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Add the docs
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‎.gitignore‎

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*.so
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*.pyc
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.classpath
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*build
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# Packages #
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############
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/data
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example_scripts/example_output/
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*/tmp/*
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venv
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docs
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venv

‎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 = "-W" # This flag turns warnings into errors.
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SPHINXBUILD = sphinx-build
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SPHINXPROJ = PackagingScientificPython
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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/make.bat‎

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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set SPHINXPROJ=PackagingScientificPython
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
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:end
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popd

‎docs/source/_static/.placeholder‎

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‎docs/source/conf.py‎

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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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#
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# constrained-matrix-factorization documentation build configuration file, created by
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# sphinx-quickstart on Thu Jun 28 12:35:56 2018.
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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 = [
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"sphinx.ext.autodoc",
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"sphinx.ext.autosummary",
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"sphinx.ext.githubpages",
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"sphinx.ext.intersphinx",
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"sphinx.ext.mathjax",
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"sphinx.ext.viewcode",
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"IPython.sphinxext.ipython_directive",
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"IPython.sphinxext.ipython_console_highlighting",
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"matplotlib.sphinxext.plot_directive",
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"numpydoc",
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"sphinx_copybutton",
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]
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# Configuration options for plot_directive. See:
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# https://github.com/matplotlib/matplotlib/blob/f3ed922d935751e08494e5fb5311d3050a3b637b/lib/matplotlib/sphinxext/plot_directive.py#L81
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plot_html_show_source_link = False
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plot_html_show_formats = False
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# Generate the API documentation when building
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autosummary_generate = True
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numpydoc_show_class_members = False
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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 = "constrained-matrix-factorization"
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copyright = "2021, Phil Maffettone"
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author = "Phil Maffettone"
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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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import constrainedmf
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# The short X.Y version.
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version = constrainedmf.__version__
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# The full version, including alpha/beta/rc tags.
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release = constrainedmf.__version__
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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 = "sphinx_rtd_theme"
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import 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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# Custom sidebar templates, must be a dictionary that maps document names
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# to template names.
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#
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# This is required for the alabaster theme
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# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
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html_sidebars = {
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"**": [
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"relations.html", # needs 'show_related': True theme option to display
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"searchbox.html",
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]
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}
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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 = "constrainedmf"
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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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(
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master_doc,
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"constrainedmf.tex",
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"constrained-matrix-factorization Documentation",
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"Contributors",
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"manual",
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),
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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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(
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master_doc,
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"constrainedmf",
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"constrained-matrix-factorization Documentation",
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[author],
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1,
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)
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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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(
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master_doc,
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"constrainedmf",
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"constrained-matrix-factorization Documentation",
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author,
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"constrainedmf",
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"Advancements on non-negative matrix factorization in PyTorch, with crystallography as a primary use case.",
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"Miscellaneous",
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),
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]
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# Example configuration for intersphinx: refer to the Python standard library.
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3/", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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"scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
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"pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
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"matplotlib": ("https://matplotlib.org/stable", None),
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}

‎docs/source/index.rst‎

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.. Packaging Scientific Python documentation master file, created by
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sphinx-quickstart on Thu Jun 28 12:35:56 2018.
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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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constrained-matrix-factorization Documentation
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==============================================
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.. toctree::
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:maxdepth: 2
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installation
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usage
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release-history
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min_versions

‎docs/source/installation.rst‎

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============
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Installation
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============
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At the command line::
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$ pip install constrainedmf

‎docs/source/min_versions.rst‎

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===================================
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Minimum Version of Python and NumPy
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===================================
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- This project supports at least the minor versions of Python
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initially released 42 months prior to a planned project release
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date.
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- The project will always support at least the 2 latest minor
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versions of Python.
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- The project will support minor versions of ``numpy`` initially
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released in the 24 months prior to a planned project release date or
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the oldest version that supports the minimum Python version
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(whichever is higher).
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- The project will always support at least the 3 latest minor
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versions of NumPy.
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The minimum supported version of Python will be set to
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``python_requires`` in ``setup``. All supported minor versions of
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Python will be in the test matrix and have binary artifacts built
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for releases.
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The project should adjust upward the minimum Python and NumPy
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version support on every minor and major release, but never on a
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patch release.
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This is consistent with NumPy `NEP 29
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<https://numpy.org/neps/nep-0029-deprecation_policy.html>`__.

‎docs/source/release-history.rst‎

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===============
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Release History
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===============
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v0.1.0 (2021-11-01)
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----------------------------
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This initial release marks the transfer of this repository to the NSLS-II organization.
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Initial publication details can be found on `the arXiv <https://arxiv.org/abs/2104.00864>`_,
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with the peer reviewed version accepted for publication in Applied Physics Reviews.

‎docs/source/usage.rst‎

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=====
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Usage
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=====
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Start by importing constrained-matrix-factorization.
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.. code-block:: python
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import constrainedmf

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