Standardise

.gitlab-ci.yml

-py27-conda-idiap:
-  script:
-    - source /idiap/group/torch5spro/conda/bin/activate bob-2.3.4-py27_0
+# 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
-    - export TMPDIR=/var/tmp
-    - python bootstrap-buildout.py
+    - 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
-    - unset TMPDIR
-    - ./bin/python --version
-    - export NOSE_WITH_COVERAGE=1
-    - export NOSE_COVER_PACKAGE=bob.bio.vein
-    - ./bin/bob_dbmanage.py vera download
-    - ./bin/nosetests -sv bob.bio.vein
-    - ./bin/sphinx-build doc html
-    - ./bin/resources.py -d --packages=bob.bio.vein
-  tags:
-    - lidiap2015
+    - 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

README.rst

 .. vim: set fileencoding=utf-8 :
-.. Fri 08 Jul 2016 15:38:56 CEST
+.. Fri 19 Aug 2016 13:32:51 CEST
 
 .. image:: http://img.shields.io/badge/docs-stable-yellow.png
    :target: http://pythonhosted.org/bob.bio.vein/index.html
 .. image:: http://img.shields.io/badge/docs-latest-orange.png
-   :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.bio.vein/master/index.html
-.. image:: https://travis-ci.org/bioidiap/bob.bio.vein.svg?branch=master
-   :target: https://travis-ci.org/bioidiap/bob.bio.vein
-.. image:: https://coveralls.io/repos/bioidiap/bob.bio.vein/badge.png
-   :target: https://coveralls.io/r/bioidiap/bob.bio.vein
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
-   :target: https://github.com/bioidiap/bob.bio.vein/tree/master
+   :target: https://www.idiap.ch/software/bob/docs/latest/bob/bob.bio.vein/master/index.html
+.. image:: https://gitlab.idiap.ch/bob/bob.bio.vein/badges/master/build.svg
+   :target: https://gitlab.idiap.ch/bob/bob.bio.vein/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+   :target: https://gitlab.idiap.ch/bob/bob.bio.vein
 .. image:: http://img.shields.io/pypi/v/bob.bio.vein.png
    :target: https://pypi.python.org/pypi/bob.bio.vein
 .. image:: http://img.shields.io/pypi/dm/bob.bio.vein.png
    :target: https://pypi.python.org/pypi/bob.bio.vein
 
 
-=========================================
- The Biometrics Vein Recognition Library
-=========================================
+==========================
+ Vein Recognition Library
+==========================
 
-Welcome to this Vein Recognition Library based on Bob. This library is designed
-to perform a fair comparison of vein recognition algorithms. It contains
-scripts to execute various of vein recognition experiments on a variety
-of vein image databases, and running the help is as easy as going to the
-command line and typing::
 
-  $ bin/verify.py --help
-
-
-About
------
-
-This library is currently developed at the `Biometrics group
-<http://www.idiap.ch/scientific-research/research-groups/biometric-person-recognition>`_
-at the `Idiap Research Institute <http://www.idiap.ch>`_.  The vein recognition
-library is designed to run vein recognition experiments in a comparable and
-reproducible manner.
-
-
-Databases
----------
-
-To achieve this goal, interfaces to some publicly available vein image
-databases are contained, and default evaluation protocols are defined, e.g.:
-
-- UTFVP - University of Twente Finger Vein Database [http://www.sas.ewi.utwente.nl/]
-- VERA - Finger vein Database [http://www.idiap.ch/scientific-research/resources]
-- PUT - The PUT biometric vein (palm and wrist) recognition dataset [http://biometrics.put.poznan.pl/vein-dataset/]
-
-
-Algorithms
-----------
-
-Together with that, implementations of a variety of traditional and
-state-of-the-art vein recognition algorithms are provided:
-
-* Maximum Curvature [MNM05]_
-* Repeated Line Tracking [MNM04]_
-* Wide Line Detector [HDLTL10]_
-
-Tools to evaluate the results can easily be used to create scientific plots. We
-also provide handles to run experiments using parallel processes or an SGE
-grid.
-
-
-Extensions
-----------
-
-On top of these already pre-coded algorithms, the vein recognition library
-provides an easy Python interface for implementing new image preprocessors,
-feature types, vein recognition algorithms or database interfaces, which
-directly integrate into the vein recognition experiment. Hence, after a short
-period of coding, researchers can compare new ideas directly with already
-existing algorithms in a fair manner.
-
-
-References
-----------
-
-.. [MNM05] *N. Miura, A. Nagasaka, and T. Miyatake*. **Extraction of Finger-Vein Pattern Using Maximum Curvature Points in Image Profiles**. Proceedings on IAPR conference on machine vision applications, 9, pp. 347--350, 2005.
-
-.. [MNM04] *N. Miura, A. Nagasaka, and T. Miyatake*. **Feature extraction of finger vein patterns based on repeated line tracking and its application to personal identification**. Machine Vision and Applications, Vol. 15, Num. 4, pp. 194--203, 2004.
-
-.. [HDLTL10] *B. Huang, Y. Dai, R. Li, D. Tang and W. Li*. **Finger-vein authentication based on wide line detector and pattern normalization**. Proceedings of the 20th International Conference on Pattern Recognition (ICPR), 2010.
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It contains resources for finger, palm and wrist vein recognition as
+`bob.bio.base`_ plugins.
 
 
 Installation
 ------------
 
-The latest version of the vein recognition library can be installed with our
-`Conda-based builds`_. Once you have installed Bob_, just go on and install
-this package using the same installation mechanism.
-
-
-Development
------------
-
-In order to develop the latest version of this package, install Bob_ as
-indicated above. Once that is done, do this::
+Follow our `installation`_ instructions. Then, using the Python interpreter
+provided by the distribution, bootstrap and buildout this package::
 
-  $ git clone https://gitlab.idiap.ch/biometrc/bob.bio.vein.git
-  $ cd bob.bio.vein
   $ python bootstrap-buildout.py
   $ ./bin/buildout
 
-After those steps, you should have a functional **development** environment to
-test the package. The python interpreter and base environment on line 3 above
-should be pre-installed with all dependencies required for Bob_ to operate
-correctly. For example, you may start from our `conda-based builds`_ and then
-use the Python interpreter in there to bootstrap your local development
-environment.
-
-
-Running tests
--------------
-
-To verify that your installation worked as expected, you might want to run our
-unit tests with::
-
-  $ ./bin/nosetests -sv
-
-
-
-Cite our paper
---------------
 
-If you use this library in any of your experiments, please cite the following
-paper::
+Contact
+-------
 
-  @inproceedings{Tome_IEEEBIOSIG2014,
-      author = {Tome, Pedro and Vanoni, Matthias and Marcel, S{\'{e}}bastien},
-      keywords = {Biometrics, Finger vein, Spoofing Attacks},
-      projects = {Idiap, BEAT},
-      month = sep,
-      title = {On the Vulnerability of Finger Vein Recognition to Spoofing},
-      booktitle = {IEEE International Conference of the Biometrics Special Interest Group (BIOSIG)},
-      volume = {230},
-      year = {2014},
-      ocation = {Darmstadt, Germay},
-      pdf = {http://publications.idiap.ch/downloads/papers/2014/Tome_IEEEBIOSIG2014.pdf}
-  }
+For questions or reporting issues to this software package, contact our
+development `mailing list`_.
 
 
-.. _bob: http://www.idiap.ch/software/bob
-.. _idiap: http://www.idiap.ch
-.. _conda-based builds: https://github.com/idiap/bob/wiki/Binary-Installation
+.. 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
+.. _bob.bio.base: https://pythonhosted.org/bob.bio.base/

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, "
-                        "the bootstrap script and buildout gets the newest "
+                  help=("Normally, if you do not specify a --version, the "
+                        "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 "

buildout.cfg

 ; vim: set fileencoding=utf-8 :
+; Fri 19 Aug 2016 13:22:13 CEST
 
 [buildout]
 parts = scripts
+eggs = bob.bio.vein
+       bob.bio.base
+       bob.measure
+       bob.extension
+       gridtk
+
 extensions = bob.buildout
-             mr.developer
-eggs =  bob.bio.vein
-        bob.bio.base
-        bob.db.base
-        bob.measure
-        bob.extension
-        gridtk
-develop = src/bob.db.vera
-          src/bob.db.putvein
-          .
-auto-checkout = *
-newest = false
+develop = .
 
-[sources]
-bob.db.vera = git git@github.com:bioidiap/bob.db.vera
-bob.db.putvein = git git@gitlab.idiap.ch:biometric/bob.db.putvein
+newest = false
+verbose = true
 
 [scripts]
 recipe = bob.buildout:scripts

develop.cfg

+; vim: set fileencoding=utf-8 :
+; Fri 19 Aug 2016 13:14:15 CEST
+
+[buildout]
+parts = scripts
+eggs = bob.bio.vein
+       bob.bio.base
+       bob.measure
+       bob.extension
+       gridtk
+
+extensions = bob.buildout
+             mr.developer
+
+auto-checkout = *
+develop = src/bob.extension
+          src/bob.blitz
+          src/bob.core
+          src/bob.math
+          src/bob.measure
+          src/bob.io.base
+          src/bob.io.image
+          src/bob.io.matlab
+          src/bob.ip.base
+          src/bob.db.base
+          src/bob.db.verafinger
+          src/bob.db.utfvp
+          src/bob.db.putvein
+          src/bob.bio.db
+          src/bob.bio.base
+          .
+
+; options for bob.buildout
+debug = true
+verbose = true
+newest = false
+
+[sources]
+bob.extension = git git@gitlab.idiap.ch:bob/bob.extension
+bob.blitz = git git@gitlab.idiap.ch:bob/bob.blitz
+bob.core = git git@gitlab.idiap.ch:bob/bob.core
+bob.math = git git@gitlab.idiap.ch:bob/bob.math
+bob.measure = git git@gitlab.idiap.ch:bob/bob.measure
+bob.io.base = git git@gitlab.idiap.ch:bob/bob.io.base
+bob.io.image = git git@gitlab.idiap.ch:bob/bob.io.image
+bob.io.matlab = git git@gitlab.idiap.ch:bob/bob.io.matlab
+bob.ip.base = git git@gitlab.idiap.ch:bob/bob.ip.base
+bob.db.base = git git@gitlab.idiap.ch:bob/bob.db.base
+bob.db.verafinger = git git@gitlab.idiap.ch:bob/bob.db.verafinger
+bob.db.utfvp = git git@gitlab.idiap.ch:bob/bob.db.utfvp
+bob.db.putvein = git git@gitlab.idiap.ch:bob.db.putvein
+bob.bio.db = git git@gitlab.idiap.ch:bob/bob.bio.db
+bob.bio.base = git git@gitlab.idiap.ch:bob/bob.bio.base
+
+[scripts]
+recipe = bob.buildout:scripts

doc/conf.py

@@ -7,11 +7,6 @@ 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.
@@ -20,26 +15,33 @@ 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.graphviz',
+    'sphinx.ext.intersphinx',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
     ]
 
+import sphinx
+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
@@ -57,12 +59,12 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'Vein Biometrics Recognition Library (bob.bio.vein)'
+project = u'bob.bio.vein'
 import time
 copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
 
 # Grab the setup entry
-distribution = pkg_resources.require('bob.bio.vein')[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
@@ -107,8 +109,10 @@ pygments_style = 'sphinx'
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
 
-# Included after all input documents
-rst_epilog = ''
+# Some variables which are useful for generated material
+project_variable = project.replace('.', '_')
+short_description = u'Vein Recognition Library'
+owner = [u'Idiap Research Institute']
 
 
 # -- Options for HTML output ---------------------------------------------------
@@ -131,7 +135,7 @@ html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 #html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+#html_short_title = project_variable
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -145,7 +149,7 @@ html_favicon = 'img/favicon.ico'
 # 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 = ['_static']
+#html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
@@ -189,70 +193,48 @@ html_favicon = 'img/favicon.ico'
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'bobbiovein_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'
+htmlhelp_basename = project_variable + u'_doc'
 
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
-    (
-      'index',
-      'bobbiovein.tex',
-      u'Vein Biometrics Recognition Library (bob.bio.vein)',
-      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 = 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
+# -- Post configuration --------------------------------------------------------
 
-# 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 = [
-    ('index', 'bobbiovein', u'Vein Biometrics Recognition Library', [u'Idiap Research Institute'], 1)
-]
+# Included after all input documents
+rst_epilog = """
+.. |project| replace:: Bob
+.. |version| replace:: %s
+.. |current-year| date:: %%Y
+""" % (version,)
 
 # 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',
-  'numpy',
-  'scipy',
-])
-
+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)

requirements.txt

@@ -9,7 +9,7 @@ bob.io.matlab
 bob.io.image
 bob.ip.base
 bob.bio.base
+bob.bio.db
 bob.db.utfvp
-bob.db.vera
+bob.db.verafinger
 bob.db.putvein
-sphinx-rtd-theme