Commit cb1ad6df authored by Steffen Möller's avatar Steffen Möller

New upstream version 0.8.1

parent 08b4a484
......@@ -5,6 +5,7 @@ os:
## - osx
python:
- 2.7
- 3.3
addons:
apt:
packages:
......
https://bitbucket.org/james_taylor/python-lzo-static/get/63987d89fd1b.zip
numpy
six
# -*- coding: utf-8 -*-
#
# BxPython documentation build configuration file, created by
# sphinx-quickstart on Fri May 08 10:18:22 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't pickleable (module imports are okay, they're removed automatically).
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys, os
# If your extensions are in another directory, add it here. If the directory
# is relative to the documentation root, use os.path.abspath to make it
# absolute, like shown here.
#sys.path.append(os.path.abspath('.'))
curr_dir = os.path.dirname( __file__ )
bx_dir = os.path.join( curr_dir, '..', '..', 'lib')
sys.path.insert( 0, bx_dir )
import bx
# General configuration
# ---------------------
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'bx-python'
copyright = u'2009, James Taylor'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = bx.__version__
# The full version, including alpha/beta/rc tags.
release = version
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of documents that shouldn't be included in the build.
#unused_docs = []
# List of directories, relative to source directory, that shouldn't be searched
# for source files.
exclude_trees = []
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# Options for HTML output
# -----------------------
# The style sheet to use for HTML and HTML Help pages. A file of that name
# must exist either in Sphinx' static/ path, or in one of the custom paths
# given in html_static_path.
html_style = 'base.css'
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['static']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
html_index = 'index.html'
html_sidebars = { 'index': 'indexsidebar.html'}
# Additional templates that should be rendered to pages, maps page names to
# template names.
##html_additional_pages = {
## 'index': 'index.html',
##}
# If false, no module index is generated.
#html_use_modindex = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, the reST sources are included in the HTML build as _sources/<name>.
#html_copy_source = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = ''
# Output file base name for HTML help builder.
htmlhelp_basename = 'bx-doc'
# Options for LaTeX output
# ------------------------
# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'
# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, document class [howto/manual]).
latex_documents = [
('index', 'bx-python.tex', ur'bx-python Documentation',
ur'James Taylor', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_use_modindex = True
# Example configuration for intersphinx: refer to the Python standard library.
#intersphinx_mapping = {'http://docs.python.org/dev': None}
# -*- coding: utf-8 -*-
#
# BxPython documentation build configuration file, created by
# sphinx-quickstart on Fri May 08 10:18:22 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't pickleable (module imports are okay, they're removed automatically).
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys, os
# If your extensions are in another directory, add it here. If the directory
# is relative to the documentation root, use os.path.abspath to make it
# absolute, like shown here.
#sys.path.append(os.path.abspath('.'))
## curr_dir = os.path.dirname( __file__ )
## bx_dir = os.path.join( curr_dir, '..', '..', 'lib')
## sys.path.insert( 0, bx_dir )
import bx
# General configuration
# ---------------------
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'bx-python'
copyright = u'2017, James Taylor'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = bx.__version__
# The full version, including alpha/beta/rc tags.
release = version
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of documents that shouldn't be included in the build.
#unused_docs = []
# List of directories, relative to source directory, that shouldn't be searched
# for source files.
exclude_trees = []
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# Options for HTML output
# -----------------------
# The style sheet to use for HTML and HTML Help pages. A file of that name
# must exist either in Sphinx' static/ path, or in one of the custom paths
# given in html_static_path.
html_style = 'base.css'
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['static']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
html_index = 'index.html'
html_sidebars = { 'index': 'indexsidebar.html'}
# Additional templates that should be rendered to pages, maps page names to
# template names.
##html_additional_pages = {
## 'index': 'index.html',
##}
# If false, no module index is generated.
#html_use_modindex = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, the reST sources are included in the HTML build as _sources/<name>.
#html_copy_source = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = ''
# Output file base name for HTML help builder.
htmlhelp_basename = 'bx-doc'
# Options for LaTeX output
# ------------------------
# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'
# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, document class [howto/manual]).
latex_documents = [
('index', 'bx-python.tex', ur'bx-python Documentation',
ur'James Taylor', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_use_modindex = True
# Example configuration for intersphinx: refer to the Python standard library.
#intersphinx_mapping = {'http://docs.python.org/dev': None}
......@@ -15,9 +15,9 @@ Contents
========
.. toctree::
:maxdepth: 2
:maxdepth: 5
modules/index.rst
Application Documentation <lib/modules>
Indices and tables
==================
......
bx.align.axt module
===================
.. automodule:: bx.align.axt
:members:
:undoc-members:
:show-inheritance:
bx.align.core module
====================
.. automodule:: bx.align.core
:members:
:undoc-members:
:show-inheritance:
bx.align.epo module
===================
.. automodule:: bx.align.epo
:members:
:undoc-members:
:show-inheritance:
bx.align.epo_tests module
=========================
.. automodule:: bx.align.epo_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.lav module
===================
.. automodule:: bx.align.lav
:members:
:undoc-members:
:show-inheritance:
bx.align.lav_tests module
=========================
.. automodule:: bx.align.lav_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.maf module
===================
.. automodule:: bx.align.maf
:members:
:undoc-members:
:show-inheritance:
bx.align.maf_tests module
=========================
.. automodule:: bx.align.maf_tests
:members:
:undoc-members:
:show-inheritance:
bx.align package
================
Subpackages
-----------
.. toctree::
bx.align.sitemask
bx.align.tools
Submodules
----------
.. toctree::
bx.align.axt
bx.align.core
bx.align.epo
bx.align.epo_tests
bx.align.lav
bx.align.lav_tests
bx.align.maf
bx.align.maf_tests
bx.align.score
bx.align.score_tests
Module contents
---------------
.. automodule:: bx.align
:members:
:undoc-members:
:show-inheritance:
bx.align.score module
=====================
.. automodule:: bx.align.score
:members:
:undoc-members:
:show-inheritance:
bx.align.score_tests module
===========================
.. automodule:: bx.align.score_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.core module
=============================
.. automodule:: bx.align.sitemask.core
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.cpg module
============================
.. automodule:: bx.align.sitemask.cpg
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.quality module
================================
.. automodule:: bx.align.sitemask.quality
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask package
=========================
Submodules
----------
.. toctree::
bx.align.sitemask.core
bx.align.sitemask.cpg
bx.align.sitemask.quality
bx.align.sitemask.sitemask_tests
Module contents
---------------
.. automodule:: bx.align.sitemask
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.sitemask_tests module
=======================================
.. automodule:: bx.align.sitemask.sitemask_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.chop module
==========================
.. automodule:: bx.align.tools.chop
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.fuse module
==========================
.. automodule:: bx.align.tools.fuse
:members:
:undoc-members: