New README and documentation strategy.

.gitignore

@@ -2,12 +2,9 @@
 *.swp
 *.pyc
 *.so
-*.so.*
 *.dylib
-CMakeLists.txt
 bin
 eggs
-src
 parts
 .installed.cfg
 .mr.developer.cfg
@@ -19,6 +16,4 @@ dist
 .gdb_history
 build
 *.egg
-opsnr.stt
-.coverage
-.DS_Store
+src/

.travis.yml

@@ -6,6 +6,7 @@ matrix:
     env:
     - secure: TEPqit10h7L/l4kbv8zbvKH9freS6f1p2pIfUuMMfASKuZHAzizljSv14NKqeXhrpr5kPbQhNAcMrme8x7Is7bQCVxN4/8K6BQNmp2V6hWxBAh+2wk/9Bxv+FNlDBhjQM3rNIM0Wjzf5JW5OM+CMeZjxI1Mi/vNI/oN2vtvFfsA=
     - secure: glYEyCLOew9QZXhgTHKkP9JGt/pAT7P/Pfk/SqyX++6wyTjyMrnj0DeSJW7khxtxo6kL+d23eojQVy6Q0izZ3US3KGt3PsLxYf+2Yi4Lhji/RjhZG4qgpz4XUb3cZcmb2wTJ/qFYZbGRjr5KvzkICvzv1IjxCeTuEwnj1ctz62Y=
+    - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
   - python: 3.2
     env:
     - NUMPYSPEC===1.7.1
@@ -15,7 +16,7 @@ matrix:
 before_install:
 - sudo add-apt-repository -y ppa:biometrics/bob
 - sudo apt-get update -qq
-- sudo apt-get install -qq --force-yes libboost-all-dev libblitz1-dev libhdf5-serial-dev
+- sudo apt-get install -qq --force-yes libboost-all-dev libblitz1-dev libhdf5-serial-dev texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
 - if [ -n "${NUMPYSPEC}" ]; then sudo apt-get install -qq libatlas-dev libatlas-base-dev liblapack-dev gfortran; fi
 - if [ -n "${NUMPYSPEC}" ]; then pip install --upgrade pip setuptools; fi
 - if [ -n "${NUMPYSPEC}" ]; then pip install --find-links http://wheels.astropy.org/ --find-links http://wheels2.astropy.org/ --use-wheel numpy$NUMPYSPEC; fi

README.rst

@@ -2,79 +2,36 @@
 .. Andre Anjos <andre.anjos@idiap.ch>
 .. Fri 13 Dec 2013 12:35:22 CET
 
-.. image:: https://travis-ci.org/bioidiap/bob.learn.activation.svg?branch=master
-   :target: https://travis-ci.org/bioidiap/bob.learn.activation
+.. image:: http://img.shields.io/badge/docs-stable-yellow.png
+   :target: http://pythonhosted.org/bob.learn.activation/index.html
 .. image:: http://img.shields.io/badge/docs-latest-orange.png
    :target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.learn.activation/master/index.html
+.. image:: https://travis-ci.org/bioidiap/bob.learn.activation.svg?branch=master
+   :target: https://travis-ci.org/bioidiap/bob.learn.activation
 .. image:: https://coveralls.io/repos/bioidiap/bob.learn.activation/badge.png
    :target: https://coveralls.io/r/bioidiap/bob.learn.activation
-.. image:: http://img.shields.io/github/tag/bioidiap/bob.learn.activation.png
-   :target: https://github.com/bioidiap/bob.learn.activation
+.. image:: https://img.shields.io/badge/github-master-0000c0.png
+   :target: https://github.com/bioidiap/bob.learn.activation/tree/master
 .. image:: http://img.shields.io/pypi/v/bob.learn.activation.png
    :target: https://pypi.python.org/pypi/bob.learn.activation
 .. image:: http://img.shields.io/pypi/dm/bob.learn.activation.png
    :target: https://pypi.python.org/pypi/bob.learn.activation
 
-=======================================================
- Python bindings for bob.machine's Activation functors
-=======================================================
+============================
+ Activation functors of Bob
+============================
 
-This package contains a set of Pythonic bindings for Bob's machine Activation
-functors.
+This package contains Bob's Activation functors, which used in several learning packages of Bob in the namespace ``bob.learn``.
 
 Installation
 ------------
-
-Install it through normal means, via PyPI or use ``zc.buildout`` to bootstrap
-the package and run test units.
+To install this package -- alone or together with other `Packages of Bob <https://github.com/idiap/bob/wiki/Packages>`_ -- please read the `Installation Instructions <https://github.com/idiap/bob/wiki/Installation>`_.
+For Bob_ to be able to work properly, some dependent packages are required to be installed.
+Please make sure that you have read the `Dependencies <https://github.com/idiap/bob/wiki/Dependencies>`_ for your operating system.
 
 Documentation
 -------------
+For further documentation on this package, please read the `Stable Version <http://pythonhosted.org/bob.learn.activation/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.learn.activation/master/index.html>`_ of the documentation.
+For a list of tutorials on this or the other packages ob Bob_, or information on submitting issues, asking questions and starting discussions, please visit its website.
 
-The latest version of the documentation can be found `here <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.learn.activation/master/index.html>`_.
-
-Otherwise, you can generate the documentation for this package yourself, after installation, using Sphinx::
-
-  $ sphinx-build -b html doc sphinx
-
-This shall place in the directory ``sphinx``, the current version for the
-documentation of the package.
-
-Testing
--------
-
-You can run a set of tests using the nose test runner::
-
-  $ nosetests -sv
-
-.. warning::
-
-   If Bob <= 1.2.1 is installed on your python path, nose will automatically
-   load the old version of the insulate plugin available in Bob, which will
-   trigger the loading of incompatible shared libraries (from Bob itself), in
-   to your working binary. This will cause a stack corruption. Either remove
-   the centrally installed version of Bob, or build your own version of Python
-   in which Bob <= 1.2.1 is not installed.
-
-You can run our documentation tests using sphinx itself::
-
-  $ sphinx-build -b doctest doc sphinx
-
-You can test overall test coverage with::
-
-  $ nosetests --with-coverage --cover-package=bob.learn.activation
-
-The ``coverage`` egg must be installed for this to work properly.
-
-Development
------------
-
-To develop this package, install using ``zc.buildout``, using the buildout
-configuration found on the root of the package::
-
-  $ python bootstrap.py
-  ...
-  $ ./bin/buildout
-
-Tweak the options in ``buildout.cfg`` to disable/enable verbosity and debug
-builds.
+.. _bob: https://www.idiap.ch/software/bob

bob/learn/activation/activation.cpp

@@ -429,7 +429,7 @@ PyDoc_STRVAR(s_load_str, "load");
 PyDoc_STRVAR(s_load_doc,
 "o.load(f) -> None\n\
 \n\
-Loads itself from a :py:class:`bob.io.HDF5File`\n\
+Loads itself from a :py:class:`bob.io.base.HDF5File`\n\
 \n\
 ");
 
@@ -463,7 +463,7 @@ PyDoc_STRVAR(s_save_str, "save");
 PyDoc_STRVAR(s_save_doc,
 "o.save(f) -> None\n\
 \n\
-Saves itself to a :py:class:`bob.io.HDF5File`\n\
+Saves itself to a :py:class:`bob.io.base.HDF5File`\n\
 \n\
 ");
 

bob/learn/activation/linear.cpp

@@ -18,7 +18,7 @@ Computes :math:`f(z) = C \\cdot z` as activation function.\n\
 The constructor builds a new linear activation function\n\
 with a given constant. Don't use this if you just want to\n\
 set constant to the default value (1.0). In such a case,\n\
-prefer to use the more efficient :py:class:`IdentityActivation`.\n\
+prefer to use the more efficient :py:class:`Identity` activation.\n\
 ");
 
 static int PyBobLearnLinearActivation_init

bob/learn/activation/mult_tanh.cpp

@@ -12,7 +12,7 @@ PyDoc_STRVAR(s_multtanhactivation_str,
     BOB_EXT_MODULE_PREFIX ".MultipliedHyperbolicTangent");
 
 PyDoc_STRVAR(s_multtanhactivation_doc,
-"MultipliedHyperbolicTangentActivation([C=1.0, [M=1.0]]) -> new multiplied hyperbolic tangent functor\n\
+"MultipliedHyperbolicTangent([C=1.0, [M=1.0]]) -> new multiplied hyperbolic tangent functor\n\
 \n\
 Computes :math:`f(z) = C \\cdot \\tanh(Mz)` as activation\n\
 function.\n\
@@ -21,7 +21,7 @@ Builds a new hyperbolic tangent activation function with a given\n\
 constant for the inner and outter products. Don't use this if you\n\
 just want to set the constants to the default values (1.0). In\n\
 such a case, prefer to use the more efficient\n\
-:py:class:`bob.learn.activation.HyperbolicTangentActivation`.\n\
+:py:class:`HyperbolicTangent` activation.\n\
 ");
 
 static int PyBobLearnMultipliedHyperbolicTangentActivation_init

bob/learn/activation/tanh.cpp

@@ -9,10 +9,10 @@
 #include <bob.learn.activation/api.h>
 
 PyDoc_STRVAR(s_hyperbolictangentactivation_str,
-    BOB_EXT_MODULE_PREFIX ".HyperbolicTangentActivation");
+    BOB_EXT_MODULE_PREFIX ".HyperbolicTangent");
 
 PyDoc_STRVAR(s_hyperbolictangentactivation_doc,
-"HyperbolicTangentActivation() -> new HyperbolicTangentActivation\n\
+"HyperbolicTangent() -> new HyperbolicTangent\n\
 \n\
 Computes :math:`f(z) = \\tanh(z)` as activation function.\n\
 \n\

buildout.cfg

@@ -17,6 +17,7 @@ develop = src/bob.extension
 ; options for bob.buildout extension
 debug = true
 verbose = true
+newest = false
 
 [sources]
 bob.extension = git https://github.com/bioidiap/bob.extension

doc/conf.py

@@ -249,36 +249,10 @@ autoclass_content = 'both'
 autodoc_member_order = 'bysource'
 autodoc_default_flags = ['members', 'undoc-members', 'inherited-members', 'show-inheritance']
 
-def smaller_than(v1, v2):
-  """Compares scipy/numpy version numbers"""
-
-  c1 = v1.split('.')
-  c2 = v2.split('.')[:len(c1)] #clip to the compared version
-  for i, k in enumerate(c2):
-    n1 = c1[i]
-    n2 = c2[i]
-    try:
-      n1 = int(n1)
-      n2 = int(n2)
-    except ValueError:
-      n1 = str(n1)
-      n2 = str(n2)
-    if n1 > n2: return False
-  return True
-
-# Some name mangling to find the correct sphinx manuals for some packages
-numpy_version = __import__('numpy').version.version
-if smaller_than(numpy_version, '1.5.z'):
-  numpy_version = '.'.join(numpy_version.split('.')[:-1]) + '.x'
-else:
-  numpy_version = '.'.join(numpy_version.split('.')[:-1]) + '.0'
-numpy_manual = 'http://docs.scipy.org/doc/numpy-%s/' % numpy_version
-
 # For inter-documentation mapping:
-intersphinx_mapping = {
-  'http://docs.python.org/%d.%d/' % sys.version_info[:2]: None,
-  numpy_manual: None,
-  }
+from bob.extension.utils import link_documentation
+intersphinx_mapping = link_documentation()
+
 
 def setup(app):
   pass

doc/index.rst

@@ -10,9 +10,8 @@
 
 .. todolist::
 
-This module contains some functionality from Bob bound to Python, available in
-the C++ counter-part ``bob::machine``. It includes Activation functors from the
-Machine Learning core.
+This module includes Activation functors from the Machine Learning core of Bob.
+These Activation functors are used in several other packages like `bob.learn.linear <http://pypi.python.org/pypi/bob.learn.linear>`_ or `bob.learn.mlp <http://pypi.python.org/pypi/bob.learn.mlp>`_.
 
 Documentation
 -------------

setup.py

@@ -84,7 +84,8 @@ setup(
     },
 
     classifiers = [
-      'Development Status :: 3 - Alpha',
+      'Framework :: Bob',
+      'Development Status :: 4 - Beta',
       'Intended Audience :: Developers',
       'License :: OSI Approved :: BSD License',
       'Natural Language :: English',
@@ -93,4 +94,4 @@ setup(
       'Topic :: Software Development :: Libraries :: Python Modules',
     ],
 
-  )
+)