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:
+    - ./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

.travis.yml

-language: python
-matrix:
-  include:
-  - python: 2.7
-    env:
-    - secure: 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
-    - secure: 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
-    - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
-    - BOB_UPLOAD_WHEEL="--universal"
-  - 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 libjpeg8-dev libnetpbm10-dev libpng12-dev libtiff4-dev libgif-dev libboost-all-dev libblitz1-dev libhdf5-serial-dev libvl-dev dvipng texlive-latex-base texlive-latex-extra texlive-math-extra texlive-latex-recommended texlive-fonts-recommended libatlas-dev libatlas-base-dev liblapack-dev gfortran
-- pip install --upgrade pip
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel sphinx nose numpy scipy matplotlib coverage
-- 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 buildout:develop=. buildout:extensions=bob.buildout buildout:auto-checkout=
-script:
-- ./bin/python -c 'import pkg_resources; from bob.bio.base import get_config; print(get_config())'
-- ./bin/coverage run --source=bob.bio.base ./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

LICENSE

+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:
+
+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
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+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

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/bio/base/test/data *.lst *.hdf5 *-dev 
+recursive-include bob/bio/base/test/data *.lst *.hdf5 *-dev

README.rst

 .. vim: set fileencoding=utf-8 :
-.. Andre Anjos <andre.anjos@idiap.ch>
-.. Thu 30 Jan 08:46:53 2014 CET
+.. Tue 16 Aug 15:00:20 CEST 2016
 
 .. image:: http://img.shields.io/badge/docs-stable-yellow.png
    :target: http://pythonhosted.org/bob.bio.base/index.html
 .. image:: http://img.shields.io/badge/docs-latest-orange.png
    :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.bio.base/master/index.html
-.. image:: http://travis-ci.org/bioidiap/bob.bio.base.svg?branch=master
-   :target: https://travis-ci.org/bioidiap/bob.bio.base?branch=master
-.. image:: https://coveralls.io/repos/bioidiap/bob.bio.base/badge.svg?branch=master
-   :target: https://coveralls.io/r/bioidiap/bob.bio.base?branch=master
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
-   :target: https://github.com/bioidiap/bob.bio.base/tree/master
+.. image:: https://gitlab.idiap.ch/bob/bob.bio.base/badges/master/build.svg
+   :target: https://gitlab.idiap.ch/bob/bob.bio.base/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+   :target: https://gitlab.idiap.ch/bob/bob.bio.base
 .. image:: http://img.shields.io/pypi/v/bob.bio.base.png
    :target: https://pypi.python.org/pypi/bob.bio.base
 .. image:: http://img.shields.io/pypi/dm/bob.bio.base.png
    :target: https://pypi.python.org/pypi/bob.bio.base
 
-==================================================
- Scripts to run biometric recognition experiments
-==================================================
 
-This package is part of the ``bob.bio`` packages, which allow to run comparable and reproducible biometric recognition experiments on publicly available databases.
+================================================
+ Tools to run biometric recognition experiments
+================================================
 
-This package contains basic functionality to run biometric recognition experiments.
-It provides a generic ``./bin/verify.py`` script that takes several parameters, including:
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It provides tools to run comparable and reproducible biometric
+recognition experiments on publicly available databases.
 
-* A database and its evaluation protocol
-* A data preprocessing algorithm
-* A feature extraction algorithm
-* A biometric recognition algorithm
+The `User Guide`_ provides installation and usage instructions.
 
-All these steps of the biometric recognition system are given as configuration files.
-
-In this base class implementation, only a few algorithms (such as PCA, LDA, PLDA, BIC) are implemented, while most algorithms that are more specialized are provided by other packages, which are usually in the ``bob.bio`` namespace, such as:
-
-* `bob.bio.spear <http://pypi.python.org/pypi/bob.bio.spear>`__ for speaker recognition recognition databases, features and algorithms
-* `bob.bio.face <http://pypi.python.org/pypi/bob.bio.face>`__ for face recognition databases, features and algorithms
-* `bob.bio.video <http://pypi.python.org/pypi/bob.bio.video>`__ for video-based databases and algorithms
-* `bob.bio.gmm <http://pypi.python.org/pypi/bob.bio.gmm>`__ for Gaussian-mixture-model-based algorithms
-* `bob.bio.csu <http://pypi.python.org/pypi/bob.bio.csu>`__ for wrapper classes of the `CSU Face Recognition Resources <http://www.cs.colostate.edu/facerec>`__ (see `Installation Instructions <http://pythonhosted.org/bob.bio.csu/installation.html>`__ of ``bob.bio.csu``).
 
+Installation
+------------
 
-Moreover, a script for score fusion ``./bin/fusion_llr.py`` is provided to do score-level fusion using Logistic regression to combine outputs from different systems.
+Follow our `installation`_ instructions. Then, using the Python interpreter
+provided by the distribution, bootstrap and buildout this package::
 
-Additionally, a generic script ``./bin/evaluate.py`` is provided that can generate several types of plots (such as ROC, DET and CMC curves) and compute several measures (such as HTER, Cllr) to evaluate your experiments.
+  $ python bootstrap-buildout.py
+  $ ./bin/buildout
 
 
-Installation
-------------
-To create your own working package using one or more of the ``bob.bio`` packages, please follow the `Installation Instructions <http://pythonhosted.org/bob.bio.base/installation.html>`__ of the ``bob.bio`` packages.
+Contact
+-------
 
-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.
+For questions or reporting issues to this software package, contact our
+development `mailing list`_.
 
-Documentation
--------------
-For further documentation on this package, please read the `Stable Version <http://pythonhosted.org/bob.bio.base/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.bio.base/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.
 
+.. 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
+.. _user guide: http://pythonhosted.org/bob.bio.base

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 :
-; Manuel Guenther <manuel.guenther@idiap.ch>
-; Thu Oct  9 16:51:06 CEST 2014
+; Tue 16 Aug 15:00:20 CEST 2016
 
 [buildout]
 parts = scripts
+develop = .
 eggs = bob.bio.base
-       gridtk
-
 extensions = bob.buildout
-             mr.developer
-auto-checkout = *
-develop = src/bob.extension
-          src/bob.blitz
-          src/bob.core
-          src/bob.io.base
-          src/bob.learn.activation
-          src/bob.math
-          src/bob.learn.linear
-          src/bob.sp
-          src/bob.learn.em
-          src/bob.measure
-          src/bob.db.base
-          src/bob.bio.db
-          src/bob.db.atnt
-          src/bob.io.image
-          .
-         
-; options for bob.buildout
-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
-bob.learn.activation = git https://github.com/bioidiap/bob.learn.activation
-bob.math = git https://github.com/bioidiap/bob.math
-bob.sp = git https://github.com/bioidiap/bob.sp
-bob.learn.linear = git https://github.com/bioidiap/bob.learn.linear
-bob.learn.em = git https://github.com/bioidiap/bob.learn.em
-bob.measure = git https://github.com/bioidiap/bob.measure
-bob.db.base = git https://github.com/bioidiap/bob.db.base
-bob.bio.db = git https://gitlab.idiap.ch/biometric/bob.bio.db
-bob.db.atnt = git https://github.com/bioidiap/bob.db.atnt
-bob.io.image = git https://github.com/bioidiap/bob.io.image
+verbose = true
 
 [scripts]
 recipe = bob.buildout:scripts

develop.cfg

+; vim: set fileencoding=utf-8 :
+; Manuel Guenther <manuel.guenther@idiap.ch>
+; Thu Oct  9 16:51:06 CEST 2014
+
+[buildout]
+parts = scripts
+eggs = bob.bio.base
+       gridtk
+
+extensions = bob.buildout
+             mr.developer
+auto-checkout = *
+develop = src/bob.extension
+          src/bob.blitz
+          src/bob.core
+          src/bob.io.base
+          src/bob.learn.activation
+          src/bob.math
+          src/bob.learn.linear
+          src/bob.sp
+          src/bob.learn.em
+          src/bob.measure
+          src/bob.db.base
+          src/bob.bio.db
+          src/bob.db.atnt
+          src/bob.io.image
+          .
+
+; options for bob.buildout
+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
+bob.learn.activation = git https://gitlab.idiap.ch/bob/bob.learn.activation
+bob.math = git https://gitlab.idiap.ch/bob/bob.math
+bob.sp = git https://gitlab.idiap.ch/bob/bob.sp
+bob.learn.linear = git https://gitlab.idiap.ch/bob/bob.learn.linear
+bob.learn.em = git https://gitlab.idiap.ch/bob/bob.learn.em
+bob.measure = git https://gitlab.idiap.ch/bob/bob.measure
+bob.db.base = git https://gitlab.idiap.ch/bob/bob.db.base
+bob.bio.db = git https://gitlab.idiap.ch/biometric/bob.bio.db
+bob.db.atnt = git https://gitlab.idiap.ch/bob/bob.db.atnt
+bob.io.image = git https://gitlab.idiap.ch/bob/bob.io.image
+
+[scripts]
+recipe = bob.buildout:scripts
+dependent-scripts = true

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) 2011-2014 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
@@ -58,12 +59,12 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'Bobs interface for running biometric recognition experiments'
+project = u'bob.bio.base'
 import time
 copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
 
 # Grab the setup entry
-distribution = pkg_resources.require('bob.bio.base')[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'Tools for running biometric recognition experiments'
+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'
+#html_short_title = project_variable
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -187,105 +193,48 @@ html_favicon = 'img/favicon.ico'
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'bob_bio_base_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_bio_base.tex', u'Bob',
-   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 = ''
-
-# -- 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.bio.base', u'Base tools to run biometric recognition experiments', [u'Idiap Research Institute'], 1)
-]
+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', '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', 'bob.bio.face', 'bob.bio.speaker', 'bob.bio.gmm', 'bob.bio.video', 'bob.bio.csu', 'bob.bio.spear', 'gridtk', 'bob.db.youtube'])
-
-
-def skip(app, what, name, obj, skip, options):
-  # Do not skip the __call__ and the __str__ functions as we have special implementations for them.
-  if name in ("__str__", "__call__"):
-    return False
-  return skip
-
-# getting dictionaries printed nicely.
-# see: http://stackoverflow.com/questions/7250659/python-code-to-generate-part-of-sphinx-documentation-is-it-possible/18143318#18143318
-try:
-    from StringIO import StringIO
-except ImportError:
-    from io import StringIO
-
-from sphinx.util.compat import Directive
-from docutils import nodes, statemachine
-
-class ExecDirective(Directive):
-    """Execute the specified python code and insert the output into the document"""
-    has_content = True
-
-    def run(self):
-        oldStdout, sys.stdout = sys.stdout, StringIO()
-
-        tab_width = self.options.get('tab-width', self.state.document.settings.tab_width)
-        source = self.state_machine.input_lines.source(self.lineno - self.state_machine.input_offset - 1)
-
-        try:
-            exec('\n'.join(self.content))
-            text = sys.stdout.getvalue()
-            lines = statemachine.string2lines(text, tab_width, convert_whitespace=True)
-            self.state_machine.insert_input(lines, source)
-            return []
-        except Exception:
-            return [nodes.error(None, nodes.paragraph(text = "Unable to execute python code at %s:%d:" % (os.path.basename(source), self.lineno)), nodes.paragraph(text = str(sys.exc_info()[1])))]
-        finally:
-            sys.stdout = oldStdout
+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):
-  app.connect("autodoc-skip-member", skip)
-  app.add_directive('exec', ExecDirective)
+  app.connect('autodoc-skip-member', member_function_test)

requirements.txt

-setuptools
-scipy
-bob.extension
+bob.bio.db
 bob.blitz
 bob.core
+bob.db.base
+bob.extension
 bob.io.base
 bob.learn.activation
-bob.math
-bob.learn.linear
-bob.sp
 bob.learn.em
+bob.learn.linear
+bob.math
 bob.measure
-bob.db.base
-bob.bio.db
-bob.db.atnt  # for test purposes
-bob.io.image # for test purposes
-matplotlib   # for plotting
+bob.sp
+scipy
+setuptools

setup.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-# Andre Anjos <andre.anjos@idiap.ch>
 # Mon 16 Apr 08:18:08 2012 CEST
-#
-# Copyright (C) Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# This file contains the python (distutils/setuptools) instructions so your
-# package can be installed on **any** host system. It defines some basic
-# information like the package name for instance, or its homepage.
-#
-# It also defines which other packages this python package depends on and that
-# are required for this package's operation. The python subsystem will make
-# sure all dependent packages are installed or will install them for you upon
-# the installation of this package.
-#
-# The 'buildout' system we use here will go further and wrap this package in
-# such a way to create an isolated python working environment. Buildout will
-# make sure that dependencies which are not yet installed do get installed, but
-# **without** requiring administrative privileges on the host system. This
-# allows you to test your package with new python dependencies w/o requiring
-# administrative interventions.
 
 from setuptools import setup, dist
 dist.Distribution(dict(setup_requires=['bob.extension']))
@@ -47,10 +16,10 @@ setup(
     # information before releasing code publicly.
     name = 'bob.bio.base',
     version = open("version.txt").read().rstrip(),
-    description = 'Basic tools for running biometric recognition experiments',
+    description = 'Tools for running biometric recognition experiments',
 
-    url = 'https://www.github.com/bioidiap/bob.bio.base',
-    license = 'GPLv3',
+    url = 'https://www.gitlab.idiap.ch/bob/bob.bio.base',
+    license = 'BSD',
     author = 'Manuel Gunther',
     author_email = 'siebenkopf@googlemail.com',
     keywords = 'bob, biometric recognition, evaluation',
@@ -157,7 +126,7 @@ setup(
       'Framework :: Bob',
       'Development Status :: 3 - Alpha',
       'Intended Audience :: Developers',
-      'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+      'License :: OSI Approved :: BSD License',
       'Natural Language :: English',
       'Programming Language :: Python',
       'Topic :: Scientific/Engineering :: Artificial Intelligence',

test-requirements.txt

+bob.db.atnt
+bob.io.image
+matplotlib