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Updated docstrings and docs
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‎DOCUMENTATION.md

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‎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 = python -msphinx
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SPHINXPROJ = QML
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SOURCEDIR = source
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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)

‎docs/source/conf.py

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# -*- coding: utf-8 -*-
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#
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# QML documentation build configuration file, created by
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# sphinx-quickstart on Sun Jun 4 14:41:04 2017.
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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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print os.getcwd()
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sys.path.insert(0, os.path.abspath('../../build/lib.linux-x86_64-2.7/'))
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import sphinx_rtd_theme
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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','sphinx.ext.mathjax']
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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'QML'
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copyright = u'2017, Anders S. Christensen'
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author = u'Anders S. Christensen'
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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'0.2.10'
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# The full version, including alpha/beta/rc tags.
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release = u'0.2.10'
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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 = []
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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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html_theme = "sphinx_rtd_theme"
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html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
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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 = 'QMLdoc'
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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, 'QML.tex', u'QML Documentation',
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u'Anders S. Christensen', '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, 'qml', u'QML 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, 'QML', u'QML Documentation',
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author, 'QML', 'One line description of project.',
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'Miscellaneous'),
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]
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html_sidebars = { '**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'], }

‎docs/source/examples.rst

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Examples
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--------
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Generating representations using the ``Compound`` class:
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The following example demonstrates how to generate a representation via
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the ``qml.Compound`` class.
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.. code:: python
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from qml import Compound
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# Read in an xyz or cif file.
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water = Compound(xyz="water.xyz")
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# Generate a molecular coulomb matrices sorted by row norm.
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water.generate_coulomb_matrix(size=5, sort="row-norm")
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print water.coulomb_matrix
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Generating representations via the ``qml.representations`` module:
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. code:: python
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from qml.representations import *
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# Dummy atomtypes and coordinates
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atomtypes = ["O", "H", H"]
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coordinates = np.array([1.464, 0.707, 1.056],
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[0.878, 1.218, 0.498],
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[2.319, 1.126, 0.952])
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# Generate a molecular coulomb matrices sorted by row norm.
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cm1 = generate_coulomb_matrix(atomtypes, coordinates,
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size=5, sort="row-norm")
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print cm1
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# Generate all atomic coulomb matrices sorted by distance to
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# query atom.
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cm2 = generate_atomic_coulomb_matrix(atomtypes, coordinates,
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size=5, sort="distance")
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print cm2

‎docs/source/index.rst

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.. QML documentation master file, created by
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sphinx-quickstart on Sun Jun 4 14:41:04 2017.
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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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|Build Status|
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QML: A Python Toolkit for Quantum Machine Learning
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==================================================
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QML is a Python2/3-compatible toolkit for representation learning of
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properties of molecules and solids. QML is not a high-level framework
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where you can do ``model.train()``, but supplies the building blocks to
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carry out efficient and accurate machine learning on chemical compounds.
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As such, the goal is to provide usable and efficient implementations of
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concepts such as representations and kernels, which can then be
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implemented in other machine learning codes.
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Current list of contributors:
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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- Anders S. Christensen (University of Basel)
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- Felix Faber (University of Basel)
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- Bing Huang (University of Basel)
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- Lars A. Bratholm (University of Copenhagen)
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- O. Anatole von Lilienfeld (University of Basel)
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1) Citing QML:
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--------------
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Until the preprint is available from arXiv, please cite this GitHub
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repository as:
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::
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AS Christensen, F Faber, B Huang, LA Bratholm, OA von Lilienfeld (2017) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml
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2) Installation
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---------------
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Please go to the QML github repository at https://github.com/qmlcode/qml/
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.. toctree::
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:maxdepth: 2
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:caption: GETTING STARTED:
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:name: index
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installation
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examples
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.. toctree::
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:maxdepth: 2
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:caption: SOURCE DOCUMENTATION:
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:name: qml
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qml
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3) License:
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-----------
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QML is freely available under the terms of the MIT license.
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.. |Build Status| image:: https://travis-ci.org/qmlcode/qml.svg?branch=master
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:target: https://travis-ci.org/qmlcode/qml

‎docs/source/installation.rst

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Installation
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---------------
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The easiest way to install the stable version from the Python Package
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Index (PyPI) is using the official, built-in Python package manager,
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``pip``:
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.. code:: bash
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pip install qml --user -U
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Alternatively, you can install the most recent stable development
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snapshot directly from GitHub:
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.. code:: bash
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pip install git+https://github.com/qmlcode/qml --user -U
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For more installation help, please see the github repository: https://github.com/qmlcode/qml/

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