Merge pull request #27 from epfl-lts2/maintenance

Some maintenance on the infrastructure. Kept in sync with
epfl-lts2/pygsp#81 to facilitate future maintenance by keeping their
infra similar.

.readthedocs.yml

@@ -1,8 +1,15 @@
+version: 2
+
 formats:
   - htmlzip
 
+sphinx:
+  builder: html
+  configuration: doc/conf.py
+
 python:
-  version: 3
-  pip_install: true
-  extra_requirements:
-    - dev
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev

.travis.yml

@@ -1,10 +1,10 @@
 language: python
 
 python:
-  - 2.7
-  - 3.5
   - 3.6
   - 3.7
+  - 3.8
+  - 3.9
 
 addons:
   apt:

doc/history.rst → CHANGELOG.rst

@@ -1,16 +1,18 @@
-=======
-History
-=======
+=========
+Changelog
+=========
 
-Versions follow `SemVer <https://semver.org>`_ (we try our best).
+All notable changes to this project will be documented in this file.
+The format is based on `Keep a Changelog <https://keepachangelog.com>`_
+and this project adheres to `Semantic Versioning <https://semver.org>`_.
 
 Unreleased
 ----------
 
-* Drop support of Python 3.4 and test with 3.7. Last version to support 2.7.
+* New function: proj_positive.
+* New function: structured_sparsity.
+* Continuous integration with Python 3.6, 3.7, 3.8, 3.9. Dropped 2.7, 3.4, 3.5.
 * Merged all the extra requirements in a single dev requirement.
-* Addition of the proj_positive function
-* Addition of the structured_sparsity function.
 
 0.5.2 (2017-12-15)
 ------------------

CONTRIBUTING.rst

@@ -27,7 +27,7 @@ If you have a nice example to demonstrate the use of the introduced
 functionality, please consider adding a tutorial in ``doc/tutorials`` or a
 short example in ``examples``.
 
-Update ``README.rst`` and ``doc/history.rst`` if applicable.
+Update ``README.rst`` and ``CHANGELOG.rst`` if applicable.
 
 After making any change, please check the style, run the tests, and build the
 documentation with the following (enforced by Travis CI)::
@@ -49,7 +49,7 @@ Making a release
 ----------------
 
 #. Update the version number and release date in ``setup.py``,
-   ``pyunlocbox/__init__.py`` and ``doc/history.rst``.
+   ``pyunlocbox/__init__.py`` and ``CHANGELOG.rst``.
 #. Create a git tag with ``git tag -a v0.5.0 -m "PyUNLocBox 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.

MANIFEST.in

@@ -1,2 +1,3 @@
 include LICENSE.txt
 include README.rst
+include CHANGELOG.rst

Makefile

@@ -1,4 +1,4 @@
-NB = $(sort $(wildcard *.ipynb))
+NB = $(sort $(wildcard examples/*.ipynb))
 .PHONY: help clean lint test doc dist release
 
 help:

README.rst

@@ -29,14 +29,14 @@ A (mostly unmaintained) `Matlab version <https://lts2.epfl.ch/unlocbox>`_ exists
    :target: https://github.com/epfl-lts2/pyunlocbox/blob/master/LICENSE.txt
 .. |pyversions| image:: https://img.shields.io/pypi/pyversions/pyunlocbox.svg
    :target: https://pypi.org/project/pyunlocbox
-.. |travis| image:: https://img.shields.io/travis/epfl-lts2/pyunlocbox.svg
-   :target: https://travis-ci.org/epfl-lts2/pyunlocbox
+.. |travis| image:: https://img.shields.io/travis/com/epfl-lts2/pyunlocbox.svg
+   :target: https://travis-ci.com/epfl-lts2/pyunlocbox
 .. |coveralls| image:: https://img.shields.io/coveralls/epfl-lts2/pyunlocbox.svg
    :target: https://coveralls.io/github/epfl-lts2/pyunlocbox
 .. |github| image:: https://img.shields.io/github/stars/epfl-lts2/pyunlocbox.svg?style=social
    :target: https://github.com/epfl-lts2/pyunlocbox
-.. |binder| image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/epfl-lts2/pyunlocbox/master?filepath=playground.ipynb
+.. |binder| image:: https://static.mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/epfl-lts2/pyunlocbox/master?urlpath=lab/tree/examples/playground.ipynb
 .. |conda| image:: https://anaconda.org/conda-forge/pyunlocbox/badges/installer/conda.svg
    :target: https://anaconda.org/conda-forge/pyunlocbox
 
@@ -115,7 +115,7 @@ Solution found after 9 iterations:
 array([3.99990766, 4.99988458, 5.99986149, 6.99983841])
 
 You can
-`try it online <https://mybinder.org/v2/gh/epfl-lts2/pyunlocbox/master?filepath=playground.ipynb>`_,
+`try it online <https://mybinder.org/v2/gh/epfl-lts2/pyunlocbox/master?urlpath=lab/tree/examples/playground.ipynb>`_,
 look at the
 `tutorials <https://pyunlocbox.readthedocs.io/en/stable/tutorials/index.html>`_
 to learn how to use it, or look at the
@@ -144,7 +144,7 @@ Acknowledgments
 The PyUNLocBoX was started in 2014 as an academic open-source project for
 research purpose at the `EPFL LTS2 laboratory <https://lts2.epfl.ch>`_.
 
-The code in this repository is released under the terms of the `BSD 3-Clause license <LICENSE.txt>`_.
+It is released under the terms of the BSD 3-Clause license.
 
 If you are using the library for your research, for the sake of
 reproducibility, please cite the version you used as indexed by

doc/changelog.rst

@@ -0,0 +1 @@
+.. include:: ../CHANGELOG.rst

doc/conf.py

@@ -2,15 +2,29 @@
 
 import pyunlocbox
 
-extensions = ['sphinx.ext.viewcode',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.inheritance_diagram',
-              'sphinxcontrib.bibtex']
+extensions = [
+        'sphinx.ext.viewcode',
+        'sphinx.ext.autosummary',
+        'sphinx.ext.mathjax',
+        'sphinx.ext.inheritance_diagram',
+]
 
 extensions.append('sphinx.ext.autodoc')
-autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance']
-autodoc_member_order = 'bysource'  # alphabetical, groupwise, bysource
+autodoc_default_options = {
+    'members': True,
+    'undoc-members': True,
+    'show-inheritance': True,
+    'member-order': 'bysource',  # alphabetical, groupwise, bysource
+}
+
+extensions.append('sphinx.ext.intersphinx')
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://numpy.org/doc/stable', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    'matplotlib': ('https://matplotlib.org', None),
+    'pygsp': ('https://pygsp.readthedocs.io/en/stable', None),
+}
 
 extensions.append('numpydoc')
 numpydoc_show_class_members = False
@@ -21,6 +35,12 @@
 plot_html_show_formats = False
 plot_working_directory = '.'
 
+extensions.append('sphinx_copybutton')
+copybutton_prompt_text = ">>> "
+
+extensions.append('sphinxcontrib.bibtex')
+bibtex_bibfiles = ['references.bib']
+
 exclude_patterns = ['_build']
 source_suffix = '.rst'
 master_doc = 'index'

doc/index.rst

@@ -6,6 +6,6 @@
    Home <self>
    tutorials/index
    reference/index
+   changelog
    contributing
-   history
    references

doc/reference/index.rst

@@ -1,6 +1,6 @@
-===============
-Reference guide
-===============
+=============
+API reference
+=============
 
 .. automodule:: pyunlocbox
 

playground.ipynb → examples/playground.ipynb

@@ -104,7 +104,7 @@
    "source": [
     "## 3 Tutorials\n",
     "\n",
-    "Try to follow one of our [tutorials](https://pyunlocbox.readthedocs.io/en/stable/tutorials/index.html)."
+    "Try our [tutorials](https://pyunlocbox.readthedocs.io/en/stable/tutorials/index.html)."
    ]
   },
   {
@@ -122,8 +122,8 @@
    "source": [
     "## 4 Playground\n",
     "\n",
-    "Or try anything that goes through your mind!\n",
-    "Look at the [reference guide](https://pyunlocbox.readthedocs.io/en/stable/reference/index.html) to know more about the API."
+    "Try something of your own!\n",
+    "The [API reference](https://pyunlocbox.readthedocs.io/en/stable/reference/index.html) is your friend."
    ]
   },
   {
@@ -152,7 +152,13 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 4
 }

pyunlocbox/__init__.py

@@ -17,17 +17,18 @@
 
 """
 
-# When importing the toolbox, you surely want these modules.
-from pyunlocbox import functions
-from pyunlocbox import solvers
-from pyunlocbox import operators
-from pyunlocbox import acceleration
-
-# Silence the code checker warning about unused symbols.
-assert functions
-assert solvers
-assert operators
-assert acceleration
+from pyunlocbox import functions  # noqa: F401
+from pyunlocbox import solvers  # noqa: F401
+from pyunlocbox import acceleration  # noqa: F401
+from pyunlocbox import operators  # noqa: F401
 
 __version__ = '0.5.2'
 __release_date__ = '2017-12-15'
+
+
+def test():  # pragma: no cover
+    """Run the test suite."""
+    import unittest
+    # Lazy as it might be slow and require additional dependencies.
+    from pyunlocbox.tests import suite
+    unittest.TextTestRunner(verbosity=2).run(suite)

pyunlocbox/tests/__init__.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+Test suite for the pyunlocbox package, broken by modules.
+
+"""
+
+import unittest
+
+from . import test_functions
+from . import test_operators
+from . import test_solvers
+from . import test_acceleration
+from . import test_docstrings
+
+
+suite = unittest.TestSuite([
+    test_functions.suite,
+    test_operators.suite,
+    test_solvers.suite,
+    test_acceleration.suite,
+    test_docstrings.suite,
+])

pyunlocbox/tests/test_docstrings.py

@@ -22,7 +22,7 @@ def test_docstrings(root, ext):
     return doctest.DocFileSuite(*files, module_relative=False)
 
 
-# Docstrings from reference documentation.
+# Docstrings from API reference.
 suite_reference = test_docstrings('pyunlocbox', '.py')
 
 # Docstrings from tutorials.

setup.py

@@ -14,32 +14,34 @@
     url='https://github.com/epfl-lts2/pyunlocbox',
     project_urls={
         'Documentation': 'https://pyunlocbox.readthedocs.io',
+        'Download': 'https://pypi.org/project/pyunlocbox',
         'Source Code': 'https://github.com/epfl-lts2/pyunlocbox',
         'Bug Tracker': 'https://github.com/epfl-lts2/pyunlocbox/issues',
-        'Try It Online': 'https://mybinder.org/v2/gh/epfl-lts2/pyunlocbox/master?filepath=playground.ipynb',  # noqa
+        'Try It Online': 'https://mybinder.org/v2/gh/epfl-lts2/pyunlocbox/master?urlpath=lab/tree/examples/playground.ipynb',  # noqa
     },
     packages=[
         'pyunlocbox',
         'pyunlocbox.tests'
     ],
-    test_suite='pyunlocbox.tests.test_all.suite',
+    test_suite='pyunlocbox.tests.suite',
     install_requires=[
         'numpy',
         'scipy'
     ],
     extras_require={
         'dev': [
-            # Testing dependencies.
+            # Run the tests.
             'flake8',
             'coverage',
             'coveralls',
-            # Dependencies to build the documentation.
+            # Build the documentation.
             'sphinx',
             'numpydoc',
             'sphinxcontrib-bibtex',
             'sphinx-rtd-theme',
+            'sphinx-copybutton',
             'matplotlib',
-            # Dependencies to build and upload packages.
+            # Build and upload packages.
             'wheel',
             'twine',
         ],
@@ -48,18 +50,18 @@
     keywords='convex optimization',
     platforms='any',
     classifiers=[
-        'Topic :: Scientific/Engineering :: Mathematics',
-        'Environment :: Console',
         'Development Status :: 4 - Beta',
+        'Topic :: Scientific/Engineering',
         'Intended Audience :: Developers',
         'Intended Audience :: Education',
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: BSD License',
-        'Natural Language :: English',
         'Operating System :: OS Independent',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
     ],
 )