diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..abbb866 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +__pycache__/ +runs/ +data/ +.idea/ \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..0afb2e5 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,216 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " applehelp to make an Apple Help Book" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + @echo " coverage to run coverage check of the documentation (if enabled)" + +.PHONY: clean +clean: + rm -rf $(BUILDDIR)/* + +.PHONY: html +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +.PHONY: dirhtml +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +.PHONY: singlehtml +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +.PHONY: pickle +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +.PHONY: json +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +.PHONY: htmlhelp +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +.PHONY: qthelp +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/AttentivePathRanking.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/AttentivePathRanking.qhc" + +.PHONY: applehelp +applehelp: + $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp + @echo + @echo "Build finished. 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The XML files are in $(BUILDDIR)/xml." + +.PHONY: pseudoxml +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..1a9cec4 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,290 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# +# AttentivePathRanking documentation build configuration file, created by +# sphinx-quickstart on Sat May 9 20:15:54 2020. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# 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 +import os + +# adding the following lines to support cython files +import pyximport +pyximport.install() + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +sys.path.insert(0, os.path.abspath('..')) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# 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', +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = 'AttentivePathRanking' +copyright = '2020, Weiyu Liu' +author = 'Weiyu Liu' + +# 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 = '0.0.1' +# The full version, including alpha/beta/rc tags. +release = '0.0.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +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 patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# 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' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +#keep_warnings = False + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'sphinx_rtd_theme' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v 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 (relative to this directory) to use as a 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'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +#html_extra_path = [] + +# 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_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = 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, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Language to be used for generating the HTML full-text search index. +# Sphinx supports the following languages: +# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja' +# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr' +#html_search_language = 'en' + +# A dictionary with options for the search language support, empty by default. +# Now only 'ja' uses this config value +#html_search_options = {'type': 'default'} + +# The name of a javascript file (relative to the configuration directory) that +# implements a search results scorer. If empty, the default will be used. +#html_search_scorer = 'scorer.js' + +# Output file base name for HTML help builder. +htmlhelp_basename = 'AttentivePathRankingdoc' + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', + +# Latex figure (float) alignment +#'figure_align': 'htbp', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + (master_doc, 'AttentivePathRanking.tex', 'AttentivePathRanking Documentation', + 'Weiyu Liu', '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 + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + (master_doc, 'attentivepathranking', 'AttentivePathRanking Documentation', + [author], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + (master_doc, 'AttentivePathRanking', 'AttentivePathRanking Documentation', + author, 'AttentivePathRanking', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +#texinfo_no_detailmenu = False diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..5193b7c --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,22 @@ +.. AttentivePathRanking documentation master file, created by + sphinx-quickstart on Sat May 9 20:15:54 2020. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to AttentivePathRanking's documentation! +================================================ + +Contents: + +.. toctree:: + :maxdepth: 2 + + modules + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/docs/main.data.rst b/docs/main.data.rst new file mode 100644 index 0000000..20d544c --- /dev/null +++ b/docs/main.data.rst @@ -0,0 +1,78 @@ +main.data package +================= + +Submodules +---------- + +main.data.Freebase15kReader module +---------------------------------- + +.. automodule:: main.data.Freebase15kReader + :members: + :undoc-members: + :show-inheritance: + +main.data.MIDFreebase15kReader module +------------------------------------- + +.. automodule:: main.data.MIDFreebase15kReader + :members: + :undoc-members: + :show-inheritance: + +main.data.RobotDataReader module +-------------------------------- + +.. automodule:: main.data.RobotDataReader + :members: + :undoc-members: + :show-inheritance: + +main.data.Split module +---------------------- + +.. automodule:: main.data.Split + :members: + :undoc-members: + :show-inheritance: + +main.data.TypedRelationInstances module +--------------------------------------- + +.. automodule:: main.data.TypedRelationInstances + :members: + :undoc-members: + :show-inheritance: + +main.data.Vocabs module +----------------------- + +.. automodule:: main.data.Vocabs + :members: + :undoc-members: + :show-inheritance: + +main.data.Word2Vec module +------------------------- + +.. automodule:: main.data.Word2Vec + :members: + :undoc-members: + :show-inheritance: + +main.data.WordnetReader module +------------------------------ + +.. automodule:: main.data.WordnetReader + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: main.data + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/main.experiments.rst b/docs/main.experiments.rst new file mode 100644 index 0000000..08ab5a3 --- /dev/null +++ b/docs/main.experiments.rst @@ -0,0 +1,38 @@ +main.experiments package +======================== + +Submodules +---------- + +main.experiments.CVSMDriver module +---------------------------------- + +.. automodule:: main.experiments.CVSMDriver + :members: + :undoc-members: + :show-inheritance: + +main.experiments.Metrics module +------------------------------- + +.. automodule:: main.experiments.Metrics + :members: + :undoc-members: + :show-inheritance: + +main.experiments.PRADriver module +--------------------------------- + +.. automodule:: main.experiments.PRADriver + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: main.experiments + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/main.features.rst b/docs/main.features.rst new file mode 100644 index 0000000..f877992 --- /dev/null +++ b/docs/main.features.rst @@ -0,0 +1,38 @@ +main.features package +===================== + +Submodules +---------- + +main.features.PRAPathReader module +---------------------------------- + +.. automodule:: main.features.PRAPathReader + :members: + :undoc-members: + :show-inheritance: + +main.features.PathExtractor module +---------------------------------- + +.. automodule:: main.features.PathExtractor + :members: + :undoc-members: + :show-inheritance: + +main.features.PathReader module +------------------------------- + +.. automodule:: main.features.PathReader + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: main.features + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/main.graphs.rst b/docs/main.graphs.rst new file mode 100644 index 0000000..7163006 --- /dev/null +++ b/docs/main.graphs.rst @@ -0,0 +1,22 @@ +main.graphs package +=================== + +Submodules +---------- + +main.graphs.AdjacencyGraph module +--------------------------------- + +.. automodule:: main.graphs.AdjacencyGraph + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: main.graphs + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/main.playground.model2.rst b/docs/main.playground.model2.rst new file mode 100644 index 0000000..2a1cadd --- /dev/null +++ b/docs/main.playground.model2.rst @@ -0,0 +1,38 @@ +main.playground.model2 package +============================== + +Submodules +---------- + +main.playground.model2.CompositionalVectorAlgorithm module +---------------------------------------------------------- + +.. automodule:: main.playground.model2.CompositionalVectorAlgorithm + :members: + :undoc-members: + :show-inheritance: + +main.playground.model2.CompositionalVectorSpaceModel module +----------------------------------------------------------- + +.. automodule:: main.playground.model2.CompositionalVectorSpaceModel + :members: + :undoc-members: + :show-inheritance: + +main.playground.model2.FeatureEmbedding module +---------------------------------------------- + +.. automodule:: main.playground.model2.FeatureEmbedding + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: main.playground.model2 + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/main.playground.rst b/docs/main.playground.rst new file mode 100644 index 0000000..960fe3a --- /dev/null +++ b/docs/main.playground.rst @@ -0,0 +1,85 @@ +main.playground package +======================= + +Subpackages +----------- + +.. toctree:: + + main.playground.model2 + +Submodules +---------- + +main.playground.Batcher module +------------------------------ + +.. automodule:: main.playground.Batcher + :members: + :undoc-members: + :show-inheritance: + +main.playground.BatcherFileList module +-------------------------------------- + +.. automodule:: main.playground.BatcherFileList + :members: + :undoc-members: + :show-inheritance: + +main.playground.CompositionalVectorAlgorithm module +--------------------------------------------------- + +.. automodule:: main.playground.CompositionalVectorAlgorithm + :members: + :undoc-members: + :show-inheritance: + +main.playground.CompositionalVectorSpaceModel module +---------------------------------------------------- + +.. automodule:: main.playground.CompositionalVectorSpaceModel + :members: + :undoc-members: + :show-inheritance: + +main.playground.FeatureEmbedding module +--------------------------------------- + +.. automodule:: main.playground.FeatureEmbedding + :members: + :undoc-members: + :show-inheritance: + +main.playground.Logger module +----------------------------- + +.. automodule:: main.playground.Logger + :members: + :undoc-members: + :show-inheritance: + +main.playground.Visualizer module +--------------------------------- + +.. automodule:: main.playground.Visualizer + :members: + :undoc-members: + :show-inheritance: + +main.playground.make_data_format module +--------------------------------------- + +.. automodule:: main.playground.make_data_format + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: main.playground + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/main.rst b/docs/main.rst new file mode 100644 index 0000000..4aaad82 --- /dev/null +++ b/docs/main.rst @@ -0,0 +1,20 @@ +main package +============ + +Subpackages +----------- + +.. toctree:: + + main.data + main.graphs + main.features + main.experiments + +Module contents +--------------- + +.. automodule:: main + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/modules.rst b/docs/modules.rst new file mode 100644 index 0000000..d2403e4 --- /dev/null +++ b/docs/modules.rst @@ -0,0 +1,7 @@ +AttentivePathRanking +==================== + +.. toctree:: + :maxdepth: 4 + + main