Commit a43a9db2 authored by valentin.emiya's avatar valentin.emiya

all files for v1.0.0

Pipeline #1394 passed with stage
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branch = True
source = pyexp
include = */pyexp/*
omit =
exclude_lines =
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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:
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def __str__(self):
# Packages
# Installer logs
# Mac OS X files
# Sphinx stuff
# jupyter notebook
# coverage
# ide
# Misc
# run the test suite
- docker
- apt install -y --no-install-recommends python3-xarray
- pip3 install --no-deps .
- pytest-3
# generate the documentation
- docker
- master
- apt install -y --no-install-recommends python3-xarray
- pip3 install --no-deps .
- python3 build_sphinx
- cp -r build/sphinx/html public
- public
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include *.txt
include *.rst
include VERSION
recursive-include doc *.rst *.py *.ipynb
include yafe/tests/*.py
prune doc/build
yafe: Yet Another Framework for Experiments.
A classical workflow consists in the following steps:
* load some data,
* generate a problem from the data,
* solve the problem,
* compute performance criteria,
* display results.
Experiments are then conducted by repeating this task while varying the
data, problem parameters, solvers and/or solver parameters. A computer
cluster may be used to run all the resulting tasks in parallel,
which requires to distribute them adequately among the available
resources and then to collect and merge the results.
The package `yafe` offers a generic framework to conduct such experiments,
aiming at saving time and avoiding errors:
* the generic framework facilitates the design of experiments,
* convenient data structures help to handle results quickly and without
confusion between multiple dimensions,
* intermediate results can be tracked,
* tasks are computed once, even when new tasks are added.
Install the current release with ``pip``::
pip install yafe
For additional details, see doc/install.rst.
See the `documentation <>`_.
Please report any bugs that you find through the `yafe GitLab project
You can also fork the repository and create a merge request.
Source code
The source code of yafe is available via its `GitLab project
You can clone the git repository of the project using the command::
git clone
Copyright © 2017-2018
* `Laboratoire d'Informatique et Systèmes <>`_
* `Université d'Aix-Marseille <>`_
* `Centre National de la Recherche Scientifique <>`_
* `Université de Toulon <>`_
* `Ronan Hamon <>`_
* `Valentin Emiya <>`_
* `Florent Jaillet <>`_
Released under the GNU General Public License version 3 or later
(see `LICENSE.txt`).
# Makefile for Sphinx documentation
# You can set these variables from the command line.
SPHINXBUILD = python -m sphinx
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest epub
@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"
-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 .)
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) build/html
@echo "Build finished. The HTML pages are in build/html."
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) build/dirhtml
@echo "Build finished. The HTML pages are in build/dirhtml."
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) build/pickle
@echo "Build finished; now you can process the pickle files."
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) build/json
@echo "Build finished; now you can process the JSON files."
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) build/htmlhelp
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in build/htmlhelp."
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) build/qthelp
@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"
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) build/epub
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) build/latex
@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."
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) build/changes
@echo "The overview file is in build/changes."
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) build/linkcheck
@echo "Link check complete; look for any errors in the above output " \
"or in build/linkcheck/output.txt."
$(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/.
python ../tools/ developer networkx \
--project-url= \
--project-ml-url= \
If you only want to get the documentation, note that a pre-built
version for the latest release is available
Sphinx is used to generate the API and reference documentation for all
packages from the [`skmad-suite`](
## Instructions to build the documentation
In addition to installing ``yafe`` 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.
This diff is collapsed.
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys
import os
from datetime import date
import yafe
# 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('../yafe/'))
# -- 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',
# 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 = 'yafe'
author = 'R. Hamon, V. Emiya, F. Jaillet'
copyright = '2017-{}, {}'.format(, 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 = yafe.__version__
# The full version, including alpha/beta/rc tags.
release = yafe.__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 = 'bizstyle'
# 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 = 'yafedoc'
# -- 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, 'yafe.tex', 'yafe Documentation', author, '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, 'yafe', 'yafe 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, 'yafe.tex', 'yafe Documentation', author, 'manual'),
# 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': ('', None),
'xarray': ('', 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
# Order members by member type
autodoc_member_order = 'groupwise'
Copyright(c) 2018
* Laboratoire d'Informatique et Systèmes <>
* Université d'Aix-Marseille <>
* Centre National de la Recherche Scientifique <>
* Université de Toulon <>
* Ronan Hamon <>
* Valentin Emiya <>
* Florent Jaillet <>
This file is part of yafe.
yafe 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
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 <>.
# -*- coding: utf-8 -*-
"""Example experiment to be deployed on a cluster grid with OAR.
.. moduleauthor:: Ronan Hamon
.. moduleauthor:: Valentin Emiya
.. moduleauthor:: Florent Jaillet
This example and the following workflow illustrates the design of a ``yafe``
experiment, its execution on a cluster and how to collect and exploit
results remotely or locally.
* On the cluster frontend, run this script to generate the experiment,
its tasks, and the OAR script (see ``__main__`` below). Note that if you are
using a virtual environment, you should add it as an argument when calling
function ``generate_oar_script`` and activate it before running this script.
* Run the tasks on the cluster by executing the command line displayed by
the script.
* Optionally, collect and exploit results on the cluster by opening a python
session and by running::
from example_oar import experiment
results, axes_labels, axes_values = experiment.load_results()
* In order to exploit results on a local machine, download the
experiment directory and all its contents into your local data path and
run the above code locally. Note that downloading all the directory
is needed to preserve the consistency of the task indexing, especially if
you want to examine some specific tasks or add new ones.
* If you only want to exploit results without downloading all the
experiment data stored in the directory, you should collect the
results remotely on the cluster and download files ``_schema.pickle`` and
``results.npz`` into your local data directory. You can then exploit the
results using ::
from example_oar import experiment
results, axes_labels, axes_values = experiment.load_results()
Be aware that only the method ``load_results`` will be usable and that the
``experiment`` object will be in an inconsistent state for all the other
import numpy as np
from yafe import Experiment
from yafe.utils import generate_oar_script
def get_sine_data(f0, signal_len=1000):
return {'signal': np.sin(2*np.pi*f0*np.arange(signal_len))}
class SimpleDenoisingProblem:
def __init__(self, snr_db):
self.snr_db = snr_db
def __call__(self, signal):
random_state = np.random.RandomState(0)
noise = random_state.randn(*signal.shape)
observation = signal + 10 ** (-self.snr_db / 20) * noise \
/ np.linalg.norm(noise) * np.linalg.norm(signal)
problem_data = {'observation': observation}
solution_data = {'signal': signal}
return problem_data, solution_data
def __str__(self):
return 'SimpleDenoisingProblem(snr_db={})'.format(self.snr_db)
class SmoothingSolver:
def __init__(self, filter_len):
self.filter_len = filter_len
def __call__(self, observation):
smoothing_filter = np.hamming(self.filter_len)
smoothing_filter /= np.sum(smoothing_filter)
return {'reconstruction': np.convolve(observation, smoothing_filter,
def __str__(self):
return 'SmoothingSolver(filter_len={})'.format(self.filter_len)
def measure(solution_data, solved_data, task_params=None, source_data=None,
euclidian_distance = np.linalg.norm(solution_data['signal']
- solved_data['reconstruction'])
sdr = 20 * np.log10(np.linalg.norm(solution_data['signal'])
/ euclidian_distance)
inf_distance = np.linalg.norm(solution_data['signal']
- solved_data['reconstruction'], ord=np.inf)