Initial commit

.gitignore

+*~
+*.swp
+*.pyc
+*.so
+bin
+eggs
+parts
+.installed.cfg
+.mr.developer.cfg
+*.egg-info
+develop-eggs
+sphinx
+dist
+.nfs*
+.gdb_history
+build
+*.egg
+src/
+opsnr.stt

LICENSE

+Copyright (c) 2013, Andre Anjos - Idiap Research Institute
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.  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.  Neither the name of the Idiap Research Institute 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.

MANIFEST.in

+include LICENSE README.rst bootstrap.py buildout.cfg
+recursive-include doc conf.py *.rst
+recursive-include xbob *.cpp *.h
+recursive-include xbob/machine/data *.*

README.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.anjos@idiap.ch>
+.. Fri 13 Dec 2013 12:35:22 CET
+
+=================================
+ Python bindings for bob.machine
+=================================
+
+This package contains a set of Pythonic bindings for Bob's machine packages and
+functionality.
+
+Installation
+------------
+
+Install it through normal means, via PyPI or use ``zc.buildout`` to bootstrap
+the package and run test units.
+
+Documentation
+-------------
+
+You can generate the documentation for this package, after installation, using
+Sphinx::
+
+  $ sphinx-build -b html doc sphinx
+
+This shall place in the directory ``sphinx``, the current version for the
+documentation of the package.
+
+Testing
+-------
+
+You can run a set of tests using the nose test runner::
+
+  $ nosetests -sv xbob.machine
+
+.. warning::
+
+   If Bob <= 1.2.1 is installed on your python path, nose will automatically
+   load the old version of the insulate plugin available in Bob, which will
+   trigger the loading of incompatible shared libraries (from Bob itself), in
+   to your working binary. This will cause a stack corruption. Either remove
+   the centrally installed version of Bob, or build your own version of Python
+   in which Bob <= 1.2.1 is not installed.
+
+You can run our documentation tests using sphinx itself::
+
+  $ sphinx-build -b doctest doc sphinx
+
+You can test overall test coverage with::
+
+  $ nosetests --with-coverage --cover-package=xbob.machine
+
+The ``coverage`` egg must be installed for this to work properly.
+
+Development
+-----------
+
+To develop this package, install using ``zc.buildout``, using the buildout
+configuration found on the root of the package:
+
+  $ python bootstrap.py
+  ...
+  $ ./bin/buildout
+
+Tweak the options in ``buildout.cfg`` to disable/enable verbosity and debug
+builds.

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
+import shutil
+import sys
+import tempfile
+
+from optparse import OptionParser
+
+tmpeggs = tempfile.mkdtemp()
+
+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 --find-links to point to local resources, you can keep
+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("-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", "--config-file",
+                  help=("Specify the path to the buildout configuration "
+                        "file to be used."))
+parser.add_option("-f", "--find-links",
+                  help=("Specify a URL to search for buildout releases"))
+
+
+options, args = parser.parse_args()
+
+######################################################################
+# load/install setuptools
+
+to_reload = False
+try:
+    import pkg_resources
+    import setuptools
+except ImportError:
+    ez = {}
+
+    try:
+        from urllib.request import urlopen
+    except ImportError:
+        from urllib2 import urlopen
+
+    # XXX use a more permanent ez_setup.py URL when available.
+    exec(urlopen('https://bitbucket.org/pypa/setuptools/raw/0.7.2/ez_setup.py'
+                ).read(), ez)
+    setup_args = dict(to_dir=tmpeggs, download_delay=0)
+    ez['use_setuptools'](**setup_args)
+
+    if to_reload:
+        reload(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)
+
+######################################################################
+# Try to best guess the version of buildout given setuptools
+if options.version is None:
+
+  try:
+    from distutils.version import LooseVersion
+    package = pkg_resources.require('setuptools')[0]
+    v = LooseVersion(package.version)
+    if v < LooseVersion('0.7'):
+      options.version = '2.1.1'
+  except:
+    pass
+
+######################################################################
+# Install buildout
+
+ws = pkg_resources.working_set
+
+cmd = [sys.executable, '-c',
+       'from setuptools.command.easy_install import main; main()',
+       '-mZqNxd', tmpeggs]
+
+find_links = os.environ.get(
+    'bootstrap-testing-find-links',
+    options.find_links or
+    ('http://downloads.buildout.org/'
+     if options.accept_buildout_test_releases else None)
+    )
+if find_links:
+    cmd.extend(['-f', find_links])
+
+setuptools_path = ws.find(
+    pkg_resources.Requirement.parse('setuptools')).location
+
+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=[setuptools_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)
+
+import subprocess
+if subprocess.call(cmd, env=dict(os.environ, PYTHONPATH=setuptools_path)) != 0:
+    raise Exception(
+        "Failed to execute command:\n%s",
+        repr(cmd)[1:-1])
+
+######################################################################
+# Import and run buildout
+
+ws.add_entry(tmpeggs)
+ws.require(requirement)
+import zc.buildout.buildout
+
+if not [a for a in args if '=' not in a]:
+    args.append('bootstrap')
+
+# if -c was provided, we push it back into args for buildout' main function
+if options.config_file is not None:
+    args[0:0] = ['-c', options.config_file]
+
+zc.buildout.buildout.main(args)
+shutil.rmtree(tmpeggs)
+

buildout.cfg

+; vim: set fileencoding=utf-8 :
+; Andre Anjos <andre.anjos@idiap.ch>
+; Mon 16 Apr 08:29:18 2012 CEST
+
+[buildout]
+parts = xbob.blitz xbob.math xbob.io xbob.math scripts
+eggs = xbob.math
+       ipdb
+extensions = mr.developer
+auto-checkout = *
+prefixes = /idiap/group/torch5spro/nightlies/last/install/linux-x86_64-release
+debug = true
+verbose = true
+
+[sources]
+xbob.buildout = git git@github.com:bioidiap/xbob.buildout
+xbob.extension = git git@github.com:bioidiap/xbob.extension branch=xbob
+
+[xbob.blitz]
+recipe = xbob.buildout:develop
+setup = src/xbob.blitz
+eggs = xbob.buildout xbob.extension
+
+[xbob.math]
+recipe = xbob.buildout:develop
+setup = src/xbob.math
+eggs = xbob.blitz xbob.buildout xbob.extension
+
+[xbob.io]
+recipe = xbob.buildout:develop
+setup = src/xbob.io
+eggs = xbob.blitz xbob.buildout xbob.extension
+
+[xbob.math]
+recipe = xbob.buildout:develop
+eggs = xbob.blitz
+
+[scripts]
+recipe = xbob.buildout:scripts

doc/c_cpp_api.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.dos.anjos@gmail.com>
+.. Tue 15 Oct 14:59:05 2013
+
+=========
+ C++ API
+=========
+
+The C++ API of ``xbob.machine`` allows users to leverage from automatic
+converters for classes in :py:class:`xbob.machine`.  To use the C API, clients
+should first, include the header file ``<xbob.machine/api.h>`` on their
+compilation units and then, make sure to call once ``import_xbob_machine()`` at
+their module instantiation, as explained at the `Python manual
+<http://docs.python.org/2/extending/extending.html#using-capsules>`_.
+
+Here is a dummy C example showing how to include the header and where to call
+the import function:
+
+.. code-block:: c++
+
+   #include <xbob.machine/api.h>
+
+   PyMODINIT_FUNC initclient(void) {
+
+     PyObject* m Py_InitModule("client", ClientMethods);
+
+     if (!m) return;
+
+     // imports the NumPy C-API
+     import_array();
+
+     // imports blitz.array C-API
+     import_xbob_blitz();
+
+     // imports xbob.io C-API
+     import_xbob_io();
+
+     // imports xbob.machine C-API
+     import_xbob_machine();
+
+   }
+
+.. note::
+
+  The include directory can be discovered using
+  :py:func:`xbob.machine.get_include`.
+
+Activation Support
+------------------
+
+.. cpp:type:: PyBobMachineActivationObject
+
+   The pythonic object representation for a ``bob::machine::Activation``
+   object.
+
+   .. code-block:: cpp
+
+      typedef struct {
+        PyObject_HEAD
+        boost::shared_ptr<bob::machine::Activation> a;
+      } PyBobIoFileObject;
+
+   .. cpp:member:: boost::shared_ptr<bob::machine::Activation> a
+
+      A pointer to the activation function implementation
+
+.. include:: links.rst

doc/conf.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Andre Anjos <andre.anjos@idiap.ch>
+# Tue 15 Oct 16:37:18 2013 CEST
+#
+# Copyright (C) 2011-2013 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 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'
+
+# 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',
+  'matplotlib.sphinxext.plot_directive',
+  ]
+
+# 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'xbob.machine'
+import time
+copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
+
+# Grab the setup entry
+distribution = pkg_resources.require('xbob.machine')[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
+# built documents.
+#
+# The short X.Y version.
+version = distribution.version
+# The full version, including alpha/beta/rc tags.
+release = distribution.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 = 'xbob_machine'
+
+# 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 = 'xbob_machine_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', 'xbob_machine.tex', u'Bob Machines',
+   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 = ''