Add release 1.0

.coveragerc

+[run]
+branch = True
+source = madarrays
+include = */madarrays/*
+omit =
+    */setup.py
+    */__init__.py
+    */test_*
+
+
+[report]
+exclude_lines =
+    pragma: no cover
+    if self.debug:
+    if settings.DEBUG
+    raise AssertionError
+    raise NotImplementedError
+    if 0:
+    if __name__ == .__main__.:
+    if obj is None: return
+    if verbose > 0:
+    if self.verbose > 0:
+    if verbose > 1:
+    if self.verbose > 1:
+    pass
+    def __str__(self):

.gitignore

+*.py[co]
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+
+# Installer logs
+pip-log.txt
+
+# Mac OS X files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Sphinx stuff
+docs/generated/
+docs/build/
+
+# jupyter notebook
+.ipynb_checkpoints
+
+# coverage
+htmlcov
+.coverage
+
+# ide 
+.idea
+.spyderproject

.gitlab-ci.yml

+# run the test suite
+
+tests_old_ubuntu:
+    image: registry.gitlab.lis-lab.fr:5005/skmad-suite/madarrays/ubuntu:16.04
+    tags:
+        - docker
+    script:
+        - pip3 install . --no-deps
+        - pytest
+
+tests_new_ubuntu:
+    image: registry.gitlab.lis-lab.fr:5005/skmad-suite/madarrays/ubuntu:rolling
+    tags:
+        - docker
+    script:
+        - pip3 install . --no-deps
+        - pytest-3
+
+
+# generate the documentation
+
+pages:
+    image: registry.gitlab.lis-lab.fr:5005/skmad-suite/madarrays/ubuntu:rolling
+    tags:
+        - docker
+    only:
+        - master
+    script:
+        - pip3 install . --no-deps
+        - python3 setup.py build_sphinx
+        - cp -r build/sphinx/html public
+    artifacts:
+        paths:
+            - public

MANIFEST.in

+include *.txt
+include *.rst
+include VERSION
+recursive-include doc *.rst *.py 
+
+include madarrays/tests/*.py
+
+prune doc/build

README.rst

+MadArrays
+=========
+
+MadArrays is a Python package that regroups various data structures adapted to
+handle audio signals with missing data.
+
+Install
+-------
+
+Install the current release with ``pip``::
+
+    pip install madarrays
+
+For additional details, see doc/install.rst.
+
+Usage
+-----
+
+See the `documentation <http://skmad-suite.pages.lis-lab.fr/madarrays/>`_.
+
+Bugs
+----
+
+Please report any bugs that you find through the `MadArrays GitLab project
+<https://gitlab.lis-lab.fr/skmad-suite/madarrays/issues>`_.
+
+You can also fork the repository and create a merge request.
+
+Source code
+-----------
+
+The source code of MadArrays is available via its `GitLab project
+<https://gitlab.lis-lab.fr/skmad-suite/madarrays>`_.
+
+You can clone the git repository of the project using the command::
+
+    git clone git@gitlab.lis-lab.fr:skmad-suite/madarrays.git
+
+Copyright © 2017-2018
+---------------------
+
+* `Laboratoire d'Informatique et Systèmes <http://www.lis-lab.fr/>`_
+* `Université d'Aix-Marseille <http://www.univ-amu.fr/>`_
+* `Centre National de la Recherche Scientifique <http://www.cnrs.fr/>`_
+* `Université de Toulon <http://www.univ-tln.fr/>`_
+
+Contributors
+------------
+
+* `Ronan Hamon <mailto:ronan.hamon@lis-lab.fr>`_
+* `Valentin Emiya <mailto:valentin.emiya@lis-lab.fr>`_
+
+License
+-------
+
+Released under the GNU General Public License version 3 or later
+(see `LICENSE.txt`).

VERSION

+madarrays:1.0

doc/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -m sphinx 
+PAPER         =
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest epub
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html      to make standalone HTML files"
+	@echo "  dirhtml   to make HTML files named index.html in directories"
+	@echo "  pickle    to make pickle files"
+	@echo "  epub       to make an epub"
+	@echo "  json      to make JSON files"
+	@echo "  htmlhelp  to make HTML files and a HTML help project"
+	@echo "  qthelp    to make HTML files and a qthelp project"
+	@echo "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  changes   to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck to check all external links for integrity"
+	@echo "  doctest   to run all doctests embedded in the documentation (if enabled)"
+	@echo "  gitwash   to update the gitwash documentation"
+
+
+clean:
+	-rm -rf build/*
+	-rm -rf ghpages_build
+	-rm -rf auto_examples modules
+	-rm -rf reference/generated reference/algorithms/generated reference/classes/generated reference/readwrite/generated
+
+dist: html
+	test -d build/latex || make latex
+	make -C build/latex all-pdf
+	-rm -rf build/dist
+	(cd build/html; cp -r . ../../build/dist)
+	(cd build/dist && tar czf ../dist.tar.gz .)
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) build/html
+	@echo
+	@echo "Build finished. The HTML pages are in build/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) build/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in build/dirhtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) build/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) build/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) build/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in build/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) build/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in build/qthelp, like this:"
+	@echo "# qcollectiongenerator build/qthelp/test.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile build/qthelp/test.qhc"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) build/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) build/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in build/latex."
+	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+	      "run these through (pdf)latex."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) build/changes
+	@echo
+	@echo "The overview file is in build/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) build/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in build/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) build/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in build/doctest/output.txt."
+
+latexpdf: latex
+	@echo "Running LaTeX files through latexmk..."
+	$(MAKE) -C build/latex all-pdf
+	@echo "latexmk finished; the PDF files are in build/latex."
+
+docs: clean html latexpdf
+	cp build/latex/networkx_reference.pdf build/html/_downloads/.
+	
+gitwash-update:
+	python ../tools/gitwash_dumper.py developer networkx \
+	--project-url=http://networkx.github.io \
+	--project-ml-url=http://groups.google.com/group/networkx-discuss/ \
+	--gitwash-url git@github.com:matthew-brett/gitwash.git

doc/README.md

+Sphinx is used to generate the API and reference documentation for all
+packages from the [`skmad-suite`](https://gitlab.lis-lab.fr/skmad-suite/).
+
+## Instructions to build the documentation
+
+In addition to installing ``madarrays`` and its dependencies, install the
+Python packages needed to build the documentation by entering
+
+```
+pip install -r ../requirements/doc.txt
+```
+in the ``doc/`` directory.
+
+To build the HTML documentation, run:
+```
+make html
+```
+in the ``doc/`` directory. This will generate a ``build/html`` subdirectory
+containing the built documentation.
+
+To build the PDF documentation, run:
+```
+make latexpdf
+```
+You will need to have Latex installed for this.

doc/_notebooks/mad_array.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "%pylab inline"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "source": [
+    "# Tutorial on how to use `MadArray` objects\n",
+    "\n",
+    "A `MadArray` is a numpy array with missing elements. It is generated using three types of parameter:\n",
+    "\n",
+    "* **data** as an array of entries, either *int*, *float* or *complex*;\n",
+    "* a **mask** indicating the missing entries;\n",
+    "* **options** to define the behaviour of the object.\n",
+    "\n",
+    "A basic initialisation requires only a data matrix.  Without mask, all elements are considered as non-missing"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "from madarrays import MadArray\n",
+    "\n",
+    "# initialisation without mask\n",
+    "data = np.random.rand(4, 6)\n",
+    "\n",
+    "A = MadArray(data)\n",
+    "print(A)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Masking\n",
+    "\n",
+    "The masking of data differs according to the type of entries:\n",
+    "\n",
+    "* if the entries are *int* or *float*, the masking is done exclusively by giving aa boolean array of the same size of the data as argument `mask`, each entry indicating if the corresponding entry in the data array is missing or not\n",
+    "* if the entries are *complex*, the masking can be done as previously, or by giving boolean arrays of the same size of the data as arguments `mask_amplitude` and `mask_phase`, each entry indicating respectively if the magnitude and the phase of the corresponding entry is missing or not."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# initialization with a mask\n",
+    "mask = np.random.random(data.shape) < 0.5\n",
+    "\n",
+    "Am = MadArray(data, mask)\n",
+    "print(mask)\n",
+    "print(Am)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "source": [
+    "A *MadArray* can also be defined from another *MadArray*, for example to copy the object:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "Am2 = MadArray(Am)\n",
+    "print('{} - {}'.format(str(Am), repr(Am)))\n",
+    "print('{} - {}'.format(str(Am2), repr(Am2)))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "source": [
+    "A different mask can also be used:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "mask2 = np.random.random(data.shape) < 0.9\n",
+    "Am3 = MadArray(Am, mask2)\n",
+    "print('{} - {}'.format(str(Am), repr(Am)))\n",
+    "print('{} - {}'.format(str(Am3), repr(Am3)))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "source": [
+    "## Properties\n",
+    "\n",
+    "A *MadArray* has attributes that give information about the masking."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# mask of non-missing elements\n",
+    "print(Am.known_mask)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# mask of missing elements\n",
+    "print(Am.unknown_mask)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "print('Is masked: {}'.format(Am.is_masked))\n",
+    "print('Ratio missing data: {}'.format(Am.ratio_missing_data))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "source": [
+    "## Indexing\n",
+    "\n",
+    "There are two different and incompatible ways to index *MadArray*. By default (`masked_indexing=False`), it is similar to the indexing of *nd-array*: both the data matrix and the mask are indexed, and a *MadArray* with the shape defined by the indices is returned:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "print(A[0:3, 1:3])\n",
+    "print(Am[0:3, 1:3])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "source": [
+    "With the other way (`masked_indexing=True`), a MadArray with the shape unchanged is returned, where non-indexed entries are considered as masked."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "Am4 = MadArray(data, mask, masked_indexing=True)\n",
+    "print(Am4[0:3, 1:3])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "source": [
+    "This latter approach is adapted to be handled with *scikit-learn* procedures."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "source": [
+    "## Numerical operations\n",
+    "Numpy functions apply on *MadArray*, but **without** taking into account the mask \n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "autoscroll": "json-false",
+    "ein.tags": [
+     "worksheet-0"
+    ],
+    "slideshow": {
+     "slide_type": "-"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "print(np.mean(A))\n",
+    "print(np.mean(Am))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.2"
+  },
+  "name": "data_structures.ipynb"
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}

doc/conf.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+import sys
+import os
+
+from datetime import date
+
+import madarrays
+
+# 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('../madarrays/'))
+
+# -- General configuration ------------------------------------------------
+
+# 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.autosummary',
+              'sphinx.ext.doctest',
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.todo',
+              'sphinx.ext.coverage',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.viewcode',
+              'sphinx_paramlinks',
+              'numpydoc',
+              'nbsphinx',
+              'IPython.sphinxext.ipython_console_highlighting',
+              ]
+
+
+# Add any paths that contain templates here, relative to this directory.
+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 = 'madarrays'
+author = 'V. Emiya and R. Hamon'
+copyright = '2017-{}, {}'.format(date.today().year, author)
+
+# 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 = madarrays.__version__
+# The full version, including alpha/beta/rc tags.
+release = madarrays.__version__.replace('_', '')
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# 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:
+# 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', '**/test_*.rst', '**.ipynb_checkpoints']
+# 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
+
+# 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 = True
+
+# -- 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 = '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
+
+# 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 = []
+
+# 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'
+
+# 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
+
+# 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'
+
+# 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 = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'madarraydoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    'papersize': 'a4paper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    'preamble': '',
+
+    # 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, 'madarray.tex', 'madarray Documentation',
+     'V. Emiya, R. Hamon.', '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 ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, 'madarray', 'madarray Documentation', [author], 1)]
+
+# If true, show URL addresses after external links.
+man_show_urls = False
+
+# -- 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, 'madarray', 'madarray Documentation', author, 'madarray',
+     '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
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'matplotlib': ('http://matplotlib.org/', None),
+}
+
+# Allow errors in notebook
+nbsphinx_allow_errors = True
+
+# Do not show class members
+numpydoc_show_class_members = False
+
+# Include todos
+todo_include_todos = True

doc/credits.rst

+Credits
+=======
+
+Copyright(c) 2018
+-----------------
+
+* Laboratoire d'Informatique et Systèmes <http://www.lis-lab.fr/>
+* Université d'Aix-Marseille <http://www.univ-amu.fr/>
+* Centre National de la Recherche Scientifique <http://www.cnrs.fr/>
+* Université de Toulon <http://www.univ-tln.fr/>
+
+Contributors
+------------
+
+* Ronan Hamon <firstname.lastname_AT_lis-lab.fr>
+* Valentin Emiya <firstname.lastname_AT_lis-lab.fr>
+
+Licence
+-------
+This file is part of madarrays.
+
+madarrays is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.

doc/index.rst

+##############################
+:mod:`madarrays` documentation
+##############################
+
+Overview
+========
+:mod:`madarrays` is a python package dedicated to the manipulation of audio
+arrays with missing entries.
+
+:mod:`madarrays` provides:
+
+* a generic data structure `MadArray` to manipulate numpy arrays with missing
+  entries
+* a data structure `Waveform` to handle waveforms and easily get access to
+  useful attributes and methods
+* amplitude and phase masking for complex entries.
+
+Documentation
+=============
+
+.. only:: html
+
+    :Release: |version|
+    :Date: |today|
+
+.. toctree::
+    :maxdepth: 1
+
+    install
+    references
+    tutorials
+    credits
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+
+

doc/install.rst

+Install
+#######
+
+``madarrays`` requires the following packages:
+
+* `python >= 3.5 <https://wiki.python.org/moin/BeginnersGuide/Download>`_
+* `numpy >= 1.11 <http://www.numpy.org>`_
+* `scipy >= 0.17 <https://www.scipy.org/scipylib/index.html>`_
+* `matplotlib >= 1.5 <http://matplotlib.org/>`_
+* `simpleaudio >= 1.0 <https://github.com/hamiltron/py-simple-audio>`_
+* `resampy >= 0.2 <https://github.com/bmcfee/resampy>`_
+
+Make sure you Python environment is properly configured. It is recommended to
+install `madarrays` in a virtual environment.
+
+Release version
+---------------
+
+First, make sure you have the latest version of pip (the Python package
+manager) installed. If you do not, refer to the `Pip documentation
+<https://pip.pypa.io/en/stable/installing/>`_ and install `pip` first.
+
+Install the current release with ``pip``::
+
+    pip install madarrays
+
+To upgrade to a newer release use the ``--upgrade`` flag::
+
+    pip install --upgrade madarrays
+
+If you do not have permission to install software systemwide, you can install
+into your user directory using the ``--user`` flag::
+
+    pip install --user madarrays
+
+Alternatively, you can manually download ``madarrays`` from its `GitLab project
+<https://gitlab.lis-lab.fr/skmad-suite/madarrays>`_  or `PyPI
+<https://pypi.python.org/pypi/madarrays>`_.  To install one of these versions,
+unpack it and run the following from the top-level source directory using the
+Terminal::
+
+    pip install .
+
+Development version
+-------------------
+
+If you have `Git <https://git-scm.com/>`_ installed on your system, it is also
+possible to install the development version of ``madarrays``.
+
+Before installing the development version, you may need to uninstall the
+standard version of ``madarrays`` using ``pip``::
+
+    pip uninstall madarrays
+
+Clone the Git repository::
+
+    git clone git@gitlab.lis-lab.fr:skmad-suite/madarrays.git
+    cd madarrays
+
+You may also need to install required packages::
+
+    pip install -r requirements/defaults.txt
+
+Then execute ``pip`` with flag ``-e`` to follow the development branch::
+
+    pip install -e .
+
+To update ``madarrays`` at any time, in the same directory do::
+
+    git pull
+
+To run unitary tests, first install required packages::
+
+    pip install -r requirements/dev.txt
+
+and execute ``pytest``::
+
+    pytest
+

doc/references.rst

+References
+==========
+
+    :Release: |release|
+    :Date: |today|
+
+madarrays\.masked\_array module
+-------------------------------
+
+.. automodule:: madarrays.mad_array
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+madarrays\.waveform module
+--------------------------
+
+.. automodule:: madarrays.waveform
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    

doc/tutorials.rst

+Tutorials
+#########
+
+Data structures
+===============
+These tutorials present data structures introduced in the module.
+
+.. toctree::
+    :maxdepth: 1
+ 
+    _notebooks/mad_array.ipynb
+    _notebooks/waveform.ipynb

docker/Dockerfile_ubuntu_16.04

+FROM ubuntu:16.04
+MAINTAINER Florent Jaillet
+WORKDIR /
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        python3 \
+        python3-pip \
+        python3-wheel \
+        python3-setuptools \
+        python3-numpy\
+        python3-scipy \
+        python3-matplotlib \
+        ipython3 \
+        python3-six \
+        python3-dev \
+        gcc \
+        libasound2-dev \
+        && \
+    apt-get clean
+RUN mkdir -p /root/.config/matplotlib && \
+    echo "backend: pdf" > /root/.config/matplotlib/matplotlibrc
+RUN pip3 install llvmlite numba resampy simpleaudio --no-deps
+RUN pip3 install pytest pytest-cov pytest-randomly

docker/Dockerfile_ubuntu_rolling

+FROM ubuntu:rolling
+MAINTAINER Florent Jaillet
+WORKDIR /
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        python3 \
+        python3-pip \
+        python3-wheel \
+        python3-setuptools \
+        python3-numpy\
+        python3-scipy \
+        python3-matplotlib \
+        ipython3 \
+        python3-six \
+        python3-numba \
+        python3-dev \
+        gcc \
+        libdpkg-perl \
+        libasound2-dev \
+        python3-pytest \
+        python3-pytest-cov \
+        python3-sphinx \
+        python3-sphinx-paramlinks \
+        python3-numpydoc \
+        python3-nbsphinx \
+        jupyter-client \
+        jupyter-notebook \
+        pandoc \        
+        && \
+    apt-get clean
+RUN mkdir -p /root/.config/matplotlib && \
+    echo "backend: pdf" > /root/.config/matplotlib/matplotlibrc
+RUN pip3 install resampy simpleaudio pytest-randomly --no-deps