diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..293eb7bc13967f6f3529d47f00468345f5470d28
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,275 @@
+# This build file is defined in two parts: 1) a generic set of instructions you
+# probably **don't** need to change and 2) a part you may have to tune to your
+# project. It heavily uses template features from YAML to help you in only
+# changing a minimal part of it and avoid code duplication to a maximum while
+# still providing a nice pipeline display on your package.
+
+
+# 1) Generic instructions (only change if you know what you're doing)
+# -------------------------------------------------------------------
+
+# Definition of our build pipeline
+stages:
+ - build
+ - test
+ - docs
+ - wheels
+
+
+# Global variables
+variables:
+ CONDA_PREFIX: env
+
+
+# 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
+ - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/7/raw | tr -d '\r' > bootstrap-conda.sh
+ - chmod 755 ./bootstrap-conda.sh
+ - ./bootstrap-conda.sh ${CONDA_FOLDER} ${PYTHON_VER} ${CONDA_PREFIX}
+ variables: &build_variables
+ BOB_DOCUMENTATION_SERVER: "http://www.idiap.ch/software/bob/docs/latest/bob/%s/master/"
+ script:
+ - BOB_PREFIX_PATH=${CONDA_FOLDER}/envs/`cat ${CONDA_FOLDER}/envs/latest-devel-${PYTHON_VER}.txt` ./bin/buildout
+ - ./bin/sphinx-build doc sphinx
+ - ./bin/python setup.py bdist_wheel
+ after_script:
+ - rm -rf ${CONDA_PREFIX}
+ artifacts:
+ expire_in: 1 day
+ paths:
+ - bootstrap-conda.sh
+ - dist/
+ - sphinx/
+
+
+# Template for building on a Linux machine
+.build_linux_template: &linux_build_job
+ <<: *build_job
+ variables: &linux_build_variables
+ <<: *build_variables
+ CONDA_FOLDER: "/local/conda"
+ CFLAGS: "-D_GLIBCXX_USE_CXX11_ABI=0 -coverage"
+ CXXFLAGS: "-D_GLIBCXX_USE_CXX11_ABI=0 -coverage"
+
+
+# Template for building on a Mac OSX machine
+.build_mac_template: &macosx_build_job
+ <<: *build_job
+ variables: &macosx_build_variables
+ <<: *build_variables
+ CONDA_FOLDER: "/opt/conda"
+ MACOSX_DEPLOYMENT_TARGET: "10.9"
+ CFLAGS: "-pthread -coverage"
+ CXXFLAGS: "-pthread -coverage"
+ LDFLAGS: "-lpthread"
+
+
+# Template for the test stage - re-install from uploaded wheels
+# Needs to run on all supported architectures, platforms and python versions
+.test_template: &test_job
+ stage: test
+ before_script:
+ - ./bootstrap-conda.sh ${CONDA_FOLDER} ${PYTHON_VER} ${CONDA_PREFIX}
+ - source ${CONDA_FOLDER}/bin/activate ${CONDA_PREFIX}
+ - pip install --use-wheel --no-index --pre dist/*.whl
+ script:
+ - cd ${CONDA_PREFIX}
+ - python -c "from ${CI_PROJECT_NAME} import get_config; print(get_config())"
+ - coverage run --source=${CI_PROJECT_NAME} ./bin/nosetests -sv ${CI_PROJECT_NAME}
+ - coverage report
+ - sphinx-build -b doctest ../doc ../sphinx
+ after_script:
+ - rm -rf ${CONDA_PREFIX}
+
+
+# Template for the wheel uploading stage
+# Needs to run against one combination of python 2.x and 3.x if it is a python
+# only package, otherwise, needs to run in both pythons to all supported
+# architectures (Linux and Mac OSX 64-bit)
+.wheels_template: &wheels_job
+ stage: wheels
+ only:
+ - master
+ - tags
+ before_script:
+ - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/8/raw | tr -d '\r' > upload-wheel.sh
+ - chmod 755 upload-wheel.sh
+ script:
+ - ./upload-wheel.sh
+
+
+# Template for (latest) documentation upload stage
+# Only one real job needs to do this
+.docs_template: &docs_job
+ stage: docs
+ only:
+ - master
+ before_script:
+ - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/9/raw | tr -d '\r' > upload-sphinx.sh
+ - chmod 755 upload-sphinx.sh
+ script:
+ - ./upload-sphinx.sh
+
+
+# 2) Package specific instructions (you may tune this if needed)
+# --------------------------------------------------------------
+
+# Linux + Python 2.7: Builds and tests
+build_linux_27:
+ <<: *linux_build_job
+ variables: &linux_27_build_variables
+ <<: *linux_build_variables
+ PYTHON_VER: "2.7"
+ 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
+ dependencies:
+ - build_linux_27
+ tags:
+ - conda-linux
+
+
+# Linux + Python 3.4: Builds and tests
+build_linux_34:
+ <<: *linux_build_job
+ variables: &linux_34_build_variables
+ <<: *linux_build_variables
+ PYTHON_VER: "3.4"
+ tags:
+ - conda-linux
+
+test_linux_34:
+ <<: *test_job
+ variables: *linux_34_build_variables
+ dependencies:
+ - build_linux_34
+ tags:
+ - conda-linux
+
+wheels_linux_34:
+ <<: *wheels_job
+ dependencies:
+ - build_linux_34
+ tags:
+ - conda-linux
+
+
+# Linux + Python 3.5: Builds and tests
+build_linux_35:
+ <<: *linux_build_job
+ variables: &linux_35_build_variables
+ <<: *linux_build_variables
+ PYTHON_VER: "3.5"
+ 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
+ dependencies:
+ - build_linux_35
+ tags:
+ - conda-linux
+
+docs_linux_35:
+ <<: *docs_job
+ dependencies:
+ - build_linux_35
+ tags:
+ - conda-linux
+
+
+# Mac OSX + Python 2.7: Builds, tests and uploads the wheel
+build_macosx_27:
+ <<: *macosx_build_job
+ variables: &macosx_27_build_variables
+ <<: *macosx_build_variables
+ PYTHON_VER: "2.7"
+ tags:
+ - conda-macosx
+
+test_macosx_27:
+ <<: *test_job
+ variables: *macosx_27_build_variables
+ dependencies:
+ - build_macosx_27
+ tags:
+ - conda-macosx
+
+wheels_macosx_27:
+ <<: *wheels_job
+ dependencies:
+ - build_macosx_27
+ tags:
+ - conda-macosx
+
+
+# Mac OSX + Python 3.4: Builds and tests
+build_macosx_34:
+ <<: *macosx_build_job
+ variables: &macosx_34_build_variables
+ <<: *macosx_build_variables
+ PYTHON_VER: "3.4"
+ tags:
+ - conda-macosx
+
+test_macosx_34:
+ <<: *test_job
+ variables: *macosx_34_build_variables
+ dependencies:
+ - build_macosx_34
+ tags:
+ - conda-macosx
+
+wheels_macosx_34:
+ <<: *wheels_job
+ dependencies:
+ - build_macosx_34
+ tags:
+ - conda-macosx
+
+
+# Mac OSX + Python 3.5: Builds, tests, uploads the wheel and the latest docs
+build_macosx_35:
+ <<: *macosx_build_job
+ variables: &macosx_35_build_variables
+ <<: *macosx_build_variables
+ PYTHON_VER: "3.5"
+ tags:
+ - conda-macosx
+
+test_macosx_35:
+ <<: *test_job
+ variables: *macosx_35_build_variables
+ dependencies:
+ - build_macosx_35
+ tags:
+ - conda-macosx
+
+wheels_macosx_35:
+ <<: *wheels_job
+ dependencies:
+ - build_macosx_35
+ tags:
+ - conda-macosx
\ No newline at end of file
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index c702afe84ac4ed5ecd4b0a2816d45045338644f8..0000000000000000000000000000000000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-language: python
-env:
- global:
- - secure: eVYI9c4v/gdgMu9/HUrdOljH6xoWucjRNlQMfh24LA3g6j1dr52+SdCP59mzFqBiAIR8eBtipIkit23sQDn+ulw3bJSrLszXsWCKGywLVG/6QtgsqN9J17/RbUA2ZnfA86famA6Z4+CtJbW7nQPYidRQshPC85iiekftN9DwdeQ=
- - secure: a+hf3j24x0fyP8OP/8IiIp5aMn+GfYxf97vWtJV1U76J8eGNLyj+n/AsPx4y6OpRWy2qTf/90W5TxU/ruRxKRl3j78+W2sYCI1LiQIlNlVX6tMrLnm2YS5zvwH3jICCmRUmY7d0Vc5MrqBRoKnmA+1QqyDrdiCjWkNSh6Jcn5KA=
- - BOB_UPLOAD_WHEEL=1
-matrix:
- include:
- - python: 2.7
- env:
- - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
- - 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 libboost-all-dev libblitz1-dev libhdf5-serial-dev libatlas-dev libatlas-base-dev liblapack-dev texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended dvipng texlive-latex-base texlive-math-extra
-- pip install --upgrade pip
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel sphinx nose numpy matplotlib coverage cpp-coveralls
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel --pre -r requirements.txt coveralls
-install:
-- python bootstrap-buildout.py
-- CPPFLAGS=--coverage LDFLAGS=--coverage ./bin/buildout buildout:debug=false buildout:develop=. buildout:extensions=bob.buildout buildout:auto-checkout=
-script:
-- ./bin/python -c 'import pkg_resources; from bob.learn.em import get_config; print(get_config())'
-- ./bin/coverage run --source=bob.learn.em ./bin/nosetests -sv
-- ./bin/sphinx-build -b doctest doc sphinx
-- ./bin/sphinx-build -b html doc sphinx
-after_success:
-- cpp-coveralls --build-root=`pwd` --exclude=src --exclude-pattern=".*Compiler.*" --dump=cpp_cov.json
-- coveralls --merge=cpp_cov.json
-- 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/LICENSE b/LICENSE
index 7ac8998a23ffd779d3e33b4fa0bc6c1301353c81..bd46ce15068f2d3b5a1b23ac6c68a33ec808d95d 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,16 +1,19 @@
-Copyright (c) 2013, Andre Anjos - Idiap Research Institute
-All rights reserved.
+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:
-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.
+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
@@ -21,4 +24,4 @@ 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.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
\ No newline at end of file
diff --git a/MANIFEST.in b/MANIFEST.in
index f333d7a38cb897e7f6f318e8bb111f8bc96799a5..8901be6b54433d29ed0ecc7940d12e5636d63367 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,4 @@
-include LICENSE README.rst bootstrap-buildout.py buildout.cfg requirements.txt version.txt
+include LICENSE README.rst bootstrap-buildout.py buildout.cfg develop.cfg requirements.txt version.txt
recursive-include doc conf.py *.rst
recursive-include bob/learn/em *.cpp *.h
recursive-include bob/learn/em/data *.*
diff --git a/README.rst b/README.rst
index 9ce1a064a70b535f7f6d6325148115372e68d6c3..8ad25551c2629497ecb4f8632fdb589fa206a68d 100644
--- a/README.rst
+++ b/README.rst
@@ -1,29 +1,39 @@
.. vim: set fileencoding=utf-8 :
-.. Andre Anjos <andre.anjos@idiap.ch>
-.. Thu 22 May 2014 15:39:03 CEST
+.. Mon 15 Aug 2016 09:48:28 CEST
.. image:: http://img.shields.io/badge/docs-stable-yellow.png
:target: http://pythonhosted.org/bob.learn.em/index.html
.. image:: http://img.shields.io/badge/docs-latest-orange.png
:target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.learn.em/master/index.html
-.. image:: https://travis-ci.org/bioidiap/bob.learn.em.svg?branch=master
- :target: https://travis-ci.org/bioidiap/bob.learn.em?branch=master
-.. image:: https://coveralls.io/repos/bioidiap/bob.learn.em/badge.svg?branch=master
- :target: https://coveralls.io/r/bioidiap/bob.learn.em?branch=master
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
- :target: https://github.com/bioidiap/bob.learn.em/tree/master
+.. image:: https://gitlab.idiap.ch/bob/bob.learn.em/badges/master/build.svg
+ :target: https://gitlab.idiap.ch/bob/bob.learn.em/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+ :target: https://gitlab.idiap.ch/bob/bob.learn.em
.. image:: http://img.shields.io/pypi/v/bob.learn.em.png
:target: https://pypi.python.org/pypi/bob.learn.em
.. image:: http://img.shields.io/pypi/dm/bob.learn.em.png
:target: https://pypi.python.org/pypi/bob.learn.em
-==================================================
- Expectation Maximization Machine Learning Tools
-==================================================
-The EM algorithm is an iterative method that estimates parameters for statistical models, where the model depends on unobserved latent variables. The EM iteration alternates between performing an expectation (E) step, which creates a function for the expectation of the log-likelihood evaluated using the current estimate for the parameters, and a maximization (M) step, which computes parameters maximizing the expected log-likelihood found on the E step. These parameter-estimates are then used to determine the distribution of the latent variables in the next E step.
+=================================================
+ Expectation Maximization Machine Learning Tools
+=================================================
+
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It contains routines for learning probabilistic models via Expectation
+Maximization (EM).
+
+The EM algorithm is an iterative method that estimates parameters for
+statistical models, where the model depends on unobserved latent variables. The
+EM iteration alternates between performing an expectation (E) step, which
+creates a function for the expectation of the log-likelihood evaluated using
+the current estimate for the parameters, and a maximization (M) step, which
+computes parameters maximizing the expected log-likelihood found on the E step.
+These parameter-estimates are then used to determine the distribution of the
+latent variables in the next E step.
The package includes the machine definition per se and a selection of different trainers for specialized purposes:
+
- Maximum Likelihood (ML)
- Maximum a Posteriori (MAP)
- K-Means
@@ -36,13 +46,22 @@ The package includes the machine definition per se and a selection of different
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.learn.em/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.learn.em/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://gitlab.idiap.ch/bob/bob/wikis/Installation
+.. _mailing list: https://groups.google.com/forum/?fromgroups#!forum/bob-devel
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 914e36e6838e8f027ec3c8791115c23821cfba11..3b7a446fdd70c7e5b29dfdfd214a9fafd0ff6f06 100644
--- a/buildout.cfg
+++ b/buildout.cfg
@@ -1,39 +1,13 @@
; vim: set fileencoding=utf-8 :
-; Andre Anjos <andre.anjos@idiap.ch>
-; Mon 16 Apr 08:29:18 2012 CEST
+; Mon 15 Aug 2016 09:48:28 CEST
[buildout]
parts = scripts
+develop = .
eggs = bob.learn.em
extensions = bob.buildout
- mr.developer
-
-auto-checkout = *
-develop = src/bob.extension
- src/bob.blitz
- src/bob.core
- src/bob.io.base
- src/bob.sp
- src/bob.math
- src/bob.learn.activation
- src/bob.learn.linear
- .
-
-; options for bob.buildout extension
-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.sp = git https://github.com/bioidiap/bob.sp
-bob.math = git https://github.com/bioidiap/bob.math
-bob.learn.activation = git https://github.com/bioidiap/bob.learn.activation
-bob.learn.linear = git https://github.com/bioidiap/bob.learn.linear
+verbose = true
[scripts]
-recipe = bob.buildout:scripts
-dependent-scripts = true
+recipe = bob.buildout:scripts
\ No newline at end of file
diff --git a/develop.cfg b/develop.cfg
new file mode 100644
index 0000000000000000000000000000000000000000..40bd10aa0e2846152a12010f8c5ee123d60b95f9
--- /dev/null
+++ b/develop.cfg
@@ -0,0 +1,39 @@
+; vim: set fileencoding=utf-8 :
+; Andre Anjos <andre.anjos@idiap.ch>
+; Mon 16 Apr 08:29:18 2012 CEST
+
+[buildout]
+parts = scripts
+eggs = bob.learn.em
+extensions = bob.buildout
+ mr.developer
+
+auto-checkout = *
+develop = src/bob.extension
+ src/bob.blitz
+ src/bob.core
+ src/bob.io.base
+ src/bob.sp
+ src/bob.math
+ src/bob.learn.activation
+ src/bob.learn.linear
+ .
+
+; options for bob.buildout extension
+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.sp = git https://gitlab.idiap.ch/bob/bob.sp
+bob.math = git https://gitlab.idiap.ch/bob/bob.math
+bob.learn.activation = git https://gitlab.idiap.ch/bob/bob.learn.activation
+bob.learn.linear = git https://gitlab.idiap.ch/bob/bob.learn.linear
+
+[scripts]
+recipe = bob.buildout:scripts
+dependent-scripts = true
diff --git a/doc/conf.py b/doc/conf.py
index 0317ae8fbae1d3e243e65ae0f899d32c72e96ca0..e545a995b9a8e110af49dff059f2808387930819 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -1,46 +1,47 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
-# Andre Anjos <andre.anjos@idiap.ch>
-# Tue 15 Oct 16:37:18 2013 CEST
-#
-# Copyright (C) 2011-2014 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')
+else:
+ extensions.append('sphinx.ext.pngmath')
# 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
@@ -63,7 +64,7 @@ import time
copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
# Grab the setup entry
-distribution = pkg_resources.require('bob.learn.em')[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
@@ -108,13 +109,18 @@ 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'Bindings for EM machines and trainers of Bob'
+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 +128,14 @@ 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_learn_em'
+#html_short_title = project_variable
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
@@ -187,72 +193,48 @@ html_favicon = 'img/favicon.ico'
#html_file_suffix = None
# Output file base name for HTML help builder.
-htmlhelp_basename = 'bob_learn_em_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_learn_em.tex', u'Bob Miscellaneous Machine Learning Tools',
- u'Biometrics Group, Idiap Research Institute', 'manual'),
-]
+htmlhelp_basename = project_variable + u'_doc'
-# 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
+# -- Post configuration --------------------------------------------------------
# Included after all input documents
rst_epilog = """
.. |project| replace:: Bob
-.. |url| replace:: https://www.idiap.ch/software/bob/
.. |version| replace:: %s
.. |current-year| date:: %%Y
""" % (version,)
-# -- 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_learn_em', u'Bob Miscellaneous Machine Learning Tools', [u'Idiap Research Institute'], 1)
-]
-
# 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()
+# 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):
- pass
+ 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/setup.py b/setup.py
index 3f560836acb26a77dc7fd9d0b70c6975b9b6a0ae..2d1961c436466a540601453ef6067ebfb6d3502b 100644
--- a/setup.py
+++ b/setup.py
@@ -22,8 +22,8 @@ setup(
name='bob.learn.em',
version=version,
- description='Bindings for emelaneous machines and trainers of Bob',
- url='http://github.com/bioidiap/bob.learn.em',
+ description='Bindings for EM machines and trainers of Bob',
+ url='http://gitlab.idiap.ch/bob/bob.learn.em',
license='BSD',
author='Andre Anjos',
author_email='andre.anjos@idiap.ch',