1.1 --- a/.hgignore	Mon Dec 13 22:16:04 2010 +0300
     1.2 +++ b/.hgignore	Mon Dec 13 22:16:37 2010 +0300
     1.3 @@ -8,6 +8,9 @@
     1.4  *.geany
     1.5  *.swp
     1.6  
     1.7 +# Temporary files from sphinx
     1.8 +docs/build
     1.9 +
    1.10  # Temporary files from debianization
    1.11  debian/python-allpy/
    1.12  debian/geometrical-core/

     2.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     2.2 +++ b/docs/Makefile	Mon Dec 13 22:16:37 2010 +0300
     2.3 @@ -0,0 +1,89 @@
     2.4 +# Makefile for Sphinx documentation
     2.5 +#
     2.6 +
     2.7 +# You can set these variables from the command line.
     2.8 +SPHINXOPTS    =
     2.9 +SPHINXBUILD   = sphinx-build
    2.10 +PAPER         =
    2.11 +BUILDDIR      = build
    2.12 +
    2.13 +# Internal variables.
    2.14 +PAPEROPT_a4     = -D latex_paper_size=a4
    2.15 +PAPEROPT_letter = -D latex_paper_size=letter
    2.16 +ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
    2.17 +
    2.18 +.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
    2.19 +
    2.20 +help:
    2.21 +	@echo "Please use \`make <target>' where <target> is one of"
    2.22 +	@echo "  html      to make standalone HTML files"
    2.23 +	@echo "  dirhtml   to make HTML files named index.html in directories"
    2.24 +	@echo "  pickle    to make pickle files"
    2.25 +	@echo "  json      to make JSON files"
    2.26 +	@echo "  htmlhelp  to make HTML files and a HTML help project"
    2.27 +	@echo "  qthelp    to make HTML files and a qthelp project"
    2.28 +	@echo "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
    2.29 +	@echo "  changes   to make an overview of all changed/added/deprecated items"
    2.30 +	@echo "  linkcheck to check all external links for integrity"
    2.31 +	@echo "  doctest   to run all doctests embedded in the documentation (if enabled)"
    2.32 +
    2.33 +clean:
    2.34 +	-rm -rf $(BUILDDIR)/*
    2.35 +
    2.36 +html:
    2.37 +	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
    2.38 +	@echo
    2.39 +	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
    2.40 +
    2.41 +dirhtml:
    2.42 +	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
    2.43 +	@echo
    2.44 +	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
    2.45 +
    2.46 +pickle:
    2.47 +	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
    2.48 +	@echo
    2.49 +	@echo "Build finished; now you can process the pickle files."
    2.50 +
    2.51 +json:
    2.52 +	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
    2.53 +	@echo
    2.54 +	@echo "Build finished; now you can process the JSON files."
    2.55 +
    2.56 +htmlhelp:
    2.57 +	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
    2.58 +	@echo
    2.59 +	@echo "Build finished; now you can run HTML Help Workshop with the" \
    2.60 +	      ".hhp project file in $(BUILDDIR)/htmlhelp."
    2.61 +
    2.62 +qthelp:
    2.63 +	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
    2.64 +	@echo
    2.65 +	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
    2.66 +	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
    2.67 +	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/allpy.qhcp"
    2.68 +	@echo "To view the help file:"
    2.69 +	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/allpy.qhc"
    2.70 +
    2.71 +latex:
    2.72 +	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
    2.73 +	@echo
    2.74 +	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
    2.75 +	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
    2.76 +	      "run these through (pdf)latex."
    2.77 +
    2.78 +changes:
    2.79 +	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
    2.80 +	@echo
    2.81 +	@echo "The overview file is in $(BUILDDIR)/changes."
    2.82 +
    2.83 +linkcheck:
    2.84 +	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
    2.85 +	@echo
    2.86 +	@echo "Link check complete; look for any errors in the above output " \
    2.87 +	      "or in $(BUILDDIR)/linkcheck/output.txt."
    2.88 +
    2.89 +doctest:
    2.90 +	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
    2.91 +	@echo "Testing of doctests in the sources finished, look at the " \
    2.92 +	      "results in $(BUILDDIR)/doctest/output.txt."

     3.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     3.2 +++ b/docs/source/_monomer.rst	Mon Dec 13 22:16:37 2010 +0300
     3.3 @@ -0,0 +1,12 @@
     3.4 +_Monomer Documentation
     3.5 +======================
     3.6 +
     3.7 +This page contains the _Monomer Module documentation.
     3.8 +
     3.9 +The :mod:`_monomer` Module
    3.10 +--------------------------
    3.11 +
    3.12 +.. automodule:: allpy._monomer
    3.13 +    :members:
    3.14 +    :undoc-members:
    3.15 +    :show-inheritance:

     4.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     4.2 +++ b/docs/source/alignment.rst	Mon Dec 13 22:16:37 2010 +0300
     4.3 @@ -0,0 +1,12 @@
     4.4 +Alignment Documentation
     4.5 +=======================
     4.6 +
     4.7 +This page contains the Alignment Module documentation.
     4.8 +
     4.9 +The :mod:`alignment` Module
    4.10 +---------------------------
    4.11 +
    4.12 +.. automodule:: allpy.alignment
    4.13 +    :members:
    4.14 +    :undoc-members:
    4.15 +    :show-inheritance:

     5.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     5.2 +++ b/docs/source/base.rst	Mon Dec 13 22:16:37 2010 +0300
     5.3 @@ -0,0 +1,12 @@
     5.4 +Base Documentation
     5.5 +==================
     5.6 +
     5.7 +This page contains the Base Module documentation.
     5.8 +
     5.9 +The :mod:`base` Module
    5.10 +----------------------
    5.11 +
    5.12 +.. automodule:: allpy.base
    5.13 +    :members:
    5.14 +    :undoc-members:
    5.15 +    :show-inheritance:

     6.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     6.2 +++ b/docs/source/block.rst	Mon Dec 13 22:16:37 2010 +0300
     6.3 @@ -0,0 +1,12 @@
     6.4 +Block Documentation
     6.5 +===================
     6.6 +
     6.7 +This page contains the Block Module documentation.
     6.8 +
     6.9 +The :mod:`block` Module
    6.10 +-----------------------
    6.11 +
    6.12 +.. automodule:: allpy.block
    6.13 +    :members:
    6.14 +    :undoc-members:
    6.15 +    :show-inheritance:

     7.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     7.2 +++ b/docs/source/conf.py	Mon Dec 13 22:16:37 2010 +0300
     7.3 @@ -0,0 +1,194 @@
     7.4 +# -*- coding: utf-8 -*-
     7.5 +#
     7.6 +# allpy documentation build configuration file, created by
     7.7 +# sphinx-quickstart on Mon Dec 13 22:14:23 2010.
     7.8 +#
     7.9 +# This file is execfile()d with the current directory set to its containing dir.
    7.10 +#
    7.11 +# Note that not all possible configuration values are present in this
    7.12 +# autogenerated file.
    7.13 +#
    7.14 +# All configuration values have a default; values that are commented out
    7.15 +# serve to show the default.
    7.16 +
    7.17 +import sys, os
    7.18 +
    7.19 +# If extensions (or modules to document with autodoc) are in another directory,
    7.20 +# add these directories to sys.path here. If the directory is relative to the
    7.21 +# documentation root, use os.path.abspath to make it absolute, like shown here.
    7.22 +#sys.path.append(os.path.abspath('.'))
    7.23 +
    7.24 +# -- General configuration -----------------------------------------------------
    7.25 +
    7.26 +# Add any Sphinx extension module names here, as strings. They can be extensions
    7.27 +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
    7.28 +extensions = ['sphinx.ext.autodoc']
    7.29 +
    7.30 +# Add any paths that contain templates here, relative to this directory.
    7.31 +templates_path = ['_templates']
    7.32 +
    7.33 +# The suffix of source filenames.
    7.34 +source_suffix = '.rst'
    7.35 +
    7.36 +# The encoding of source files.
    7.37 +#source_encoding = 'utf-8'
    7.38 +
    7.39 +# The master toctree document.
    7.40 +master_doc = 'index'
    7.41 +
    7.42 +# General information about the project.
    7.43 +project = u'allpy'
    7.44 +copyright = u'2010, many people'
    7.45 +
    7.46 +# The version info for the project you're documenting, acts as replacement for
    7.47 +# |version| and |release|, also used in various other places throughout the
    7.48 +# built documents.
    7.49 +#
    7.50 +# The short X.Y version.
    7.51 +version = '0.0'
    7.52 +# The full version, including alpha/beta/rc tags.
    7.53 +release = '0.0'
    7.54 +
    7.55 +# The language for content autogenerated by Sphinx. Refer to documentation
    7.56 +# for a list of supported languages.
    7.57 +#language = None
    7.58 +
    7.59 +# There are two options for replacing |today|: either, you set today to some
    7.60 +# non-false value, then it is used:
    7.61 +#today = ''
    7.62 +# Else, today_fmt is used as the format for a strftime call.
    7.63 +#today_fmt = '%B %d, %Y'
    7.64 +
    7.65 +# List of documents that shouldn't be included in the build.
    7.66 +#unused_docs = []
    7.67 +
    7.68 +# List of directories, relative to source directory, that shouldn't be searched
    7.69 +# for source files.
    7.70 +exclude_trees = []
    7.71 +
    7.72 +# The reST default role (used for this markup: `text`) to use for all documents.
    7.73 +#default_role = None
    7.74 +
    7.75 +# If true, '()' will be appended to :func: etc. cross-reference text.
    7.76 +#add_function_parentheses = True
    7.77 +
    7.78 +# If true, the current module name will be prepended to all description
    7.79 +# unit titles (such as .. function::).
    7.80 +#add_module_names = True
    7.81 +
    7.82 +# If true, sectionauthor and moduleauthor directives will be shown in the
    7.83 +# output. They are ignored by default.
    7.84 +#show_authors = False
    7.85 +
    7.86 +# The name of the Pygments (syntax highlighting) style to use.
    7.87 +pygments_style = 'sphinx'
    7.88 +
    7.89 +# A list of ignored prefixes for module index sorting.
    7.90 +#modindex_common_prefix = []
    7.91 +
    7.92 +
    7.93 +# -- Options for HTML output ---------------------------------------------------
    7.94 +
    7.95 +# The theme to use for HTML and HTML Help pages.  Major themes that come with
    7.96 +# Sphinx are currently 'default' and 'sphinxdoc'.
    7.97 +html_theme = 'default'
    7.98 +
    7.99 +# Theme options are theme-specific and customize the look and feel of a theme
   7.100 +# further.  For a list of options available for each theme, see the
   7.101 +# documentation.
   7.102 +#html_theme_options = {}
   7.103 +
   7.104 +# Add any paths that contain custom themes here, relative to this directory.
   7.105 +#html_theme_path = []
   7.106 +
   7.107 +# The name for this set of Sphinx documents.  If None, it defaults to
   7.108 +# "<project> v<release> documentation".
   7.109 +#html_title = None
   7.110 +
   7.111 +# A shorter title for the navigation bar.  Default is the same as html_title.
   7.112 +#html_short_title = None
   7.113 +
   7.114 +# The name of an image file (relative to this directory) to place at the top
   7.115 +# of the sidebar.
   7.116 +#html_logo = None
   7.117 +
   7.118 +# The name of an image file (within the static path) to use as favicon of the
   7.119 +# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
   7.120 +# pixels large.
   7.121 +#html_favicon = None
   7.122 +
   7.123 +# Add any paths that contain custom static files (such as style sheets) here,
   7.124 +# relative to this directory. They are copied after the builtin static files,
   7.125 +# so a file named "default.css" will overwrite the builtin "default.css".
   7.126 +html_static_path = ['_static']
   7.127 +
   7.128 +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
   7.129 +# using the given strftime format.
   7.130 +#html_last_updated_fmt = '%b %d, %Y'
   7.131 +
   7.132 +# If true, SmartyPants will be used to convert quotes and dashes to
   7.133 +# typographically correct entities.
   7.134 +#html_use_smartypants = True
   7.135 +
   7.136 +# Custom sidebar templates, maps document names to template names.
   7.137 +#html_sidebars = {}
   7.138 +
   7.139 +# Additional templates that should be rendered to pages, maps page names to
   7.140 +# template names.
   7.141 +#html_additional_pages = {}
   7.142 +
   7.143 +# If false, no module index is generated.
   7.144 +#html_use_modindex = True
   7.145 +
   7.146 +# If false, no index is generated.
   7.147 +#html_use_index = True
   7.148 +
   7.149 +# If true, the index is split into individual pages for each letter.
   7.150 +#html_split_index = False
   7.151 +
   7.152 +# If true, links to the reST sources are added to the pages.
   7.153 +#html_show_sourcelink = True
   7.154 +
   7.155 +# If true, an OpenSearch description file will be output, and all pages will
   7.156 +# contain a <link> tag referring to it.  The value of this option must be the
   7.157 +# base URL from which the finished HTML is served.
   7.158 +#html_use_opensearch = ''
   7.159 +
   7.160 +# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
   7.161 +#html_file_suffix = ''
   7.162 +
   7.163 +# Output file base name for HTML help builder.
   7.164 +htmlhelp_basename = 'allpydoc'
   7.165 +
   7.166 +
   7.167 +# -- Options for LaTeX output --------------------------------------------------
   7.168 +
   7.169 +# The paper size ('letter' or 'a4').
   7.170 +#latex_paper_size = 'letter'
   7.171 +
   7.172 +# The font size ('10pt', '11pt' or '12pt').
   7.173 +#latex_font_size = '10pt'
   7.174 +
   7.175 +# Grouping the document tree into LaTeX files. List of tuples
   7.176 +# (source start file, target name, title, author, documentclass [howto/manual]).
   7.177 +latex_documents = [
   7.178 +  ('index', 'allpy.tex', u'allpy Documentation',
   7.179 +   u'many people', 'manual'),
   7.180 +]
   7.181 +
   7.182 +# The name of an image file (relative to this directory) to place at the top of
   7.183 +# the title page.
   7.184 +#latex_logo = None
   7.185 +
   7.186 +# For "manual" documents, if this is true, then toplevel headings are parts,
   7.187 +# not chapters.
   7.188 +#latex_use_parts = False
   7.189 +
   7.190 +# Additional stuff for the LaTeX preamble.
   7.191 +#latex_preamble = ''
   7.192 +
   7.193 +# Documents to append as an appendix to all manuals.
   7.194 +#latex_appendices = []
   7.195 +
   7.196 +# If false, no module index is generated.
   7.197 +#latex_use_modindex = True

     8.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     8.2 +++ b/docs/source/data.rst	Mon Dec 13 22:16:37 2010 +0300
     8.3 @@ -0,0 +1,5 @@
     8.4 +Data Documentation
     8.5 +==================
     8.6 +
     8.7 +This page contains the Data Package documentation.
     8.8 +

     9.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     9.2 +++ b/docs/source/dna.rst	Mon Dec 13 22:16:37 2010 +0300
     9.3 @@ -0,0 +1,12 @@
     9.4 +Dna Documentation
     9.5 +=================
     9.6 +
     9.7 +This page contains the Dna Module documentation.
     9.8 +
     9.9 +The :mod:`dna` Module
    9.10 +---------------------
    9.11 +
    9.12 +.. automodule:: allpy.dna
    9.13 +    :members:
    9.14 +    :undoc-members:
    9.15 +    :show-inheritance:

    10.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    10.2 +++ b/docs/source/fasta.rst	Mon Dec 13 22:16:37 2010 +0300
    10.3 @@ -0,0 +1,12 @@
    10.4 +Fasta Documentation
    10.5 +===================
    10.6 +
    10.7 +This page contains the Fasta Module documentation.
    10.8 +
    10.9 +The :mod:`fasta` Module
   10.10 +-----------------------
   10.11 +
   10.12 +.. automodule:: allpy.fasta
   10.13 +    :members:
   10.14 +    :undoc-members:
   10.15 +    :show-inheritance:

    11.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    11.2 +++ b/docs/source/graph.rst	Mon Dec 13 22:16:37 2010 +0300
    11.3 @@ -0,0 +1,12 @@
    11.4 +Graph Documentation
    11.5 +===================
    11.6 +
    11.7 +This page contains the Graph Module documentation.
    11.8 +
    11.9 +The :mod:`graph` Module
   11.10 +-----------------------
   11.11 +
   11.12 +.. automodule:: allpy.graph
   11.13 +    :members:
   11.14 +    :undoc-members:
   11.15 +    :show-inheritance:

    12.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    12.2 +++ b/docs/source/index.rst	Mon Dec 13 22:16:37 2010 +0300
    12.3 @@ -0,0 +1,20 @@
    12.4 +.. allpy documentation master file, created by
    12.5 +   sphinx-quickstart on Mon Dec 13 22:14:23 2010.
    12.6 +   You can adapt this file completely to your liking, but it should at least
    12.7 +   contain the root `toctree` directive.
    12.8 +
    12.9 +Welcome to allpy's documentation!
   12.10 +=================================
   12.11 +
   12.12 +Contents:
   12.13 +
   12.14 +.. toctree::
   12.15 +   :maxdepth: 2
   12.16 +
   12.17 +Indices and tables
   12.18 +==================
   12.19 +
   12.20 +* :ref:`genindex`
   12.21 +* :ref:`modindex`
   12.22 +* :ref:`search`
   12.23 +

    13.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    13.2 +++ b/docs/source/markup.rst	Mon Dec 13 22:16:37 2010 +0300
    13.3 @@ -0,0 +1,12 @@
    13.4 +Markup Documentation
    13.5 +====================
    13.6 +
    13.7 +This page contains the Markup Module documentation.
    13.8 +
    13.9 +The :mod:`markup` Module
   13.10 +------------------------
   13.11 +
   13.12 +.. automodule:: allpy.markup
   13.13 +    :members:
   13.14 +    :undoc-members:
   13.15 +    :show-inheritance:

    14.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    14.2 +++ b/docs/source/modules.rst	Mon Dec 13 22:16:37 2010 +0300
    14.3 @@ -0,0 +1,24 @@
    14.4 +Project Documentation
    14.5 +=====================
    14.6 +
    14.7 +This page contains the Project Modules documentation.
    14.8 +
    14.9 +Modules:
   14.10 +--------
   14.11 +
   14.12 +.. toctree::
   14.13 +   :maxdepth: 4
   14.14 +
   14.15 +   _monomer
   14.16 +   alignment
   14.17 +   base
   14.18 +   block
   14.19 +   data
   14.20 +   dna
   14.21 +   fasta
   14.22 +   graph
   14.23 +   markup
   14.24 +   pdb
   14.25 +   protein
   14.26 +   rna
   14.27 +   sequence

    15.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    15.2 +++ b/docs/source/pdb.rst	Mon Dec 13 22:16:37 2010 +0300
    15.3 @@ -0,0 +1,12 @@
    15.4 +Pdb Documentation
    15.5 +=================
    15.6 +
    15.7 +This page contains the Pdb Module documentation.
    15.8 +
    15.9 +The :mod:`pdb` Module
   15.10 +---------------------
   15.11 +
   15.12 +.. automodule:: allpy.pdb
   15.13 +    :members:
   15.14 +    :undoc-members:
   15.15 +    :show-inheritance:

    16.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    16.2 +++ b/docs/source/protein.rst	Mon Dec 13 22:16:37 2010 +0300
    16.3 @@ -0,0 +1,12 @@
    16.4 +Protein Documentation
    16.5 +=====================
    16.6 +
    16.7 +This page contains the Protein Module documentation.
    16.8 +
    16.9 +The :mod:`protein` Module
   16.10 +-------------------------
   16.11 +
   16.12 +.. automodule:: allpy.protein
   16.13 +    :members:
   16.14 +    :undoc-members:
   16.15 +    :show-inheritance:

    17.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    17.2 +++ b/docs/source/rna.rst	Mon Dec 13 22:16:37 2010 +0300
    17.3 @@ -0,0 +1,12 @@
    17.4 +Rna Documentation
    17.5 +=================
    17.6 +
    17.7 +This page contains the Rna Module documentation.
    17.8 +
    17.9 +The :mod:`rna` Module
   17.10 +---------------------
   17.11 +
   17.12 +.. automodule:: allpy.rna
   17.13 +    :members:
   17.14 +    :undoc-members:
   17.15 +    :show-inheritance:

    18.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
    18.2 +++ b/docs/source/sequence.rst	Mon Dec 13 22:16:37 2010 +0300
    18.3 @@ -0,0 +1,12 @@
    18.4 +Sequence Documentation
    18.5 +======================
    18.6 +
    18.7 +This page contains the Sequence Module documentation.
    18.8 +
    18.9 +The :mod:`sequence` Module
   18.10 +--------------------------
   18.11 +
   18.12 +.. automodule:: allpy.sequence
   18.13 +    :members:
   18.14 +    :undoc-members:
   18.15 +    :show-inheritance: