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Adds inference code and documentation
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Diff for: ‎doc_requirements.txt

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Sphinx==1.5

Diff for: ‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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SPHINXPROJ = hdhppy
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

Diff for: ‎docs/conf.py

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# -*- coding: utf-8 -*-
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#
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# hdhp.py documentation build configuration file, created by
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# sphinx-quickstart on Fri Dec 9 22:35:31 2016.
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#
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# This file is execfile()d with the current directory set to its
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# containing dir.
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#
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# Note that not all possible configuration values are present in this
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# autogenerated file.
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#
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# All configuration values have a default; values that are commented out
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# serve to show the default.
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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# import os
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# import sys
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# sys.path.insert(0, os.path.abspath('.'))
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# -- General configuration ------------------------------------------------
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# If your documentation needs a minimal Sphinx version, state it here.
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#
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# needs_sphinx = '1.0'
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = ['sphinx.ext.autodoc',
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'sphinx.ext.napoleon',
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'sphinx.ext.mathjax',
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'sphinx.ext.viewcode']
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# Napoleon settings
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napoleon_numpy_docstring = True
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napoleon_include_init_with_doc = True
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napoleon_include_private_with_doc = False
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napoleon_include_special_with_doc = True
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napoleon_use_admonition_for_examples = False
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napoleon_use_admonition_for_notes = False
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napoleon_use_admonition_for_references = False
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napoleon_use_ivar = False
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napoleon_use_param = True
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napoleon_use_rtype = True
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# The suffix(es) of source filenames.
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# You can specify multiple suffix as a list of string:
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#
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# source_suffix = ['.rst', '.md']
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source_suffix = '.rst'
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# The master toctree document.
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master_doc = 'index'
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# General information about the project.
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project = u'hdhp.py'
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copyright = u'2016, Charalampos Mavroforakis and contributors'
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author = u'Charalampos Mavroforakis and contributors'
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the
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# built documents.
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#
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# The short X.Y version.
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version = u'1.0'
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# The full version, including alpha/beta/rc tags.
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release = u'1.0'
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.
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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
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language = None
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This patterns also effect to html_static_path and html_extra_path
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'sphinx'
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# If true, `todo` and `todoList` produce output, else they produce nothing.
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todo_include_todos = False
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# -- Options for HTML output ----------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'alabaster'
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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# documentation.
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#
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# html_theme_options = {}
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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# -- Options for HTMLHelp output ------------------------------------------
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# Output file base name for HTML help builder.
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htmlhelp_basename = 'hdhppydoc'
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# -- Options for LaTeX output ---------------------------------------------
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latex_elements = {
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# The paper size ('letterpaper' or 'a4paper').
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#
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# 'papersize': 'letterpaper',
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# The font size ('10pt', '11pt' or '12pt').
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#
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# 'pointsize': '10pt',
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# Additional stuff for the LaTeX preamble.
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#
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# 'preamble': '',
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# Latex figure (float) alignment
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#
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# 'figure_align': 'htbp',
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}
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# Grouping the document tree into LaTeX files. List of tuples
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# (source start file, target name, title,
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# author, documentclass [howto, manual, or own class]).
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latex_documents = [
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(master_doc, 'hdhppy.tex', u'hdhp.py Documentation',
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u'Charalampos Mavroforakis and contributors', 'manual'),
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]
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# -- Options for manual page output ---------------------------------------
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [
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(master_doc, 'hdhppy', u'hdhp.py Documentation',
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[author], 1)
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]
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# -- Options for Texinfo output -------------------------------------------
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# Grouping the document tree into Texinfo files. List of tuples
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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(master_doc, 'hdhppy', u'hdhp.py Documentation',
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author, 'hdhppy', 'One line description of project.',
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'Miscellaneous'),
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]
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Diff for: ‎docs/index.rst

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.. hdhp.py documentation master file, created by
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sphinx-quickstart on Fri Dec 9 22:35:31 2016.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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Welcome to hdhp.py's documentation!
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===================================
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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The ``infer`` function
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======================
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.. automodule:: hdhp
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:members: infer
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The ``HDHProcess`` object
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=========================
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.. autoclass:: HDHProcess
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:members:
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.. Indices and tables
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.. ==================
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.. * :ref:`genindex`
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.. * :ref:`modindex`
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.. * :ref:`search`

Diff for: ‎hdhp/__init__.py

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from generative_model import HDHProcess
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from smc import Particle, infer
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__all__ = ['utils']

Diff for: ‎hdhp/generative_model.py

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:copyright: 2016 Charalampos Mavroforakis, <[email protected]> and contributors.
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:license: ISC
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"""
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from __future__ import division
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from __future__ import division, print_function
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import datetime
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from collections import defaultdict
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plt.savefig(filename + '.pdf', transparent=True)
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sns.set_style(None)
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return fig
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def user_patterns(self, user):
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"""Returns a list with the patterns that a user has adopted.
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Parameters
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----------
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user : int
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"""
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pattern_list = [self.dish_on_table_per_user[user][table]
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for table in self.table_history_per_user[user]]
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return list(set(pattern_list))
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def show_annotated_events(self, user=None, patterns=None, show_time=True,
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T_min=0, T_max=None):
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"""Returns a string where each event is annotated with the inferred
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pattern.
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Parameters
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----------
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user : int, default is None
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If given, the events returned are limited to the selected user
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patterns : list, default is None
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If not None, an event is return only if it belongs to one of the
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selected patterns
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show_time : bool, default is True
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Controls whether the time of the event will be shown
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T_min : float, default is 0
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Controls the minimum timestamp after which the events will be shown
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T_max : float, default is None
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If given, T_max controls the maximum timestamp shown
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Returns
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-------
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str
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"""
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if patterns is not None and type(patterns) is not set:
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patterns = set(patterns)
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if show_time:
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return '\n'.join(['%5.3g pattern=%3d task=%3d (u=%d) %s' %
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(t, dish, table, u, doc)
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for u in range(self.num_users)
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for ((t, doc), (table, dish)) in
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zip([(t, d)
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for t, d in zip(self.time_history_per_user[u],
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self.document_history_per_user[u])],
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[(table, self.dish_on_table_per_user[u][table])
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for table in self.table_history_per_user[u]])
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if (user is None or user == u) and
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(patterns is None or dish in patterns)
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and t >= T_min
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and (T_max is None or (T_max is not None and t <= T_max))])
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else:
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return '\n'.join(['pattern=%3d task=%3d (u=%d) %s'
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% (dish, table, u, doc)
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for u in range(self.num_users)
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for ((t, doc), (table, dish)) in
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zip([(t, d)
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for t, d in zip(self.time_history_per_user[u],
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self.document_history_per_user[u])],
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[(table, self.dish_on_table_per_user[u][table])
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for table in self.table_history_per_user[u]])
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if (user is None or user == u) and
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(patterns is None or dish in patterns)
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and t >= T_min
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and (T_max is None or (T_max is not None and t <= T_max))])
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def show_pattern_content(self, patterns=None, words=0, detail_threshold=5):
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"""Shows the content distrubution of the inferred patterns.
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Parameters
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----------
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patterns : list, default is None
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If not None, only the content of the selected patterns will be
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shown
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words : int, default is 0
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A positive number that control how many words will be shown.
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The words are being shown sorted by their likelihood, starting
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with the most probable.
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detail_threshold : int, default is 5
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A positive number that sets the lower bound in the number of times
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that a word appeared in a pattern so that its count is shown.
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Returns
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-------
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str
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"""
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if patterns is None:
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patterns = self.per_pattern_word_count.keys()
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text = ['___Pattern %d___ \n%s\n%s'
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% (pattern,
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'\n'.join(['%s : %d'
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% (k, v)
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for i, (k, v)
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in enumerate(sorted(self.per_pattern_word_counts[pattern].iteritems(),
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key=lambda x: (x[1], x[0]),
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reverse=True))
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if v >= detail_threshold and (words == 0 or i < words)]
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),
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' '.join([k for i, (k, v)
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in enumerate(sorted(self.per_pattern_word_counts[pattern].iteritems(),
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key=lambda x: (x[1], x[0]),
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reverse=True))
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if v < detail_threshold and (words == 0 or i < words)])
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)
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for pattern in self.per_pattern_word_counts if pattern in patterns]
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return '\n\n'.join(text)

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