diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..fa11e075cc0fd8c54733fead8bc84daabc081f0b
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,249 @@
+# This build file heavily uses template features from YAML so it is generic
+# enough for any Bob project. Don't modify it unless you know what you're
+# doing.
+
+
+# Definition of our build pipeline
+stages:
+ - build
+ - test
+ - docs
+ - wheels
+ - deploy
+
+
+# ---------
+# Templates
+# ---------
+
+# Template for the build stage
+# Needs to run on all supported architectures, platforms and python versions
+.build_template: &build_job
+ stage: build
+ before_script:
+ - git clean -ffdx
+ - mkdir _ci
+ - curl --silent "https://gitlab.idiap.ch/bob/bob.admin/raw/master/gitlab/install.sh" > _ci/install.sh
+ - chmod 755 _ci/install.sh
+ - ./_ci/install.sh _ci #updates
+ - ./_ci/before_build.sh
+ script:
+ - ./_ci/build.sh
+ after_script:
+ - ./_ci/after_build.sh
+ artifacts:
+ expire_in: 1 week
+ paths:
+ - _ci/
+ - dist/
+ - sphinx/
+
+
+# Template for the test stage - re-installs from uploaded wheels
+# Needs to run on all supported architectures, platforms and python versions
+.test_template: &test_job
+ stage: test
+ before_script:
+ - ./_ci/install.sh _ci #updates
+ - ./_ci/before_test.sh
+ script:
+ - ./_ci/test.sh
+ after_script:
+ - ./_ci/after_test.sh
+
+
+# Template for the wheel uploading stage
+# Needs to run against one supported architecture, platform and python version
+.wheels_template: &wheels_job
+ stage: wheels
+ environment: intranet
+ only:
+ - master
+ - /^v\d+\.\d+\.\d+([abc]\d*)?$/ # PEP-440 compliant version (tags)
+ before_script:
+ - ./_ci/install.sh _ci #updates
+ - ./_ci/before_wheels.sh
+ script:
+ - ./_ci/wheels.sh
+ after_script:
+ - ./_ci/after_wheels.sh
+
+
+# Template for (latest) documentation upload stage
+# Only one real job needs to do this
+.docs_template: &docs_job
+ stage: docs
+ environment: intranet
+ only:
+ - master
+ before_script:
+ - ./_ci/install.sh _ci #updates
+ - ./_ci/before_docs.sh
+ script:
+ - ./_ci/docs.sh
+ after_script:
+ - ./_ci/after_docs.sh
+
+
+# Template for the deployment stage - re-installs from uploaded wheels
+# Needs to run on a single architecture only
+# Will deploy your package to PyPI and other required services
+# Only runs for tags
+.deploy_template: &deploy_job
+ stage: deploy
+ environment: internet
+ only:
+ - /^v\d+\.\d+\.\d+([abc]\d*)?$/ # PEP-440 compliant version (tags)
+ except:
+ - branches
+ before_script:
+ - ./_ci/install.sh _ci #updates
+ - ./_ci/before_deploy.sh
+ script:
+ - ./_ci/deploy.sh
+ after_script:
+ - ./_ci/after_deploy.sh
+
+
+# -------------
+# Build Targets
+# -------------
+
+# Linux + Python 2.7: Builds, tests, uploads wheel and deploys (if needed)
+build_linux_27:
+ <<: *build_job
+ variables: &linux_27_build_variables
+ PYTHON_VERSION: "2.7"
+ WHEEL_TAG: "py27"
+ tags:
+ - conda-linux
+
+test_linux_27:
+ <<: *test_job
+ variables: *linux_27_build_variables
+ dependencies:
+ - build_linux_27
+ tags:
+ - conda-linux
+
+wheels_linux_27:
+ <<: *wheels_job
+ variables: *linux_27_build_variables
+ dependencies:
+ - build_linux_27
+ tags:
+ - conda-linux
+
+deploy_linux_27:
+ <<: *deploy_job
+ variables: *linux_27_build_variables
+ dependencies:
+ - build_linux_27
+ tags:
+ - conda-linux
+
+
+# Linux + Python 3.4: Builds and tests
+build_linux_34:
+ <<: *build_job
+ variables: &linux_34_build_variables
+ PYTHON_VERSION: "3.4"
+ WHEEL_TAG: "py3"
+ tags:
+ - conda-linux
+
+test_linux_34:
+ <<: *test_job
+ variables: *linux_34_build_variables
+ dependencies:
+ - build_linux_34
+ tags:
+ - conda-linux
+
+
+# Linux + Python 3.5: Builds, tests and uploads wheel
+build_linux_35:
+ <<: *build_job
+ variables: &linux_35_build_variables
+ PYTHON_VERSION: "3.5"
+ WHEEL_TAG: "py3"
+ tags:
+ - conda-linux
+
+test_linux_35:
+ <<: *test_job
+ variables: *linux_35_build_variables
+ dependencies:
+ - build_linux_35
+ tags:
+ - conda-linux
+
+wheels_linux_35:
+ <<: *wheels_job
+ variables: *linux_35_build_variables
+ dependencies:
+ - build_linux_35
+ tags:
+ - conda-linux
+
+docs_linux_35:
+ <<: *docs_job
+ variables: *linux_35_build_variables
+ dependencies:
+ - build_linux_35
+ tags:
+ - conda-linux
+
+
+# Mac OSX + Python 2.7: Builds and tests
+build_macosx_27:
+ <<: *build_job
+ variables: &macosx_27_build_variables
+ PYTHON_VERSION: "2.7"
+ WHEEL_TAG: "py27"
+ tags:
+ - conda-macosx
+
+test_macosx_27:
+ <<: *test_job
+ variables: *macosx_27_build_variables
+ dependencies:
+ - build_macosx_27
+ tags:
+ - conda-macosx
+
+
+# Mac OSX + Python 3.4: Builds and tests
+build_macosx_34:
+ <<: *build_job
+ variables: &macosx_34_build_variables
+ PYTHON_VERSION: "3.4"
+ WHEEL_TAG: "py3"
+ tags:
+ - conda-macosx
+
+test_macosx_34:
+ <<: *test_job
+ variables: *macosx_34_build_variables
+ dependencies:
+ - build_macosx_34
+ tags:
+ - conda-macosx
+
+
+# Mac OSX + Python 3.5: Builds and tests
+build_macosx_35:
+ <<: *build_job
+ variables: &macosx_35_build_variables
+ PYTHON_VERSION: "3.5"
+ WHEEL_TAG: "py3"
+ tags:
+ - conda-macosx
+
+test_macosx_35:
+ <<: *test_job
+ variables: *macosx_35_build_variables
+ dependencies:
+ - build_macosx_35
+ tags:
+ - conda-macosx
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 38b238cb16ea2268c27c98354aaa92b4bacac4fc..0000000000000000000000000000000000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-language: python
-matrix:
- include:
- - python: 2.7
- env:
- - secure: 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
- - secure: 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
- - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
- - BOB_UPLOAD_WHEEL="--universal"
- - python: 3.3
- - python: 3.4
- - python: 3.5
-before_install:
-- sudo add-apt-repository -y ppa:biometrics/bob
-- sudo apt-get update -qq
-- sudo apt-get install -qq --force-yes libjpeg8-dev libnetpbm10-dev libpng12-dev libtiff4-dev libgif-dev libboost-all-dev libblitz1-dev libhdf5-serial-dev libvl-dev dvipng texlive-latex-base texlive-latex-extra texlive-math-extra texlive-latex-recommended texlive-fonts-recommended libatlas-dev libatlas-base-dev liblapack-dev gfortran
-- pip install --upgrade pip
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel sphinx nose numpy scipy matplotlib 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.bio.gmm import get_config; print(get_config())'
-- ./bin/coverage run --source=bob.bio.gmm ./bin/nosetests -sv
-- ./bin/sphinx-build -b doctest doc sphinx
-- ./bin/sphinx-build -b html doc sphinx
-after_success:
-- coveralls
-- wget https://raw.githubusercontent.com/bioidiap/bob.extension/master/scripts/upload-{sphinx,wheel}.sh
-- chmod a+x upload-sphinx.sh upload-wheel.sh
-- ./upload-sphinx.sh
-- ./upload-wheel.sh
diff --git a/COPYING b/COPYING
deleted file mode 100644
index 94a9ed024d3859793618152ea559a168bbcbb5e2..0000000000000000000000000000000000000000
--- a/COPYING
+++ /dev/null
@@ -1,674 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
- The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
- The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works. By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users. We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors. You can apply it to
-your programs, too.
-
- When we speak of free software, we are referring to freedom, not
-price. Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
-free programs, and that you know you can do these things.
-
- To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights. Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
-
- For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must pass on to the recipients the same
-freedoms that you received. You must make sure that they, too, receive
-or can get the source code. And you must show them these terms so they
-know their rights.
-
- Developers that use the GNU GPL protect your rights with two steps:
-(1) assert copyright on the software, and (2) offer you this License
-giving you legal permission to copy, distribute and/or modify it.
-
- For the developers' and authors' protection, the GPL clearly explains
-that there is no warranty for this free software. For both users' and
-authors' sake, the GPL requires that modified versions be marked as
-changed, so that their problems will not be attributed erroneously to
-authors of previous versions.
-
- Some devices are designed to deny users access to install or run
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- The precise terms and conditions for copying, distribution and
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- TERMS AND CONDITIONS
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diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..0c3160331a4198b350981b4eb39a1b2f851813f6
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,27 @@
+Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
+Written by Andre Anjos <andre.anjos@idiap.ch>
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. 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.
+
+3. Neither the name of the copyright holder 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.
diff --git a/MANIFEST.in b/MANIFEST.in
index 9e7fb7d306498dd0902979b5bc46fe0d02de3414..302f250d7ca47fc0236ba812a337315b30bbc658 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
-include README.rst bootstrap-buildout.py buildout.cfg COPYING version.txt requirements.txt
+include README.rst bootstrap-buildout.py buildout.cfg develop.cfg COPYING version.txt requirements.txt
recursive-include doc *.py *.rst
recursive-include bob/bio/gmm/test/data *.hdf5 *-dev
diff --git a/README.rst b/README.rst
index 367d64d859f7ae8450664f594d8cf04524a2614e..d041ab1057f84f549593c5bfa15d839ef01ab5e0 100644
--- a/README.rst
+++ b/README.rst
@@ -1,26 +1,26 @@
.. vim: set fileencoding=utf-8 :
-.. Andre Anjos <andre.anjos@idiap.ch>
-.. Thu 30 Jan 08:46:53 2014 CET
+.. Sun Aug 21 21:38:15 CEST 2016
-.. image:: http://img.shields.io/badge/docs-stable-yellow.png
+.. image:: http://img.shields.io/badge/docs-stable-yellow.svg
:target: http://pythonhosted.org/bob.bio.gmm/index.html
-.. image:: http://img.shields.io/badge/docs-latest-orange.png
- :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.bio.gmm/master/index.html
-.. image:: http://travis-ci.org/bioidiap/bob.bio.gmm.svg?branch=master
- :target: https://travis-ci.org/bioidiap/bob.bio.gmm?branch=master
-.. image:: https://coveralls.io/repos/bioidiap/bob.bio.gmm/badge.svg?branch=master
- :target: https://coveralls.io/r/bioidiap/bob.bio.gmm?branch=master
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
- :target: https://github.com/bioidiap/bob.bio.gmm/tree/master
-.. image:: http://img.shields.io/pypi/v/bob.bio.gmm.png
+.. image:: http://img.shields.io/badge/docs-latest-orange.svg
+ :target: https://www.idiap.ch/software/bob/docs/latest/bob/bob.bio.gmm/master/index.html
+.. image:: https://gitlab.idiap.ch/bob/bob.bio.gmm/badges/master/build.svg
+ :target: https://gitlab.idiap.ch/bob/bob.bio.gmm/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+ :target: https://gitlab.idiap.ch/bob/bob.bio.gmm
+.. image:: http://img.shields.io/pypi/v/bob.bio.gmm.svg
:target: https://pypi.python.org/pypi/bob.bio.gmm
-.. image:: http://img.shields.io/pypi/dm/bob.bio.gmm.png
+.. image:: http://img.shields.io/pypi/dm/bob.bio.gmm.svg
:target: https://pypi.python.org/pypi/bob.bio.gmm
-=============================================
+
+============================================
Run Gaussian mixture model based algorithms
-=============================================
+============================================
+This package is part of the signal-processing and machine learning toolbox
+Bob_.
This package is part of the ``bob.bio`` packages, which allow to run comparable and reproducible biometric recognition experiments on publicly available databases.
This package contains functionality to run biometric recognition algorithms based on Gaussian mixture models (GMMs).
@@ -31,15 +31,25 @@ In this package, utilities that are specific for using GMM-based algorithms are
* Scripts to run the training of these algorithms in parallel
+
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.bio.gmm/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.bio.gmm/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.
+Follow our `installation`_ instructions. Then, using the Python interpreter
+provided by the distribution, bootstrap and buildout this package::
+
+ $ python bootstrap-buildout.py
+ $ ./bin/buildout
+
+
+Contact
+-------
+
+For questions or reporting issues to this software package, contact our
+development `mailing list`_.
+
+.. Place your references here:
.. _bob: https://www.idiap.ch/software/bob
+.. _installation: https://www.idiap.ch/software/bob/install
+.. _mailing list: https://www.idiap.ch/software/bob/discuss
diff --git a/bob/bio/gmm/algorithm/__init__.py b/bob/bio/gmm/algorithm/__init__.py
index 18612fe9cbde0c3e590e946bd0768013a5686231..c64ce2b4a62cb889ef39ea9df2d6ae6da07a1f35 100644
--- a/bob/bio/gmm/algorithm/__init__.py
+++ b/bob/bio/gmm/algorithm/__init__.py
@@ -4,4 +4,24 @@ from .ISV import ISV
from .IVector import IVector
# gets sphinx autodoc done right - don't remove it
+def __appropriate__(*args):
+ """Says object was actually declared here, and not in the import module.
+ Fixing sphinx warnings of not being able to find classes, when path is shortened.
+ Parameters:
+
+ *args: An iterable of objects to modify
+
+ Resolves `Sphinx referencing issues
+ <https://github.com/sphinx-doc/sphinx/issues/3048>`
+ """
+
+ for obj in args: obj.__module__ = __name__
+
+__appropriate__(
+ GMM,
+ GMMRegular,
+ JFA,
+ ISV,
+ IVector,
+ )
__all__ = [_ for _ in dir() if not _.startswith('_')]
diff --git a/bob/bio/gmm/script/verify_gmm.py b/bob/bio/gmm/script/verify_gmm.py
index c186a494322b16ee4476e94cef9d3290b4cfb612..5f7a69c269c7d1fd36f8332531b5c23d874d0ee2 100644
--- a/bob/bio/gmm/script/verify_gmm.py
+++ b/bob/bio/gmm/script/verify_gmm.py
@@ -58,6 +58,13 @@ def parse_arguments(command_line_parameters, exclude_resources_from = []):
if tools.base(args.algorithm).__class__ not in (algorithm.GMM, algorithm.GMMRegular):
raise ValueError("The given algorithm %s is not a (pure) GMM algorithm" % type(args.algorithm))
+ # check if one of the parameters is given wothout the sub-task
+ if args.sub_task is None:
+ if args.iteration is not None: raise ValueError("The option --iteration is an internal option and cannot be used to define experiments")
+ if args.model_type is not None: raise ValueError("The option --model-type is an internal option and cannot be used to define experiments")
+ if args.score_type is not None: raise ValueError("The option --score-type is an internal option and cannot be used to define experiments")
+ if args.group is not None: raise ValueError("The option --group is an internal option and cannot be used to define experiments; did you mean to use --groups?")
+
return args
def add_gmm_jobs(args, job_ids, deps, submitter):
diff --git a/bob/bio/gmm/script/verify_isv.py b/bob/bio/gmm/script/verify_isv.py
index 61804f8e74d8ee46c626a043be07464aede34d19..9b390cdd42600810c99eb4074f5920184c1ae251 100644
--- a/bob/bio/gmm/script/verify_isv.py
+++ b/bob/bio/gmm/script/verify_isv.py
@@ -58,6 +58,13 @@ def parse_arguments(command_line_parameters, exclude_resources_from = []):
if tools.base(args.algorithm).__class__ != algorithm.ISV:
raise ValueError("The given algorithm %s is not a (pure) ISV algorithm" % type(args.algorithm))
+ # check if one of the parameters is given wothout the sub-task
+ if args.sub_task is None:
+ if args.iteration is not None: raise ValueError("The option --iteration is an internal option and cannot be used to define experiments")
+ if args.model_type is not None: raise ValueError("The option --model-type is an internal option and cannot be used to define experiments")
+ if args.score_type is not None: raise ValueError("The option --score-type is an internal option and cannot be used to define experiments")
+ if args.group is not None: raise ValueError("The option --group is an internal option and cannot be used to define experiments; did you mean to use --groups?")
+
return args
from .verify_gmm import add_gmm_jobs
diff --git a/bob/bio/gmm/script/verify_ivector.py b/bob/bio/gmm/script/verify_ivector.py
index c3a3a33c8038632643ca60244226c5a9162273bd..bafedfc1c40e13bd8b7caf4ec268f6d779f2b413 100644
--- a/bob/bio/gmm/script/verify_ivector.py
+++ b/bob/bio/gmm/script/verify_ivector.py
@@ -23,7 +23,7 @@ def parse_arguments(command_line_parameters, exclude_resources_from = []):
tools.add_parallel_gmm_options(parsers, sub_module = 'ivector')
# override some parameters
- parsers['config'].add_argument('-a', '--algorithm', metavar = 'x', nargs = '+', default = ['ivector'],
+ parsers['config'].add_argument('-a', '--algorithm', metavar = 'x', nargs = '+', default = ['ivector-cosine'],
help = 'Face recognition; only GMM-related algorithms are allowed')
@@ -58,6 +58,13 @@ def parse_arguments(command_line_parameters, exclude_resources_from = []):
if tools.base(args.algorithm).__class__ != algorithm.IVector:
raise ValueError("The given algorithm %s is not a (pure) IVector algorithm" % type(args.algorithm))
+ # check if one of the parameters is given wothout the sub-task
+ if args.sub_task is None:
+ if args.iteration is not None: raise ValueError("The option --iteration is an internal option and cannot be used to define experiments")
+ if args.model_type is not None: raise ValueError("The option --model-type is an internal option and cannot be used to define experiments")
+ if args.score_type is not None: raise ValueError("The option --score-type is an internal option and cannot be used to define experiments")
+ if args.group is not None: raise ValueError("The option --group is an internal option and cannot be used to define experiments; did you mean to use --groups?")
+
return args
from .verify_gmm import add_gmm_jobs
diff --git a/bob/bio/gmm/test/test_scripts.py b/bob/bio/gmm/test/test_scripts.py
index 742ec4cdfd63a14493724668f5b46398eaa8ff65..603e609ffbb64f812a0eebb648266178a46e66ea 100644
--- a/bob/bio/gmm/test/test_scripts.py
+++ b/bob/bio/gmm/test/test_scripts.py
@@ -1,11 +1,10 @@
-from __future__ import print_function
-
import bob.measure
import os
import shutil
import tempfile
import numpy
+import nose
import bob.io.image
import bob.bio.base
@@ -75,8 +74,6 @@ def test_gmm_sequential():
'--preferred-package', 'bob.bio.gmm'
]
- print (bob.bio.base.tools.command_line(parameters))
-
_verify(parameters, test_dir, 'test_gmm_sequential', ref_modifier='-gmm')
@@ -100,8 +97,6 @@ def test_gmm_parallel():
'--preferred-package', 'bob.bio.gmm'
]
- print (bob.bio.base.tools.command_line(parameters))
-
_verify(parameters, test_dir, 'test_gmm_parallel', executable=main, ref_modifier='-gmm')
@@ -120,8 +115,6 @@ def test_isv_sequential():
'--preferred-package', 'bob.bio.gmm'
]
- print (bob.bio.base.tools.command_line(parameters))
-
_verify(parameters, test_dir, 'test_isv_sequential', ref_modifier='-isv')
@@ -145,8 +138,6 @@ def test_isv_parallel():
'--preferred-package', 'bob.bio.gmm'
]
- print (bob.bio.base.tools.command_line(parameters))
-
_verify(parameters, test_dir, 'test_isv_parallel', executable=main, ref_modifier='-isv')
@@ -164,7 +155,7 @@ def test_ivector_cosine_sequential():
'--result-directory', test_dir,
'--preferred-package', 'bob.bio.gmm'
]
- print (bob.bio.base.tools.command_line(parameters))
+
_verify(parameters, test_dir, 'test_ivector_cosine_sequential', ref_modifier='-ivector-cosine')
@@ -187,7 +178,7 @@ def test_ivector_cosine_parallel():
'--result-directory', test_dir,
'--preferred-package', 'bob.bio.gmm'
]
- print (bob.bio.base.tools.command_line(parameters))
+
_verify(parameters, test_dir, 'test_ivector_cosine_parallel', executable=main, ref_modifier='-ivector-cosine')
def test_ivector_lda_wccn_plda_sequential():
@@ -203,7 +194,7 @@ def test_ivector_lda_wccn_plda_sequential():
'--temp-directory', test_dir,
'--result-directory', test_dir
]
- print (bob.bio.base.tools.command_line(parameters))
+
_verify(parameters, test_dir, 'test_ivector_lda_wccn_plda_sequential', ref_modifier='-ivector-lda-wccn-plda')
@@ -226,5 +217,39 @@ def test_ivector_lda_wccn_plda_parallel():
'--result-directory', test_dir,
'--preferred-package', 'bob.bio.gmm'
]
- print (bob.bio.base.tools.command_line(parameters))
+
_verify(parameters, test_dir, 'test_ivector_lda_wccn_plda_parallel', executable=main, ref_modifier='-ivector-lda-wccn-plda')
+
+
+def test_internal_raises():
+ test_dir = tempfile.mkdtemp(prefix='bobtest_')
+ test_database = os.path.join(test_dir, "submitted.sql3")
+ # define dummy parameters
+ parameters = [
+ '-d', 'dummy',
+ '-p', 'dummy',
+ '-e', 'dummy2d',
+ '-g', 'bob.bio.base.grid.Grid(grid_type = "local", number_of_parallel_processes = 2, scheduler_sleep_time = 0.1)', '-G', test_database, '--run-local-scheduler', '--stop-on-failure',
+ '--import', 'bob.bio.gmm', 'bob.io.image',
+ '--clean-intermediate',
+ '--zt-norm',
+ '-vs', 'test_raises',
+ '--temp-directory', test_dir,
+ '--result-directory', test_dir,
+ '--preferred-package', 'bob.bio.gmm'
+ ]
+
+ from bob.bio.gmm.script.verify_gmm import main as gmm
+ from bob.bio.gmm.script.verify_isv import main as isv
+ from bob.bio.gmm.script.verify_ivector import main as ivector
+
+ for script, algorithm in (
+ (gmm, "bob.bio.gmm.algorithm.GMM(2, 2, 2)"),
+ (isv, "bob.bio.gmm.algorithm.ISV(10, number_of_gaussians=2, kmeans_training_iterations=2, gmm_training_iterations=2, isv_training_iterations=2)"),
+ (ivector, "bob.bio.gmm.algorithm.IVector(10, number_of_gaussians=2, kmeans_training_iterations=2, gmm_training_iterations=2, tv_training_iterations=2, use_lda=True, use_wccn=True, use_plda=True, lda_dim=2, plda_dim_F=2, plda_dim_G=2, plda_training_iterations=2)")):
+
+ for option, value in (("--iteration", "0"), ("--group", "dev"), ("--model-type", "N"), ("--score-type", "A")):
+ internal = parameters + ["--algorithm", algorithm, option, value]
+
+ nose.tools.assert_raises(ValueError, script, internal)
+ shutil.rmtree(test_dir)
diff --git a/bootstrap-buildout.py b/bootstrap-buildout.py
index a629566735c1c84fbec7173f0f30015b2b432512..a4599211f741c468cd37a29861d1c7f2c3a641d1 100644
--- a/bootstrap-buildout.py
+++ b/bootstrap-buildout.py
@@ -25,7 +25,10 @@ import tempfile
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]
@@ -40,8 +43,9 @@ 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("--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,
@@ -59,25 +63,33 @@ parser.add_option("-f", "--find-links",
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 @@ if not options.allow_site_packages:
# 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 @@ for path in sys.path:
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 @@ find_links = os.environ.get(
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 @@ if 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])
diff --git a/buildout.cfg b/buildout.cfg
index a07d6e5d3bcbbf0d07344841d005c9a847a6fac6..6f84c9a7d526317e56e1c9243e49d21c08fa1049 100644
--- a/buildout.cfg
+++ b/buildout.cfg
@@ -1,55 +1,13 @@
; vim: set fileencoding=utf-8 :
-; Manuel Guenther <manuel.guenther@idiap.ch>
-; Thu Oct 9 16:51:06 CEST 2014
+; Sun Aug 21 21:38:14 CEST 2016
[buildout]
parts = scripts
+develop = .
eggs = bob.bio.gmm
- gridtk
-
extensions = bob.buildout
- mr.developer
-auto-checkout = *
-develop = src/bob.extension
- src/bob.blitz
- src/bob.core
- src/bob.io.base
- src/bob.learn.activation
- src/bob.math
- src/bob.learn.linear
- src/bob.sp
- src/bob.learn.em
- src/bob.measure
- src/bob.db.base
- src/bob.db.verification.utils
- src/bob.db.verification.filelist
- src/bob.db.atnt
- src/bob.io.image
- src/bob.bio.base
- .
-
-; options for bob.buildout
-debug = true
-verbose = true
newest = false
-
-[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.learn.activation = git https://github.com/bioidiap/bob.learn.activation
-bob.math = git https://github.com/bioidiap/bob.math
-bob.sp = git https://github.com/bioidiap/bob.sp
-bob.learn.linear = git https://github.com/bioidiap/bob.learn.linear
-bob.learn.em = git https://github.com/bioidiap/bob.learn.em
-bob.measure = git https://github.com/bioidiap/bob.measure
-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
-bob.db.atnt = git https://github.com/bioidiap/bob.db.atnt
-bob.io.image = git https://github.com/bioidiap/bob.io.image
-bob.bio.base = git https://github.com/bioidiap/bob.bio.base
+verbose = true
[scripts]
recipe = bob.buildout:scripts
diff --git a/develop.cfg b/develop.cfg
new file mode 100644
index 0000000000000000000000000000000000000000..497ac8e077aff0cfc389d708c27da2d1b1d79b04
--- /dev/null
+++ b/develop.cfg
@@ -0,0 +1,52 @@
+; vim: set fileencoding=utf-8 :
+; Manuel Guenther <manuel.guenther@idiap.ch>
+; Thu Oct 9 16:51:06 CEST 2014
+
+[buildout]
+parts = scripts
+eggs = bob.bio.gmm
+ gridtk
+
+extensions = bob.buildout
+ mr.developer
+auto-checkout = *
+develop = src/bob.extension
+ src/bob.blitz
+ src/bob.core
+ src/bob.io.base
+ src/bob.learn.activation
+ src/bob.math
+ src/bob.learn.linear
+ src/bob.sp
+ src/bob.learn.em
+ src/bob.measure
+ src/bob.db.base
+ src/bob.db.atnt
+ src/bob.io.image
+ src/bob.bio.base
+ .
+
+; options for bob.buildout
+debug = true
+verbose = true
+newest = false
+
+[sources]
+bob.extension = git https://gitlab.idiap.ch/bob/bob.extension
+bob.blitz = git https://gitlab.idiap.ch/bob/bob.blitz
+bob.core = git https://gitlab.idiap.ch/bob/bob.core
+bob.io.base = git https://gitlab.idiap.ch/bob/bob.io.base
+bob.learn.activation = git https://gitlab.idiap.ch/bob/bob.learn.activation
+bob.math = git https://gitlab.idiap.ch/bob/bob.math
+bob.sp = git https://gitlab.idiap.ch/bob/bob.sp
+bob.learn.linear = git https://gitlab.idiap.ch/bob/bob.learn.linear
+bob.learn.em = git https://gitlab.idiap.ch/bob/bob.learn.em
+bob.measure = git https://gitlab.idiap.ch/bob/bob.measure
+bob.db.base = git https://gitlab.idiap.ch/bob/bob.db.base
+bob.db.atnt = git https://gitlab.idiap.ch/bob/bob.db.atnt
+bob.io.image = git https://gitlab.idiap.ch/bob/bob.io.image
+bob.bio.base = git https://gitlab.idiap.ch/bob/bob.bio.base
+
+[scripts]
+recipe = bob.buildout:scripts
+dependent-scripts = true
diff --git a/doc/conf.py b/doc/conf.py
index fee975858837048a52cbdeaa3bea5717dbe75767..39120fc21288f402af36bfab544d5be29bd84b68 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -1,46 +1,67 @@
#!/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) 2011-2014 Idiap Research Institute, Martigny, Switzerland
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'
+needs_sphinx = '1.3'
# 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',
- ]
+ 'sphinx.ext.todo',
+ 'sphinx.ext.coverage',
+ 'sphinx.ext.ifconfig',
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.autosummary',
+ 'sphinx.ext.doctest',
+ 'sphinx.ext.graphviz',
+ 'sphinx.ext.intersphinx',
+ 'sphinx.ext.napoleon',
+ 'sphinx.ext.viewcode',
+ ]
-# The viewcode extension appeared only on Sphinx >= 1.0.0
import sphinx
-if sphinx.__version__ >= "1.0":
- extensions.append('sphinx.ext.viewcode')
+if sphinx.__version__ >= "1.4.1":
+ extensions.append('sphinx.ext.imgmath')
+ imgmath_image_format = 'svg'
+else:
+ extensions.append('sphinx.ext.pngmath')
+
+# Be picky about warnings
+nitpicky = True
+
+# Ignores stuff we can't easily resolve on other project's sphinx manuals
+nitpick_ignore = []
+
+# Allows the user to override warnings from a separate file
+if os.path.exists('nitpick-exceptions.txt'):
+ for line in open('nitpick-exceptions.txt'):
+ if line.strip() == "" or line.startswith("#"):
+ continue
+ dtype, target = line.split(None, 1)
+ target = target.strip()
+ try: # python 2.x
+ target = unicode(target)
+ except NameError:
+ pass
+ nitpick_ignore.append((dtype, target))
# Always includes todos
todo_include_todos = True
+# Generates auto-summary automatically
+autosummary_generate = True
+
+# Create numbers on figures with captions
+numfig = 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
@@ -58,12 +79,12 @@ source_suffix = '.rst'
master_doc = 'index'
# General information about the project.
-project = u'Gaussian Mixture Model based algorithms for bob.bio'
+project = u'bob.bio.gmm'
import time
copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
# Grab the setup entry
-distribution = pkg_resources.require('bob.bio.gmm')[0]
+distribution = pkg_resources.require(project)[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
@@ -86,7 +107,7 @@ release = distribution.version
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
-exclude_patterns = ['links.rst', 'references.rst']
+exclude_patterns = ['links.rst']
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
@@ -108,13 +129,18 @@ pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
+# Some variables which are useful for generated material
+project_variable = project.replace('.', '_')
+short_description = u'Tools for running biometric recognition experiments using GMM-based approximation'
+owner = [u'Idiap Research Institute']
+
# -- 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'
+import sphinx_rtd_theme
+html_theme = 'sphinx_rtd_theme'
# 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
@@ -122,14 +148,14 @@ if sphinx.__version__ >= "1.0":
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+html_theme_path = [sphinx_rtd_theme.get_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'
+#html_short_title = project_variable
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
@@ -187,73 +213,53 @@ html_favicon = 'img/favicon.ico'
#html_file_suffix = None
# Output file base name for HTML help builder.
-htmlhelp_basename = 'bob_bio_gmm_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', 'bob_bio_gmm.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 = ''
+htmlhelp_basename = project_variable + u'_doc'
-# 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
+# -- Post configuration --------------------------------------------------------
# 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.bio.gmm', u'Gaussian Mixture Models in bob.bio Documentation', [u'Idiap Research Institute'], 1)
-]
+rst_epilog = """
+.. |project| replace:: Bob
+.. |version| replace:: %s
+.. |current-year| date:: %%Y
+""" % (version,)
# Default processing flags for sphinx
-autoclass_content = 'both'
+autoclass_content = 'class'
autodoc_member_order = 'bysource'
-autodoc_default_flags = ['members', 'undoc-members', 'inherited-members', 'show-inheritance']
+autodoc_default_flags = [
+ 'members',
+ 'undoc-members',
+ 'inherited-members',
+ 'show-inheritance',
+ ]
# For inter-documentation mapping:
-from bob.extension.utils import link_documentation
-intersphinx_mapping = link_documentation(['python', 'numpy', 'bob.io.gmm'])
-
-
-def skip(app, what, name, obj, skip, options):
- # Do not skip the __call__ and the __str__ functions as we have special implementations for them.
- if name in ("__call__"):
- return False
- return skip
+from bob.extension.utils import link_documentation, load_requirements
+sphinx_requirements = "extra-intersphinx.txt"
+if os.path.exists(sphinx_requirements):
+ intersphinx_mapping = link_documentation(additional_packages=load_requirements(sphinx_requirements))
+else:
+ intersphinx_mapping = link_documentation()
+
+
+# We want to remove all private (i.e. _. or __.__) members
+# that are not in the list of accepted functions
+accepted_private_functions = ['__array__']
+
+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 skip
+ else:
+ # test if the method is documented
+ if not hasattr(obj, '__doc__') or not obj.__doc__:
+ return skip
+ return False
def setup(app):
- app.connect("autodoc-skip-member", skip)
+ app.connect('autodoc-skip-member', member_function_test)
diff --git a/doc/img/logo.png b/doc/img/logo.png
index b9dd573a01019afd1af58a881996930e5212699d..b60858a7068bf45c1ed8e3da12fe244ccdcfe85d 100644
Binary files a/doc/img/logo.png and b/doc/img/logo.png differ
diff --git a/doc/nitpick-exceptions.txt b/doc/nitpick-exceptions.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14c3632ef2dc0c19608a93a7af18fdac75d55333
--- /dev/null
+++ b/doc/nitpick-exceptions.txt
@@ -0,0 +1 @@
+py:exc ValueError
diff --git a/doc/parallel.rst b/doc/parallel.rst
index 1709e876bee5c3599cbd970625aaedd9e2ed30b2..f6c59f0a5f2a789c7b8f957e50cebd59d29f4f68 100644
--- a/doc/parallel.rst
+++ b/doc/parallel.rst
@@ -14,7 +14,7 @@ These scripts integrate perfectly into the ``bob.bio`` packages.
Particularly, they have exactly the same set of options as documented in :ref:`bob.bio.base.experiments`.
In fact, the scripts above only run in parallelized mode, i.e., either the ``--grid`` or ``--parallel`` option is required.
-During the submission of the jobs, several hundred jobs might be created (depending on the ``number_of_..._training_iterations`` that you specify in the :py:class:`bob.bio.gmm.algorithms.GMM` constructor).
+During the submission of the jobs, several hundred jobs might be created (depending on the ``number_of_..._training_iterations`` that you specify in the :py:class:`bob.bio.gmm.algorithm.GMM` constructor).
However, after the training has finished, it is possible to use the normal ``./bin/verify.py`` script to run similar experiments, e.g., if you want to change the protocol of your experiment.
.. todo:: improve the documentation of the parallelized scripts.
diff --git a/requirements.txt b/requirements.txt
index cc2aba6c358ed80121c5372774cb69db1caa6c66..1feea38a47ba8ce0b1a3514e48c31219cd136d09 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -10,9 +10,5 @@ bob.sp
bob.learn.em
bob.measure
bob.db.base
-bob.db.verification.utils
-bob.db.verification.filelist
-bob.db.atnt # for test purposes
-bob.io.image # for test purposes
bob.bio.base
matplotlib # for plotting
diff --git a/setup.py b/setup.py
index 76960817833291a3b511ca67a6720bc7933da098..12a07ab2bbda996fce6c958fdb247f883820e94c 100644
--- a/setup.py
+++ b/setup.py
@@ -49,8 +49,8 @@ setup(
version = open("version.txt").read().rstrip(),
description = 'Tools for running biometric recognition experiments using GMM-based approximation',
- url = 'https://www.github.com/bioidiap/bob.bio.gmm',
- license = 'GPLv3',
+ url = 'https://gitlab.idiap.ch/bob/bob.bio.gmm',
+ license = 'BSD',
author = '<YourName>',
author_email = '<YourEmail>',
keywords = 'bob, biometric recognition, evaluation',
@@ -80,7 +80,7 @@ setup(
#
# Our database packages are good examples of namespace implementations
# using several layers. You can check them out here:
- # https://github.com/idiap/bob/wiki/Satellite-Packages
+ # https://www.idiap.ch/software/bob/packages
# This entry defines which scripts you will have inside the 'bin' directory
@@ -137,7 +137,7 @@ setup(
'Framework :: Bob',
'Development Status :: 3 - Alpha',
'Intended Audience :: Developers',
- 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+ 'License :: OSI Approved :: BSD License',
'Natural Language :: English',
'Programming Language :: Python',
'Topic :: Scientific/Engineering :: Artificial Intelligence',
diff --git a/test-requirements.txt b/test-requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b43739e4acef80d6cc73773077529240de759eef
--- /dev/null
+++ b/test-requirements.txt
@@ -0,0 +1,2 @@
+bob.db.atnt # for test purposes
+bob.io.image # for test purposes
\ No newline at end of file
diff --git a/version.txt b/version.txt
index 7c000e15dfb84e6feeb14890c35bc3248fa645a4..f044c2aa769acd6ae1b2a2b3634ef8d97122e238 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-2.0.6b0
\ No newline at end of file
+3.0.1b0
\ No newline at end of file