Merge branch 'master' into faster

.gitignore

@@ -1,7 +1,4 @@
-*.py[cod]
-
-# C extensions
-*.so
+__pycache__/
 
 # Packages
 *.egg
@@ -15,39 +12,26 @@ var
 sdist
 develop-eggs
 .installed.cfg
-lib
-lib64
 
 # Installer logs
 pip-log.txt
 
-# Unit test / coverage reports
+# Coverage reports
 .coverage
-.tox
-nosetests.xml
 htmlcov
 
-# Translations
-*.mo
-
-# Mr Developer
-.mr.developer.cfg
-.project
-.pydevproject
-
 # Complexity
 output/*.html
 output/*/index.html
 
-# Sphinx
+# Sphinx documentation
 doc/_build
-doc/tutorials/img/*\.pdf
-doc/tutorials/img/*\.png
+
 # Vim swap files
 .*.swp
-.*.swo
-docs/_build
 
-.ropeproject
+# Mac OS garbage
+.DS_Store
 
-.eggs/*
+# Jupyter notebook
+.ipynb_checkpoints/

.readthedocs.yml

@@ -0,0 +1,9 @@
+formats:
+  - htmlzip
+
+python:
+  version: 3
+  pip_install: true
+  extra_requirements:
+    - alldeps
+    - doc

.travis.yml

@@ -1,34 +1,27 @@
-# Configuration file for automatic testing at travis-ci.org
-
-language: python
-
+dist: trusty  # need glibc >= 2.17 for pyqt5
 sudo: false
 
+language: python
+cache: pip  # cache wheels for faster tests (PySide build can timeout)
 python:
-  - "2.7"
-  - "3.4"
-  - "3.5"
+  - 2.7
+  - 3.4
+  - 3.5
+  - 3.6
 
 addons:
   apt:
     packages:
-    - python-dev
-    - pkg-config
-    - libfreetype6-dev
-    - libpng-dev
-    - liblapack-dev
-    - libatlas-dev
-    - gfortran
-    - libatlas-base-dev
-    - libx11-xcb1
-    - xvfb
-
-before_install:
-    - pip install -U pip
-    - pip install -U -r requirements.txt
+      - xvfb
 
 install:
-    - python setup.py install
+  - pip install -U pip setuptools
+  - pip install -U .[alldeps,test,doc]
 
 script:
-    - xvfb-run python setup.py test
+# - make lint
+  - make test
+  - make doc
+
+after_success:
+  - coveralls

.zenodo.json

@@ -0,0 +1,39 @@
+{
+	"title": "PyGSP: Graph Signal Processing in Python",
+	"description": "The PyGSP facilitates a wide variety of operations on graphs, like computing their Fourier basis, filtering or interpolating signals, plotting graphs, signals, and filters.",
+	"upload_type": "software",
+	"license": "BSD-3-Clause",
+	"access_right": "open",
+	"creators": [
+		{
+			"name": "Micha\u00ebl Defferrard",
+			"affiliation": "EPFL",
+			"orcid": "0000-0002-6028-9024"
+		},
+		{
+			"name": "Lionel Martin",
+			"affiliation": "EPFL"
+		},
+		{
+			"name": "Rodrigo Pena",
+			"affiliation": "EPFL"
+		},
+		{
+			"name": "Nathana\u00ebl Perraudin",
+			"affiliation": "EPFL",
+			"orcid": "0000-0001-8285-1308"
+		}
+	],
+	"related_identifiers": [
+		{
+			"scheme": "url",
+			"identifier": "https://github.com/epfl-lts2/pygsp",
+			"relation": "isSupplementTo"
+		},
+		{
+			"scheme": "doi",
+			"identifier": "10.5281/zenodo.1003157",
+			"relation": "isPartOf"
+		}
+	]
+}

CONTRIBUTING.rst

@@ -2,114 +2,97 @@
 Contributing
 ============
 
-Contributions are welcome, and they are greatly appreciated! Every
-little bit helps, and credit will always be given. 
-
-You can contribute in many ways:
-
-Types of Contributions
-----------------------
-
-Report Bugs
-~~~~~~~~~~~
-
-Report bugs at https://github.com/epfl-lts2/pygsp/issues.
-
-If you are reporting a bug, please include:
-
-* Your operating system name and version.
-* Any details about your local setup that might be helpful in troubleshooting.
-* Detailed steps to reproduce the bug.
-
-Fix Bugs
-~~~~~~~~
-
-Look through the GitHub issues for bugs. Anything tagged with "bug"
-is open to whoever wants to fix it.
-
-Implement Features
-~~~~~~~~~~~~~~~~~~
-
-Look through the GitHub issues for features. Anything tagged with "feature"
-is open to whoever wants to implement it.
-
-Write Documentation
-~~~~~~~~~~~~~~~~~~~
-
-PyGSP could always use more documentation, whether as part of the 
-official PyGSP docs, in docstrings, or even on the web in blog posts,
-articles, and such.
-
-Submit Feedback
-~~~~~~~~~~~~~~~
-
-The best way to send feedback is to file an issue at https://github.com/epfl-lts2/pygsp/issues.
-
-If you are proposing a feature:
-
-* Explain in detail how it would work.
-* Keep the scope as narrow as possible, to make it easier to implement.
-* Remember that this is a volunteer-driven project, and that contributions
-  are welcome :)
-
-Get Started!
-------------
-
-Ready to contribute? Here's how to set up `pygsp` for local development.
-
-1. Fork the `pygsp` repo on GitHub.
-2. Clone your fork locally::
-
-    $ git clone git@github.com:your_name_here/pygsp.git
-
-3. Install your local copy into a virtualenv. Assuming you have `virtualenvwrapper <https://virtualenvwrapper.readthedocs.org/en/latest/>`_ installed, this is how you set up your fork for local development::
-
-    $ mkvirtualenv pygsp
-    $ cd pygsp/
-    $ python setup.py develop
-
-Note: alternatively, the third step could be replaced by::
-
-    $ pip install -e .
-
-4. Create a branch for local development::
-
-    $ git checkout -b name-of-your-bugfix-or-feature
-   
-   Now you can make your changes locally.
-
-5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
-
-    $ flake8 pygsp tests
-    $ python setup.py test
-    $ tox
-
-   To get flake8 and tox, just pip install them into your virtualenv. 
-
-6. Commit your changes and push your branch to GitHub::
-
-    $ git add *
-    $ git commit -m "Your detailed description of your changes."
-    $ git push --set-upstream origin name-of-your-branch
-
-7. Submit a pull request through the GitHub website.
-
-Pull Request Guidelines
+Contributions are welcome, and they are greatly appreciated! The development of
+this package takes place on `GitHub <https://github.com/epfl-lts2/pygsp>`_.
+Issues, bugs, and feature requests should be reported `there
+<https://github.com/epfl-lts2/pygsp/issues>`_.
+Code and documentation can be improved by submitting a `pull request
+<https://github.com/epfl-lts2/pygsp/pulls>`_. Please add documentation and
+tests for any new code.
+
+The package can be set up (ideally in a virtual environment) for local
+development with the following::
+
+    $ git clone https://github.com/epfl-lts2/pygsp.git
+    $ pip install -U -e pygsp[alldeps,test,doc,pkg]
+
+You can improve or add functionality in the ``pygsp`` folder, along with
+corresponding unit tests in ``pygsp/tests/test_*.py`` (with reasonable
+coverage) and documentation in ``doc/reference/*.rst``. If you have a nice
+example to demonstrate the use of the introduced functionality, please consider
+adding a tutorial in ``doc/tutorials``.
+
+Do not forget to update ``README.rst`` and ``doc/history.rst`` with e.g. new
+features. The version number needs to be updated in ``setup.py`` and
+``pyunlocbox/__init__.py``.
+
+After making any change, please check the style, run the tests, and build the
+documentation with the following (enforced by Travis CI)::
+
+    $ make lint
+    $ make test
+    $ make doc
+
+Check the generated coverage report at ``htmlcov/index.html`` to make sure the
+tests reasonably cover the changes you've introduced.
+
+Making a release
+----------------
+
+#. Update the version number and release date in ``setup.py``,
+   ``pygsp/__init__.py`` and ``doc/history.rst``.
+#. Create a git tag with ``git tag -a v0.5.0 -m "PyGSP v0.5.0"``.
+#. Push the tag to GitHub with ``git push github v0.5.0``. The tag should now
+   appear in the releases and tags tab.
+#. `Create a release <https://github.com/epfl-lts2/pygsp/releases/new>`_ on
+   GitHub and select the created tag. A DOI should then be issued by Zenodo.
+#. Go on Zenodo and fix the metadata if necessary.
+#. Build the distribution with ``make dist`` and check that the
+   ``dist/PyGSP-0.5.0.tar.gz`` source archive contains all required files. The
+   binary wheel should be found as ``dist/PyGSP-0.5.0-py2.py3-none-any.whl``.
+#. Test the upload and installation process::
+
+    $ twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+    $ pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple pygsp
+
+   Log in as the LTS2 user.
+#. Build and upload the distribution to the real PyPI with ``make release``.
+#. Update the conda feedstock (at least the version number and sha256 in
+   ``recipe/meta.yaml``) by sending a PR to
+   `conda-forge <https://github.com/conda-forge/pygsp-feedstock>`_.
+
+Repository organization
 -----------------------
 
-Before you submit a pull request, check that it meets these guidelines:
-
-1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. Put
-   your new functionality into a function with a docstring, and add the
-   feature to the list in README.rst.
-3. The pull request should work for Python 2.7, 3.2, and 3.4, and for PyPy. Check 
-   https://travis-ci.org/epfl-lts2/pygsp/pull_requests
-   and make sure that the tests pass for all supported Python versions.
-
-Tips
-----
-
-To run a subset of tests::
-
-	$ python -m unittest tests.test_pygsp
+::
+
+  LICENSE.txt         Project license
+  *.rst               Important documentation
+  Makefile            Targets for make
+  setup.py            Meta information about package (published on PyPI)
+  .gitignore          Files ignored by the git revision control system
+  .travis.yml         Defines testing on Travis continuous integration
+
+  pygsp/              Contains the modules (the actual toolbox implementation)
+   __init.py__        Load modules at package import
+   *.py               One file per module
+
+  pygsp/tests/        Contains the test suites (will be distributed to end user)
+   __init.py__        Load modules at package import
+   test_*.py          One test suite per module
+   test_docstrings.py Test the examples in the docstrings (reference doc)
+   test_tutorials.py  Test the tutorials in doc/tutorials
+   test_all.py        Launch all the tests (docstrings, tutorials, modules)
+
+  doc/                Package documentation
+   conf.py            Sphinx configuration
+   index.rst          Documentation entry page
+   *.rst              Include doc files from root directory
+
+  doc/reference/      Reference documentation
+   index.rst          Reference entry page
+   *.rst              Only directives, the actual doc is alongside the code
+
+  doc/tutorials/
+   index.rst          Tutorials entry page
+   *.rst              One file per tutorial