Initial port of the ATNT database as a satellite package for bob

.gitignore

+*~
+*.swp
+*.pyc
+bin
+eggs
+parts
+.installed.cfg
+.mr.developer.cfg
+*.egg-info
+src
+develop-eggs
+dist
+sphinx

MANIFEST.in

+include README.rst
+recursive-include docs *.py *.rst
+recursive-include xbob *.txt

README.rst

+===================
+ ATNT/ORL Database
+===================
+
+The ATNT/ORL database is a database of faces.
+
+The actual raw data for the database should be downloaded from the original
+URL. This package only contains the `Bob <http://www.idiap.ch/software/bob/>`_
+accessor methods to use the DB directly from python, with our certified
+protocols.
+
+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/bioidiap/xbob.db.nuaa>`_. 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.
+
+You can mix and match points 1/2 and a/b above based on your requirements. Here
+are some examples:
+
+Modify your setup.py and download from PyPI
+===========================================
+
+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)::
+
+    install_requires=[
+      ...
+      "xbob.db.atnt",
+    ],
+
+Proceed normally with your ``boostrap/buildout`` steps and you should be all
+set. That means you can now import the namespace ``xbob.db.atnt`` into your scripts.
+
+Modify your buildout.cfg and download from git
+==============================================
+
+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::
+
+  [buildout]
+  ...
+  extensions = mr.developer
+  auto-checkout = *
+  eggs = bob
+         ...
+         xbob.db.atnt
+
+  [sources]
+  xbob.db.atnt = git https://github.com/bioidiap/xbob.db.atnt.git
+  ...

bootstrap.py

+##############################################################################
+#
+# Copyright (c) 2006 Zope Foundation and Contributors.
+# All Rights Reserved.
+#
+# This software is subject to the provisions of the Zope Public License,
+# Version 2.1 (ZPL).  A copy of the ZPL should accompany this distribution.
+# THIS SOFTWARE IS PROVIDED "AS IS" AND ANY AND ALL EXPRESS OR IMPLIED
+# WARRANTIES ARE DISCLAIMED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF TITLE, MERCHANTABILITY, AGAINST INFRINGEMENT, AND FITNESS
+# FOR A PARTICULAR PURPOSE.
+#
+##############################################################################
+"""Bootstrap a buildout-based project
+
+Simply run this script in a directory containing a buildout.cfg.
+The script accepts buildout command-line options, so you can
+use the -c option to specify an alternate configuration file.
+"""
+
+import os, shutil, sys, tempfile, urllib, urllib2, subprocess
+from optparse import OptionParser
+
+if sys.platform == 'win32':
+    def quote(c):
+        if ' ' in c:
+            return '"%s"' % c  # work around spawn lamosity on windows
+        else:
+            return c
+else:
+    quote = str
+
+# See zc.buildout.easy_install._has_broken_dash_S for motivation and comments.
+stdout, stderr = subprocess.Popen(
+    [sys.executable, '-Sc',
+     'try:\n'
+     '    import ConfigParser\n'
+     'except ImportError:\n'
+     '    print 1\n'
+     'else:\n'
+     '    print 0\n'],
+    stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+has_broken_dash_S = bool(int(stdout.strip()))
+
+# In order to be more robust in the face of system Pythons, we want to
+# run without site-packages loaded.  This is somewhat tricky, in
+# particular because Python 2.6's distutils imports site, so starting
+# with the -S flag is not sufficient.  However, we'll start with that:
+if not has_broken_dash_S and 'site' in sys.modules:
+    # We will restart with python -S.
+    args = sys.argv[:]
+    args[0:0] = [sys.executable, '-S']
+    args = map(quote, args)
+    os.execv(sys.executable, args)
+# Now we are running with -S.  We'll get the clean sys.path, import site
+# because distutils will do it later, and then reset the path and clean
+# out any namespace packages from site-packages that might have been
+# loaded by .pth files.
+clean_path = sys.path[:]
+import site  # imported because of its side effects
+sys.path[:] = clean_path
+for k, v in sys.modules.items():
+    if k in ('setuptools', 'pkg_resources') or (
+        hasattr(v, '__path__') and
+        len(v.__path__) == 1 and
+        not os.path.exists(os.path.join(v.__path__[0], '__init__.py'))):
+        # This is a namespace package.  Remove it.
+        sys.modules.pop(k)
+
+is_jython = sys.platform.startswith('java')
+
+setuptools_source = 'http://peak.telecommunity.com/dist/ez_setup.py'
+distribute_source = 'http://python-distribute.org/distribute_setup.py'
+
+
+# parsing arguments
+def normalize_to_url(option, opt_str, value, parser):
+    if value:
+        if '://' not in value:  # It doesn't smell like a URL.
+            value = 'file://%s' % (
+                urllib.pathname2url(
+                    os.path.abspath(os.path.expanduser(value))),)
+        if opt_str == '--download-base' and not value.endswith('/'):
+            # Download base needs a trailing slash to make the world happy.
+            value += '/'
+    else:
+        value = None
+    name = opt_str[2:].replace('-', '_')
+    setattr(parser.values, name, value)
+
+usage = '''\
+[DESIRED PYTHON FOR BUILDOUT] bootstrap.py [options]
+
+Bootstraps a buildout-based project.
+
+Simply run this script in a directory containing a buildout.cfg, using the
+Python that you want bin/buildout to use.
+
+Note that by using --setup-source and --download-base to point to
+local resources, you can keep this script from going over the network.
+'''
+
+parser = OptionParser(usage=usage)
+parser.add_option("-v", "--version", dest="version",
+                          help="use a specific zc.buildout version")
+parser.add_option("-d", "--distribute",
+                   action="store_true", dest="use_distribute", default=False,
+                   help="Use Distribute rather than Setuptools.")
+parser.add_option("--setup-source", action="callback", dest="setup_source",
+                  callback=normalize_to_url, nargs=1, type="string",
+                  help=("Specify a URL or file location for the setup file. "
+                        "If you use Setuptools, this will default to " +
+                        setuptools_source + "; if you use Distribute, this "
+                        "will default to " + distribute_source + "."))
+parser.add_option("--download-base", action="callback", dest="download_base",
+                  callback=normalize_to_url, nargs=1, type="string",
+                  help=("Specify a URL or directory for downloading "
+                        "zc.buildout and either Setuptools or Distribute. "
+                        "Defaults to PyPI."))
+parser.add_option("--eggs",
+                  help=("Specify a directory for storing eggs.  Defaults to "
+                        "a temporary directory that is deleted when the "
+                        "bootstrap script completes."))
+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 --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 "
+                        "even if they are alphas or betas."))
+parser.add_option("-c", None, action="store", dest="config_file",
+                   help=("Specify the path to the buildout configuration "
+                         "file to be used."))
+
+options, args = parser.parse_args()
+
+# if -c was provided, we push it back into args for buildout's main function
+if options.config_file is not None:
+    args += ['-c', options.config_file]
+
+if options.eggs:
+    eggs_dir = os.path.abspath(os.path.expanduser(options.eggs))
+else:
+    eggs_dir = tempfile.mkdtemp()
+
+if options.setup_source is None:
+    if options.use_distribute:
+        options.setup_source = distribute_source
+    else:
+        options.setup_source = setuptools_source
+
+if options.accept_buildout_test_releases:
+    args.append('buildout:accept-buildout-test-releases=true')
+args.append('bootstrap')
+
+try:
+    import pkg_resources
+    import setuptools  # A flag.  Sometimes pkg_resources is installed alone.
+    if not hasattr(pkg_resources, '_distribute'):
+        raise ImportError
+except ImportError:
+    ez_code = urllib2.urlopen(
+        options.setup_source).read().replace('\r\n', '\n')
+    ez = {}
+    exec ez_code in ez
+    setup_args = dict(to_dir=eggs_dir, download_delay=0)
+    if options.download_base:
+        setup_args['download_base'] = options.download_base
+    if options.use_distribute:
+        setup_args['no_fake'] = True
+    ez['use_setuptools'](**setup_args)
+    if 'pkg_resources' in sys.modules:
+        reload(sys.modules['pkg_resources'])
+    import pkg_resources
+    # This does not (always?) update the default working set.  We will
+    # do it.
+    for path in sys.path:
+        if path not in pkg_resources.working_set.entries:
+            pkg_resources.working_set.add_entry(path)
+
+cmd = [quote(sys.executable),
+       '-c',
+       quote('from setuptools.command.easy_install import main; main()'),
+       '-mqNxd',
+       quote(eggs_dir)]
+
+if not has_broken_dash_S:
+    cmd.insert(1, '-S')
+
+find_links = options.download_base
+if not find_links:
+    find_links = os.environ.get('bootstrap-testing-find-links')
+if find_links:
+    cmd.extend(['-f', quote(find_links)])
+
+if options.use_distribute:
+    setup_requirement = 'distribute'
+else:
+    setup_requirement = 'setuptools'
+ws = pkg_resources.working_set
+setup_requirement_path = ws.find(
+    pkg_resources.Requirement.parse(setup_requirement)).location
+env = dict(
+    os.environ,
+    PYTHONPATH=setup_requirement_path)
+
+requirement = 'zc.buildout'
+version = options.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
+    _final_parts = '*final-', '*final'
+
+    def _final_version(parsed_version):
+        for part in parsed_version:
+            if (part[:1] == '*') and (part not in _final_parts):
+                return False
+        return True
+    index = setuptools.package_index.PackageIndex(
+        search_path=[setup_requirement_path])
+    if find_links:
+        index.add_find_links((find_links,))
+    req = pkg_resources.Requirement.parse(requirement)
+    if index.obtain(req) is not None:
+        best = []
+        bestv = None
+        for dist in index[req.project_name]:
+            distv = dist.parsed_version
+            if _final_version(distv):
+                if bestv is None or distv > bestv:
+                    best = [dist]
+                    bestv = distv
+                elif distv == bestv:
+                    best.append(dist)
+        if best:
+            best.sort()
+            version = best[-1].version
+if version:
+    requirement = '=='.join((requirement, version))
+cmd.append(requirement)
+
+if is_jython:
+    import subprocess
+    exitcode = subprocess.Popen(cmd, env=env).wait()
+else:  # Windows prefers this, apparently; otherwise we would prefer subprocess
+    exitcode = os.spawnle(*([os.P_WAIT, sys.executable] + cmd + [env]))
+if exitcode != 0:
+    sys.stdout.flush()
+    sys.stderr.flush()
+    print ("An error occurred when trying to install zc.buildout. "
+           "Look above this message for any errors that "
+           "were output by easy_install.")
+    sys.exit(exitcode)
+
+ws.add_entry(eggs_dir)
+ws.require(requirement)
+import zc.buildout.buildout
+zc.buildout.buildout.main(args)
+if not options.eggs:  # clean up temporary egg directory
+    shutil.rmtree(eggs_dir)

buildout.cfg

+; vim: set fileencoding=utf-8 :
+; Andre Anjos <andre.anjos@idiap.ch>
+; Mon 16 Apr 08:29:18 2012 CEST
+
+[buildout]
+parts = external tests sphinx python
+develop = .
+versions = versions
+eggs = bob
+       xbob.db.atnt
+
+[versions]
+;If you would like to pin-down the recipes package version so you are not
+;bothered with eventual updates, do it here. Note that, by pinning the version
+;of the package, you will be also excluded from bug fixes.
+;xbob.buildout = 0.1
+
+[external]
+recipe = xbob.buildout:external
+egg-directories = /idiap/group/torch5spro/nightlies/last/install/linux-x86_64-release/lib
+
+[tests]
+recipe = xbob.buildout:nose
+eggs = ${buildout:eggs}
+script = tests.py
+
+[sphinx]
+recipe = xbob.buildout:sphinx
+eggs = ${buildout:eggs}
+source = ${buildout:directory}/docs
+build = ${buildout:directory}/sphinx
+
+[python]
+recipe = z3c.recipe.scripts
+eggs = ${buildout:eggs}
+interpreter = python
+dependent-scripts = true

docs/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) 2011-2012 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/>.
+
+import sys, os
+
+# 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'
+
+# 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',
+  'bob.sphinxext.plot', # ours add source copying to install directory
+  ]
+
+# The viewcode extension appeared only on Sphinx >= 1.0.0
+import sphinx
+if sphinx.__version__ >= "1.0":
+  extensions.append('sphinx.ext.viewcode')
+
+# Always includes todos
+todo_include_todos = 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
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'AT&T/ORL Database (Bob API)'
+import time
+copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+from xbob.db.atnt.driver import Interface
+version = Interface().version()
+# The full version, including alpha/beta/rc tags.
+release = version
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['**/links.rst']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- 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'
+
+# 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
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#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'
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = ''
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+html_favicon = ''
+
+# 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']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'bobdbdoc'
+
+
+# -- 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', 'bobdbman.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,
+# 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 = ''
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples