Commit c3d900c0 authored by Laurent EL SHAFEY's avatar Laurent EL SHAFEY
Browse files

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

parents
*~
*.swp
*.pyc
bin
eggs
parts
.installed.cfg
.mr.developer.cfg
*.egg-info
src
develop-eggs
built-docs
dist
sphinx
db.sql3
include README.rst
recursive-include docs *.py *.rst
recursive-include xbob *.sql3
================
MOBIO Database
================
This package contains the access API and descriptions for the `MOBIO
Database <http://www.idiap.ch/dataset/mobio/>`_. 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.mobio>`_. 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.mobio",
],
Proceed normally with your ``boostrap/buildout`` steps and you should be all
set. That means you can now import the ``xbob.db.mobio`` namespace 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.mobio
[sources]
xbob.db.mobio = git https://github.com/bioidiap/xbob.db.mobio.git
...
##############################################################################
#
# 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)
; 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.mobio
[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
#!/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'MOBIO 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.mobio.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 --------------------------------------------