Updates to package structure, license and ci

.travis.yml

@@ -1,11 +1,12 @@
 language: python
+env:
+  global:
+  - secure: MPgfLy1TeHcTfPcRqnKAqzvDAeHoAGEf7+O6KqI0R71vtUc5tz/RdCmG/pbPzNRSo5m8nPWs4/R04enbC/mjb8ibxqZixTQ8ZLOEZDrLFwpzn7aVIS7Dr0dLrk1/gFQKUy1jpQF554VZK02dYz03E6UkjRLuyIn0aA1N0jJF2bM=
+  - secure: R//IYVHP3G4JQah/AhEhT8HCmESN5FsC1JGjFQK05/q9QFm6Ztgqk86EZ2bDA1DW0eTZ47dmyQ3wJwoWI6DcgQeWAIred/iK2ZtKAMefmvwRjnxEDcE+D9F2ZCOB0HNW5o7LtuwsbXWNE2Z880pOBKVkQJyFKLfnwkywOv6/irI=
+  - BOB_UPLOAD_WHEEL=1
 matrix:
   include:
   - python: 2.7
-    env:
-    - secure: Xxn/9bwmKulVZX1zsoPbCIjNPxwC2PtN8J0kdDWRDV45ATUE0FIbh3CiWa26D7jFgSdUN9gUm8hbvjBbffnDlEnKQIKBzEO9E2q+R1dtBaevNZxOEQu9miM+GUYaf2Rr4ed8EAIHoKO0yGCOVRG+p+6qyBDVW9bhOqLNAESY6rc=
-    - secure: Qs6A6w5jj8NlxTjXt4v844IC2tE9117Zsx1lYlVeQN+baXD8Bo/bFBjGCTsnvruIZQRdnX/ZCT/Gece1Hqlw06Iy8WEfN8nPH1MR8e3+QqRY2okpbtAdGjC2CPdG6WKp8DjLchnZccWE8QV1YdfinJ0qAh6wguS86fTbyq/hyyo=
-    - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
   - python: 3.3
   - python: 3.4
   - python: 3.5
@@ -14,13 +15,13 @@ before_install:
 - 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 --upgrade pip
-- 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 sphinx nose coverage cpp-coveralls pillow
 - 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=
+- ./bin/buildout
 script:
-- ./bin/python -c 'import pkg_resources; from bob.db.utfvp import get_config; print(get_config())'
+- ./bin/python -c 'from bob.db.utfvp import get_config; print(get_config())'
 - ./bin/bob_dbmanage.py utfvp download
 - ./bin/coverage run --source=bob.db.utfvp ./bin/nosetests -sv
 - ./bin/sphinx-build -b doctest doc sphinx

LICENSE

@@ -0,0 +1,24 @@
+Copyright (c) 2016, 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.

README.rst

@@ -1,6 +1,5 @@
 .. vim: set fileencoding=utf-8 :
-.. Pedro Tome <pedro.tome@idiap.ch>
-.. Tus Jan  13 19:35:05 CEST 2015
+.. Wed 03 Aug 2016 09:05:32 CEST
 
 .. image:: http://img.shields.io/badge/docs-stable-yellow.png
    :target: http://pythonhosted.org/bob.db.utfvp/index.html
@@ -20,26 +19,24 @@
    :target: http://www.sas.ewi.utwente.nl
 
 
-==============================================================================
+=============================================
  UTFVP Fingervein Database Interface for Bob
-==============================================================================
+=============================================
 
-This package contains an interface for the evaluation protocol of the `UTFVP Fingervein Database <http://www.sas.ewi.utwente.nl>`_.
-This package does not contain the original `UTFVP Fingervein <http://www.sas.ewi.utwente.nl>`_ data files, which need to be obtained through the links above.
+This package contains an interface for the evaluation protocols of the `UTFVP
+Fingervein Database`_. Notice this package does not contain the raw data files
+from this dataset, which need to be obtained through the link above.
 
 
 Installation
 ------------
-To install this package -- alone or together with other `Packages of Bob <https://github.com/idiap/bob/wiki/Packages>`_ -- please read the `Installation Instructions <https://github.com/idiap/bob/wiki/Installation>`_.
-For Bob_ to be able to work properly, some dependent packages are required to be installed.
-Please make sure that you have read the `Dependencies <https://github.com/idiap/bob/wiki/Dependencies>`_ for your operating system.
-
-Documentation
--------------
-For further documentation on this package, please read the `Stable Version <http://pythonhosted.org/bob.db.utfvp/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.db.utfvp/master/index.html>`_ of the documentation.
-For a list of tutorials on this or the other packages ob Bob_, or information on submitting issues, asking questions and starting discussions, please visit its website.
-
-.. _bob: https://www.idiap.ch/software/bob
 
+This package only contains database access functions so it is easy to
+programatically reproduce evaluation results obtained in papers. You normally
+don't install this package, unless you're modifying it. Instead, install one of
+our top-level frameworks for vein image processing, such as ``bob.bio.vein``.
 
 
+.. Write your references here:
+.. _bob: https://www.idiap.ch/software/bob
+.. _utfvp fingervein database: http://www.sas.ewi.utwente.nl

bob/__init__.py

@@ -1,2 +1,3 @@
+# see https://docs.python.org/3/library/pkgutil.html
 from pkgutil import extend_path
 __path__ = extend_path(__path__, __name__)

bob/db/__init__.py

@@ -1,2 +1,3 @@
+# see https://docs.python.org/3/library/pkgutil.html
 from pkgutil import extend_path
 __path__ = extend_path(__path__, __name__)

bootstrap-buildout.py

@@ -25,7 +25,10 @@
 
 from optparse import OptionParser
 
-tmpeggs = tempfile.mkdtemp()
+__version__ = '2015-07-01'
+# See zc.buildout's changelog if this version is up to date.
+
+tmpeggs = tempfile.mkdtemp(prefix='bootstrap-')
 
 usage = '''\
 [DESIRED PYTHON FOR BUILDOUT] bootstrap.py [options]
@@ -40,13 +43,14 @@
 '''
 
 parser = OptionParser(usage=usage)
-parser.add_option("-v", "--version", help="use a specific zc.buildout version")
-
+parser.add_option("--version",
+                  action="store_true", default=False,
+                  help=("Return bootstrap.py 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 "
+                  help=("Normally, if you do not specify a --buildout-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 "
@@ -59,25 +63,33 @@
 parser.add_option("--allow-site-packages",
                   action="store_true", default=False,
                   help=("Let bootstrap.py use existing site packages"))
+parser.add_option("--buildout-version",
+                  help="Use a specific zc.buildout version")
 parser.add_option("--setuptools-version",
-                  help="use a specific setuptools version")
-
+                  help="Use a specific setuptools version")
+parser.add_option("--setuptools-to-dir",
+                  help=("Allow for re-use of existing directory of "
+                        "setuptools versions"))
 
 options, args = parser.parse_args()
+if options.version:
+    print("bootstrap.py version %s" % __version__)
+    sys.exit(0)
+
 
 ######################################################################
 # load/install setuptools
 
 try:
-    if options.allow_site_packages:
-        import setuptools
-        import pkg_resources
     from urllib.request import urlopen
 except ImportError:
     from urllib2 import urlopen
 
 ez = {}
-exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
+if os.path.exists('ez_setup.py'):
+    exec(open('ez_setup.py').read(), ez)
+else:
+    exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
 
 if not options.allow_site_packages:
     # ez_setup imports site, which adds site packages
@@ -88,12 +100,19 @@
     # We can't remove these reliably
     if hasattr(site, 'getsitepackages'):
         for sitepackage_path in site.getsitepackages():
-            sys.path[:] = [x for x in sys.path if sitepackage_path not in x]
+            # Strip all site-packages directories from sys.path that
+            # are not sys.prefix; this is because on Windows
+            # sys.prefix is a site-package directory.
+            if sitepackage_path != sys.prefix:
+                sys.path[:] = [x for x in sys.path
+                               if sitepackage_path not in x]
 
 setup_args = dict(to_dir=tmpeggs, download_delay=0)
 
 if options.setuptools_version is not None:
     setup_args['version'] = options.setuptools_version
+if options.setuptools_to_dir is not None:
+    setup_args['to_dir'] = options.setuptools_to_dir
 
 ez['use_setuptools'](**setup_args)
 import setuptools
@@ -110,7 +129,12 @@
 
 ws = pkg_resources.working_set
 
+setuptools_path = ws.find(
+    pkg_resources.Requirement.parse('setuptools')).location
+
+# Fix sys.path here as easy_install.pth added before PYTHONPATH
 cmd = [sys.executable, '-c',
+       'import sys; sys.path[0:0] = [%r]; ' % setuptools_path +
        'from setuptools.command.easy_install import main; main()',
        '-mZqNxd', tmpeggs]
 
@@ -123,11 +147,8 @@
 if find_links:
     cmd.extend(['-f', find_links])
 
-setuptools_path = ws.find(
-    pkg_resources.Requirement.parse('setuptools')).location
-
 requirement = 'zc.buildout'
-version = options.version
+version = options.buildout_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
@@ -167,7 +188,7 @@ def _final_version(parsed_version):
 cmd.append(requirement)
 
 import subprocess
-if subprocess.call(cmd, env=dict(os.environ, PYTHONPATH=setuptools_path)) != 0:
+if subprocess.call(cmd) != 0:
     raise Exception(
         "Failed to execute command:\n%s" % repr(cmd)[1:-1])
 

buildout.cfg

@@ -1,13 +1,15 @@
 ; vim: set fileencoding=utf-8 :
-; Pedro Tome <pedro.tome@idiap.ch>
-; Tue Jan  16 19:35:15 CEST 2015
+; Tue 02 Aug 2016 15:44:30 CEST
 
 [buildout]
 parts = scripts
 eggs = bob.db.utfvp
+       bob.db.base
+extensions = bob.buildout
 develop = .
+
+verbose = true
 newest = false
 
 [scripts]
 recipe = bob.buildout:scripts
-dependent-scripts=true

requirements.txt

@@ -1,4 +1,3 @@
-setuptools
 six
 bob.io.base
 bob.db.base

setup.py

@@ -1,43 +1,25 @@
 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-# Pedro Tome <Pedro.Tome@idiap.ch>
-#
-# Copyright (C) 2014-2015 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/>.
 
-from setuptools import setup, find_packages, dist
+from setuptools import setup, dist
 dist.Distribution(dict(setup_requires=['bob.extension']))
 
-from bob.extension.utils import load_requirements
+from bob.extension.utils import load_requirements, find_packages
 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='bob.db.utfvp',
-    version=version,
-    description='UTFVP Database Access API for Bob',
-    url='https://github.com/bioidiap/bob.db.utfvp',
-    license='GPLv3',
-    author='Pedro Tome',
-    author_email='pedro.tome@idiap.ch',
+    version=open("version.txt").read().rstrip(),
+    description='VERA Fingervein Database Access API for Bob',
+    url='https://github.com/bioidiap/bob.db.vera',
+    license='BSD',
+
+    author='Andre Anjos,Pedro Tome',
+    author_email='andre.anjos@idiap.ch,pedro.tome@idiap.ch',
+
     keywords='fingervein recognition, bob, bob.db, UTFVP',
+
     long_description=open('README.rst').read(),
 
     # This line is required for any distutils based packaging.
@@ -48,6 +30,7 @@
     install_requires=install_requires,
 
     entry_points = {
+      # bob database declaration
       'bob.db': [
         'utfvp = bob.db.utfvp.driver:Interface',
         ],
@@ -60,7 +43,7 @@
       'Intended Audience :: Developers',
       'Intended Audience :: Education',
       'Intended Audience :: Science/Research',
-      'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+      'License :: OSI Approved :: BSD License',
       'Natural Language :: English',
       'Programming Language :: Python',
       'Programming Language :: Python :: 3',