Commit 642e03cd authored by Manuel Günther's avatar Manuel Günther
Browse files

New README and documentation strategy.

parent 37b5f78c
......@@ -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/
......@@ -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
......
......@@ -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
......@@ -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\
");
......
......@@ -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
......
......@@ -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
......
......@@ -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\
......
......@@ -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
......
......@@ -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
......@@ -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
-------------
......
......@@ -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',
],
)
)
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