Update doc and correct utf8 reading pb in setup.py

MANIFEST.in

 recursive-include doc *.rst *.py *.png *.bib
-prune splearn/tests
+#prune splearn/tests
 include *.txt
 include *.rst
 include VERSION

doc/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = scikit-splearn
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

doc/automaton.rst

-automaton module
-================
-
-.. automodule:: automaton
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/conf.py

-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 #
-# scikit-splearn documentation build configuration file, created by
-# sphinx-quickstart on Fri Nov  6 17:21:52 2015.
+# Configuration file for the Sphinx documentation builder.
 #
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/stable/config
 
-import sys
-import os
-import shlex
+# -- Path setup --------------------------------------------------------------
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('../splearn'))
+#
+import os
+import sys
+import shlex
+# sys.path.insert(0, os.path.abspath('.'))
 
-# -- General configuration ------------------------------------------------
+
+# -- Project information -----------------------------------------------------
+
+project = 'scikit-splearn'
+copyright = u'2018, François Denis, Remi Eyraud, Dominique Benielli, Denis Arrivault'
+author = 'François Denis, Remi Eyraud, Dominique Benielli, Denis Arrivault'
+
+# The short X.Y version.
+import splearn
+version = splearn.__version__
+# The full version, including alpha/beta/rc tags.
+release = version
+
+# -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+#
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
-    'sphinx.ext.imgmath'
+    'sphinx.ext.imgmath',
+    'sphinx.ext.doctest',
+    'sphinx.ext.coverage',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-# templates_path = ['_templates']
+templates_path = ['_templates']
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
+#
 # source_suffix = ['.rst', '.md']
 source_suffix = '.rst'
 
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
 # The master toctree document.
 master_doc = 'index'
 
-# General information about the project.
-project = 'scikit-splearn'
-copyright = '2016, François Denis, Rémi Eyraud and Denis Arrivault and Dominique Benielli'
-author = 'François Denis, Rémi Eyraud and Denis Arrivault and Dominique Benielli'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '1'
-# The full version, including alpha/beta/rc tags.
-release = '0'
-
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
@@ -70,220 +65,99 @@ release = '0'
 # Usually you set "language" from the command line for these cases.
 language = None
 
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-# exclude_patterns = ['_build']
-
-# The reST default role (used for this markup: `text`) to use for all
-# documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = False
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'splearn.tests*']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-# If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = False
-
 
-# -- Options for HTML output ----------------------------------------------
+# -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'alabaster'
+#
+html_theme = 'nature'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents.  If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-#html_logo = None
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
+#
+# html_theme_options = {}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ['_static']
-
-# Add any extra paths that contain custom files (such as robots.txt or
-# .htaccess) here, relative to this directory. These files are copied
-# directly to the root of the documentation.
-#html_extra_path = []
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_domain_indices = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+html_static_path = ['_static']
 
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it.  The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Language to be used for generating the HTML full-text search index.
-# Sphinx supports the following languages:
-#   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
-#   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr'
-#html_search_language = 'en'
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
 
-# A dictionary with options for the search language support, empty by default.
-# Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
 
-# The name of a javascript file (relative to the configuration directory) that
-# implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
+# -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'scikit-splearndoc'
 
-# -- Options for LaTeX output ---------------------------------------------
+
+# -- Options for LaTeX output ------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
 
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  (master_doc, 'scikit-splearn.tex', 'scikit splearn Documentation',
-   'François Denis, Rémi Eyraud, Denis Arrivault and dominique Benielli',
-   'manual'),
+    (master_doc, 'scikit-splearn.tex', 'scikit-splearn Documentation',
+     'François Denis, Remi Eyraud, Dominique Benielli, Denis Arrivault', 'manual'),
 ]
 
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
 
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
+# -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'scikit-splearn', 'scikit splearn Documentation',
+    (master_doc, 'scikit-splearn', 'scikit-splearn Documentation',
      [author], 1)
 ]
 
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
 
-# -- Options for Texinfo output -------------------------------------------
+# -- Options for Texinfo output ----------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'scikit-splearn', 'scikit splearn Documentation',
-   author, 'scikit-splearn', 'One line description of project.',
-   'Miscellaneous'),
+    (master_doc, 'scikit-splearn', 'scikit-splearn Documentation',
+     author, 'scikit-splearn', 'One line description of project.',
+     'Miscellaneous'),
 ]
 
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-#texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
 
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# -- Extension configuration -------------------------------------------------
\ No newline at end of file

doc/hankel.rst

-hankel module
-===============
-
-.. automodule:: hankel
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-

doc/index.rst

 .. scikit-splearn documentation master file, created by
-   sphinx-quickstart on Fri Nov  6 17:21:52 2015.
+   sphinx-quickstart on Fri Feb 16 11:42:36 2018.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
 Welcome to scikit-splearn's documentation!
 ==========================================
 
-Contents:
-
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
+   :caption: Contents:
+
 
-   modules
 
 Indices and tables
 ==================
@@ -19,4 +18,3 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-

doc/modules.rst

@@ -2,9 +2,6 @@ splearn
 =======
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 4
 
-   automaton
-   spectral
-   hankel
-   splearn.datasets
+   splearn

doc/spectral.rst

-spectral module
-===============
-
-.. automodule:: spectral
-    :members: Learning, Spectral
-    :undoc-members:
-    :show-inheritance:

doc/splearn.datasets.rst

-splearn.datasets
-================
+splearn.datasets package
+========================
 
+Submodules
+----------
 
-base
-----
+splearn.datasets.base module
+----------------------------
 
 .. automodule:: splearn.datasets.base
-    :members: load_data_sample
+    :members:
     :undoc-members:
     :show-inheritance:
 
-
-data_sample
------------
+splearn.datasets.data\_sample module
+------------------------------------
 
 .. automodule:: splearn.datasets.data_sample
-    :members: DataSample , Splearn_array
+    :members:
     :undoc-members:
     :show-inheritance:
 
 
+Module contents
+---------------
 
+.. automodule:: splearn.datasets
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/splearn.rst

+splearn package
+===============
+
+Subpackages
+-----------
+
+.. toctree::
+
+    splearn.datasets
+
+Submodules
+----------
+
+splearn.automaton module
+------------------------
+
+.. automodule:: splearn.automaton
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+splearn.hankel module
+---------------------
+
+.. automodule:: splearn.hankel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+splearn.serializer module
+-------------------------
+
+.. automodule:: splearn.serializer
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+splearn.spectral module
+-----------------------
+
+.. automodule:: splearn.spectral
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: splearn
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/splearn.tests.datasets.rst

+splearn.tests.datasets package
+==============================
+
+Submodules
+----------
+
+splearn.tests.datasets.get\_dataset\_path module
+------------------------------------------------
+
+.. automodule:: splearn.tests.datasets.get_dataset_path
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: splearn.tests.datasets
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/splearn.tests.rst

+splearn.tests package
+=====================
+
+Submodules
+----------
+
+splearn.tests.test\_automaton module
+------------------------------------
+
+.. automodule:: splearn.tests.test_automaton
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+splearn.tests.test\_base module
+-------------------------------
+
+.. automodule:: splearn.tests.test_base
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+splearn.tests.test\_data\_sample module
+---------------------------------------
+
+.. automodule:: splearn.tests.test_data_sample
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+splearn.tests.test\_hankel module
+---------------------------------
+
+.. automodule:: splearn.tests.test_hankel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+splearn.tests.test\_serializer module
+-------------------------------------
+
+.. automodule:: splearn.tests.test_serializer
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+splearn.tests.test\_spectral module
+-----------------------------------
+
+.. automodule:: splearn.tests.test_spectral
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: splearn.tests
+    :members:
+    :undoc-members:
+    :show-inheritance:

docker/Dockerfile

@@ -7,7 +7,7 @@ RUN apt-get update && apt-get install -y \
     python3-scipy \
     graphviz-dev
 RUN pip3 install --upgrade pip
-RUN pip3 install nose coverage sphinx sphinxcontrib-bibtex
+RUN pip3 install pyyaml nose coverage sphinx sphinxcontrib-bibtex
 
 # Copy the scikit-splearn sdist in the docker directory and uncomment the following line
 # if you want to include grackelpy sources in the docker image :

setup.py

@@ -147,7 +147,8 @@ def setup_package():
           long_description=(read('README.rst') + '\n\n' +
                             read('HISTORY.rst') + '\n\n' +
                             read('AUTHORS.rst')),
-          packages=["splearn", "splearn.datasets"],
+          packages=["splearn", "splearn.datasets", "splearn.tests", "splearn.tests.datasets"],
+          package_data={'splearn.tests.datasets': ['*.*']},
           url="https://gitlab.lif.univ-mrs.fr/dominique.benielli/scikit-splearn.git",
           license='new BSD',
           author='François Denis and Rémi Eyraud and Denis Arrivault and Dominique Benielli',

splearn/automaton.py

@@ -662,6 +662,7 @@ class Automaton(object):
     
     def get_dot(self, threshold = 0., nb_dec = 2, title = "Weighted Automata"):
         """ Return a string that contains the Automata into dot (graphviz) format
+        
         :Example:
 
         >>> from splearn.datasets.base import load_data_sample
@@ -681,7 +682,7 @@ class Automaton(object):
         - Input:
 
         :param  Automaton self
-        :param float threshold for the value to keep. If |weight| < threshold, the 
+        :param float threshold for the value to keep. If \|weight\| < threshold, the 
         corresponding transition is not kept as an edge in the final dot string.
         :param int nb_dec is the number of decimals to keep for the weights.
         :param string title corresponds to the top comment of the string

splearn/hankel.py

@@ -45,7 +45,7 @@ class Hankel(object):
     """ A Hankel instance , compute the list of Hankel matrices
 
     :Example:
-
+    
     >>> from splearn import Learning, Hankel , Spectral
     >>> train_file = '0.spice.train'
     >>> pT = load_data_sample(adr=train_file)
@@ -56,9 +56,9 @@ class Hankel(object):
     >>>                   nbL=pT.nbL, nbEx=pT.nbEx,
     >>>                   lrows=6, lcolumns=6, version="classic",
     >>>                   partial=True, sparse=True, mode_quiet=True).lhankel
-
+    
     - Input:
-
+    
     :param dict sample_instance: sample dictionary
     :param dict pref: prefix dictionary
     :param dict suff: suffix dictionary
@@ -81,7 +81,7 @@ class Hankel(object):
            matrix is sparse
     :param boolean mode_quiet: (default value = False) True for no
            output message.
-    :param list of all Hankel matrices. At least one of the two parameters 
+    :param list lhankel: list of all Hankel matrices. At least one of the two parameters 
            *sample_instance* or *lhankel* has to be not None. If *sample_instance* is given,
            the **Hankel** instance is built directly from the sample dictionnary,
            else it is deduced from the *lhankels* list of matrices.