Merge branch 'issue_1' into 'master'

Issue 1

Closes #1

See merge request !1

.gitlab-ci.yml

+# This build file heavily uses template features from YAML so it is generic
+# enough for any Bob project. Don't modify it unless you know what you're
+# doing.
+
+
+# Definition of our build pipeline
+stages:
+  - build
+  - test
+  - docs
+  - wheels
+  - deploy
+
+
+# ---------
+# Templates
+# ---------
+
+# 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
+    - mkdir _ci
+    - curl --silent "https://gitlab.idiap.ch/bob/bob.admin/raw/master/gitlab/install.sh" > _ci/install.sh
+    - chmod 755 _ci/install.sh
+    - ./_ci/install.sh _ci #updates
+    - ./_ci/before_build.sh
+  script:
+    - ./_ci/build.sh
+  after_script:
+    - ./_ci/after_build.sh
+  artifacts:
+    expire_in: 1 week
+    paths:
+      - _ci/
+      - dist/
+      - sphinx/
+
+
+# Template for the test stage - re-installs from uploaded wheels
+# Needs to run on all supported architectures, platforms and python versions
+.test_template: &test_job
+  stage: test
+  before_script:
+    - ./_ci/install.sh _ci #updates
+    - ./_ci/before_test.sh
+  script:
+    - ./_ci/test.sh
+  after_script:
+    - ./_ci/after_test.sh
+
+
+# Template for the wheel uploading stage
+# Needs to run against one supported architecture, platform and python version
+.wheels_template: &wheels_job
+  stage: wheels
+  environment: intranet
+  only:
+    - master
+    - /^v\d+\.\d+\.\d+([abc]\d*)?$/  # PEP-440 compliant version (tags)
+  before_script:
+    - ./_ci/install.sh _ci #updates
+    - ./_ci/before_wheels.sh
+  script:
+    - ./_ci/wheels.sh
+  after_script:
+    - ./_ci/after_wheels.sh
+
+
+# Template for (latest) documentation upload stage
+# Only one real job needs to do this
+.docs_template: &docs_job
+  stage: docs
+  environment: intranet
+  only:
+    - master
+  before_script:
+    - ./_ci/install.sh _ci #updates
+    - ./_ci/before_docs.sh
+  script:
+    - ./_ci/docs.sh
+  after_script:
+    - ./_ci/after_docs.sh
+
+
+# Template for the deployment stage - re-installs from uploaded wheels
+# Needs to run on a single architecture only
+# Will deploy your package to PyPI and other required services
+# Only runs for tags
+.deploy_template: &deploy_job
+  stage: deploy
+  environment: internet
+  only:
+    - /^v\d+\.\d+\.\d+([abc]\d*)?$/  # PEP-440 compliant version (tags)
+  except:
+    - branches
+  before_script:
+    - ./_ci/install.sh _ci #updates
+    - ./_ci/before_deploy.sh
+  script:
+    - ./_ci/deploy.sh
+  after_script:
+    - ./_ci/after_deploy.sh
+
+
+# -------------
+# Build Targets
+# -------------
+
+# Linux + Python 2.7: Builds, tests, uploads wheel and deploys (if needed)
+build_linux_27:
+  <<: *build_job
+  variables: &linux_27_build_variables
+    PYTHON_VERSION: "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
+  variables: *linux_27_build_variables
+  dependencies:
+    - build_linux_27
+  tags:
+    - conda-linux
+
+deploy_linux_27:
+  <<: *deploy_job
+  variables: *linux_27_build_variables
+  dependencies:
+    - build_linux_27
+  tags:
+    - conda-linux
+
+
+# Linux + Python 3.4: Builds and tests
+build_linux_34:
+  <<: *build_job
+  variables: &linux_34_build_variables
+    PYTHON_VERSION: "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 and uploads wheel
+build_linux_35:
+  <<: *build_job
+  variables: &linux_35_build_variables
+    PYTHON_VERSION: "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
+  variables: *linux_35_build_variables
+  dependencies:
+    - build_linux_35
+  tags:
+    - conda-linux
+
+docs_linux_35:
+  <<: *docs_job
+  variables: *linux_35_build_variables
+  dependencies:
+    - build_linux_35
+  tags:
+    - conda-linux
+
+
+# Mac OSX + Python 2.7: Builds and tests
+build_macosx_27:
+  <<: *build_job
+  variables: &macosx_27_build_variables
+    PYTHON_VERSION: "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:
+  <<: *build_job
+  variables: &macosx_34_build_variables
+    PYTHON_VERSION: "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:
+  <<: *build_job
+  variables: &macosx_35_build_variables
+    PYTHON_VERSION: "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

.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 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 numpy 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/bob_dbmanage.py kboc16 download
-- ./bin/coverage run --source=bob.db.kboc16 ./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 Universidad Autonoma de Madrid, http://atvs.ii.uam.es/
+Written by Marta Gomez-Barrero <marta.gomez-barrero@h-da.de>
+
+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.

README.rst

+.. vim: set fileencoding=utf-8 :
+.. Thu Aug 18 20:54:15 CEST 2016
+
 .. image:: http://img.shields.io/badge/docs-stable-yellow.png
    :target: http://pythonhosted.org/bob.db.kboc16/index.html
 .. image:: http://img.shields.io/badge/docs-latest-orange.png
-   :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.db.kboc16/master/index.html
-.. image:: https://travis-ci.org/bioidiap/bob.db.kboc16.svg?branch=master
-   :target: https://travis-ci.org/bioidiap/bob.db.kboc16?branch=master
-.. image:: https://coveralls.io/repos/bioidiap/bob.db.kboc16/badge.svg?branch=master
-   :target: https://coveralls.io/r/bioidiap/bob.db.kboc16?branch=master
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
-   :target: https://github.com/bioidiap/bob.db.kboc16/tree/master
+   :target: https://www.idiap.ch/software/bob/docs/latest/bob/bob.db.kboc16/master/index.html
+.. image:: https://gitlab.idiap.ch/bob/bob.db.kboc16/badges/master/build.svg
+   :target: https://gitlab.idiap.ch/bob/bob.db.kboc16/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+   :target: https://gitlab.idiap.ch/bob/bob.db.kboc16
 .. image:: http://img.shields.io/pypi/v/bob.db.kboc16.png
    :target: https://pypi.python.org/pypi/bob.db.kboc16
 .. image:: http://img.shields.io/pypi/dm/bob.db.kboc16.png
    :target: https://pypi.python.org/pypi/bob.db.kboc16
 
 
-==================
+=================
  KBOC16 Database
-==================
-
-This package contains the access API and descriptions for the `KBOC16
-Database`_.
-
-You would normally not install this package unless you are maintaining it. What
-you would do instead is to tie it in at the package you need to **use** it.
-There are a few ways to achieve this:
-
-1. You can add this package as a requirement at the ``setup.py`` for your own
-   `satellite package
-   <https://github.com/idiap/bob/wiki/Virtual-Work-Environments-with-Buildout>`_
-   or to your Buildout ``.cfg`` file, if you prefer it that way. With this
-   method, this package gets automatically downloaded and installed on your
-   working environment, or
-
-2. You can manually download and install this package using commands like
-   ``easy_install`` or ``pip``.
-
-The package is available in two different distribution formats:
-
-1. You can download it from `PyPI <http://pypi.python.org/pypi>`_, or
+=================
 
-2. You can download it in its source form from `its git repository
-   <https://github.com/mgbarrero/bob.db.KBOC16>`_. When you download the
-   version at the git repository, you will need to run a command to recreate
-   the backend SQLite file required for its operation. This means that the
-   database raw files must be installed somewhere in this case. With option
-   ``a`` you can run in `dummy` mode and only download the raw data files for
-   the database once you are happy with your setup.
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It contains the access API and descriptions for the `KBOC16 Database`_.
 
-You can mix and match points 1/2 above based on your requirements. Here are
-some examples:
 
-Modify your setup.py and download from PyPI
-===========================================
+Installation
+------------
 
-That is the easiest. Edit your ``setup.py`` in your satellite package and add
-the following entry in the ``install_requires`` section (note: ``...`` means
-`whatever extra stuff you may have in-between`, don't put that on your
-script)::
+Follow our `installation`_ instructions. Then, using the Python interpreter
+provided by the distribution, bootstrap and buildout this package::
 
-    install_requires=[
-      ...
-      "bob.db.kboc16",
-    ],
+  $ python bootstrap-buildout.py
+  $ ./bin/buildout
 
-Proceed normally with your ``boostrap/buildout`` steps and you should be all
-set. That means you can now import the ``bob.db.kboc16`` namespace into your
-scripts.
 
-Modify your buildout.cfg and download from git
-==============================================
+Contact
+-------
 
-You will need to add a dependence to `mr.developer
-<http://pypi.python.org/pypi/mr.developer/>`_ to be able to install from our
-git repositories. Your ``buildout.cfg`` file should contain the following
-lines::
+For questions or reporting issues to this software package, contact our
+development `mailing list`_.
 
-  [buildout]
-  ...
-  extensions =mr.developer
-  auto-checkout = *
-  eggs = ...
-         bob.db.kboc16
 
-  [sources]
-  bob.db.KBOC16 = git https://github.com/mgbarrero/bob.db.kboc16.git
-  ...
+.. 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
+.. _kboc16 database: http://atvs.ii.uam.es/databases.jsp

bob/db/kboc16/__init__.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-#
-# 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/>.
 
-"""The ATVSKeystroke database
+"""The ATVS Keystroke database
 """
 
 from .query import Database

bob/db/kboc16/create.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-#
-# 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 script creates the KBOC16 database in a single pass.
 """

bob/db/kboc16/driver.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-#
-# 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/>.
 
 """Commands this database can respond to.
 """

bob/db/kboc16/models.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-#
-# 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/>.
 
 """Table models and functionality for the KBOC16 database.
 """
@@ -22,7 +10,7 @@ from bob.db.base.sqlalchemy_migration import Enum, relationship
 from sqlalchemy.orm import backref
 from sqlalchemy.ext.declarative import declarative_base
 
-import bob.db.verification.utils
+import bob.db.base
 
 Base = declarative_base()
 
@@ -48,7 +36,7 @@ class Client(Base):
     return "Client(`%s`)" % (self.id)
 
 
-class File(Base, bob.db.verification.utils.File):
+class File(Base, bob.db.base.File):
   """Generic file container"""
 
   __tablename__ = 'file'
@@ -69,7 +57,7 @@ class File(Base, bob.db.verification.utils.File):
 
   def __init__(self, client_id, path, session_id, shot_id):
     # call base class constructor
-    bob.db.verification.utils.File.__init__(self, client_id = client_id, path = path)
+    bob.db.base.File.__init__(self, client_id = client_id, path = path)
 
     self.session_id = session_id
     self.shot_id = shot_id

bob/db/kboc16/query.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-#
-# 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 module provides the Dataset interface allowing the user to query the
 KBOC16 database in the most obvious ways.
 """
 
-import os
 import six
 from .models import *
 from .driver import Interface
 
-import bob.db.verification.utils
+import bob.db.base
 
 SQLITE_FILE = Interface().files()[0]
 
-class Database(bob.db.verification.utils.SQLiteDatabase,bob.db.verification.utils.Database):
+class Database(bob.db.base.SQLiteDatabase):
   """The dataset class opens and maintains a connection opened to the Database.
 
   It provides many different ways to probe for the characteristics of the data
@@ -35,8 +22,9 @@ class Database(bob.db.verification.utils.SQLiteDatabase,bob.db.verification.util
 
   def __init__(self, original_directory = None, original_extension = db_file_extension):
     # call base class constructor
-    bob.db.verification.utils.SQLiteDatabase.__init__(self, SQLITE_FILE, File)
-    bob.db.verification.utils.Database.__init__(self, original_directory=original_directory, original_extension=original_extension)
+    super(Database, self).__init__(SQLITE_FILE, File)
+    self.original_directory = original_directory
+    self.original_extension = original_extension
 
   def __group_replace_eval_by_genuine__(self, l):
     """Replace 'eval' by 'Genuine' and returns the new list"""

bob/db/kboc16/test.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-#
-# 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/>.
 
 """A few checks at the KBOC16 database.
 """
@@ -56,7 +44,7 @@ class kboc16DatabaseTest(unittest.TestCase):
       assert len(db.objects(protocol='A', groups='eval', purposes='probe', model_ids=[1], classes='client')) == 20
       assert len(db.objects(protocol='A', groups='eval', purposes='probe', model_ids=[1,2])) == 40
       assert len(db.objects(protocol='A', groups='eval', purposes='probe', model_ids=[1,2], classes='client')) == 40
-      
+
       # D
       assert len(db.objects(protocol='D')) == 2400
       assert len(db.objects(protocol='D', groups='eval')) == 2400

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])
 

doc/extra-intersphinx.txt

+bob.bio.base

doc/nitpick-exceptions.txt

+# This is an undocumented, dynamic type
+py:class sqlalchemy.ext.declarative.api.Base
+
+# This is not documented as py:exc in Python 2.7 - works in Python 3.x
+py:exc ValueError

requirements.txt

 setuptools
 six
 bob.db.base
-bob.db.verification.utils

setup.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-# Marta Gomez-Barrero <marta.barrero@uam.es>
-#