Commit c66b7d0b authored by André Anjos's avatar André Anjos 💬

Merge branch 'various_fixes' into 'master'

Various fixes

Closes #1 as well.

See merge request !2
parents 9a6f3a67 fa52c419
Pipeline #4582 passed with stages
in 100 minutes and 47 seconds
# 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.
# 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.
# 1) Generic instructions (only change if you know what you're doing)
# -------------------------------------------------------------------
# Definition of our build pipeline
stages:
- build
- test
- docs
- wheels
- deploy
# Global variables
variables:
CONDA_PREFIX: env
# ---------
# Templates
# ---------
# Template for the build stage
# Needs to run on all supported architectures, platforms and python versions
......@@ -27,104 +22,98 @@ variables:
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/"
- 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:
- ./bin/buildout
- if [ -x ./bin/bob_dbmanage.py ]; then ./bin/bob_dbmanage.py all download --force; fi
- ./bin/sphinx-build doc sphinx
- ./bin/python setup.py bdist_wheel --python-tag ${WHEEL_TAG}
- ./_ci/build.sh
after_script:
- rm -rf ${CONDA_PREFIX}
- ./_ci/after_build.sh
artifacts:
expire_in: 1 day
expire_in: 1 week
paths:
- bootstrap-conda.sh
- _ci/
- 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
# 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:
- ./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
- ./_ci/install.sh _ci #updates
- ./_ci/before_test.sh
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
- ./_ci/test.sh
after_script:
- rm -rf ${CONDA_PREFIX}
- ./_ci/after_test.sh
# Template for the wheel uploading stage
# Needs to run against one combination of python 2.x and 3.x if it is a python
# only package, otherwise, needs to run in both pythons to all supported
# architectures (Linux and Mac OSX 64-bit)
# Needs to run against one supported architecture, platform and python version
.wheels_template: &wheels_job
stage: wheels
environment: intranet
only:
- master
- tags
- /^v\d+\.\d+\.\d+([abc]\d*)?$/ # PEP-440 compliant version (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
- ./_ci/install.sh _ci #updates
- ./_ci/before_wheels.sh
script:
- ./upload-wheel.sh
- ./_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:
- curl --silent https://gitlab.idiap.ch/bob/bob/snippets/9/raw | tr -d '\r' > upload-sphinx.sh
- chmod 755 upload-sphinx.sh
- ./_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:
- ./upload-sphinx.sh
- ./_ci/deploy.sh
after_script:
- ./_ci/after_deploy.sh
# 2) Package specific instructions (you may tune this if needed)
# --------------------------------------------------------------
# -------------
# Build Targets
# -------------
# Linux + Python 2.7: Builds, tests, uploads wheel
# Linux + Python 2.7: Builds, tests, uploads wheel and deploys (if needed)
build_linux_27:
<<: *linux_build_job
<<: *build_job
variables: &linux_27_build_variables
<<: *linux_build_variables
PYTHON_VER: "2.7"
PYTHON_VERSION: "2.7"
WHEEL_TAG: "py27"
tags:
- conda-linux
......@@ -139,6 +128,15 @@ test_linux_27:
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:
......@@ -147,10 +145,9 @@ wheels_linux_27:
# Linux + Python 3.4: Builds and tests
build_linux_34:
<<: *linux_build_job
<<: *build_job
variables: &linux_34_build_variables
<<: *linux_build_variables
PYTHON_VER: "3.4"
PYTHON_VERSION: "3.4"
WHEEL_TAG: "py3"
tags:
- conda-linux
......@@ -164,12 +161,11 @@ test_linux_34:
- conda-linux
# Linux + Python 3.5: Builds, tests, uploads wheel
# Linux + Python 3.5: Builds, tests and uploads wheel
build_linux_35:
<<: *linux_build_job
<<: *build_job
variables: &linux_35_build_variables
<<: *linux_build_variables
PYTHON_VER: "3.5"
PYTHON_VERSION: "3.5"
WHEEL_TAG: "py3"
tags:
- conda-linux
......@@ -184,6 +180,7 @@ test_linux_35:
wheels_linux_35:
<<: *wheels_job
variables: *linux_35_build_variables
dependencies:
- build_linux_35
tags:
......@@ -191,6 +188,7 @@ wheels_linux_35:
docs_linux_35:
<<: *docs_job
variables: *linux_35_build_variables
dependencies:
- build_linux_35
tags:
......@@ -199,10 +197,9 @@ docs_linux_35:
# Mac OSX + Python 2.7: Builds and tests
build_macosx_27:
<<: *macosx_build_job
<<: *build_job
variables: &macosx_27_build_variables
<<: *macosx_build_variables
PYTHON_VER: "2.7"
PYTHON_VERSION: "2.7"
WHEEL_TAG: "py27"
tags:
- conda-macosx
......@@ -218,10 +215,9 @@ test_macosx_27:
# Mac OSX + Python 3.4: Builds and tests
build_macosx_34:
<<: *macosx_build_job
<<: *build_job
variables: &macosx_34_build_variables
<<: *macosx_build_variables
PYTHON_VER: "3.4"
PYTHON_VERSION: "3.4"
WHEEL_TAG: "py3"
tags:
- conda-macosx
......@@ -237,10 +233,9 @@ test_macosx_34:
# Mac OSX + Python 3.5: Builds and tests
build_macosx_35:
<<: *macosx_build_job
<<: *build_job
variables: &macosx_35_build_variables
<<: *macosx_build_variables
PYTHON_VER: "3.5"
PYTHON_VERSION: "3.5"
WHEEL_TAG: "py3"
tags:
- conda-macosx
......@@ -251,4 +246,4 @@ test_macosx_35:
dependencies:
- build_macosx_35
tags:
- conda-macosx
\ No newline at end of file
- conda-macosx
Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
Written by Andre Anjos <andre.anjos@idiap.ch>
Written by Pedro Tome <pedro.tome@idiap.ch>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
......@@ -24,4 +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.
\ No newline at end of file
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
include README.rst bootstrap-buildout.py buildout.cfg develop.cfg COPYING requirements.txt version.txt
include README.rst bootstrap-buildout.py buildout.cfg develop.cfg LICENSE requirements.txt version.txt
recursive-include doc *.py *.rst
recursive-include bob *.sql3
......@@ -39,7 +39,7 @@ class Database(bob.db.base.SQLiteDatabase):
Parameters:
protocol (str, Optional): One of the UTFVP protocols:
protocol (:py:class:`str`, optional): One of the UTFVP protocols:
* ``1vsall``
* ``nom``
......@@ -50,8 +50,8 @@ class Database(bob.db.base.SQLiteDatabase):
* ``nomRightMiddle``
* ``nomRightRing``
groups (str, Optional): ignored (The clients belong both to ``world`` and
``dev``)
groups (:py:class:`str`, Optional): ignored (The clients belong both to
``world`` and ``dev``)
Returns
......@@ -88,7 +88,7 @@ class Database(bob.db.base.SQLiteDatabase):
Parameters:
protocol (str, Optional): One of the UTFVP protocols:
protocol (:py:class:`str`, optional): One of the UTFVP protocols:
* ``1vsall``
* ``nom``
......@@ -99,7 +99,8 @@ class Database(bob.db.base.SQLiteDatabase):
* ``nomRightMiddle``
* ``nomRightRing``
groups (str, Optional): Groups the clients belong to. Should be one of:
groups (:py:class:`str`, optional): Groups the clients belong to. Should
be one of:
* ``world``
* ``dev``
......@@ -119,7 +120,7 @@ class Database(bob.db.base.SQLiteDatabase):
Parameters:
protocol (str, Optional): One of the UTFVP protocols:
protocol (:py:class:`str`, optional): One of the UTFVP protocols:
* ``1vsall``
* ``nom``
......@@ -130,7 +131,8 @@ class Database(bob.db.base.SQLiteDatabase):
* ``nomRightMiddle``
* ``nomRightRing``
groups (str, Optional): Groups the clients belong to. Should be one of:
groups (:py:class:`str`, optional): Groups the clients belong to. Should
be one of:
* ``dev``
* ``eval``
......@@ -161,7 +163,7 @@ class Database(bob.db.base.SQLiteDatabase):
Parameters:
protocol (str, Optional): One of the UTFVP protocols:
protocol (:py:class:`str`, optional): One of the UTFVP protocols:
* ``1vsall``
* ``nom``
......@@ -172,7 +174,8 @@ class Database(bob.db.base.SQLiteDatabase):
* ``nomRightMiddle``
* ``nomRightRing``
groups (str, Optional): Groups the clients belong to. Should be one of:
groups (:py:class:`str`, optional): Groups the clients belong to. Should
be one of:
* ``world``
* ``dev``
......@@ -224,7 +227,8 @@ class Database(bob.db.base.SQLiteDatabase):
Parameters:
protocol (str, list, Optional): One or several of:
protocol (:py:class:`str`, :py:class:`list`, optional): One or several
of:
* ``1vsall``
* ``nom``
......@@ -235,35 +239,36 @@ class Database(bob.db.base.SQLiteDatabase):
* ``nomRightMiddle``
* ``nomRightRing``
purposes (str, list, Optional): One or several of:
purposes (:py:class:`str`, :py:class:`list`, optional): One or several
of:
* ``train``
* ``enroll``
* ``probe``
model_ids (str, list, Optional): Only retrieves the files for the
provided list of model ids. If ``None`` is given (this is the default),
no filter over the model_ids is performed.
model_ids (:py:class:`str`, :py:class:`list`, optional): Only retrieves
the files for the provided list of model ids. If ``None`` is given
(this is the default), no filter over the model_ids is performed.
groups (str, list, Optional): Groups the clients belong to. Should be one
or several of:
groups (:py:class:`str`, :py:class:`list`, optional): Groups the clients
belong to. Should be one or several of:
* ``world``
* ``dev``
* ``eval``
classes (str, list, Optional): The classes (types of accesses) to be
retrieved (``client`` or ``impostor``) or a tuple with several of them.
If ``None`` is given (this is the default), it is considered the same
as a tuple with all possible values.
classes (:py:class:`str`, :py:class:`list`, optional): The classes (types
of accesses) to be retrieved (``client`` or ``impostor``) or a tuple
with several of them. If ``None`` is given (this is the default), it
is considered the same as a tuple with all possible values.
finger_ids (str, list, Optional): Only retrieves the files for the
provided list of finger ids. If ``None`` is given (this is the
default), no filter over the finger_ids is performed.
finger_ids (:py:class:`str`, :py:class:`list`, optional): Only retrieves
the files for the provided list of finger ids. If ``None`` is given
(this is the default), no filter over the finger_ids is performed.
session_ids (str, list, Optional): Only retrieves the files for the
provided list of session ids. If ``None`` is given (this is the
default), no filter over the session_ids is performed.
session_ids (:py:class:`str`, :py:class:`list`, optional): Only retrieves
the files for the provided list of session ids. If ``None`` is given
(this is the default), no filter over the session_ids is performed.
Returns:
......
......@@ -30,9 +30,29 @@ extensions = [
import sphinx
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
......@@ -216,8 +236,13 @@ autodoc_default_flags = [
]
# For inter-documentation mapping:
from bob.extension.utils import link_documentation
intersphinx_mapping = link_documentation()
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
......
py:class bob.db.base.file.File
py:class bob.db.base.database.SQLiteDatabase
py:class sqlalchemy.ext.declarative.api.Base
......@@ -15,8 +15,10 @@ setup(
url='https://gitlab.idiap.ch/bob/bob.db.vera',
license='BSD',
author='Andre Anjos,Pedro Tome',
author_email='andre.anjos@idiap.ch,pedro.tome@idiap.ch',
author='Pedro Tome',
author_email='pedro.tome@idiap.ch',
maintainer='Andre Anjos',
maintainer_email='andre.anjos@idiap.ch',
keywords='fingervein recognition, bob, bob.db, UTFVP',
......
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