Standardise

6a040930 · André Anjos · eac6a7e6 · 6a040930 · eac6a7e6 · 6a040930
Commit 6a040930 authored 8 years ago by André Anjos
--- a/.gitlab-ci.yml
+++ b/.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:
+    - ./bin/buildout
+    - if [ -x ./bin/bob_dbmanage.py ]; then ./bin/bob_dbmanage.py all download --force; fi
+    - ./bin/sphinx-build doc sphinx
+    - ./bin/python setup.py bdist_wheel --python-tag ${WHEEL_TAG}
+  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, tests, uploads wheel
+build_linux_27:
+  <<: *linux_build_job
+  variables: &linux_27_build_variables
+    <<: *linux_build_variables
+    PYTHON_VER: "2.7"
+    WHEEL_TAG: "py27"
+  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"
+    WHEEL_TAG: "py3"
+  tags:
+    - conda-linux
+test_linux_34:
+  <<: *test_job
+  variables: *linux_34_build_variables
+  dependencies:
+    - build_linux_34
+  tags:
+    - conda-linux
+# Linux + Python 3.5: Builds, tests, uploads wheel
+build_linux_35:
+  <<: *linux_build_job
+  variables: &linux_35_build_variables
+    <<: *linux_build_variables
+    PYTHON_VER: "3.5"
+    WHEEL_TAG: "py3"
+  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 and tests
+build_macosx_27:
+  <<: *macosx_build_job
+  variables: &macosx_27_build_variables
+    <<: *macosx_build_variables
+    PYTHON_VER: "2.7"
+    WHEEL_TAG: "py27"
+  tags:
+    - conda-macosx
+test_macosx_27:
+  <<: *test_job
+  variables: *macosx_27_build_variables
+  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"
+    WHEEL_TAG: "py3"
+  tags:
+    - conda-macosx
+test_macosx_34:
+  <<: *test_job
+  variables: *macosx_34_build_variables
+  dependencies:
+    - build_macosx_34
+  tags:
+    - conda-macosx
+# Mac OSX + Python 3.5: Builds and tests
+build_macosx_35:
+  <<: *macosx_build_job
+  variables: &macosx_35_build_variables
+    <<: *macosx_build_variables
+    PYTHON_VER: "3.5"
+    WHEEL_TAG: "py3"
+  tags:
+    - conda-macosx
+test_macosx_35:
+  <<: *test_job
+  variables: *macosx_35_build_variables
+  dependencies:
+    - build_macosx_35
+  tags:
+    - conda-macosx
\ No newline at end of file
--- a/.travis.yml
+++ b/.travis.yml
-language: python
-env:
-  global:
-  - secure: GaAguRxF+QilM0/DBfG7lZNdv4vtRpLGBLXrrLgeK53nEd71rtRS4CN8bDlSvSfGRvJP1kSGBAeQ8GfdQMalk1X4k2rOdoE2wUI16hffDaiiIep0NgIP0AAyk6lArCMZDvQsSzhNymO1ecUd37BB9fIyyrOPFrrOA0yRh3DVJGU=
-  - secure: jvMgMwM/BY7+mIujPcCFKLOJl+HCChhNVUYTK4b7+kkn+bE7+5tfYrXcKsxt6hOY1YeKPtQJafsWgFmR9Rj1i0NzFA9oBPRgtavE3eLlPOLNRJaolY7A1FQwKTS3X5IbHyHb9hhKz1q916nDY14bkKP35HmtN14k4RozhdiXqRk=
-  - 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 pillow
- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel --pre -r requirements.txt coveralls
-install:
- python bootstrap-buildout.py
- ./bin/buildout
-script:
- ./bin/python -c 'from bob.db.verafinger import get_config; print(get_config())'
- ./bin/bob_dbmanage.py verafinger download
- ./bin/coverage run --source=bob.db.verafinger ./bin/nosetests -sv
- ./bin/sphinx-build -b doctest doc sphinx
- ./bin/sphinx-build -b html doc sphinx
-after_success:
- coveralls
- 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
--- a/LICENSE
+++ b/LICENSE
-Copyright (c) 2016, Andre Anjos - Idiap Research Institute
+Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
-All rights reserved.
+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
+1. Redistributions of source code must retain the above copyright notice, this
-list of conditions and the following disclaimer.  Redistributions in binary
+list of conditions and the following disclaimer.
-form must reproduce the above copyright notice, this list of conditions and the
-following disclaimer in the documentation and/or other materials provided with
+2. Redistributions in binary form must reproduce the above copyright notice,
-the distribution.  Neither the name of the Idiap Research Institute nor the
+this list of conditions and the following disclaimer in the documentation
-names of its contributors may be used to endorse or promote products derived
+and/or other materials provided with the distribution.
-from this software without specific prior written permission.
+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.
\ No newline at end of file
--- a/MANIFEST.in
+++ b/MANIFEST.in
-include README.rst bootstrap-buildout.py buildout.cfg COPYING version.txt requirements.txt
+include README.rst bootstrap-buildout.py buildout.cfg develop.cfg COPYING version.txt requirements.txt
 recursive-include doc *.py *.rst
 recursive-include bob *.sql3
--- a/README.rst
+++ b/README.rst
 .. vim: set fileencoding=utf-8 :
-.. Tue 02 Aug 2016 15:43:29 CEST
+.. Tue 16 Aug 17:34:26 CEST 2016
 .. image:: http://img.shields.io/badge/docs-stable-yellow.png
   :target: http://pythonhosted.org/bob.db.verafinger/index.html
 .. image:: http://img.shields.io/badge/docs-latest-orange.png
-   :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.db.verafinger/master/index.html
+   :target: https://www.idiap.ch/software/bob/docs/latest/bob/bob.db.verafinger/master/index.html
-.. image:: https://travis-ci.org/bioidiap/bob.db.verafinger.svg?branch=master
+.. image:: https://gitlab.idiap.ch/bob/bob.db.verafinger/badges/master/build.svg
-   :target: https://travis-ci.org/bioidiap/bob.db.verafinger
+   :target: https://gitlab.idiap.ch/bob/bob.db.verafinger/commits/master
-.. image:: https://coveralls.io/repos/bioidiap/bob.db.verafinger/badge.png
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
-   :target: https://coveralls.io/r/bioidiap/bob.db.verafinger
+   :target: https://gitlab.idiap.ch/bob/bob.db.verafinger
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
-   :target: https://github.com/bioidiap/bob.db.verafinger/tree/master
 .. image:: http://img.shields.io/pypi/v/bob.db.verafinger.png
   :target: https://pypi.python.org/pypi/bob.db.verafinger
 .. image:: http://img.shields.io/pypi/dm/bob.db.verafinger.png
   :target: https://pypi.python.org/pypi/bob.db.verafinger
-.. image:: https://img.shields.io/badge/real-data--files-a000a0.png
-   :target: https://www.idiap.ch/dataset/vera-fingervein
-.. image:: https://img.shields.io/badge/spoofing-data--files-a000a0.png
-   :target: https://www.idiap.ch/dataset/vera-spoofingfingervein
 ============================================
 VERA Fingervein Database Interface for Bob
 ============================================
-This package contains an interface for the evaluation protocols of the `VERA
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It contains an interface for the evaluation protocols of the `VERA
 Fingervein Database`_. Notice this package does not contain the raw data files
 from this dataset, which need to be obtained through the link above.
-About
+Installation
-----
+------------
+Follow our `installation`_ instructions. Then, using the Python interpreter
+provided by the distribution, bootstrap and buildout this package::
-This package is currently developed at the `Biometrics group`_ at the `Idiap
+  $ python bootstrap-buildout.py
-Research Institute`_.
+  $ ./bin/buildout
-Installation
+Contact
------------
+-------
-This package only contains database access functions so it is easy to
+For questions or reporting issues to this software package, contact our
-programatically reproduce evaluation results obtained in papers. You normally
+development `mailing list`_.
-don't install this package, unless you're modifying it. Instead, install one of
-our top-level frameworks for vein image processing, such as ``bob.bio.vein``.
-.. Write your references here:
+.. 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
 .. _vera fingervein database: https://www.idiap.ch/dataset/vera-fingervein
-.. _biometrics group: http://www.idiap.ch/scientific-research/research-groups/biometric-person-recognition
-.. _idiap research institute: http://www.idiap.ch
--- a/bootstrap-buildout.py
+++ b/bootstrap-buildout.py
@@ -49,8 +49,8 @@ parser.add_option("--version",
 parser.add_option("-t", "--accept-buildout-test-releases",
                  dest='accept_buildout_test_releases',
                  action="store_true", default=False,
-                  help=("Normally, if you do not specify a --buildout-version, "
+                  help=("Normally, if you do not specify a --version, the "
-                        "the bootstrap script and buildout gets the newest "
+                        "bootstrap script and buildout gets the newest "
                        "*final* versions of zc.buildout and its recipes and "
                        "extensions for you.  If you use this flag, "
                        "bootstrap and buildout will get the newest releases "

--- a/buildout.cfg
+++ b/buildout.cfg
 ; vim: set fileencoding=utf-8 :
-; Tue 02 Aug 2016 15:44:30 CEST
+; Tue 16 Aug 17:34:25 CEST 2016
 [buildout]
 parts = scripts
+develop = .
 eggs = bob.db.verafinger
-       bob.db.base
 extensions = bob.buildout
-develop = .
-verbose = true
 newest = false
+verbose = true
 [scripts]
 recipe = bob.buildout:scripts
+dependent-scripts = true
\ No newline at end of file
--- a/develop.cfg
+++ b/develop.cfg
+; vim: set fileencoding=utf-8 :
+; Tue 02 Aug 2016 15:44:30 CEST
+[buildout]
+parts = scripts
+eggs = bob.db.verafinger
+       bob.db.base
+extensions = bob.buildout
+develop = .
+verbose = true
+newest = false
+[scripts]
+recipe = bob.buildout:scripts
--- a/doc/conf.py
+++ b/doc/conf.py
 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-# Andre Anjos <andre.anjos@idiap.ch>
-# Mon 13 Aug 2012 12:38:15 CEST
-#
-# Copyright (C) 2011-2015 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.todo',
-  'sphinx.ext.coverage',
+    'sphinx.ext.coverage',
-  'sphinx.ext.pngmath',
+    'sphinx.ext.ifconfig',
-  'sphinx.ext.ifconfig',
+    'sphinx.ext.autodoc',
-  'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
-  'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
-  'sphinx.ext.doctest',
+    'sphinx.ext.graphviz',
-  'sphinx.ext.intersphinx',
+    '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":
+if sphinx.__version__ >= "1.4.1":
-  extensions.append('sphinx.ext.viewcode')
+    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
@@ -58,12 +59,12 @@ source_suffix = '.rst'
 master_doc = 'index'
 # General information about the project.
-project = u'VERA Fingervein Database (Bob API)'
+project = u'bob.db.verafinger'
 import time
 copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
 # Grab the setup entry
-distribution = pkg_resources.require('bob.db.verafinger')[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
@@ -86,7 +87,7 @@ release = distribution.version
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['**/links.rst']
+exclude_patterns = ['links.rst']
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
@@ -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'VERA Fingervein Database Access API for Bob'
+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":
+import sphinx_rtd_theme
-  html_theme = 'nature'
+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'
+#html_short_title = project_variable
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -187,67 +193,48 @@ html_favicon = 'img/favicon.ico'
 #html_file_suffix = None
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'bob_db_verafinger_doc'
+htmlhelp_basename = project_variable + u'_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_db_verafinger.tex', u'Bob',
-   u'Biometrics Group, Idiap Research Institute', 'manual'),
-]
-# 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,
+# -- Post configuration --------------------------------------------------------
-# 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
 # Included after all input documents
-rst_epilog = ''
+rst_epilog = """
+.. |project| replace:: Bob
-# -- Options for manual page output --------------------------------------------
+.. |version| replace:: %s
+.. |current-year| date:: %%Y
-# One entry per manual page. List of tuples
+""" % (version,)
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'bob', u'VERA Fingervein Database (Bob API) 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(['python', 'bob.db.base', 'bob.db.verification.utils'])
+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)
--- a/doc/img/logo.png
+++ b/doc/img/logo.png