Package update to gitlab

.gitlab-ci.yml

+# 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: "-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"
+
+
+# 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 ${CONDA_PREFIX}
+
+
+# Template for the wheel uploading stage
+# Needs to run against one combination of python 2.x and 3.x if it is a python
+# only package, otherwise, needs to run in both pythons to all supported
+# architectures (Linux and Mac OSX 64-bit)
+.wheels_template: &wheels_job
+  stage: wheels
+  only:
+    - master
+    - tags
+  script:
+    - curl --silent --insecure --upload-file dist/*.whl https://${DOCUSER}:${DOCPASS}@www.idiap.ch/software/bob/wheels-upload/gitlab/
+
+
+# Template for (latest) documentation upload stage
+# Only one real job needs to do this
+.docs_template: &docs_job
+  stage: docs
+  only:
+    - master
+  script:
+    - echo "repo=${CI_PROJECT_PATH}" > sphinx/.gitlab-ci.info
+    - echo "branch=${CI_BUILD_REF_NAME}" >> sphinx/.gitlab-ci.info
+    - echo "tag=${CI_BUILD_TAG}" >> sphinx/.gitlab-ci.info
+    - echo "build=${CI_BUILD_ID}" >> sphinx/.gitlab-ci.info
+    - echo "commit=${CI_BUILD_REF}" >> sphinx/.gitlab-ci.info
+    - echo "runner=${CI_RUNNER_DESCRIPTION}" >> sphinx/.gitlab-ci.info
+    - tar cfj ${CI_PROJECT_NAME}-${CI_BUILD_REF}.tar.bz2 sphinx
+    - curl --silent --insecure --upload-file *.tar.bz2 https://${DOCUSER}:${DOCPASS}@www.idiap.ch/software/bob/docs-upload/
+
+
+
+# 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

.travis.yml

-language: python
-env:
-  global:
-  - secure: DCsVw4Y5hFxTH8iYFb80gJyBu4IEOJzRNuA7YGXsh6Sx4hsLXJ5D2e7t7pUUSjE5fv5SfBj+J5zS3wyZfNtLx/yi3Le1WjBYxv4WPbaUcRgEdH5NUSamJKrf0eGuoIYvus8fPLeLcKyfj05sQYKhMiVlACtKkfBzUzoSVDEg7RE=
-  - secure: YLwf/svdpy6rI3YvfYb/1t4EzvBtoaluBMvr+tCOKwB/kWu5/UuDr/lujbCyMNAvRi1LQutAaqiNnKlbFMNOQD47n/yy5yHlC6cBm45ptWs1XV4hb5oqE2EAkNEfh7LIFus60RnlI1bq4D+jkBNLiFJ+0jj59h9WNqzLcpQxTKI=
-  - 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 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 coverage cpp-coveralls
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel -r requirements.txt --pre 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.math import get_config; print(get_config())'
-- ./bin/coverage run --source=bob.math ./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

LICENSE

-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

MANIFEST.in

-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 *.cpp *.h

README.rst

 .. vim: set fileencoding=utf-8 :
-.. Andre Anjos <andre.anjos@idiap.ch>
-.. Thu 29 Aug 2013 16:07:57 CEST
+.. Thu 11 Aug 2016 09:34:29 CEST
 
 .. image:: http://img.shields.io/badge/docs-stable-yellow.png
    :target: http://pythonhosted.org/bob.math/index.html
 .. image:: http://img.shields.io/badge/docs-latest-orange.png
    :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.math/master/index.html
-.. image:: https://travis-ci.org/bioidiap/bob.math.svg?branch=master
-   :target: https://travis-ci.org/bioidiap/bob.math?branch=master
-.. image:: https://coveralls.io/repos/bioidiap/bob.math/badge.svg?branch=master
-   :target: https://coveralls.io/r/bioidiap/bob.math?branch=master
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
-   :target: https://github.com/bioidiap/bob.math/tree/master
+.. image:: https://gitlab.idiap.ch/bob/bob.math/badges/master/build.svg
+   :target: https://gitlab.idiap.ch/bob/bob.math/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+   :target: https://gitlab.idiap.ch/bob/bob.math
 .. image:: http://img.shields.io/pypi/v/bob.math.png
    :target: https://pypi.python.org/pypi/bob.math
 .. image:: http://img.shields.io/pypi/dm/bob.math.png
    :target: https://pypi.python.org/pypi/bob.math
 
+
 ===============================
  Mathematical Functions of Bob
 ===============================
 
-This package contains Bob's math functionality.
+This package is part of the signal-processing and machine learning toolbox
+Bob_. This package contains Bob's math functionality.
+
 
 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.math/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.math/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

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])
 

buildout.cfg

 ; vim: set fileencoding=utf-8 :
-; Andre Anjos <andre.anjos@idiap.ch>
-; Mon 16 Apr 08:29:18 2012 CEST
+; Thu 11 Aug 09:55:30 CEST 2016
 
 [buildout]
 parts = scripts
+develop = .
 eggs = bob.math
 extensions = bob.buildout
-             mr.developer
-auto-checkout = *
-develop = src/bob.extension
-          src/bob.blitz
-          src/bob.core
-          .
-
-; 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
+verbose = true
 
 [scripts]
-recipe = bob.buildout:scripts
+recipe = bob.buildout:scripts
\ No newline at end of file

develop.cfg

+; vim: set fileencoding=utf-8 :
+; Andre Anjos <andre.anjos@idiap.ch>
+; Mon 16 Apr 08:29:18 2012 CEST
+
+[buildout]
+parts = scripts
+eggs = bob.math
+extensions = bob.buildout
+             mr.developer
+auto-checkout = *
+develop = src/bob.extension
+          src/bob.blitz
+          src/bob.core
+          .
+
+; 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
+
+[scripts]
+recipe = bob.buildout:scripts

doc/conf.py

@@ -25,7 +25,6 @@ import pkg_resources
 extensions = [
   'sphinx.ext.todo',
   'sphinx.ext.coverage',
-  'sphinx.ext.pngmath',
   'sphinx.ext.ifconfig',
   'sphinx.ext.autodoc',
   'sphinx.ext.autosummary',
@@ -38,6 +37,11 @@ import sphinx
 if sphinx.__version__ >= "1.0":
   extensions.append('sphinx.ext.viewcode')
 
+if sphinx.__version__ >= "1.4":
+    extensions.append('sphinx.ext.imgmath')
+  else:
+      extensions.append('sphinx.ext.pngmath')
+
 # Always includes todos
 todo_include_todos = True