Standardise

.gitlab-ci.yml

+# This build file is defined in two parts: 1) a generic set of instructions you
+# probably **don't** need to change and 2) a part you may have to tune to your
+# project. It heavily uses template features from YAML to help you in only
+# changing a minimal part of it and avoid code duplication to a maximum while
+# still providing a nice pipeline display on your package.
+
+
+# 1) Generic instructions (only change if you know what you're doing)
+# -------------------------------------------------------------------
+
+# Definition of our build pipeline
+stages:
+  - build
+  - test
+  - docs
+  - wheels
+
+
+# Global variables
+variables:
+  CONDA_PREFIX: env
+
+
+# Template for the build stage
+# Needs to run on all supported architectures, platforms and python versions
+.build_template: &build_job
+  stage: build
+  before_script:
+    - git clean -ffdx
+    - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/7/raw | tr -d '\r' > bootstrap-conda.sh
+    - chmod 755 ./bootstrap-conda.sh
+    - ./bootstrap-conda.sh ${CONDA_FOLDER} ${PYTHON_VER} ${CONDA_PREFIX}
+  variables: &build_variables
+    BOB_DOCUMENTATION_SERVER: "http://www.idiap.ch/software/bob/docs/latest/bob/%s/master/"
+  script:
+    - BOB_PREFIX_PATH=${CONDA_FOLDER}/envs/`cat ${CONDA_FOLDER}/envs/latest-devel-${PYTHON_VER}.txt` ./bin/buildout
+    - ./bin/sphinx-build doc sphinx
+    - ./bin/python setup.py bdist_wheel
+  after_script:
+    - rm -rf ${CONDA_PREFIX}
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - bootstrap-conda.sh
+      - dist/
+      - sphinx/
+
+
+# Template for building on a Linux machine
+.build_linux_template: &linux_build_job
+  <<: *build_job
+  variables: &linux_build_variables
+    <<: *build_variables
+    CONDA_FOLDER: "/local/conda"
+    CFLAGS: "-D_GLIBCXX_USE_CXX11_ABI=0 -coverage"
+    CXXFLAGS: "-D_GLIBCXX_USE_CXX11_ABI=0 -coverage"
+
+
+# Template for building on a Mac OSX machine
+.build_mac_template: &macosx_build_job
+  <<: *build_job
+  variables: &macosx_build_variables
+    <<: *build_variables
+    CONDA_FOLDER: "/opt/conda"
+    MACOSX_DEPLOYMENT_TARGET: "10.9"
+    CFLAGS: "-pthread -coverage"
+    CXXFLAGS: "-pthread -coverage"
+    LDFLAGS: "-lpthread"
+
+
+# Template for the test stage - re-install from uploaded wheels
+# Needs to run on all supported architectures, platforms and python versions
+.test_template: &test_job
+  stage: test
+  before_script:
+    - ./bootstrap-conda.sh ${CONDA_FOLDER} ${PYTHON_VER} ${CONDA_PREFIX}
+    - source ${CONDA_FOLDER}/bin/activate ${CONDA_PREFIX}
+    - pip install --use-wheel --no-index --pre dist/*.whl
+  script:
+    - cd ${CONDA_PREFIX}
+    - python -c "from ${CI_PROJECT_NAME} import get_config; print(get_config())"
+    - coverage run --source=${CI_PROJECT_NAME} ./bin/nosetests -sv ${CI_PROJECT_NAME}
+    - coverage report
+    - sphinx-build -b doctest ../doc ../sphinx
+  after_script:
+    - rm -rf ${CONDA_PREFIX}
+
+
+# Template for the wheel uploading stage
+# Needs to run against one combination of python 2.x and 3.x if it is a python
+# only package, otherwise, needs to run in both pythons to all supported
+# architectures (Linux and Mac OSX 64-bit)
+.wheels_template: &wheels_job
+  stage: wheels
+  only:
+    - master
+    - tags
+  before_script:
+    - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/8/raw | tr -d '\r' > upload-wheel.sh
+    - chmod 755 upload-wheel.sh
+  script:
+    - ./upload-wheel.sh
+
+
+# Template for (latest) documentation upload stage
+# Only one real job needs to do this
+.docs_template: &docs_job
+  stage: docs
+  only:
+    - master
+  before_script:
+    - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/9/raw | tr -d '\r' > upload-sphinx.sh
+    - chmod 755 upload-sphinx.sh
+  script:
+    - ./upload-sphinx.sh
+
+
+# 2) Package specific instructions (you may tune this if needed)
+# --------------------------------------------------------------
+
+# Linux + Python 2.7: Builds and tests
+build_linux_27:
+  <<: *linux_build_job
+  variables: &linux_27_build_variables
+    <<: *linux_build_variables
+    PYTHON_VER: "2.7"
+  tags:
+    - conda-linux
+
+test_linux_27:
+  <<: *test_job
+  variables: *linux_27_build_variables
+  dependencies:
+    - build_linux_27
+  tags:
+    - conda-linux
+
+wheels_linux_27:
+  <<: *wheels_job
+  dependencies:
+    - build_linux_27
+  tags:
+    - conda-linux
+
+
+# Linux + Python 3.4: Builds and tests
+build_linux_34:
+  <<: *linux_build_job
+  variables: &linux_34_build_variables
+    <<: *linux_build_variables
+    PYTHON_VER: "3.4"
+  tags:
+    - conda-linux
+
+test_linux_34:
+  <<: *test_job
+  variables: *linux_34_build_variables
+  dependencies:
+    - build_linux_34
+  tags:
+    - conda-linux
+
+wheels_linux_34:
+  <<: *wheels_job
+  dependencies:
+    - build_linux_34
+  tags:
+    - conda-linux
+
+
+# Linux + Python 3.5: Builds and tests
+build_linux_35:
+  <<: *linux_build_job
+  variables: &linux_35_build_variables
+    <<: *linux_build_variables
+    PYTHON_VER: "3.5"
+  tags:
+    - conda-linux
+
+test_linux_35:
+  <<: *test_job
+  variables: *linux_35_build_variables
+  dependencies:
+    - build_linux_35
+  tags:
+    - conda-linux
+
+wheels_linux_35:
+  <<: *wheels_job
+  dependencies:
+    - build_linux_35
+  tags:
+    - conda-linux
+
+docs_linux_35:
+  <<: *docs_job
+  dependencies:
+    - build_linux_35
+  tags:
+    - conda-linux
+
+
+# Mac OSX + Python 2.7: Builds, tests and uploads the wheel
+build_macosx_27:
+  <<: *macosx_build_job
+  variables: &macosx_27_build_variables
+    <<: *macosx_build_variables
+    PYTHON_VER: "2.7"
+  tags:
+    - conda-macosx
+
+test_macosx_27:
+  <<: *test_job
+  variables: *macosx_27_build_variables
+  dependencies:
+    - build_macosx_27
+  tags:
+    - conda-macosx
+
+wheels_macosx_27:
+  <<: *wheels_job
+  dependencies:
+    - build_macosx_27
+  tags:
+    - conda-macosx
+
+
+# Mac OSX + Python 3.4: Builds and tests
+build_macosx_34:
+  <<: *macosx_build_job
+  variables: &macosx_34_build_variables
+    <<: *macosx_build_variables
+    PYTHON_VER: "3.4"
+  tags:
+    - conda-macosx
+
+test_macosx_34:
+  <<: *test_job
+  variables: *macosx_34_build_variables
+  dependencies:
+    - build_macosx_34
+  tags:
+    - conda-macosx
+
+wheels_macosx_34:
+  <<: *wheels_job
+  dependencies:
+    - build_macosx_34
+  tags:
+    - conda-macosx
+
+
+# Mac OSX + Python 3.5: Builds, tests, uploads the wheel and the latest docs
+build_macosx_35:
+  <<: *macosx_build_job
+  variables: &macosx_35_build_variables
+    <<: *macosx_build_variables
+    PYTHON_VER: "3.5"
+  tags:
+    - conda-macosx
+
+test_macosx_35:
+  <<: *test_job
+  variables: *macosx_35_build_variables
+  dependencies:
+    - build_macosx_35
+  tags:
+    - conda-macosx
+
+wheels_macosx_35:
+  <<: *wheels_job
+  dependencies:
+    - build_macosx_35
+  tags:
+    - conda-macosx
\ No newline at end of file

.travis.yml

-language: python
-env:
-  global:
-  - secure: TEPqit10h7L/l4kbv8zbvKH9freS6f1p2pIfUuMMfASKuZHAzizljSv14NKqeXhrpr5kPbQhNAcMrme8x7Is7bQCVxN4/8K6BQNmp2V6hWxBAh+2wk/9Bxv+FNlDBhjQM3rNIM0Wjzf5JW5OM+CMeZjxI1Mi/vNI/oN2vtvFfsA=
-  - secure: glYEyCLOew9QZXhgTHKkP9JGt/pAT7P/Pfk/SqyX++6wyTjyMrnj0DeSJW7khxtxo6kL+d23eojQVy6Q0izZ3US3KGt3PsLxYf+2Yi4Lhji/RjhZG4qgpz4XUb3cZcmb2wTJ/qFYZbGRjr5KvzkICvzv1IjxCeTuEwnj1ctz62Y=
-  - BOB_UPLOAD_WHEEL=1
-matrix:
-  include:
-  - python: 2.7
-    env:
-    - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
-  - python: 3.3
-  - python: 3.4
-  - python: 3.5
-before_install:
-- sudo add-apt-repository -y ppa:biometrics/bob
-- sudo apt-get update -qq
-- sudo apt-get install -qq --force-yes libboost-all-dev libblitz1-dev libhdf5-serial-dev libatlas-dev libatlas-base-dev liblapack-dev texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
-- pip install --upgrade pip
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel sphinx nose coverage cpp-coveralls
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel --pre -r requirements.txt coveralls
-install:
-- python bootstrap-buildout.py
-- CPPFLAGS=--coverage LDFLAGS=--coverage ./bin/buildout buildout:debug=false buildout:develop=. buildout:extensions=bob.buildout buildout:auto-checkout=
-script:
-- ./bin/python -c 'import pkg_resources; from bob.learn.activation import get_config; print(get_config())'
-- ./bin/coverage run --source=bob.learn.activation ./bin/nosetests -sv
-- ./bin/sphinx-build -b doctest doc sphinx
-- ./bin/sphinx-build -b html doc sphinx
-after_success:
-- cpp-coveralls --build-root=`pwd` --exclude=src --exclude-pattern=".*Compiler.*" --dump=cpp_cov.json
-- coveralls --merge=cpp_cov.json
-- wget https://raw.githubusercontent.com/bioidiap/bob.extension/master/scripts/upload-{sphinx,wheel}.sh
-- chmod a+x upload-sphinx.sh upload-wheel.sh
-- ./upload-sphinx.sh
-- ./upload-wheel.sh

LICENSE

-Copyright (c) 2013, Andre Anjos - Idiap Research Institute
-All rights reserved.
+Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
+Written by Andre Anjos <andre.anjos@idiap.ch>
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 
-Redistributions of source code must retain the above copyright notice, this
-list of conditions and the following disclaimer.  Redistributions in binary
-form must reproduce the above copyright notice, this list of conditions and the
-following disclaimer in the documentation and/or other materials provided with
-the distribution.  Neither the name of the Idiap Research Institute nor the
-names of its contributors may be used to endorse or promote products derived
-from this software without specific prior written permission.
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
 
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
@@ -21,4 +24,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
\ No newline at end of file

MANIFEST.in

-include LICENSE README.rst bootstrap-buildout.py buildout.cfg requirements.txt version.txt
+include LICENSE README.rst bootstrap-buildout.py buildout.cfg develop.cfg requirements.txt version.txt
 recursive-include doc conf.py *.rst
 recursive-include bob/learn/activation *.cpp *.h

README.rst

 .. vim: set fileencoding=utf-8 :
-.. Andre Anjos <andre.anjos@idiap.ch>
-.. Fri 13 Dec 2013 12:35:22 CET
+.. Sun 14 Aug 2016 20:48:25 CEST
 
 .. image:: http://img.shields.io/badge/docs-stable-yellow.png
    :target: http://pythonhosted.org/bob.learn.activation/index.html
 .. image:: http://img.shields.io/badge/docs-latest-orange.png
    :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.learn.activation/master/index.html
-.. image:: https://travis-ci.org/bioidiap/bob.learn.activation.svg?branch=master
-   :target: https://travis-ci.org/bioidiap/bob.learn.activation?branch=master
-.. image:: https://coveralls.io/repos/bioidiap/bob.learn.activation/badge.svg?branch=master
-   :target: https://coveralls.io/r/bioidiap/bob.learn.activation?branch=master
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
-   :target: https://github.com/bioidiap/bob.learn.activation/tree/master
+.. image:: https://gitlab.idiap.ch/bob/bob.learn.activation/badges/master/build.svg
+   :target: https://gitlab.idiap.ch/bob/bob.learn.activation/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+   :target: https://gitlab.idiap.ch/bob/bob.learn.activation
 .. image:: http://img.shields.io/pypi/v/bob.learn.activation.png
    :target: https://pypi.python.org/pypi/bob.learn.activation
 .. image:: http://img.shields.io/pypi/dm/bob.learn.activation.png
    :target: https://pypi.python.org/pypi/bob.learn.activation
 
+
 ============================
  Activation functors of Bob
 ============================
 
-This package contains Bob's Activation functors, which used in several learning packages of Bob in the namespace ``bob.learn``.
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It contains Bob's Activation functors, which used in several learning
+packages of Bob in the namespace ``bob.learn``.
+
 
 Installation
 ------------
-To install this package -- alone or together with other `Packages of Bob <https://github.com/idiap/bob/wiki/Packages>`_ -- please read the `Installation Instructions <https://github.com/idiap/bob/wiki/Installation>`_.
-For Bob_ to be able to work properly, some dependent packages are required to be installed.
-Please make sure that you have read the `Dependencies <https://github.com/idiap/bob/wiki/Dependencies>`_ for your operating system.
 
-Documentation
--------------
-For further documentation on this package, please read the `Stable Version <http://pythonhosted.org/bob.learn.activation/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.learn.activation/master/index.html>`_ of the documentation.
-For a list of tutorials on this or the other packages ob Bob_, or information on submitting issues, asking questions and starting discussions, please visit its website.
+Follow our `installation`_ instructions. Then, using the Python interpreter
+provided by the distribution, bootstrap and buildout this package::
+
+  $ python bootstrap-buildout.py
+  $ ./bin/buildout
+
+
+Contact
+-------
+
+For questions or reporting issues to this software package, contact our
+development `mailing list`_.
+
 
+.. Place your references here:
 .. _bob: https://www.idiap.ch/software/bob
+.. _installation: https://gitlab.idiap.ch/bob/bob/wikis/Installation
+.. _mailing list: https://groups.google.com/forum/?fromgroups#!forum/bob-devel

bootstrap-buildout.py

@@ -25,7 +25,10 @@ import tempfile
 
 from optparse import OptionParser
 
-tmpeggs = tempfile.mkdtemp()
+__version__ = '2015-07-01'
+# See zc.buildout's changelog if this version is up to date.
+
+tmpeggs = tempfile.mkdtemp(prefix='bootstrap-')
 
 usage = '''\
 [DESIRED PYTHON FOR BUILDOUT] bootstrap.py [options]
@@ -40,8 +43,9 @@ this script from going over the network.
 '''
 
 parser = OptionParser(usage=usage)
-parser.add_option("-v", "--version", help="use a specific zc.buildout version")
-
+parser.add_option("--version",
+                  action="store_true", default=False,
+                  help=("Return bootstrap.py version."))
 parser.add_option("-t", "--accept-buildout-test-releases",
                   dest='accept_buildout_test_releases',
                   action="store_true", default=False,
@@ -59,25 +63,33 @@ parser.add_option("-f", "--find-links",
 parser.add_option("--allow-site-packages",
                   action="store_true", default=False,
                   help=("Let bootstrap.py use existing site packages"))
+parser.add_option("--buildout-version",
+                  help="Use a specific zc.buildout version")
 parser.add_option("--setuptools-version",
-                  help="use a specific setuptools version")
-
+                  help="Use a specific setuptools version")
+parser.add_option("--setuptools-to-dir",
+                  help=("Allow for re-use of existing directory of "
+                        "setuptools versions"))
 
 options, args = parser.parse_args()
+if options.version:
+    print("bootstrap.py version %s" % __version__)
+    sys.exit(0)
+
 
 ######################################################################
 # load/install setuptools
 
 try:
-    if options.allow_site_packages:
-        import setuptools
-        import pkg_resources
     from urllib.request import urlopen
 except ImportError:
     from urllib2 import urlopen
 
 ez = {}
-exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
+if os.path.exists('ez_setup.py'):
+    exec(open('ez_setup.py').read(), ez)
+else:
+    exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
 
 if not options.allow_site_packages:
     # ez_setup imports site, which adds site packages
@@ -88,12 +100,19 @@ if not options.allow_site_packages:
     # We can't remove these reliably
     if hasattr(site, 'getsitepackages'):
         for sitepackage_path in site.getsitepackages():
-            sys.path[:] = [x for x in sys.path if sitepackage_path not in x]
+            # Strip all site-packages directories from sys.path that
+            # are not sys.prefix; this is because on Windows
+            # sys.prefix is a site-package directory.
+            if sitepackage_path != sys.prefix:
+                sys.path[:] = [x for x in sys.path
+                               if sitepackage_path not in x]
 
 setup_args = dict(to_dir=tmpeggs, download_delay=0)
 
 if options.setuptools_version is not None:
     setup_args['version'] = options.setuptools_version
+if options.setuptools_to_dir is not None:
+    setup_args['to_dir'] = options.setuptools_to_dir
 
 ez['use_setuptools'](**setup_args)
 import setuptools
@@ -110,7 +129,12 @@ for path in sys.path:
 
 ws = pkg_resources.working_set
 
+setuptools_path = ws.find(
+    pkg_resources.Requirement.parse('setuptools')).location
+
+# Fix sys.path here as easy_install.pth added before PYTHONPATH
 cmd = [sys.executable, '-c',
+       'import sys; sys.path[0:0] = [%r]; ' % setuptools_path +
        'from setuptools.command.easy_install import main; main()',
        '-mZqNxd', tmpeggs]
 
@@ -123,11 +147,8 @@ find_links = os.environ.get(
 if find_links:
     cmd.extend(['-f', find_links])
 
-setuptools_path = ws.find(
-    pkg_resources.Requirement.parse('setuptools')).location
-
 requirement = 'zc.buildout'
-version = options.version
+version = options.buildout_version
 if version is None and not options.accept_buildout_test_releases:
     # Figure out the most recent final version of zc.buildout.
     import setuptools.package_index
@@ -167,7 +188,7 @@ if version:
 cmd.append(requirement)
 
 import subprocess
-if subprocess.call(cmd, env=dict(os.environ, PYTHONPATH=setuptools_path)) != 0:
+if subprocess.call(cmd) != 0:
     raise Exception(
         "Failed to execute command:\n%s" % repr(cmd)[1:-1])
 

buildout.cfg

 ; vim: set fileencoding=utf-8 :
-; Andre Anjos <andre.anjos@idiap.ch>
-; Mon 16 Apr 08:29:18 2012 CEST
+; Sun 14 Aug 2016 20:48:25 CEST
 
 [buildout]
 parts = scripts
+develop = .
 eggs = bob.learn.activation
 extensions = bob.buildout
-             mr.developer
-auto-checkout = *
-develop = src/bob.extension
-          src/bob.blitz
-          src/bob.core
-          src/bob.io.base
-          .
-
-; options for bob.buildout extension
-debug = true
-verbose = true
 newest = false
-
-[sources]
-bob.extension = git https://github.com/bioidiap/bob.extension
-bob.blitz = git https://github.com/bioidiap/bob.blitz
-bob.core = git https://github.com/bioidiap/bob.core
-bob.io.base = git https://github.com/bioidiap/bob.io.base
+verbose = true
 
 [scripts]
-recipe = bob.buildout:scripts
+recipe = bob.buildout:scripts
\ No newline at end of file

develop.cfg

+; vim: set fileencoding=utf-8 :
+; Andre Anjos <andre.anjos@idiap.ch>
+; Mon 16 Apr 08:29:18 2012 CEST
+
+[buildout]
+parts = scripts
+eggs = bob.learn.activation
+extensions = bob.buildout
+             mr.developer
+auto-checkout = *
+develop = src/bob.extension
+          src/bob.blitz
+          src/bob.core
+          src/bob.io.base
+          .
+
+; options for bob.buildout extension
+debug = true
+verbose = true
+newest = false
+
+[sources]
+bob.extension = git https://gitlab.idiap.ch/bob/bob.extension
+bob.blitz = git https://gitlab.idiap.ch/bob/bob.blitz
+bob.core = git https://gitlab.idiap.ch/bob/bob.core
+bob.io.base = git https://gitlab.idiap.ch/bob/bob.io.base
+
+[scripts]
+recipe = bob.buildout:scripts

doc/conf.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-# Andre Anjos <andre.anjos@idiap.ch>
-# Tue 15 Oct 16:37:18 2013 CEST
-#
-# Copyright (C) 2011-2014 Idiap Research Institute, Martigny, Switzerland
 
 import os
 import sys
 import glob
 import pkg_resources
 
-# 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('.'))
 
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+needs_sphinx = '1.3'
 
 # 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.todo',
-  'sphinx.ext.coverage',
-  'sphinx.ext.pngmath',
-  'sphinx.ext.ifconfig',
-  'sphinx.ext.autodoc',
-  'sphinx.ext.autosummary',
-  'sphinx.ext.doctest',
-  'sphinx.ext.intersphinx',
-  ]
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.graphviz',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    ]
 
-# The viewcode extension appeared only on Sphinx >= 1.0.0
 import sphinx
-if sphinx.__version__ >= "1.0":
-  extensions.append('sphinx.ext.viewcode')
+if sphinx.__version__ >= "1.4.1":
+    extensions.append('sphinx.ext.imgmath')
+else:
+    extensions.append('sphinx.ext.pngmath')
 
 # Always includes todos
 todo_include_todos = True
 
+# Generates auto-summary automatically
+autosummary_generate = True
+
+# Create numbers on figures with captions
+numfig = True
+
 # If we are on OSX, the 'dvipng' path maybe different
 dvipng_osx = '/opt/local/libexec/texlive/binaries/dvipng'
 if os.path.exists(dvipng_osx): pngmath_dvipng = dvipng_osx
@@ -63,7 +64,7 @@ import time
 copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
 
 # Grab the setup entry
-distribution = pkg_resources.require('bob.learn.activation')[0]
+distribution = pkg_resources.require(project)[0]
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -108,13 +109,18 @@ pygments_style = 'sphinx'
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
 
+# Some variables which are useful for generated material
+project_variable = project.replace('.', '_')
+short_description = u'Bindings for Activation functors'
+owner = [u'Idiap Research Institute']
+
 
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-if sphinx.__version__ >= "1.0":
-  html_theme = 'nature'
+import sphinx_rtd_theme
+html_theme = 'sphinx_rtd_theme'
 
 # 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
@@ -122,14 +128,14 @@ if sphinx.__version__ >= "1.0":
 #html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+html_theme_path = [sphinx_rtd_theme.get_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 = 'bob_learn_activation'
+#html_short_title = project_variable
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -187,72 +193,48 @@ html_favicon = 'img/favicon.ico'
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'bob_learn_activation_doc'
-
-
-# -- Options for LaTeX output --------------------------------------------------
-
-# The paper size ('letter' or 'a4').
-latex_paper_size = 'a4'
-
-# The font size ('10pt', '11pt' or '12pt').
-latex_font_size = '10pt'
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
-  ('index', 'bob_learn_activation.tex', u'Bob Activation Functions',
-   u'Biometrics Group, Idiap Research Institute', 'manual'),
-]
+htmlhelp_basename = project_variable + u'_doc'
 
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-latex_logo = ''
 
-# 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
-
-# Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
+# -- Post configuration --------------------------------------------------------
 
 # Included after all input documents
 rst_epilog = """
 .. |project| replace:: Bob
-.. |url| replace:: https://www.idiap.ch/software/bob/
 .. |version| replace:: %s
 .. |current-year| date:: %%Y
 """ % (version,)
 
-# -- Options for manual page output --------------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'bob_learn_activation', u'Bob Activation Function Documentation', [u'Idiap Research Institute'], 1)
-]
-
 # Default processing flags for sphinx
-autoclass_content = 'both'
+autoclass_content = 'class'
 autodoc_member_order = 'bysource'
-autodoc_default_flags = ['members', 'undoc-members', 'inherited-members', 'show-inheritance']
+autodoc_default_flags = [
+  'members',
+  'undoc-members',
+  'inherited-members',
+  'show-inheritance',
+  ]
 
 # For inter-documentation mapping:
 from bob.extension.utils import link_documentation
 intersphinx_mapping = link_documentation()
 
+# We want to remove all private (i.e. _. or __.__) members
+# that are not in the list of accepted functions
+accepted_private_functions = ['__array__']
+
+def member_function_test(app, what, name, obj, skip, options):
+  # test if we have a private function
+  if len(name) > 1 and name[0] == '_':
+    # test if this private function should be allowed
+    if name not in accepted_private_functions:
+      # omit privat functions that are not in the list of accepted private functions
+      return skip
+    else:
+      # test if the method is documented
+      if not hasattr(obj, '__doc__') or not obj.__doc__:
+        return skip
+  return False
 
 def setup(app):
-  pass
+  app.connect('autodoc-skip-member', member_function_test)

setup.py

@@ -22,8 +22,8 @@ setup(
 
     name='bob.learn.activation',
     version=version,
-    description='Bindings for bob.machine\'s Activation functors',
-    url='http://github.com/bioidiap/bob.learn.activation',
+    description='Bindings for Activation functors',
+    url='http://gitlab.idiap.ch/bob/bob.learn.activation',
     license='BSD',
     author='Andre Anjos',
     author_email='andre.anjos@idiap.ch',