[sphinx] cleanup and fixes

bob/pad/base/database/__init__.py

 from .database import PadDatabase
 from .file import PadFile
 
+# to fix sphinx warnings of not able to find classes, when path is shortened
+PadDatabase.__module__ = "database"
+PadFile.__module__ = "database"
 # gets sphinx autodoc done right - don't remove it
 __all__ = [_ for _ in dir() if not _.startswith('_')]

doc/experiments.rst

@@ -86,15 +86,12 @@ To change this behavior, you can use the ``--verbose`` option several times to i
 2) Informative messages
 3) Debug messages
 
-When running experiments, my personal preference is verbose level 2, which can be enabled by using the short version: ``-vv``.
-So, a typical PAD experiment (in this case, attacks detection in speech) could look something like:
+When running experiments, it is a good idea to set verbose level 2, which can be enabled by using the short version: ``-vv``.
+So, a typical PAD experiment (in this case, attacks detection in speech) would look like the following:
 
 .. code-block:: sh
 
-   $ ./bin/spoof.py --database avspoof --preprocessor vad_energy --extractor lbp_hist --algorithm logregr --sub-directory pad_speech -vv
-
-.. note::
-   To be able to run exactly the command line from above, it requires to have :ref:`bob.pad.voice <bob.pad.voice>` installed.
+   $ ./bin/spoof.py --database <database-name> --preprocessor <preprocessor> --extractor <extractor> --algorithm <algorithm> --sub-directory <folder_name> -vv
 
 Before running an experiment, it is recommended to add the ``--dry-run`` option, so that it will only print, which steps would be executed, without actually executing them, and make sure that everything works as expected.
 
@@ -151,7 +148,7 @@ Hence, to run the same experiment as above using four parallel threads on the lo
 
 .. code-block:: sh
 
-   $ ./bin/spoof.py --database avspoof --preprocessor vad_energy --extractor lbp_hist --algorithm logregr --sub-directory pad_speech -vv --grid local-p4 --run-local-scheduler --nice 10
+   $ ./bin/spoof.py --database <database-name> --preprocessor <preprocessor> --extractor <extractor> --algorithm <algorithm> --sub-directory <folder_name> -vv --grid local-p4 --run-local-scheduler --nice 10
 
 .. note::
    You might realize that the second execution of the same experiment is much faster than the first one.
@@ -198,7 +195,7 @@ To change the protocol, you can either modify the configuration file, or simply
 
 Some databases define several kinds of evaluation setups.
 For example, often two groups of data are defined, a so-called *development set* and an *evaluation set*.
-The scores of the two groups will be concatenated into two files called **scores-dev** and **scores-eval**, which are located in the score directory (see above).
+The scores of the two groups will be concatenated into several files called **scores-dev** and **scores-eval**, which are located in the score directory (see above).
 In this case, by default only the development set is employed.
 To use both groups, just specify ``--groups dev eval`` (of course, you can also only use the ``'eval'`` set by calling ``--groups eval``).
 

doc/index.rst

@@ -34,7 +34,7 @@ The implementation of (most of) the tools is separated into other packages in th
 All these packages can be easily combined.
 Here is a growing list of derived packages:
 
-* :ref:`bob.pad.voice <bob.pad.voice>` Tools to run presentation attack detection experiments for speech, including Cepstral-based feature and LBP-based feature extraction, GMM-based and logistic regression based algorithms, plot processing and score fusion scripts.
+* `bob.pad.voice <http://pypi.python.org/pypi/bob.pad.voice>`__` Tools to run presentation attack detection experiments for speech, including several Cepstral-based features and LBP-based feature extraction, GMM-based and logistic regression based algorithms, as well as plot and score fusion scripts.
 
 If you are interested, please continue reading:
 

doc/installation.rst

@@ -29,10 +29,6 @@ There, in the ``eggs`` section of the ``buildout.cfg`` file, simply list the ``b
           gridtk
 
 in order to download and install all packages that are required for your experiments.
-In the example above, you might want to run a simple speech presentation attack detection
-experiment using the :py:class:`bob.bio.spear.preprocessor.Mod_4Hz` and
-the :py:class:`bob.pad.voice.extractor.LBPHistograms` feature extractor
-defined in :ref:`bob.pad.voice <bob.pad.voice>`, using the AVspoof database interface defined in :ref:`bob.db.avspoof <bob.db.avspoof>`.
 Running the simple command line:
 
 .. code-block:: sh
@@ -67,7 +63,7 @@ Please use ``./bin/databases.py`` for a list of known databases, where you can s
 
 
 .. note::
-   If you have installed only ``bob.pad.base``, there is no database listed -- as all databases are included in other packages, such as :ref:`bob.pad.voice <bob.pad.voice>`.
+   If you have installed only ``bob.pad.base``, there is no database listed -- as all databases are included in other extension packages, such as :ref:`bob.pad.voice <bob.pad.voice>`.
 
 
 Test your Installation

doc/py_api.rst

@@ -40,10 +40,6 @@ Details
 
 .. automodule:: bob.pad.base
 
-   .. attribute:: valid_keywords
-
-      Valid keywords, for which resources are defined, are ``('database', 'preprocessor', 'extractor', 'algorithm', 'grid')``
-
 
 .. automodule:: bob.pad.base.tools