diff --git a/.gitignore b/.gitignore
index 234ed7ae298c484971dbc36646f6ef1bcba9e022..37d1fef28e90f91a21e60cf18907a75030fd75b4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,7 +18,8 @@ dist
.gdb_history
build
*.egg
-src/
*.sql3
record.txt
*.DS_Store
+.gitlab-ci-local*
+html/
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 845b719f2378d396a8b75296a68d1e32c840e7c7..feea02856cf6935a78083041f6e125e391c46170 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1 +1,4 @@
-include: 'https://gitlab.idiap.ch/bob/bob.devtools/raw/master/bob/devtools/data/gitlab-ci/single-package.yaml'
+include:
+ - project: bob/dev-profile
+ ref: main
+ file: /gitlab/python.yml
diff --git a/MANIFEST.in b/MANIFEST.in
index 1b422a5d6892f59d701c62183e3601418148b795..08b0470c9f6818bda1dc326fd7e537ceeb617ec3 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,8 +1,8 @@
-include README.rst bootstrap-buildout.py buildout.cfg develop.cfg version.txt requirements.txt
+include README.rst
recursive-include doc *.py *.rst
recursive-include bob *.txt *.hdf5
recursive-include bob *.sql3
-recursive-include bob/pad/base/test/data scores-* *.sql3 *.wav
-recursive-include bob/pad/base/test/data/example_filelist *.lst
-recursive-include bob/pad/base/test/ *.csv
-recursive-include bob/pad/base/test/ *.tar.gz
+recursive-include tests/data scores-* *.sql3 *.wav
+recursive-include tests/example_filelist *.lst
+recursive-include tests/ *.csv
+recursive-include tests/ *.tar.gz
diff --git a/README.rst b/README.rst
index a33a489b99f7979d519bb53cf0b9b1d88061a1e0..fcd5ff686a96487a7272a64c74d67c26e7cb388f 100644
--- a/README.rst
+++ b/README.rst
@@ -3,11 +3,11 @@
.. Wed 19 Oct 22:36:22 2016 CET
.. image:: https://img.shields.io/badge/docs-latest-orange.svg
- :target: https://www.idiap.ch/software/bob/docs/bob/bob.pad.base/master/index.html
+ :target: https://www.idiap.ch/software/bob/docs/bob/bob.pad.base/master/sphinx/index.html
.. image:: https://gitlab.idiap.ch/bob/bob.pad.base/badges/master/pipeline.svg
:target: https://gitlab.idiap.ch/bob/bob.pad.base/commits/master
.. image:: https://gitlab.idiap.ch/bob/bob.pad.base/badges/master/coverage.svg
- :target: https://gitlab.idiap.ch/bob/bob.pad.base/commits/master
+ :target: https://www.idiap.ch/software/bob/docs/bob/bob.pad.base/master/coverage/
.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
:target: https://gitlab.idiap.ch/bob/bob.pad.base
diff --git a/bob/pad/base/test/data/test_db.sql3 b/bob/pad/base/test/data/test_db.sql3
deleted file mode 100755
index 3ed135e225dd562d40e5175ac310aa92f661675f..0000000000000000000000000000000000000000
Binary files a/bob/pad/base/test/data/test_db.sql3 and /dev/null differ
diff --git a/buildout.cfg b/buildout.cfg
deleted file mode 100644
index 0b85449b386e39996ad91d9187f57616f0090702..0000000000000000000000000000000000000000
--- a/buildout.cfg
+++ /dev/null
@@ -1,14 +0,0 @@
-; vim: set fileencoding=utf-8 :
-; Tue 16 Aug 15:00:20 CEST 2016
-
-[buildout]
-parts = scripts
-develop = .
-eggs = bob.pad.base
-extensions = bob.buildout
-newest = false
-verbose = true
-
-[scripts]
-recipe = bob.buildout:scripts
-dependent-scripts = true
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 0f7d57f2954c3010fc3163d28e9b8640cf87b83e..1201d1cfff885a7a554cb8ac11eca142401d266d 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -1,22 +1,20 @@
-{% set name = 'bob.pad.base' %}
-{% set project_dir = environ.get('RECIPE_DIR') + '/..' %}
+{% set data = load_file_data(RECIPE_DIR + '/../pyproject.toml') %}
+{% set name = data['project']['name'] %}
package:
name: {{ name }}
- version: {{ environ.get('BOB_PACKAGE_VERSION', '0.0.1') }}
+ version: {{ data['project']['version'] }}
+
+source:
+ path: ..
build:
- entry_points:
- - spoof.py = bob.pad.base.script.spoof:main
+ noarch: python
number: {{ environ.get('BOB_BUILD_NUMBER', 0) }}
run_exports:
- {{ pin_subpackage(name) }}
script:
- - cd {{ project_dir }}
- {% if environ.get('BUILD_EGG') %}
- - "{{ PYTHON }} setup.py sdist --formats=zip"
- {% endif %}
- - "{{ PYTHON }} -m pip install . -vv"
+ - "{{ PYTHON }} -m pip install {{ SRC_DIR }} -vv"
requirements:
host:
@@ -40,35 +38,30 @@ requirements:
run:
- python
- setuptools
+ - bob.extension
+ - bob.io.base
+ - bob.pipelines
+ - bob.measure
+ - bob.bio.base
- {{ pin_compatible('click') }}
- {{ pin_compatible('click-plugins') }}
- {{ pin_compatible('dask') }}
- {{ pin_compatible('matplotlib') }}
- {{ pin_compatible('numpy') }}
- - {{ pin_compatible('scikit-learn', min_pin='x.x') }}
+ - {{ pin_compatible('scikit-learn') }}
- {{ pin_compatible('scipy') }}
- {{ pin_compatible('sqlalchemy') }}
- {{ pin_compatible('tabulate') }}
test:
imports:
- - {{ name }}
+ - {{ name.replace('-','_') }}
commands:
- - bob pad --help
- - pytest --verbose --cov {{ name }} --cov-report term-missing --cov-report html:{{ project_dir }}/sphinx/coverage --cov-report xml:{{ project_dir }}/coverage.xml --pyargs {{ name }}
- - sphinx-build -aEW {{ project_dir }}/doc {{ project_dir }}/sphinx
- - sphinx-build -aEb doctest {{ project_dir }}/doc sphinx
- conda inspect linkages -p $PREFIX {{ name }} # [not win]
- conda inspect objects -p $PREFIX {{ name }} # [osx]
- requires:
- - pytest {{ pytest }}
- - pytest-cov {{ pytest_cov }}
- - coverage {{ coverage }}
- - sphinx {{ sphinx }}
- - sphinx_rtd_theme {{ sphinx_rtd_theme }}
about:
- home: https://www.idiap.ch/software/bob/
- license: GNU General Public License v3 (GPLv3)
- summary: A framework for executing the chain of presentation attack detection (PAD) experiments
+ home: {{ data['project']['urls']['homepage'] }}
+ summary: {{ data['project']['description'] }}
+ license: {{ data['project']['license']['text'] }}
license_family: GPL
diff --git a/doc/catalog.json b/doc/catalog.json
new file mode 100644
index 0000000000000000000000000000000000000000..d502c82dc61d364048fac634fef3c9e8332b15c3
--- /dev/null
+++ b/doc/catalog.json
@@ -0,0 +1,8 @@
+{
+ "bob.extension": {
+ "versions": {
+ "latest": "https://www.idiap.ch/software/bob/docs/bob/bob.extension/master"
+ },
+ "sources": {}
+ }
+}
diff --git a/doc/conf.py b/doc/conf.py
index 2c71f27125dfd482ab653f57d6163fc8e6970e38..20a84dc67d274fb159e6085dd241cacc7f4900e1 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -24,6 +24,7 @@ extensions = [
"sphinx.ext.napoleon",
"sphinx.ext.viewcode",
"sphinx.ext.mathjax",
+ "auto_intersphinx",
]
# Be picky about warnings
@@ -234,13 +235,15 @@ autodoc_default_options = {
"show-inheritance": True,
}
-# For inter-documentation mapping:
-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()
+auto_intersphinx_packages = [
+ ("python", "3"),
+ "numpy",
+ "bob.extension",
+ "bob.pipelines",
+ "bob.bio.base",
+ "bob.pad.face",
+ "setuptools",
+ "dask",
+ "scikit-learn",
+]
+auto_intersphinx_catalog = "catalog.json"
diff --git a/doc/extra-intersphinx.txt b/doc/extra-intersphinx.txt
index 989e8b49ce55345f4155769927d8f27f96ba7576..b5fd3457bb3738edca78133420d3779f48ed7f55 100644
--- a/doc/extra-intersphinx.txt
+++ b/doc/extra-intersphinx.txt
@@ -1,7 +1,19 @@
python
numpy
+bob.extension
+bob.pipelines
+bob.measure
bob.io.base
bob.bio.base
bob.bio.spear
bob.bio.face
bob.pad.face
+setuptools
+click
+click-plugins
+dask
+matplotlib
+scikit-learn
+scipy
+sqlalchemy
+tabulate
diff --git a/pyproject.toml b/pyproject.toml
index b738dc847ff9705c5769673db7415f2eb9a75f4d..971265f780d7c96db274b1385161c59880aba729 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,95 @@
[build-system]
- requires = ["setuptools", "wheel", "bob.extension"]
+ requires = ["setuptools>=61.0.0", "wheel"]
build-backend = "setuptools.build_meta"
+[project]
+ name = "bob.pad.base"
+ version = "5.0.5b0"
+ requires-python = ">=3.9"
+ description = "A framework for executing the chain of presentation attack detection (PAD) experiments"
+ dynamic = ["readme"]
+ license = {text = "GPLv3 License"}
+ authors = [
+ {name = "Pavel Korshunov"},
+ {email = "pavel.korshunov@idiap.ch"},
+ ]
+ keywords = ["PAD framework", "grid support", "pipeline organization"]
+
+ classifiers=[
+ "Framework :: Bob",
+ "Development Status :: 3 - Alpha",
+ "Intended Audience :: Developers",
+ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+ "Natural Language :: English",
+ "Programming Language :: Python",
+ "Topic :: Scientific/Engineering :: Artificial Intelligence",
+ ]
+ dependencies = [
+ "setuptools",
+ "bob.extension",
+ "bob.io.base",
+ "bob.pipelines",
+ "bob.measure",
+ "bob.bio.base",
+ "click",
+ "click-plugins",
+ "dask",
+ "matplotlib",
+ "numpy",
+ "scikit-learn",
+ "scipy",
+ "sqlalchemy",
+ "tabulate",
+ ]
+
+[project.urls]
+ documentation = "https://www.idiap.ch/software/bob/docs/bob/bob.pad.base/stable/"
+ homepage = "https://pypi.org/project/bob.pad.base/"
+ repository = "https://gitlab.idiap.ch/bob/bob.pad.base"
+ changelog = "https://gitlab.idiap.ch/bob/bob.pad.base/-/releases"
+
+[project.optional-dependencies]
+ qa = ["pre-commit"]
+ doc = [
+ "sphinx",
+ "sphinx_rtd_theme",
+ "sphinx-autodoc-typehints",
+ "auto-intersphinx",
+ "sphinxcontrib-programoutput",
+ "matplotlib",
+ "bob.pad.face",
+ ]
+ test = [
+ "pytest",
+ "pytest-cov",
+ "coverage",
+ ]
+
+[tool.setuptools]
+ zip-safe = false
+ package-dir = {"" = "src"}
+
+[tool.setuptools.dynamic]
+ readme = {file = "README.rst"}
+
+[project.entry-points."bob.cli"]
+ pad = "bob.pad.base.script.pad:pad"
+
+[project.entry-points."bob.pad.cli"]
+ metrics = "bob.pad.base.script.pad_commands:metrics"
+ multi-metrics = "bob.pad.base.script.pad_commands:multi_metrics"
+ hist = "bob.pad.base.script.pad_commands:hist"
+ det = "bob.pad.base.script.pad_commands:det"
+ roc = "bob.pad.base.script.pad_commands:roc"
+ epc = "bob.pad.base.script.pad_commands:epc"
+ gen = "bob.pad.base.script.pad_commands:gen"
+ evaluate = "bob.pad.base.script.pad_commands:evaluate"
+ cross = "bob.pad.base.script.cross:cross"
+ finalize-scores = "bob.pad.base.script.finalize_scores:finalize_scores"
+ run-pipeline = "bob.pad.base.script.run_pipeline:run_pipeline"
+
+[tool.distutils.bdist_wheel]
+ universal = true
[tool.isort]
profile = "black"
line_length = 80
@@ -10,3 +98,12 @@
[tool.black]
line-length = 80
+
+[tool.pytest.ini_options]
+ addopts = [
+ "--import-mode=append",
+ "--cov-report=term-missing",
+ "--cov=bob.pad.base",
+ ]
+ junit_logging = "all"
+ junit_log_passing_tests = false
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 17185041e64d6ef9bfdbfaebb2c9536736c40a54..0000000000000000000000000000000000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-setuptools
-bob.extension
-bob.io.base
-bob.pipelines
-bob.measure
-bob.bio.base
-click
-click-plugins
-dask
-matplotlib
-numpy
-scikit-learn
-scipy
-sqlalchemy
-tabulate
diff --git a/setup.py b/setup.py
index de4d81bd6a02826eb65d6d036633955685d02e40..606849326a4002007fd42060b51e69a19c18675c 100644
--- a/setup.py
+++ b/setup.py
@@ -1,125 +1,3 @@
-#!/usr/bin/env python
-# vim: set fileencoding=utf-8 :
-# Andre Anjos <andre.anjos@idiap.ch>
-# Mon 16 Apr 08:18:08 2012 CEST
-#
-# Copyright (C) Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
+from setuptools import setup
-# This file contains the python (distutils/setuptools) instructions so your
-# package can be installed on **any** host system. It defines some basic
-# information like the package name for instance, or its homepage.
-#
-# It also defines which other packages this python package depends on and that
-# are required for this package's operation. The python subsystem will make
-# sure all dependent packages are installed or will install them for you upon
-# the installation of this package.
-#
-# The 'buildout' system we use here will go further and wrap this package in
-# such a way to create an isolated python working environment. Buildout will
-# make sure that dependencies which are not yet installed do get installed, but
-# **without** requiring administrative privileges on the host system. This
-# allows you to test your package with new python dependencies w/o requiring
-# administrative interventions.
-
-from setuptools import dist, setup
-
-dist.Distribution(dict(setup_requires=["bob.extension"]))
-
-from bob.extension.utils import find_packages, load_requirements
-
-install_requires = load_requirements()
-
-# The only thing we do in this file is to call the setup() function with all
-# parameters that define our package.
-setup(
- # This is the basic information about your project. Modify all this
- # information before releasing code publicly.
- name="bob.pad.base",
- version=open("version.txt").read().rstrip(),
- description="A framework for executing the chain of presentation attack detection (PAD) experiments",
- url="https://gitlab.idiap.ch/bob/bob.pad.base",
- license="GPLv3",
- author="Pavel Korshunov",
- author_email="pavel.korshunov@idiap.ch",
- keywords="PAD framework, grid support, pipeline organization",
- # If you have a better, long description of your package, place it on the
- # 'doc' directory and then hook it here
- long_description=open("README.rst").read(),
- # This line is required for any distutils based packaging.
- packages=find_packages(),
- include_package_data=True,
- # This line defines which packages should be installed when you "install"
- # this package. All packages that are mentioned here, but are not installed
- # on the current system will be installed locally and only visible to the
- # scripts of this package. Don't worry - You won't need administrative
- # privileges when using buildout.
- install_requires=install_requires,
- # Your project should be called something like 'bob.<foo>' or
- # 'bob.<foo>.<bar>'. To implement this correctly and still get all your
- # packages to be imported w/o problems, you need to implement namespaces
- # on the various levels of the package and declare them here. See more
- # about this here:
- # http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
- #
- # 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
- # This entry defines which scripts you will have inside the 'bin' directory
- # once you install the package (or run 'bin/buildout'). The order of each
- # entry under 'console_scripts' is like this:
- # script-name-at-bin-directory = module.at.your.library:function
- #
- # The module.at.your.library is the python file within your library, using
- # the python syntax for directories (i.e., a '.' instead of '/' or '\').
- # This syntax also omits the '.py' extension of the filename. So, a file
- # installed under 'example/foo.py' that contains a function which
- # implements the 'main()' function of particular script you want to have
- # should be referred as 'example.foo:main'.
- #
- # In this simple example we will create a single program that will print
- # the version of bob.
- entry_points={
- # main entry for bob pad cli
- "bob.cli": [
- "pad = bob.pad.base.script.pad:pad",
- ],
- # bob pad scripts
- "bob.pad.cli": [
- "metrics = bob.pad.base.script.pad_commands:metrics",
- "multi-metrics = bob.pad.base.script.pad_commands:multi_metrics",
- "hist = bob.pad.base.script.pad_commands:hist",
- "det = bob.pad.base.script.pad_commands:det",
- "roc = bob.pad.base.script.pad_commands:roc",
- "epc = bob.pad.base.script.pad_commands:epc",
- "gen = bob.pad.base.script.pad_commands:gen",
- "evaluate = bob.pad.base.script.pad_commands:evaluate",
- "cross = bob.pad.base.script.cross:cross",
- "finalize-scores = bob.pad.base.script.finalize_scores:finalize_scores",
- "run-pipeline = bob.pad.base.script.run_pipeline:run_pipeline",
- ],
- },
- # Classifiers are important if you plan to distribute this package through
- # PyPI. You can find the complete list of classifiers that are valid and
- # useful here (http://pypi.python.org/pypi?%3Aaction=list_classifiers).
- classifiers=[
- "Framework :: Bob",
- "Development Status :: 3 - Alpha",
- "Intended Audience :: Developers",
- "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
- "Natural Language :: English",
- "Programming Language :: Python",
- "Topic :: Scientific/Engineering :: Artificial Intelligence",
- ],
-)
+setup()
diff --git a/bob/__init__.py b/src/bob/__init__.py
similarity index 100%
rename from bob/__init__.py
rename to src/bob/__init__.py
diff --git a/bob/pad/__init__.py b/src/bob/pad/__init__.py
similarity index 100%
rename from bob/pad/__init__.py
rename to src/bob/pad/__init__.py
diff --git a/bob/pad/base/__init__.py b/src/bob/pad/base/__init__.py
similarity index 54%
rename from bob/pad/base/__init__.py
rename to src/bob/pad/base/__init__.py
index 11bb1980cd3f9714cb47296e6eda828e233f196f..9e6fb4ebc5a14df31da6cef271f8541721efb933 100644
--- a/bob/pad/base/__init__.py
+++ b/src/bob/pad/base/__init__.py
@@ -2,15 +2,6 @@
from . import database # noqa: F401
from . import error_utils # noqa: F401
from . import script # noqa: F401
-from . import test # noqa: F401
-
-
-def get_config():
- """Returns a string containing the configuration information."""
- import bob.extension
-
- return bob.extension.get_config(__name__)
-
# gets sphinx autodoc done right - don't remove it
__all__ = [_ for _ in dir() if not _.startswith("_")]
diff --git a/bob/pad/base/config/__init__.py b/src/bob/pad/base/config/__init__.py
similarity index 100%
rename from bob/pad/base/config/__init__.py
rename to src/bob/pad/base/config/__init__.py
diff --git a/bob/pad/base/database/__init__.py b/src/bob/pad/base/database/__init__.py
similarity index 100%
rename from bob/pad/base/database/__init__.py
rename to src/bob/pad/base/database/__init__.py
diff --git a/bob/pad/base/database/csv_dataset.py b/src/bob/pad/base/database/csv_dataset.py
similarity index 100%
rename from bob/pad/base/database/csv_dataset.py
rename to src/bob/pad/base/database/csv_dataset.py
diff --git a/bob/pad/base/error_utils.py b/src/bob/pad/base/error_utils.py
similarity index 100%
rename from bob/pad/base/error_utils.py
rename to src/bob/pad/base/error_utils.py
diff --git a/bob/pad/base/pipelines/__init__.py b/src/bob/pad/base/pipelines/__init__.py
similarity index 100%
rename from bob/pad/base/pipelines/__init__.py
rename to src/bob/pad/base/pipelines/__init__.py
diff --git a/bob/pad/base/pipelines/abstract_classes.py b/src/bob/pad/base/pipelines/abstract_classes.py
similarity index 100%
rename from bob/pad/base/pipelines/abstract_classes.py
rename to src/bob/pad/base/pipelines/abstract_classes.py
diff --git a/bob/pad/base/script/__init__.py b/src/bob/pad/base/script/__init__.py
similarity index 100%
rename from bob/pad/base/script/__init__.py
rename to src/bob/pad/base/script/__init__.py
diff --git a/bob/pad/base/script/cross.py b/src/bob/pad/base/script/cross.py
similarity index 90%
rename from bob/pad/base/script/cross.py
rename to src/bob/pad/base/script/cross.py
index 62b8f26fe0ab140b832427bc43ab4ee618de0d6c..a3ab03e2c50b5a0271b2a4a33262d129bf6d216d 100644
--- a/bob/pad/base/script/cross.py
+++ b/src/bob/pad/base/script/cross.py
@@ -10,14 +10,10 @@ import click
import jinja2
import yaml
+from exposed.click import log_parameters, verbosity_option
from tabulate import tabulate
from bob.bio.base.score.load import get_negatives_positives, load_score
-from bob.extension.scripts.click_helper import (
- bool_option,
- log_parameters,
- verbosity_option,
-)
from bob.measure import farfrr
from bob.measure.script import common_options
from bob.measure.utils import get_fta
@@ -28,6 +24,47 @@ from .pad_commands import CRITERIA
logger = logging.getLogger(__name__)
+def bool_option(name, short_name, desc, dflt=False, **kwargs):
+ """Generic provider for boolean options
+
+ Parameters
+ ----------
+ name : str
+ name of the option
+ short_name : str
+ short name for the option
+ desc : str
+ short description for the option
+ dflt : bool or None
+ Default value
+ **kwargs
+ All kwargs are passed to click.option.
+
+ Returns
+ -------
+ ``callable``
+ A decorator to be used for adding this option.
+ """
+
+ def custom_bool_option(func):
+ def callback(ctx, param, value):
+ ctx.meta[name.replace("-", "_")] = value
+ return value
+
+ return click.option(
+ "-%s/-n%s" % (short_name, short_name),
+ "--%s/--no-%s" % (name, name),
+ default=dflt,
+ help=desc,
+ show_default=True,
+ callback=callback,
+ is_eager=True,
+ **kwargs,
+ )(func)
+
+ return custom_bool_option
+
+
def _ordered_load(stream, Loader=yaml.Loader, object_pairs_hook=dict):
"""Loads the contents of the YAML stream into :py:class:`collections.OrderedDict`'s
@@ -234,7 +271,7 @@ Examples:
@common_options.table_option()
@common_options.output_log_metric_option()
@common_options.decimal_option(dflt=2, short="-dec")
-@verbosity_option()
+@verbosity_option(logger)
@click.pass_context
def cross(
ctx,
diff --git a/bob/pad/base/script/finalize_scores.py b/src/bob/pad/base/script/finalize_scores.py
similarity index 92%
rename from bob/pad/base/script/finalize_scores.py
rename to src/bob/pad/base/script/finalize_scores.py
index 6164d901a886782907a19b831719432f264da69a..7d81e0b9a54ca12cbdf2a903b1af7a514d1fe0c6 100644
--- a/bob/pad/base/script/finalize_scores.py
+++ b/src/bob/pad/base/script/finalize_scores.py
@@ -1,8 +1,12 @@
"""Finalizes the scores that are produced by bob pad run-pipeline.
"""
+import logging
+
import click
-from bob.extension.scripts.click_helper import log_parameters, verbosity_option
+from exposed.click import log_parameters, verbosity_option
+
+logger = logging.getLogger(__name__)
@click.command(
@@ -27,7 +31,7 @@ Examples:
@click.option(
"--backup/--no-backup", default=True, help="Whether to backup scores."
)
-@verbosity_option()
+@verbosity_option(logger)
def finalize_scores(scores, method, backup, verbose):
"""Finalizes the scores given by bob pad run-pipeline
When using bob.pad.base, Algorithms can produce several score values for
@@ -37,13 +41,11 @@ def finalize_scores(scores, method, backup, verbose):
The conversion is done in-place (original files will be backed up).
The order of scores will change.
"""
- import logging
import shutil
import numpy
import pandas as pd
- logger = logging.getLogger(__name__)
log_parameters(logger)
mean = {
diff --git a/bob/pad/base/script/pad.py b/src/bob/pad/base/script/pad.py
similarity index 82%
rename from bob/pad/base/script/pad.py
rename to src/bob/pad/base/script/pad.py
index e798bb200f6b9c5fd348bc7395a125576ea42bdc..518ebb2a50ea9e1bfa7b8f8c9ce93003f243eb44 100644
--- a/bob/pad/base/script/pad.py
+++ b/src/bob/pad/base/script/pad.py
@@ -4,8 +4,7 @@ import click
import pkg_resources
from click_plugins import with_plugins
-
-from bob.extension.scripts.click_helper import AliasedGroup
+from exposed.click import AliasedGroup
@with_plugins(pkg_resources.iter_entry_points("bob.pad.cli"))
diff --git a/bob/pad/base/script/pad_commands.py b/src/bob/pad/base/script/pad_commands.py
similarity index 98%
rename from bob/pad/base/script/pad_commands.py
rename to src/bob/pad/base/script/pad_commands.py
index 4fdabe9cb94173ed7c1b7cc9253a3a7f94bd0daa..b8227131279b3699e1ac867de4a2bf1d6b09ba6a 100644
--- a/bob/pad/base/script/pad_commands.py
+++ b/src/bob/pad/base/script/pad_commands.py
@@ -1,5 +1,6 @@
"""The main entry for bob pad commands.
"""
+import logging
import os
from csv import DictWriter
@@ -8,14 +9,17 @@ from functools import partial
import click
import numpy
+from exposed.click import verbosity_option
+
import bob.measure.script.figure as measure_figure
-from bob.extension.scripts.click_helper import verbosity_option
from bob.measure.script import common_options
from ..error_utils import split_csv_pad, split_csv_pad_per_pai
from . import pad_figure as figure
+logger = logging.getLogger(__name__)
+
SCORE_FORMAT = "Files must be in CSV format."
CRITERIA = (
"eer",
@@ -190,7 +194,7 @@ def gen_pad_csv_scores(
)
@click.option("-s", "--n-samples", default=2, type=click.INT, show_default=True)
@click.option("-a", "--n-attacks", default=2, type=click.INT, show_default=True)
-@verbosity_option()
+@verbosity_option(logger)
@click.pass_context
def gen(
ctx,
diff --git a/bob/pad/base/script/pad_figure.py b/src/bob/pad/base/script/pad_figure.py
similarity index 100%
rename from bob/pad/base/script/pad_figure.py
rename to src/bob/pad/base/script/pad_figure.py
diff --git a/bob/pad/base/script/run_pipeline.py b/src/bob/pad/base/script/run_pipeline.py
similarity index 98%
rename from bob/pad/base/script/run_pipeline.py
rename to src/bob/pad/base/script/run_pipeline.py
index 1686efeab0855b9372803f43104999e270a1e87c..f8f7e77fe635fa6c049b22a23f09e97167f57857 100644
--- a/bob/pad/base/script/run_pipeline.py
+++ b/src/bob/pad/base/script/run_pipeline.py
@@ -5,11 +5,13 @@ import logging
import click
-from bob.extension.scripts.click_helper import (
+from exposed.click import (
ConfigCommand,
ResourceOption,
+ log_parameters,
verbosity_option,
)
+
from bob.pipelines.distributed import (
VALID_DASK_CLIENT_STRINGS,
dask_get_partition_size,
@@ -113,7 +115,7 @@ logger = logging.getLogger(__name__)
help="If set, it will not use Dask for the execution of the pipeline.",
cls=ResourceOption,
)
-@verbosity_option(cls=ResourceOption)
+@verbosity_option(cls=ResourceOption, logger=logger)
def run_pipeline(
pipeline,
decision_function,
@@ -129,8 +131,6 @@ def run_pipeline(
):
"""Runs the simplest PAD pipeline."""
- from bob.extension.scripts.click_helper import log_parameters
-
log_parameters(logger)
execute_pipeline(
diff --git a/bob/pad/base/test/__init__.py b/tests/__init__.py
similarity index 100%
rename from bob/pad/base/test/__init__.py
rename to tests/__init__.py
diff --git a/bob/pad/base/test/data/csv_dataset.tar.gz b/tests/data/csv_dataset.tar.gz
similarity index 100%
rename from bob/pad/base/test/data/csv_dataset.tar.gz
rename to tests/data/csv_dataset.tar.gz
diff --git a/bob/pad/base/test/data/csv_dataset/protocol1/dev/for_attack.csv b/tests/data/csv_dataset/protocol1/dev/for_attack.csv
similarity index 100%
rename from bob/pad/base/test/data/csv_dataset/protocol1/dev/for_attack.csv
rename to tests/data/csv_dataset/protocol1/dev/for_attack.csv
diff --git a/bob/pad/base/test/data/csv_dataset/protocol1/dev/for_real.csv b/tests/data/csv_dataset/protocol1/dev/for_real.csv
similarity index 100%
rename from bob/pad/base/test/data/csv_dataset/protocol1/dev/for_real.csv
rename to tests/data/csv_dataset/protocol1/dev/for_real.csv
diff --git a/bob/pad/base/test/data/csv_dataset/protocol1/eval/for_attack.csv b/tests/data/csv_dataset/protocol1/eval/for_attack.csv
similarity index 100%
rename from bob/pad/base/test/data/csv_dataset/protocol1/eval/for_attack.csv
rename to tests/data/csv_dataset/protocol1/eval/for_attack.csv
diff --git a/bob/pad/base/test/data/csv_dataset/protocol1/eval/for_real.csv b/tests/data/csv_dataset/protocol1/eval/for_real.csv
similarity index 100%
rename from bob/pad/base/test/data/csv_dataset/protocol1/eval/for_real.csv
rename to tests/data/csv_dataset/protocol1/eval/for_real.csv
diff --git a/bob/pad/base/test/data/csv_dataset/protocol1/train/for_attack.csv b/tests/data/csv_dataset/protocol1/train/for_attack.csv
similarity index 100%
rename from bob/pad/base/test/data/csv_dataset/protocol1/train/for_attack.csv
rename to tests/data/csv_dataset/protocol1/train/for_attack.csv
diff --git a/bob/pad/base/test/data/csv_dataset/protocol1/train/for_real.csv b/tests/data/csv_dataset/protocol1/train/for_real.csv
similarity index 100%
rename from bob/pad/base/test/data/csv_dataset/protocol1/train/for_real.csv
rename to tests/data/csv_dataset/protocol1/train/for_real.csv
diff --git a/bob/pad/base/test/data/csv_scores/scores-dev.csv b/tests/data/csv_scores/scores-dev.csv
similarity index 100%
rename from bob/pad/base/test/data/csv_scores/scores-dev.csv
rename to tests/data/csv_scores/scores-dev.csv
diff --git a/bob/pad/base/test/data/csv_scores/scores-eval.csv b/tests/data/csv_scores/scores-eval.csv
similarity index 100%
rename from bob/pad/base/test/data/csv_scores/scores-eval.csv
rename to tests/data/csv_scores/scores-eval.csv
diff --git a/bob/pad/base/test/data/example_filelist/dev/for_attack.lst b/tests/data/example_filelist/dev/for_attack.lst
similarity index 100%
rename from bob/pad/base/test/data/example_filelist/dev/for_attack.lst
rename to tests/data/example_filelist/dev/for_attack.lst
diff --git a/bob/pad/base/test/data/example_filelist/dev/for_real.lst b/tests/data/example_filelist/dev/for_real.lst
similarity index 100%
rename from bob/pad/base/test/data/example_filelist/dev/for_real.lst
rename to tests/data/example_filelist/dev/for_real.lst
diff --git a/bob/pad/base/test/data/example_filelist/eval/for_attack.lst b/tests/data/example_filelist/eval/for_attack.lst
similarity index 100%
rename from bob/pad/base/test/data/example_filelist/eval/for_attack.lst
rename to tests/data/example_filelist/eval/for_attack.lst
diff --git a/bob/pad/base/test/data/example_filelist/eval/for_real.lst b/tests/data/example_filelist/eval/for_real.lst
similarity index 100%
rename from bob/pad/base/test/data/example_filelist/eval/for_real.lst
rename to tests/data/example_filelist/eval/for_real.lst
diff --git a/bob/pad/base/test/data/example_filelist/train/for_attack.lst b/tests/data/example_filelist/train/for_attack.lst
similarity index 100%
rename from bob/pad/base/test/data/example_filelist/train/for_attack.lst
rename to tests/data/example_filelist/train/for_attack.lst
diff --git a/bob/pad/base/test/data/example_filelist/train/for_real.lst b/tests/data/example_filelist/train/for_real.lst
similarity index 100%
rename from bob/pad/base/test/data/example_filelist/train/for_real.lst
rename to tests/data/example_filelist/train/for_real.lst
diff --git a/bob/pad/base/test/data/licit/scores-dev b/tests/data/licit/scores-dev
similarity index 100%
rename from bob/pad/base/test/data/licit/scores-dev
rename to tests/data/licit/scores-dev
diff --git a/bob/pad/base/test/data/licit/scores-eval b/tests/data/licit/scores-eval
similarity index 100%
rename from bob/pad/base/test/data/licit/scores-eval
rename to tests/data/licit/scores-eval
diff --git a/bob/pad/base/test/data/per_pai_scores/scores-dev b/tests/data/per_pai_scores/scores-dev
similarity index 100%
rename from bob/pad/base/test/data/per_pai_scores/scores-dev
rename to tests/data/per_pai_scores/scores-dev
diff --git a/bob/pad/base/test/data/per_pai_scores/scores-dev-0.hdf5 b/tests/data/per_pai_scores/scores-dev-0.hdf5
similarity index 100%
rename from bob/pad/base/test/data/per_pai_scores/scores-dev-0.hdf5
rename to tests/data/per_pai_scores/scores-dev-0.hdf5
diff --git a/bob/pad/base/test/data/per_pai_scores/scores-dev-1.hdf5 b/tests/data/per_pai_scores/scores-dev-1.hdf5
similarity index 100%
rename from bob/pad/base/test/data/per_pai_scores/scores-dev-1.hdf5
rename to tests/data/per_pai_scores/scores-dev-1.hdf5
diff --git a/bob/pad/base/test/data/per_pai_scores/scores-dev.csv b/tests/data/per_pai_scores/scores-dev.csv
similarity index 100%
rename from bob/pad/base/test/data/per_pai_scores/scores-dev.csv
rename to tests/data/per_pai_scores/scores-dev.csv
diff --git a/bob/pad/base/test/data/scores-dev b/tests/data/scores-dev
similarity index 100%
rename from bob/pad/base/test/data/scores-dev
rename to tests/data/scores-dev
diff --git a/bob/pad/base/test/data/scores-dev-attack b/tests/data/scores-dev-attack
similarity index 100%
rename from bob/pad/base/test/data/scores-dev-attack
rename to tests/data/scores-dev-attack
diff --git a/bob/pad/base/test/data/scores-dev-real b/tests/data/scores-dev-real
similarity index 100%
rename from bob/pad/base/test/data/scores-dev-real
rename to tests/data/scores-dev-real
diff --git a/bob/pad/base/test/data/scores-eval b/tests/data/scores-eval
similarity index 100%
rename from bob/pad/base/test/data/scores-eval
rename to tests/data/scores-eval
diff --git a/bob/pad/base/test/data/scores-eval-attack b/tests/data/scores-eval-attack
similarity index 100%
rename from bob/pad/base/test/data/scores-eval-attack
rename to tests/data/scores-eval-attack
diff --git a/bob/pad/base/test/data/scores-eval-real b/tests/data/scores-eval-real
similarity index 100%
rename from bob/pad/base/test/data/scores-eval-real
rename to tests/data/scores-eval-real
diff --git a/bob/pad/base/test/data/scores-train b/tests/data/scores-train
similarity index 100%
rename from bob/pad/base/test/data/scores-train
rename to tests/data/scores-train
diff --git a/bob/pad/base/test/data/scores-train-attack b/tests/data/scores-train-attack
similarity index 100%
rename from bob/pad/base/test/data/scores-train-attack
rename to tests/data/scores-train-attack
diff --git a/bob/pad/base/test/data/scores-train-real b/tests/data/scores-train-real
similarity index 100%
rename from bob/pad/base/test/data/scores-train-real
rename to tests/data/scores-train-real
diff --git a/bob/pad/base/test/data/spoof/scores-dev b/tests/data/spoof/scores-dev
similarity index 100%
rename from bob/pad/base/test/data/spoof/scores-dev
rename to tests/data/spoof/scores-dev
diff --git a/bob/pad/base/test/data/spoof/scores-eval b/tests/data/spoof/scores-eval
similarity index 100%
rename from bob/pad/base/test/data/spoof/scores-eval
rename to tests/data/spoof/scores-eval
diff --git a/bob/pad/base/test/test_commands.py b/tests/test_commands.py
similarity index 81%
rename from bob/pad/base/test/test_commands.py
rename to tests/test_commands.py
index 53d570025d7b897816a72710725086bd24c73cac..4192bb5b6753ec7949c268a86b1b17f25b02f624 100644
--- a/bob/pad/base/test/test_commands.py
+++ b/tests/test_commands.py
@@ -4,17 +4,16 @@ import pkg_resources
from click.testing import CliRunner
-from bob.extension.scripts.click_helper import assert_click_runner_result
-
-from ..script import pad_commands
+from bob.io.base.testing_utils import assert_click_runner_result
+from bob.pad.base.script import pad_commands
def test_gen_pad():
dev_ref_file = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-dev.csv"
+ __name__, "data/csv_scores/scores-dev.csv"
)
eval_ref_file = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-eval.csv"
+ __name__, "data/csv_scores/scores-eval.csv"
)
with open(dev_ref_file, "r") as f:
dev_ref = f.readlines()
@@ -48,10 +47,10 @@ def test_gen_pad():
def test_det_pad():
dev = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-dev.csv"
+ __name__, "data/csv_scores/scores-dev.csv"
)
test = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-eval.csv"
+ __name__, "data/csv_scores/scores-eval.csv"
)
runner = CliRunner()
with runner.isolated_filesystem():
@@ -63,10 +62,10 @@ def test_det_pad():
def test_hist_pad():
dev = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-dev.csv"
+ __name__, "data/csv_scores/scores-dev.csv"
)
test = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-eval.csv"
+ __name__, "data/csv_scores/scores-eval.csv"
)
runner = CliRunner()
with runner.isolated_filesystem():
@@ -108,10 +107,10 @@ def test_hist_pad():
def test_metrics_pad():
dev = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-dev.csv"
+ __name__, "data/csv_scores/scores-dev.csv"
)
test = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-eval.csv"
+ __name__, "data/csv_scores/scores-eval.csv"
)
runner = CliRunner()
with runner.isolated_filesystem():
@@ -121,10 +120,10 @@ def test_metrics_pad():
def test_evaluate_pad():
dev = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-dev.csv"
+ __name__, "data/csv_scores/scores-dev.csv"
)
test = pkg_resources.resource_filename(
- "bob.pad.base.test", "data/csv_scores/scores-eval.csv"
+ __name__, "data/csv_scores/scores-eval.csv"
)
runner = CliRunner()
with runner.isolated_filesystem():
diff --git a/bob/pad/base/test/test_error_utils.py b/tests/test_error_utils.py
similarity index 98%
rename from bob/pad/base/test/test_error_utils.py
rename to tests/test_error_utils.py
index 43fd9026d704c639beda1a232d78bb16b7486c53..8ebc9083fa79397b1fffcc30b116e60cb5a4f040 100644
--- a/bob/pad/base/test/test_error_utils.py
+++ b/tests/test_error_utils.py
@@ -1,7 +1,7 @@
import h5py
import numpy as np
-from bob.io.base.test_utils import datafile
+from bob.io.base.testing_utils import datafile
from bob.pad.base.error_utils import (
apcer_bpcer,
calc_threshold,
diff --git a/bob/pad/base/test/test_pipelines.py b/tests/test_pipelines.py
similarity index 95%
rename from bob/pad/base/test/test_pipelines.py
rename to tests/test_pipelines.py
index ade45f615b2450ff4d8417ecd2280693e6fff9e6..39c8efdabc64a5da1cd3ea7556be8925c505322c 100644
--- a/bob/pad/base/test/test_pipelines.py
+++ b/tests/test_pipelines.py
@@ -11,7 +11,7 @@ from sklearn.pipeline import Pipeline
import bob.measure
import bob.pipelines as mario
-from bob.extension.scripts.click_helper import assert_click_runner_result
+from bob.io.base.testing_utils import assert_click_runner_result
from bob.pad.base.error_utils import split_csv_pad
from bob.pad.base.pipelines import Database
from bob.pad.base.script.run_pipeline import run_pipeline as run_pipeline_cli
@@ -73,7 +73,7 @@ def _create_config_file(path):
with open(path, "w") as f:
f.write(
"""
-from bob.pad.base.test.test_pipelines import DummyPadDatabase, dummy_pipeline
+from tests.test_pipelines import DummyPadDatabase, dummy_pipeline
database = DummyPadDatabase()
pipeline = dummy_pipeline()
"""
diff --git a/version.txt b/version.txt
deleted file mode 100644
index f4939080b892a87661f310207a4c09a52639a640..0000000000000000000000000000000000000000
--- a/version.txt
+++ /dev/null
@@ -1 +0,0 @@
-5.0.5b0