Added tons of documentation

bob/bio/base/algorithm/__init__.py

@@ -3,3 +3,6 @@
 from .LDA import LDA
 from .PLDA import PLDA
 from .BIC import BIC
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/bio/base/extractor/__init__.py

@@ -1,8 +1,5 @@
-#!/usr/bin/env python
-# vim: set fileencoding=utf-8 :
-# Laurent El Shafey <Laurent.El-Shafey@idiap.ch>
-
-"""Basic features for biometric recognition"""
-
 from .Extractor import Extractor
 from .Linearize import Linearize
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/bio/base/grid.py

@@ -106,3 +106,6 @@ def queue(self, params):
   def is_local(self):
     """Returns whether this grid setup should use the local submission or the SGE grid."""
     return self.grid_type == 'local'
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/bio/base/preprocessor/__init__.py

@@ -1 +1,4 @@
 from .Preprocessor import Preprocessor
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/bio/base/script/resources.py

@@ -39,7 +39,7 @@ def resources():
 
 def databases():
   import argparse
-  database_replacement = "/idiap/home/%s/.bob_bio_databases.txt" % os.environ["USER"] if os.path.isdir("/idiap") else "/home/%s/.bob_bio_databases.txt" % os.environ["USER"]
+  database_replacement = "%s/.bob_bio_databases.txt" % os.environ["HOME"]
 
   parser = argparse.ArgumentParser(description="Prints a list of directories for registered databases", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
   parser.add_argument('-D', '--database-directories-file', metavar = 'FILE', default = database_replacement, help = 'The file, where database directories are stored (to avoid changing the database configurations)')

bob/bio/base/tools/__init__.py

@@ -5,3 +5,6 @@
 from .scoring import *
 from .command_line import *
 from .grid import *
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/bio/base/tools/command_line.py

@@ -5,7 +5,7 @@
 import bob.core
 logger = bob.core.log.setup("bob.bio.base")
 
-from ..utils import load_resource, resource_keys
+from .. import utils
 from . import FileSelector
 
 """Execute biometric recognition algorithms on a certain biometric database.
@@ -23,13 +23,13 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
   ############## options that are required to be specified #######################
   config_group = parser.add_argument_group('\nParameters defining the experiment. Most of these parameters can be a registered resource, a configuration file, or even a string that defines a newly created object')
   config_group.add_argument('-d', '--database', metavar = 'x', nargs = '+', required = True,
-      help = 'Database and the protocol; registered databases are: %s' % resource_keys('database', exclude_resources_from))
+      help = 'Database and the protocol; registered databases are: %s' % utils.resource_keys('database', exclude_resources_from))
   config_group.add_argument('-p', '--preprocessor', metavar = 'x', nargs = '+', required = True,
-      help = 'Data preprocessing; registered preprocessors are: %s' % resource_keys('preprocessor', exclude_resources_from))
+      help = 'Data preprocessing; registered preprocessors are: %s' % utils.resource_keys('preprocessor', exclude_resources_from))
   config_group.add_argument('-e', '--extractor', metavar = 'x', nargs = '+', required = True,
-      help = 'Feature extraction; registered feature extractors are: %s' % resource_keys('extractor', exclude_resources_from))
+      help = 'Feature extraction; registered feature extractors are: %s' % utils.resource_keys('extractor', exclude_resources_from))
   config_group.add_argument('-a', '--algorithm', metavar = 'x', nargs = '+', required = True,
-      help = 'Biometric recognition; registered algorithms are: %s' % resource_keys('algorithm', exclude_resources_from))
+      help = 'Biometric recognition; registered algorithms are: %s' % utils.resource_keys('algorithm', exclude_resources_from))
   config_group.add_argument('-g', '--grid', metavar = 'x', nargs = '+',
       help = 'Configuration for the grid setup; if not specified, the commands are executed sequentially on the local machine.')
   config_group.add_argument('--imports', metavar = 'LIB', nargs = '+', default = ['bob.bio.base'],
@@ -48,7 +48,7 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
   is_idiap = os.path.isdir("/idiap")
   temp = "/idiap/temp/%s/database-name/sub-directory" % os.environ["USER"] if is_idiap else "temp"
   results = "/idiap/user/%s/database-name/sub-directory" % os.environ["USER"] if is_idiap else "results"
-  database_replacement = "/idiap/home/%s/.bob_bio_databases.txt" % os.environ["USER"] if is_idiap else "/home/%s/.bob_bio_databases.txt" % os.environ["USER"]
+  database_replacement = "%s/.bob_bio_databases.txt" % os.environ["HOME"]
 
   dir_group = parser.add_argument_group('\nDirectories that can be changed according to your requirements')
   dir_group.add_argument('-T', '--temp-directory', metavar = 'DIR',
@@ -150,12 +150,12 @@ def initialize(parsers, command_line_parameters = None, skips = []):
     args.timer = ('real', 'system', 'user')
 
   # load configuration resources
-  args.database = load_resource(' '.join(args.database), 'database', imports = args.imports)
-  args.preprocessor = load_resource(' '.join(args.preprocessor), 'preprocessor', imports = args.imports)
-  args.extractor = load_resource(' '.join(args.extractor), 'extractor', imports = args.imports)
-  args.algorithm = load_resource(' '.join(args.algorithm), 'algorithm', imports = args.imports)
+  args.database = utils.load_resource(' '.join(args.database), 'database', imports = args.imports)
+  args.preprocessor = utils.load_resource(' '.join(args.preprocessor), 'preprocessor', imports = args.imports)
+  args.extractor = utils.load_resource(' '.join(args.extractor), 'extractor', imports = args.imports)
+  args.algorithm = utils.load_resource(' '.join(args.algorithm), 'algorithm', imports = args.imports)
   if args.grid is not None:
-    args.grid = load_resource(' '.join(args.grid), 'grid', imports = args.imports)
+    args.grid = utils.load_resource(' '.join(args.grid), 'grid', imports = args.imports)
 
   # set base directories
   is_idiap = os.path.isdir("/idiap")
@@ -237,8 +237,8 @@ def write_info(args, command_line_parameters, executable):
     f.write(command_line([executable] + command_line_parameters) + "\n\n")
     f.write("Configuration:\n")
     f.write("Database:\n%s\n\n" % args.database)
-    f.write("Preprocessing:\n%s\n\n" % args.preprocessor)
-    f.write("Feature Extraction:\n%s\n\n" % args.extractor)
+    f.write("Preprocessor:\n%s\n\n" % args.preprocessor)
+    f.write("Extractor:\n%s\n\n" % args.extractor)
     f.write("Algorithm:\n%s\n\n" % args.algorithm)
   except IOError:
     logger.error("Could not write the experimental setup into file '%s'", args.info_file)

bob/bio/base/tools/grid.py

@@ -3,7 +3,7 @@
 import sys
 import os
 import math
-from ..grid import Grid
+from .. import grid
 from .command_line import command_line
 
 import bob.core
@@ -48,7 +48,7 @@ def __init__(self, args, command_line_parameters, executable = 'verify.py', firs
     self.executable = executable
 
     if args.grid is not None:
-      assert isinstance(args.grid, Grid)
+      assert isinstance(args.grid, grid.Grid)
 
       # find, where jman is installed
       jmans = bob.extension.find_executable('jman', prefixes = ['bin'])

bob/bio/base/utils/resources.py

@@ -174,7 +174,7 @@ def list_resources(keyword, strip=['dummy']):
   entry_points = _get_entry_points(keyword, strip)
   last_dist = None
   retval = ""
-  length = max(len(entry_point.name) for entry_point in entry_points)
+  length = max(len(entry_point.name) for entry_point in entry_points) if entry_points else 1
 
   for entry_point in sorted(entry_points):
     if last_dist != str(entry_point.dist):
@@ -198,7 +198,6 @@ def database_directories(strip=['dummy'], replacements = None):
       db = load_resource(entry_point.name, 'database')
       db.replace_directories(replacements)
       dirs[entry_point.name] = [db.original_directory]
-#      import ipdb; ipdb.set_trace()
       if db.annotation_directory is not None:
         dirs[entry_point.name].append(db.annotation_directory)
     except (AttributeError, ValueError):

doc/conf.py

@@ -86,7 +86,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-#exclude_patterns = ['**/links.rst']
+exclude_patterns = ['links.rst']
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None