs/source/references/monomulti/utils/multiclass.rst

-Utils Multiclass module
-=======================
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.utils.multiclass
-:members:
-       :inherited-members:

docs/source/references/monomultidoc.rst

-Mono and mutliview classification
-=================================
-
-.. toctree::
-   :maxdepth: 3
-   :caption: Contents:
-
-   monomulti/metrics
-   monomulti/monoview_classifier/classifiers
-   monomulti/multiview_classifier
-   monomulti/exec_classif
-   monomulti/multiview_classifiers/diversity_fusion
-   monomulti/utils/execution
-   monomulti/utils/multiclass

docs/source/references/multiview_platform.mono_multi_view_classifiers.multiview_classifiers.difficulty_fusion.rst

-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.difficulty_fusion package
-==============================================================================================
-
-Submodules
-----------
-
-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.difficulty_fusion.analyze_results module
--------------------------------------------------------------------------------------------------------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.difficulty_fusion.analyze_results
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.difficulty_fusion.difficulty_fusion module
----------------------------------------------------------------------------------------------------------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.difficulty_fusion.difficulty_fusion
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.difficulty_fusion
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/references/multiview_platform.mono_multi_view_classifiers.multiview_classifiers.disagree_fusion.rst

-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.disagree_fusion package
-============================================================================================
-
-Submodules
-----------
-
-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.disagree_fusion.analyze_results module
------------------------------------------------------------------------------------------------------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.disagree_fusion.analyze_results
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.disagree_fusion.disagree_fusion module
------------------------------------------------------------------------------------------------------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.disagree_fusion.disagree_fusion
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.disagree_fusion
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/references/multiview_platform.mono_multi_view_classifiers.multiview_classifiers.double_fault_fusion.rst

-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.double_fault_fusion package
-================================================================================================
-
-Submodules
-----------
-
-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.double_fault_fusion.analyze_results module
----------------------------------------------------------------------------------------------------------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.double_fault_fusion.analyze_results
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.double_fault_fusion.double_fault_fusion module
--------------------------------------------------------------------------------------------------------------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.double_fault_fusion.double_fault_fusion
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.double_fault_fusion
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/source/references/multiview_platform.mono_multi_view_classifiers.multiview_classifiers.entropy_fusion.rst

-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.entropy_fusion package
-===========================================================================================
-
-Submodules
-----------
-
-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.entropy_fusion.analyze_results module
-----------------------------------------------------------------------------------------------------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.entropy_fusion.analyze_results
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-multiview_platform.mono_multi_view_classifiers.multiview_classifiers.entropy_fusion.entropy_fusion module
----------------------------------------------------------------------------------------------------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.entropy_fusion.entropy_fusion
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: multiview_platform.mono_multi_view_classifiers.multiview_classifiers.entropy_fusion
-    :members:
-    :undoc-members:
-    :show-inheritance: