diff --git a/bob/bio/base/script/annotate.py b/bob/bio/base/script/annotate.py
index 2918590eec60532410d4fd6af529f44228311027..03abb154893832b51bcd94d03fd0941d0fc1af29 100644
--- a/bob/bio/base/script/annotate.py
+++ b/bob/bio/base/script/annotate.py
@@ -5,66 +5,49 @@ import json
import click
from os.path import dirname, isfile, expanduser
from bob.extension.scripts.click_helper import (
- verbosity_option, ConfigCommand, ResourceOption)
+ verbosity_option, ConfigCommand, ResourceOption, log_parameters)
from bob.io.base import create_directories_safe
from bob.bio.base.tools.grid import indices
logger = logging.getLogger(__name__)
-@click.command(entry_point_group='bob.bio.config', cls=ConfigCommand)
+ANNOTATE_EPILOG = '''\b
+Examples:
+
+ $ bob bio annotate -vvv -d <database> -a <annotator> -o /tmp/annotations
+ $ jman submit --array 64 -- bob bio annotate ... --array 64
+'''
+
+
+@click.command(entry_point_group='bob.bio.config', cls=ConfigCommand,
+ epilog=ANNOTATE_EPILOG)
@click.option('--database', '-d', required=True, cls=ResourceOption,
- entry_point_group='bob.bio.database')
+ entry_point_group='bob.bio.database',
+ help='''The database that you want to annotate.''')
@click.option('--annotator', '-a', required=True, cls=ResourceOption,
- entry_point_group='bob.bio.annotator')
-@click.option('--output-dir', '-o', required=True, cls=ResourceOption)
-@click.option('--force', '-f', is_flag=True, cls=ResourceOption)
-@click.option('--array', type=click.INT, default=1, cls=ResourceOption)
+ entry_point_group='bob.bio.annotator',
+ help='A callable that takes the database and a sample (biofile) '
+ 'of the database and returns the annotations in a dictionary.')
+@click.option('--output-dir', '-o', required=True, cls=ResourceOption,
+ help='The directory to save the annotations.')
+@click.option('--force', '-f', is_flag=True, cls=ResourceOption,
+ help='Whether to overwrite existing annotations.')
+@click.option('--array', type=click.INT, default=1, cls=ResourceOption,
+ help='Use this option alongside gridtk to submit this script as '
+ 'an array job.')
@click.option('--database-directories-file', cls=ResourceOption,
- default=expanduser('~/.bob_bio_databases.txt'))
+ default=expanduser('~/.bob_bio_databases.txt'),
+ help='(Deprecated) To support loading of old databases.')
@verbosity_option(cls=ResourceOption)
def annotate(database, annotator, output_dir, force, array,
database_directories_file, **kwargs):
"""Annotates a database.
+
The annotations are written in text file (json) format which can be read
back using :any:`bob.db.base.read_annotation_file` (annotation_type='json')
-
- \b
- Parameters
- ----------
- database : :any:`bob.bio.database`
- The database that you want to annotate. Can be a ``bob.bio.database``
- entry point or a path to a Python file which contains a variable
- named `database`.
- annotator : callable
- A function that takes the database and a sample (biofile) of the
- database and returns the annotations in a dictionary. Can be a
- ``bob.bio.annotator`` entry point or a path to a Python file which
- contains a variable named `annotator`.
- output_dir : str
- The directory to save the annotations.
- force : bool, optional
- Whether to overwrite existing annotations.
- array : int, optional
- Use this option alongside gridtk to submit this script as an array job.
- verbose : int, optional
- Increases verbosity (see help for --verbose).
-
- \b
- [CONFIG]... Configuration files. It is possible to pass one or
- several Python files (or names of ``bob.bio.config``
- entry points) which contain the parameters listed
- above as Python variables. The options through the
- command-line (see below) will override the values of
- configuration files.
"""
- logger.debug('database: %s', database)
- logger.debug('annotator: %s', annotator)
- logger.debug('force: %s', force)
- logger.debug('output_dir: %s', output_dir)
- logger.debug('array: %s', array)
- logger.debug('database_directories_file: %s', database_directories_file)
- logger.debug('kwargs: %s', kwargs)
+ log_parameters(logger)
# Some databases need their original_directory to be replaced
database.replace_directories(database_directories_file)
diff --git a/bob/bio/base/script/baseline.py b/bob/bio/base/script/baseline.py
index 63758fae181dea04221cf19dab78c614f1731677..e0c2091238b1b7764705d0775df88d296c9841cc 100644
--- a/bob/bio/base/script/baseline.py
+++ b/bob/bio/base/script/baseline.py
@@ -25,7 +25,7 @@ logger = logging.getLogger("bob.bio.base")
@click.argument('database', required=True)
@verbosity_option()
@click.pass_context
-def baseline(ctx, baseline, database):
+def baseline(ctx, baseline, database, **kwargs):
"""Run a biometric recognition baseline.
\b
@@ -65,7 +65,7 @@ def baseline(ctx, baseline, database):
sub_directory = os.path.join(database, baseline)
else:
sub_directory = baseline
-
+
logger.debug('Database groups are %s', database_data["groups"])
# call verify with newly generated config file. We will create a new config
diff --git a/bob/bio/base/script/gen.py b/bob/bio/base/script/gen.py
index 0c4d382756ecdbc703e12281b5717fd46b3f76f1..547c4baa1114c36278e8207208239611b121b38c 100644
--- a/bob/bio/base/script/gen.py
+++ b/bob/bio/base/script/gen.py
@@ -87,7 +87,7 @@ def write_scores_to_file(neg, pos, filename, n_sys=1, five_col=False):
@click.option('-n', '--n-sys', default=1, type=click.INT, show_default=True)
@click.option('--five-col/--four-col', default=False, show_default=True)
@verbosity_option()
-def gen(outdir, mean_match, mean_non_match, n_sys, five_col):
+def gen(outdir, mean_match, mean_non_match, n_sys, five_col, **kwargs):
"""Generate random scores.
Generates random scores in 4col or 5col format. The scores are generated
using Gaussian distribution whose mean is an input