diff --git a/.gitignore b/.gitignore
index 6954e9b210ca1a355c84bd660549ae86d08312b7..dae95ef0644140d1c14bdc82855252e51625a8de 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,8 +2,7 @@
*.swp
*.pyc
*.so
-*.so.*
-CMakeLists.txt
+*.dylib
bin
eggs
parts
@@ -18,4 +17,3 @@ dist
build
*.egg
src/
-opsnr.stt
diff --git a/.travis.yml b/.travis.yml
index b4cf96d73f30f361ca57a0b109959d8bfd90a945..de2acbb79d6eef42e3030a2f52af5012027cf79f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,21 +1,22 @@
language: python
matrix:
include:
- - python: 2.6
- - python: 2.7
- env:
- - secure: Mjicore21483fMCADQLzOqhWQ9jWlfoppAMK+8cHYrz6pluK8cv/lBou4JXdE5Y/1z8svn44boMpCSldppDImqFfJGLFE0mvAl8CiSHtXp3mxQxpS2yDd4pCAfxMzr+K4M0/bfOrhAviI/3itKG5GiwCviLeTIiQ7dAJJrnU1C8=
- - secure: QgHg0wGSy8ZGRELq7nXAAdv17q2/NDinAoFA3aNjJ5ZAUsi9ymKJGtwa1HbJN6npQgMDAew+joj85VeKMEDv7dCcNp2ySm2q23qIppoAutdBH23tvaMmvzgKsSvtFqq7SL52vcx9HY13mVXhhUenr1XeGlxRV2RFTeQz276arsg=
- - python: 3.2
- env:
- - NUMPYSPEC===1.7.1
- - python: 3.3
- env:
- - NUMPYSPEC===1.8.0
+ - python: 2.6
+ - python: 2.7
+ env:
+ - secure: Mjicore21483fMCADQLzOqhWQ9jWlfoppAMK+8cHYrz6pluK8cv/lBou4JXdE5Y/1z8svn44boMpCSldppDImqFfJGLFE0mvAl8CiSHtXp3mxQxpS2yDd4pCAfxMzr+K4M0/bfOrhAviI/3itKG5GiwCviLeTIiQ7dAJJrnU1C8=
+ - secure: QgHg0wGSy8ZGRELq7nXAAdv17q2/NDinAoFA3aNjJ5ZAUsi9ymKJGtwa1HbJN6npQgMDAew+joj85VeKMEDv7dCcNp2ySm2q23qIppoAutdBH23tvaMmvzgKsSvtFqq7SL52vcx9HY13mVXhhUenr1XeGlxRV2RFTeQz276arsg=
+ - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
+ - python: 3.2
+ env:
+ - NUMPYSPEC===1.7.1
+ - python: 3.3
+ env:
+ - NUMPYSPEC===1.8.0
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 libatlas-dev libatlas-base-dev liblapack-dev libhdf5-serial-dev;
+- sudo apt-get install -qq --force-yes libboost-all-dev libblitz1-dev libatlas-dev libatlas-base-dev liblapack-dev libhdf5-serial-dev texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
- if [ -n "${NUMPYSPEC}" ]; then sudo apt-get install -qq gfortran; fi
- if [ -n "${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
diff --git a/README.rst b/README.rst
index 8672712917e14fc25ed55f3711e4f12252f9ca0f..efe635434ed98460ad103bf0ad3309b9825eb777 100644
--- a/README.rst
+++ b/README.rst
@@ -2,78 +2,34 @@
.. Andre Anjos <andre.anjos@idiap.ch>
.. Thu 29 Aug 2013 16:07:57 CEST
-.. image:: https://travis-ci.org/bioidiap/bob.io.base.svg?branch=master
- :target: https://travis-ci.org/bioidiap/bob.io.base
+.. image:: http://img.shields.io/badge/docs-stable-yellow.png
+ :target: http://pythonhosted.org/bob.io.base/index.html
.. image:: http://img.shields.io/badge/docs-latest-orange.png
:target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.io.base/master/index.html
+.. image:: https://travis-ci.org/bioidiap/bob.io.base.svg?branch=master
+ :target: https://travis-ci.org/bioidiap/bob.io.base
.. image:: https://coveralls.io/repos/bioidiap/bob.io.base/badge.png
:target: https://coveralls.io/r/bioidiap/bob.io.base
-.. image:: http://img.shields.io/github/tag/bioidiap/bob.io.base.png
- :target: https://github.com/bioidiap/bob.io.base
.. image:: http://img.shields.io/pypi/v/bob.io.base.png
:target: https://pypi.python.org/pypi/bob.io.base
.. image:: http://img.shields.io/pypi/dm/bob.io.base.png
:target: https://pypi.python.org/pypi/bob.io.base
-=============================
- Python bindings for bob::io
-=============================
+=========================================
+ Basic Input/Output functionality of Bob
+=========================================
-This package contains a set of Pythonic bindings for core Bob I/O functionality.
+This package contains Bob's basic I/O functionality.
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.io.base/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.io.base/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.io.base/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.io.base
-
-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
diff --git a/bob/io/base/__init__.py b/bob/io/base/__init__.py
index 71dbc365c21a2f0faac7b906ed280ad1e409388e..47ce5c211d7c2a8eef6f160324939596c9131343 100644
--- a/bob/io/base/__init__.py
+++ b/bob/io/base/__init__.py
@@ -52,7 +52,7 @@ def create_directories_safe(directory, dryrun=False):
def load(inputs):
"""Loads the contents of a file, an iterable of files, or an iterable of
- :py:class:`bob.io.File`'s into a :py:class:`numpy.ndarray`.
+ :py:class:`bob.io.base.File`'s into a :py:class:`numpy.ndarray`.
Parameters:
@@ -67,11 +67,11 @@ def load(inputs):
would assume that each file contains a single 1D sample or a set of 1D
samples, load them in memory and concatenate them into a single and
returned 2D numpy ndarray.
- 3. An iterable of :py:class:`bob.io.File`. In this case, this would assume
- that each :py:class:`bob.io.File` contains a single 1D sample or a set
+ 3. An iterable of :py:class:`bob.io.base.File`. In this case, this would assume
+ that each :py:class:`bob.io.base.File` contains a single 1D sample or a set
of 1D samples, load them in memory if required and concatenate them into
a single and returned 2D numpy ndarray.
- 4. An iterable with mixed filenames and :py:class:`bob.io.File`. In this
+ 4. An iterable with mixed filenames and :py:class:`bob.io.base.File`. In this
case, this would returned a 2D :py:class:`numpy.ndarray`, as described
by points 2 and 3 above.
"""
@@ -88,14 +88,14 @@ def load(inputs):
elif isinstance(obj, File):
retval.append(obj.read())
else:
- raise TypeError("Iterable contains an object which is not a filename nor a bob.io.File.")
+ raise TypeError("Iterable contains an object which is not a filename nor a bob.io.base.File.")
return numpy.vstack(retval)
else:
- raise TypeError("Unexpected input object. This function is expecting a filename, or an iterable of filenames and/or bob.io.File's")
+ raise TypeError("Unexpected input object. This function is expecting a filename, or an iterable of filenames and/or bob.io.base.File's")
def merge(filenames):
"""Converts an iterable of filenames into an iterable over read-only
- bob.io.File's.
+ bob.io.base.File's.
Parameters:
@@ -104,9 +104,9 @@ def merge(filenames):
This might represent:
1. A single filename. In this case, an iterable with a single
- :py:class:`bob.io.File` is returned.
+ :py:class:`bob.io.base.File` is returned.
2. An iterable of filenames to be converted into an iterable of
- :py:class:`bob.io.File`'s.
+ :py:class:`bob.io.base.File`'s.
"""
from collections import Iterable
@@ -121,9 +121,9 @@ def merge(filenames):
def save(array, filename, create_directories = False):
"""Saves the contents of an array-like object to file.
- Effectively, this is the same as creating a :py:class:`bob.io.File` object
+ Effectively, this is the same as creating a :py:class:`bob.io.base.File` object
with the mode flag set to `w` (write with truncation) and calling
- :py:meth:`bob.io.File.write` passing `array` as parameter.
+ :py:meth:`bob.io.base.File.write` passing `array` as parameter.
Parameters:
@@ -149,9 +149,9 @@ read = load
def append(array, filename):
"""Appends the contents of an array-like object to file.
- Effectively, this is the same as creating a :py:class:`bob.io.File` object
+ Effectively, this is the same as creating a :py:class:`bob.io.base.File` object
with the mode flag set to `a` (append) and calling
- :py:meth:`bob.io.File.append` passing `array` as parameter.
+ :py:meth:`bob.io.base.File.append` passing `array` as parameter.
Parameters:
@@ -166,9 +166,9 @@ def append(array, filename):
def peek(filename):
"""Returns the type of array (frame or sample) saved in the given file.
- Effectively, this is the same as creating a :py:class:`bob.io.File` object
+ Effectively, this is the same as creating a :py:class:`bob.io.base.File` object
with the mode flag set to `r` (read-only) and returning
- :py:attr:`bob.io.File.describe()`.
+ :py:func:`bob.io.base.File.describe`.
Parameters:
@@ -180,9 +180,9 @@ def peek(filename):
def peek_all(filename):
"""Returns the type of array (for full readouts) saved in the given file.
- Effectively, this is the same as creating a :py:class:`bob.io.File` object
+ Effectively, this is the same as creating a :py:class:`bob.io.base.File` object
with the mode flag set to `r` (read-only) and returning
- :py:attr:`bob.io.File.describe(all=True)`.
+ ``bob.io.base.File.describe(all=True)``.
Parameters:
diff --git a/bob/io/base/file.cpp b/bob/io/base/file.cpp
index 58d760c5bf52455de8cddd27715d2ce8ff1a1ca5..2adb35620b744c0b1c23031cf26b33fa78f76f7f 100644
--- a/bob/io/base/file.cpp
+++ b/bob/io/base/file.cpp
@@ -478,7 +478,7 @@ Parameters:\n\
\n\
array\n\
[array] The array to be written into the file. It can be a\n\
- numpy, a bob.blitz.array or any other object which can be\n\
+ :py:class:`numpy.array`, a :py:class:`bob.blitz.array` or any other object which can be\n\
converted to either of them, as long as the number of\n\
dimensions and scalar type are supported by\n\
:py:class:`bob.blitz.array`.\n\
@@ -531,7 +531,7 @@ Parameters:\n\
\n\
array\n\
[array] The array to be added into the file. It can be a\n\
- numpy, a bob.blitz.array or any other object which can be\n\
+ :py:class:`numpy.ndarray`, a :py:class`bob.blitz.array` or any other object which can be\n\
converted to either of them, as long as the number of\n\
dimensions and scalar type are supported by\n\
:py:class:`bob.blitz.array`.\n\
diff --git a/bob/io/base/hdf5.cpp b/bob/io/base/hdf5.cpp
index d2dbcc74451e6337efdca3131bee35df4ec470fe..b68dce773a30aa2ded8c4cccd28460c0886807b0 100644
--- a/bob/io/base/hdf5.cpp
+++ b/bob/io/base/hdf5.cpp
@@ -299,7 +299,7 @@ path. ``'..'`` and ``'.'`` are supported. This object should\n\
be an :py:class:`str` object. If the value is relative, it is\n\
added to the current path. If it is absolute, it causes the\n\
prefix to be reset. Note all operations taking a relative path,\n\
-following a ``cd()``, will be considered relative to the value\n\
+following a :py:func:`cd`, will be considered relative to the value\n\
defined by the ``cwd`` property of this object.\n\
");
@@ -386,7 +386,7 @@ path\n\
Creates a new directory (i.e., a *group* in HDF5 parlance) inside\n\
the file. A relative path is taken w.r.t. to the current\n\
directory. If the directory already exists (check it with\n\
-:py:meth:`HDF5File.has_group()`, an exception will be raised.\n\
+:py:meth:`bob.io.base.HDF5File.has_group`, an exception will be raised.\n\
");
static PyObject* PyBobIoHDF5File_HasDataset(PyBobIoHDF5FileObject* self, PyObject *args, PyObject* kwds) {
@@ -1946,18 +1946,18 @@ Parameters:\n\
\n\
name\n\
[str] The name of the attribute to retrieve. If the attribute\n\
- is not available, a :py:class:`RuntimeError` is raised.\n\
+ is not available, a ``RuntimeError`` is raised.\n\
\n\
path\n\
[str, optional] The path leading to the resource (dataset or\n\
group|directory) you would like to get an attribute from.\n\
- If the path does not exist, a :py:class:`RuntimeError` is\n\
+ If the path does not exist, a ``RuntimeError`` is\n\
raised.\n\
\n\
This method returns a single value corresponding to what is\n\
stored inside the attribute container for the given resource.\n\
If you would like to retrieve all attributes at once, use\n\
-:py:meth:`HDF5File.get_attributes()` instead.\n\
+:py:meth:`bob.io.base.HDF5File.get_attributes` instead.\n\
");
static PyObject* PyBobIoHDF5File_GetAttributes(PyBobIoHDF5FileObject* self, PyObject *args, PyObject* kwds) {
@@ -2011,13 +2011,13 @@ Parameters:\n\
path\n\
[str, optional] The path leading to the resource (dataset or\n\
group|directory) you would like to get all attributes from.\n\
- If the path does not exist, a :py:class:`RuntimeError` is\n\
+ If the path does not exist, a ``RuntimeError`` is\n\
raised.\n\
\n\
Attributes are returned in a dictionary in which each key\n\
corresponds to the attribute name and each value corresponds\n\
to the value stored inside the HDF5 file. To retrieve only\n\
-a specific attribute, use :py:meth:`HDF5File.get_attribute()`.\n\
+a specific attribute, use :py:meth:`bob.io.base.HDF5File.get_attribute`.\n\
");
template <typename T> PyObject* PyBobIoHDF5File_WriteScalarAttribute
@@ -2334,14 +2334,14 @@ Parameters:\n\
\n\
name\n\
[str] The name of the attribute to delete. A\n\
- :py:class:`RuntimeError` is raised if the attribute does\n\
+ ``RuntimeError`` is raised if the attribute does\n\
not exist.\n\
\n\
\n\
path\n\
[str, optional] The path leading to the resource (dataset or\n\
group|directory) you would like to set an attribute at.\n\
- If the path does not exist, a :py:class:`RuntimeError` is\n\
+ If the path does not exist, a ``RuntimeError`` is\n\
raised.\n\
\n\
");
@@ -2430,13 +2430,13 @@ Parameters:\n\
\n\
attrs\n\
[list] An iterable containing the names of the attributes to\n\
- be removed. If not given or set to :py:class:`None`, then\n\
+ be removed. If not given or set to ``None``, then\n\
remove all attributes at the named resource.\n\
\n\
path\n\
[str, optional] The path leading to the resource (dataset or\n\
group|directory) you would like to set attributes at.\n\
- If the path does not exist, a :py:class:`RuntimeError` is\n\
+ If the path does not exist, a ``RuntimeError`` is\n\
raised.\n\
\n\
");
@@ -2482,7 +2482,7 @@ name\n\
path\n\
[str, optional] The path leading to the resource (dataset or\n\
group|directory) you would like to set an attribute at.\n\
- If the path does not exist, a :py:class:`RuntimeError` is\n\
+ If the path does not exist, a ``RuntimeError`` is\n\
raised.\n\
\n\
");
diff --git a/doc/conf.py b/doc/conf.py
index bb21f932ed474f32cb9c4a95e577a8fd3fb6f57d..34108fbbb9cf0f0c5f5db25d498f2072f3c85806 100644
--- a/doc/conf.py
+++ b/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
diff --git a/doc/guide.rst b/doc/guide.rst
index b6ffc51cb5e0213814893e16bc5078398950074a..0554cd4c7233c7f9f3fa7830e7d35f6d3e5920e5 100644
--- a/doc/guide.rst
+++ b/doc/guide.rst
@@ -145,7 +145,7 @@ as it was defined.
If you need to place lots of variables in a subfolder, it may be better to
setup the prefix folder before starting the writing operations on the
:py:class:`bob.io.base.HDF5File` object. You can do this using the method
- :py:meth:`HDF5File.cd`. Look up its help for more information and usage
+ :py:meth:`bob.io.base.HDF5File.cd`. Look up its help for more information and usage
instructions.
Writing arrays is a little simpler as the :py:class:`numpy.ndarray` objects
@@ -175,8 +175,8 @@ The result of running ``h5dump`` on the file ``testfile3.hdf5`` should be:
...
You don't need to limit yourself to single variables, you can also save lists
-of scalars and arrays using the function :py:meth:`bob.io.base.HDF5.append`
-instead of :py:meth:`bob.io.base.HDF5.set`.
+of scalars and arrays using the function :py:meth:`bob.io.base.HDF5File.append`
+instead of :py:meth:`bob.io.base.HDF5File.set`.
Reading operations
------------------
@@ -264,7 +264,7 @@ What we have shown so far is the generic API to read and write data using HDF5.
You will use it when you want to import or export data from |project| into
other software frameworks, debug your data or just implement your own classes
that can serialize and de-serialize from HDF5 file containers. In |project|,
-most of the time you will be working with :py:class:`numpy.ndarrays`\s. In
+most of the time you will be working with :py:class:`numpy.ndarray`\s. In
special situations though, you may be asked to handle
:py:class:`bob.io.base.File`\s. :py:class:`bob.io.base.File` objects create a
transparent connection between C++ (`Blitz++`_) / Python (`NumPy`_) arrays and
@@ -323,7 +323,7 @@ through the :py:class:`bob.io.base.File` container:
[ 0., 3., 6., 9., 12., 15., 18., 21., 24., 27.]])
You can also directly save :py:class:`numpy.ndarray`\s without going through
-the :py:class:`bob.io.base.Array` container:
+the :py:class:`bob.io.base.File` container:
.. doctest::
diff --git a/setup.py b/setup.py
index 2c6d99cb01f75322e7fdb04a5db8c2afd6a71b91..85cf84f873f978b50d28e557c462ecd8be1f9281 100644
--- a/setup.py
+++ b/setup.py
@@ -133,7 +133,7 @@ setup(
name='bob.io.base',
version=version,
- description='Base bindings for bob.io',
+ description='Basic IO for Bob',
url='http://github.com/bioidiap/bob.io.base',
license='BSD',
author='Andre Anjos',
@@ -222,7 +222,8 @@ setup(
},
classifiers = [
- 'Development Status :: 3 - Alpha',
+ 'Framework :: Bob',
+ 'Development Status :: 4 - Beta',
'Intended Audience :: Developers',
'License :: OSI Approved :: BSD License',
'Natural Language :: English',