Massive update to Bob v2

.gitignore

@@ -3,7 +3,7 @@
 *.pyc
 .DS_Store
 .installed.cfg
-xbob.db.atvskeystroke.egg-info/
+bob.db.atvskeystroke.egg-info/
 parts
 develop-eggs
 bin

.travis.yml

+language: python
+matrix:
+  include:
+  - python: 2.7
+    env:
+    - secure: nFUUA3ju4Y+JTuLS4N2u+9FZtvWMIKij8wz4OzpLNtPhAitdzZJSiAUgE5uY94MbRlsyBkLuyUiJ144RVRoRmZuaw4Dkr/ntW3Z/zqIni7IYJ4yl3QUPXGSbTH7HR2LQIid7mHkeWcEguyfiusSYhBhmEtxPJoHN4SfaFfveX28=
+    - secure: bN9g+XWFSBHYsJdjNVk/h0ijua42yi5pfw2EIEpSGAg5IoIVP2ZwwC5Nc3z+w08+TpdyHjFqP7wVj0e0Ltcz2+Ia3sG8sprqC4jaVrEe4E2xaImvzxRUpLBzgO7jbPsi8Kulz1BCuSKcE+P9/wHpGi92DX42+lVw4f2iFtKWEaM=
+    - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
+    - BOB_UPLOAD_WHEEL="--universal"
+  - python: 3.3
+  - python: 3.4
+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 --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/python -c 'import pkg_resources; from bob.db.atvskeystroke import get_config; print(get_config())'
+- ./bin/coverage run --source=bob.db.atvskeystroke ./bin/nosetests -sv
+after_success:
+- coveralls
+- wget https://raw.githubusercontent.com/bioidiap/bob.extension/master/scripts/upload-wheel.sh
+- chmod a+x upload-wheel.sh
+- ./upload-wheel.sh

MANIFEST.in

 include README.rst bootstrap-buildout.py buildout.cfg COPYING
 recursive-include docs *.py *.rst
-recursive-include xbob *.sql3
+recursive-include bob *.sql3

README.rst

+.. image:: http://img.shields.io/badge/docs-stable-yellow.png
+   :target: http://pythonhosted.org/bob.db.atvskeystroke/index.html
+.. image:: http://img.shields.io/badge/docs-latest-orange.png
+   :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.db.atvskeystroke/master/index.html
+.. image:: https://travis-ci.org/bioidiap/bob.db.atvskeystroke.svg?branch=master
+   :target: https://travis-ci.org/bioidiap/bob.db.atvskeystroke
+.. image:: https://coveralls.io/repos/bioidiap/bob.db.atvskeystroke/badge.png
+   :target: https://coveralls.io/r/bioidiap/bob.db.atvskeystroke
+.. image:: https://img.shields.io/badge/github-master-0000c0.png
+   :target: https://github.com/bioidiap/bob.db.atvskeystroke/tree/master
+.. image:: http://img.shields.io/pypi/v/bob.db.atvskeystroke.png
+   :target: https://pypi.python.org/pypi/bob.db.atvskeystroke
+.. image:: http://img.shields.io/pypi/dm/bob.db.atvskeystroke.png
+   :target: https://pypi.python.org/pypi/bob.db.atvskeystroke
+
+
 =========================
  ATVS Keystroke Database
 =========================
@@ -24,7 +40,7 @@ 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/xbob.db.atvskeystroke>`_. When you download the
+   <https://github.com/mgbarrero/bob.db.atvskeystroke>`_. 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
@@ -44,11 +60,11 @@ script)::
 
     install_requires=[
       ...
-      "xbob.db.atvskeystroke",
+      "bob.db.atvskeystroke",
     ],
 
 Proceed normally with your ``boostrap/buildout`` steps and you should be all
-set. That means you can now import the ``xbob.db.atvskeystroke`` namespace into your scripts.
+set. That means you can now import the ``bob.db.atvskeystroke`` namespace into your scripts.
 
 Modify your buildout.cfg and download from git
 ==============================================
@@ -60,12 +76,11 @@ lines::
 
   [buildout]
   ...
-  extensions = mr.developer
+  extensions =mr.developer
   auto-checkout = *
-  eggs = bob
-         ...
-         xbob.db.atvskeystroke
+  eggs = ...
+         bob.db.atvskeystroke
 
   [sources]
-  xbob.db.atvskeystroke = git https://github.com/mgbarrero/xbob.db.atvskeystroke.git
+  bob.db.atvskeystroke = git https://github.com/mgbarrero/bob.db.atvskeystroke.git
   ...

bob/__init__.py

+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)

bob/db/__init__.py

+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)

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

@@ -13,10 +13,18 @@
 # 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 BiosecurID database
+"""The ATVSKeystroke database
 """
 
 from .query import Database
 from .models import Client, File, Protocol, ProtocolPurpose
 
-__all__ = dir()
+def get_config():
+  """Returns a string containing the configuration information.
+  """
+  import bob.extension
+  return bob.extension.get_config(__name__)
+
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

xbob/db/atvskeystroke/create.py → bob/db/atvskeystroke/create.py

@@ -13,7 +13,7 @@
 # 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 BiosecurId database in a single pass.
+"""This script creates the ATVSKeystroke database in a single pass.
 """
 
 import os,string

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

@@ -18,7 +18,7 @@
 
 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"""
@@ -36,7 +36,7 @@ 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:
@@ -64,7 +64,7 @@ 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:
@@ -83,7 +83,7 @@ def reverse(args):
 
   output = sys.stdout
   if args.selftest:
-    from bob.db.utils import null
+    from bob.db.base.utils import null
     output = null()
 
   r = db.reverse(args.path)
@@ -101,7 +101,7 @@ def path(args):
 
   output = sys.stdout
   if args.selftest:
-    from bob.db.utils import null
+    from bob.db.base.utils import null
     output = null()
 
   r = db.paths(args.id, prefix=args.directory, suffix=args.extension)
@@ -119,7 +119,7 @@ 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):
 

xbob/db/atvskeystroke/models.py → bob/db/atvskeystroke/models.py

@@ -13,17 +13,16 @@
 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
-"""Table models and functionality for the BiosecurId database.
+"""Table models and functionality for the ATVSKeystroke database.
 """
 
 import os, numpy
-import bob.db.utils
 from sqlalchemy import Table, Column, Integer, String, ForeignKey, or_, and_, not_
-from bob.db.sqlalchemy_migration import Enum, relationship
+from bob.db.base.sqlalchemy_migration import Enum, relationship
 from sqlalchemy.orm import backref
 from sqlalchemy.ext.declarative import declarative_base
 
-import xbob.db.verification.utils
+import bob.db.verification.utils
 
 Base = declarative_base()
 
@@ -53,7 +52,7 @@ class Client(Base):
     return "Client(`%s`, `%s`)" % (self.id, self.stype)
 
 
-class File(Base, xbob.db.verification.utils.File):
+class File(Base, bob.db.verification.utils.File):
   """Generic file container"""
 
   __tablename__ = 'file'
@@ -74,7 +73,7 @@ class File(Base, xbob.db.verification.utils.File):
 
   def __init__(self, client_id, path, session_id, shot_id):
     # call base class constructor
-    xbob.db.verification.utils.File.__init__(self, client_id = client_id, path = path)
+    bob.db.verification.utils.File.__init__(self, client_id = client_id, path = path)
 
     self.session_id = session_id
     self.shot_id = shot_id

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

@@ -14,20 +14,19 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 """This module provides the Dataset interface allowing the user to query the
-BiosecurID database in the most obvious ways.
+ATVSKeystroke database in the most obvious ways.
 """
 
 import os
 import six
-from bob.db import utils
 from .models import *
 from .driver import Interface
 
-import xbob.db.verification.utils
+import bob.db.verification.utils
 
 SQLITE_FILE = Interface().files()[0]
 
-class Database(xbob.db.verification.utils.SQLiteDatabase,xbob.db.verification.utils.Database):
+class Database(bob.db.verification.utils.SQLiteDatabase,bob.db.verification.utils.Database):
   """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
@@ -36,8 +35,8 @@ class Database(xbob.db.verification.utils.SQLiteDatabase,xbob.db.verification.ut
 
   def __init__(self, original_directory = None, original_extension = db_file_extension):
     # call base class constructor
-    xbob.db.verification.utils.SQLiteDatabase.__init__(self, SQLITE_FILE, File)
-    xbob.db.verification.utils.Database.__init__(self, original_directory=original_directory, original_extension=original_extension)
+    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)
 
   def __group_replace_eval_by_genuine__(self, l):
     """Replace 'eval' by 'Genuine' and returns the new list"""
@@ -103,7 +102,7 @@ class Database(xbob.db.verification.utils.SQLiteDatabase,xbob.db.verification.ut
       The groups to which the subjects attached to the models belong ('Genuine')
       Note that 'dev', 'eval' and 'world' are alias for 'Genuine'.
 
-    Returns: A list containing all the models (model <-> client in BiosecurID) belonging
+    Returns: A list containing all the models (model <-> client in AVTSKeystroke) belonging
              to the given group.
     """
 
@@ -157,7 +156,7 @@ class Database(xbob.db.verification.utils.SQLiteDatabase,xbob.db.verification.ut
     Keyword Parameters:
 
     protocol
-      One of the Biosecurid protocols ('A').
+      One of the ATVSKeystroke protocols ('A').
 
     purposes
       The purposes required to be retrieved ('enrol', 'probe') or a tuple

buildout.cfg

-; vim: set fileencoding=utf-8 :
-; author: Manuel Guenther <manuel.guenther@idiap.ch>
-; date:   Wed Feb 13 12:35:29 CET 2013
-
 [buildout]
 parts = scripts
 develop = .
-eggs = xbob.db.atvskeystroke
+eggs = bob.db.atvskeystroke
 newest = false
 
 [scripts]
-recipe = xbob.buildout:scripts
+recipe = bob.buildout:scripts
 dependent-scripts = true

docs/conf.py

@@ -4,16 +4,16 @@
 # 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/>.
 
@@ -40,7 +40,6 @@ extensions = [
   '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
@@ -248,7 +247,7 @@ man_pages = [
 ]
 
 
-# We want to remove all private (i.e. _. or __.__) members 
+# We want to remove all private (i.e. _. or __.__) members
 # that are not in the list of accepted functions
 accepted_private_functions = ['__call__']
 
@@ -263,10 +262,10 @@ def member_function_test(app, what, name, obj, skip, options):
       # 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. 
+  # 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
@@ -276,7 +275,7 @@ def member_function_test(app, what, name, obj, skip, options):
         return True
 
     return False
-  
+
 # Default processing flags for sphinx
 autoclass_content = 'both'
 autodoc_member_order = 'bysource'

requirements.txt

+setuptools
+six
+bob.db.base

setup.py

@@ -16,16 +16,23 @@
 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
-from setuptools import setup, find_packages
+from setuptools import setup, find_packages, dist
+dist.Distribution(dict(setup_requires=['bob.extension']))
+
+from bob.extension.utils import load_requirements
+install_requires = load_requirements()
+
+# Define package version
+version = open("version.txt").read().rstrip()
 
 # The only thing we do in this file is to call the setup() function with all
 # parameters that define our package.
 setup(
 
-    name='xbob.db.atvskeystroke',
-    version='0.0.1',
+    name='bob.db.atvskeystroke',
+    version=version,
     description='ATVS-Keystroke Database Access API for Bob',
-    url='http://github.com/mgbarrero/xbob.db.atvskeystroke',
+    url='http://github.com/mgbarrero/bob.db.atvskeystroke',
     license='GPLv3',
     author='Marta Gomez-Barrero',
     author_email='marta.barrero@uam.es',
@@ -36,28 +43,13 @@ setup(
     include_package_data=True,
     zip_safe=False,
 
-    install_requires=[
-      'setuptools',
-      'six',  # py2/3 compatibility library
-      'bob',  # base signal proc./machine learning library
-      'xbob.db.verification.utils>=0.1.4' # defines a set of utilities for face verification databases like this one.
-    ],
-
-    namespace_packages = [
-      'xbob',
-      'xbob.db',
-      ],
+    install_requires=install_requires,
 
     entry_points={
 
       # declare database to bob
       'bob.db': [
-        'atvskeystroke = xbob.db.atvskeystroke.driver:Interface',
-        ],
-
-      # declare tests to bob
-      'bob.test': [
-        'atvskeystroke = xbob.db.atvskeystroke.test:ATVSKeystrokeDatabaseTest',
+        'atvskeystroke = bob.db.atvskeystroke.driver:Interface',
         ],
 
       },

version.txt

+2.0.0

xbob/__init__.py

-#see http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
-__import__('pkg_resources').declare_namespace(__name__)

xbob/db/__init__.py

-#see http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
-__import__('pkg_resources').declare_namespace(__name__)