Switched to new bob version.

.travis.yml

+language: python
+matrix:
+  include:
+  - python: 2.6
+  - python: 2.7
+    env:
+    - secure: HYFSm84gCi+EnE3hDeRfPFojhfPx7RS7xfP2cYs+tzOvE2DdL62D4ZA/bnBTCbIl4FyOKxS/3biLYu40d8UIjDYvMgx8xaT/byJB6iw4my9vnzkFl2NcbBNQA0NvoU8lBrS/zXrbz3U/JMLNDXlGDFx/GTMmvAYt2Hrttq9kxD4=
+    - secure: Yfaf3JfZ7QWuEqOmExFD81KD0SDiAIB84x122zCYpcHCyqqAjWQw2v7+YBBR3F3m0sdMhrVuj/gBkmccEU/M3KLYR8jm9DiPfeenW2mdJwUBdcmM+9DCeYtnkZx8DYo3Uxpxi0WkvXmED6l6mkWHyPVSi3que9h1t3aOv/zt+2I=
+  - python: 3.2
+    env:
+    - NUMPYSPEC===1.8.0
+  - python: 3.3
+    env:
+    - NUMPYSPEC===1.8.0
+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
+- if [ -n "${NUMPYSPEC}" ]; then sudo apt-get install -qq gfortran; fi
+- if [ -n "${NUMPYSPEC}" ]; then pip install --upgrade pip setuptools; fi
+- if [ -n "${NUMPYSPEC}" ]; then pip install --find-links http://wheels.astropy.org/ --find-links http://wheels2.astropy.org/ --use-wheel numpy$NUMPYSPEC; fi
+- pip install --find-links http://wheels.astropy.org/ --find-links http://wheels2.astropy.org/ --use-wheel matplotlib==1.3.0 sphinx nose==1.3.0 jinja2==2.6 coveralls
+install:
+- python bootstrap.py
+- ./bin/buildout
+script:
+- ./bin/python -c 'from bob.db.voxforge import get_config; print(get_config())'
+- ./bin/coverage run --source=bob.db.voxforge ./bin/nosetests -sv
+- ./bin/sphinx-build -b doctest doc sphinx
+- ./bin/sphinx-build -b html doc sphinx
+after_success:
+- coveralls
+- ./src/bob.extension/scripts/upload-sphinx.sh

MANIFEST.in

 include README.rst bootstrap.py buildout.cfg COPYING
-recursive-include xbob *.lst
+recursive-include doc *.py *.rst
+recursive-include bob *.lst

xbob/db/voxforge/__init__.py → bob/db/voxforge/__init__.py

@@ -23,8 +23,23 @@ http://www.voxforge.org/
 """
 
 from .query import Database
-from xbob.db.verification.filelist.models import File, Client
+from bob.db.verification.filelist.models import File, Client
 
-__all__ = dir()
+def get_config():
+  """Returns a string containing the configuration information.
+  """
 
+  import pkg_resources
 
+  packages = pkg_resources.require(__name__)
+  this = packages[0]
+  deps = packages[1:]
+
+  retval =  "%s: %s (%s)\n" % (this.key, this.version, this.location)
+  retval += "  - python dependencies:\n"
+  for d in deps: retval += "    - %s: %s (%s)\n" % (d.key, d.version, d.location)
+
+  return retval.strip()
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

xbob/db/voxforge/driver.py → bob/db/voxforge/driver.py

@@ -22,7 +22,7 @@
 
 import os
 import sys
-from bob.db.driver import Interface as BaseInterface
+from bob.db.base.driver import Interface as BaseInterface
 
 def dumplist(args):
   """Dumps lists of files based on your criteria"""
@@ -37,7 +37,7 @@ def dumplist(args):
 
   output = sys.stdout
   if args.selftest:
-    from bob.db.utils import null
+    from bob.db.base.utils import null
     output = null()
 
   for f in r:
@@ -63,7 +63,7 @@ def checkfiles(args):
   # report
   output = sys.stdout
   if args.selftest:
-    from bob.db.utils import null
+    from bob.db.base.utils import null
     output = null()
 
   if bad:
@@ -81,7 +81,7 @@ class Interface(BaseInterface):
 
   def version(self):
     import pkg_resources # part of setuptools
-    return pkg_resources.require('xbob.db.%s' % self.name())[0].version
+    return pkg_resources.require('bob.db.%s' % self.name())[0].version
 
   def files(self):
     return ()

xbob/db/voxforge/query.py → bob/db/voxforge/query.py

@@ -17,16 +17,16 @@
 # 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 xbob.db.verification.filelist
+import bob.db.verification.filelist
 
-class Database(xbob.db.verification.filelist.Database):
+class Database(bob.db.verification.filelist.Database):
   """Wrapper class for the subVoxforge database for speaker recognition (http://www.voxforge.org/).
   this class defines a simple protocol for training, dev and and by splitting the audio files of the database in three main parts.
   """
 
-  def __init__(self):
+  def __init__(self, original_directory = None, original_extension = None):
     # call base class constructor
     from pkg_resources import resource_filename
     lists = resource_filename(__name__, 'lists')
-    xbob.db.verification.filelist.Database.__init__(self, lists)
-    
+    bob.db.verification.filelist.Database.__init__(self, lists, original_directory = original_directory, original_extension = original_extension)
+

bob/db/voxforge/test.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Laurent El Shafey <laurent.el-shafey@idiap.ch>
+# Fri Aug 23 16:27:27 CEST 2013
+#
+# Copyright (C) 2011-2014 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/>.
+
+"""A few checks on the protocols of a subset of the VoxForge database
+"""
+
+import bob.db.voxforge
+
+def test_query():
+  db = bob.db.voxforge.Database()
+
+  assert len(db.client_ids()) == 30 # 10 client ids for world, dev and eval
+  assert len(db.client_ids(groups='world')) == 10 # 10 client ids for world
+  assert len(db.client_ids(groups='optional_world_1')) == 10 # 10 client ids for optional world 1
+  assert len(db.client_ids(groups='optional_world_2')) == 10 # 10 client ids for optional world 2
+  assert len(db.client_ids(groups='dev')) == 10 # 10 client ids for dev
+  assert len(db.client_ids(groups='eval')) == 10 # 10 client ids for eval
+
+  assert len(db.model_ids()) == 30 # 30 model ids for world, dev and eval
+  assert len(db.model_ids(groups='world')) == 10 # 10 model ids for world
+  assert len(db.model_ids(groups='optional_world_1')) == 10 # 10 model ids for optional world 1
+  assert len(db.model_ids(groups='optional_world_2')) == 10 # 10 model ids for optional world 2
+  assert len(db.model_ids(groups='dev')) == 10 # 10 model ids for dev
+  assert len(db.model_ids(groups='eval')) == 10 # 10 model ids for eval
+
+  assert len(db.objects(groups='world')) == 3148 # 3148 samples in the world set
+
+  assert len(db.objects(groups='dev', purposes='enrol')) == 1304 # 1304 samples for enrollment in the dev set
+  assert len(db.objects(groups='dev', purposes='enrol', model_ids='Dcoetzee')) == 240 # 240 samples to enroll model 'Dcoetzee' in the dev set
+  assert len(db.objects(groups='dev', purposes='enrol', model_ids='rortiz')) == 0 # 0 samples to enroll model 'rortiz' (it is an eval model)
+  assert len(db.objects(groups='dev', purposes='probe')) == 300 # 300 samples as probes in the dev set
+
+  assert len(db.objects(groups='eval', purposes='enrol')) == 1509 # 1509 samples for enrollment in the eval set
+  assert len(db.objects(groups='eval', purposes='enrol', model_ids='rortiz')) == 120 # 120 samples to enroll model 'rortiz' in the eval set
+  assert len(db.objects(groups='eval', purposes='enrol', model_ids='Dcoetzee')) == 0 # 0 samples to enroll model 'Dcoetzee' (it is a dev model)
+  assert len(db.objects(groups='eval', purposes='probe')) == 300 # 300 samples as probes in the eval set
+

buildout.cfg

 ; vim: set fileencoding=utf-8 :
-; Elie Khoury <Elie.Khoury@idiap.ch>
-; Thu Aug 22 20:38:47 CEST 2013
+; Manuel Guenther <manuel.guenther@idiap.ch>
+; Thu Sep  4 18:24:14 CEST 2014
 
 [buildout]
-parts = scripts 
-develop = .
-eggs =  bob>=1.2.0
-        xbob.db.verification.filelist
-        xbob.db.voxforge
-        vanity
+parts = scripts
+eggs = bob.db.voxforge
+extensions = bob.buildout
+             mr.developer
+auto-checkout = *
+develop = src/bob.extension
+          src/bob.blitz
+          src/bob.core
+          src/bob.io.base
+          src/bob.db.base
+          src/bob.db.verification.utils
+          src/bob.db.verification.filelist
+          .
+
+; options for bob.buildout extension
+debug = true
+verbose = true
 newest = false
 
-; Look at this directory to find bob
-prefixes = /idiap/group/torch5spro/releases/bob-1.2.0/install/linux-x86_64-release
+[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.db.base = git https://github.com/bioidiap/bob.db.base
+bob.db.verification.utils = git https://github.com/bioidiap/bob.db.verification.utils
+bob.db.verification.filelist = git https://github.com/bioidiap/bob.db.verification.filelist
 
 [scripts]
-recipe = xbob.buildout: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) 2011-2012 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',
+  ]
+
+# 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'BANCA 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 bob.db.voxforge.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
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'bob', u'BANCA (Bob API) Documentation', [u'Idiap Research Institute'], 1)
+]
+
+
+# We want to remove all private (i.e. _. or __.__) members
+# that are not in the list of accepted functions
+accepted_private_functions = ['__call__']
+
+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 True
+    else:
+      # test if the method is documented
+      if not hasattr(obj, '__doc__') or not obj.__doc__:
+        return True
+
+  # Skips selected members in auto-generated documentation. Unfortunately, old
+  # versions of Boost.Python will not generate a __self__ member for static
+  # methods and that screws-up Sphinx processing.
+  if sphinx.__version__ < "1.0":
+    # We have to remove objects that do not have a __self__ attribute set
+    import types
+    if isinstance(obj, types.BuiltinFunctionType) and \
+      not hasattr(obj, '__self__') and what == 'class':
+        app.warn("Skipping %s %s (no __self__)" % (what, name))
+        return True
+
+    return False
+
+# Default processing flags for sphinx
+autoclass_content = 'both'
+autodoc_member_order = 'bysource'
+autodoc_default_flags = ['members', 'undoc-members', 'special-members', 'inherited-members', 'show-inheritance']
+
+def setup(app):
+  app.connect('autodoc-skip-member', member_function_test)

doc/guide.rst

+.. vim: set fileencoding=utf-8 :
+.. @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
+.. @date:   Thu Dec  6 12:28:25 CET 2012
+
+==============
+ User's Guide
+==============
+
+.. todo::
+   Write users guide.

doc/index.rst

+.. vim: set fileencoding=utf-8 :
+.. @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
+.. @date:   Tue Aug 26 09:42:18 CEST 2014
+
+=======================================
+ BANCA Database Verification Protocols
+=======================================
+
+.. todolist::
+
+Documentation
+-------------
+
+.. toctree::
+   :maxdepth: 2
+
+   guide
+   py_api
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+