move untrack doc and requirement files (#41)

* move untrack doc and requirement files

* add requirement in run.txt

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.gitattributes

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+diffpy.srmise/_version.py export-subst

doc/source/api/diffpy.srmise.example_package.rst

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+.. _example_package documentation:
+
+|title|
+=======
+
+.. |title| replace:: diffpy.srmise.example_package package
+
+.. automodule:: diffpy.srmise.example_package
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+|foo|
+-----
+
+.. |foo| replace:: diffpy.srmise.example_package.foo module
+
+.. automodule::  diffpy.srmise.example_package.foo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+|bar|
+-----
+
+.. |bar| replace:: diffpy.srmise.example_package.bar module
+
+.. automodule:: diffpy.srmise.example_package.foo
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/diffpy.srmise.rst

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+:tocdepth: -1
+
+|title|
+=======
+
+.. |title| replace:: diffpy.srmise package
+
+.. automodule:: diffpy.srmise
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   diffpy.srmise.example_package
+
+Submodules
+----------
+
+|module|
+--------
+
+.. |module| replace:: diffpy.srmise.example_submodule module
+
+.. automodule:: diffpy.srmise.example_submodule
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/conf.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# diffpy.srmise documentation build configuration file, created by
+# sphinx-quickstart on Thu Jan 30 15:49:41 2014.
+#
+# 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 time
+from importlib.metadata import version
+from pathlib import Path
+
+# 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 Path().resolve() to make it absolute, like shown here.
+# sys.path.insert(0, str(Path(".").resolve()))
+sys.path.insert(0, str(Path("../..").resolve()))
+sys.path.insert(0, str(Path("../../src").resolve()))
+
+# abbreviations
+ab_authors = "Billinge Group members and community contributors"
+
+# -- 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",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx_rtd_theme",
+    "m2r",
+]
+
+# 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"]
+
+# The encoding of source files.
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+project = "diffpy.srmise"
+copyright = "%Y, The Trustees of Columbia University in the City of New York"
+
+# 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.
+
+fullversion = version(project)
+# The short X.Y version.
+version = "".join(fullversion.split(".post")[:1])
+# The full version, including alpha/beta/rc tags.
+release = fullversion
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+# language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+# today = ''
+today = time.strftime("%B %d, %Y", time.localtime())
+year = today.split()[-1]
+# Else, today_fmt is used as the format for a strftime call.
+# today_fmt = '%B %d, %Y'
+# substitute YEAR in the copyright string
+copyright = copyright.replace("%Y", year)
+
+# 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 = ["diffpy.srmise"]
+
+# Display all warnings for missing links.
+nitpicky = True
+
+# -- 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 = {
+    "navigation_with_keys": "true",
+}
+
+# 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
+# "<project> v<release> 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 (within the static path) to use as 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 <link> 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
+
+# Output file base name for HTML help builder.
+basename = "diffpy.srmise".replace(" ", "").replace(".", "")
+htmlhelp_basename = basename + "doc"
+
+
+# -- 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': '',
+}
+
+# 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 = [
+    ("index", "diffpy.srmise.tex", "diffpy.srmise Documentation", ab_authors, "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 = [("index", "diffpy.srmise", "diffpy.srmise Documentation", ab_authors, 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 = [
+    (
+        "index",
+        "diffpy.srmise",
+        "diffpy.srmise Documentation",
+        ab_authors,
+        "diffpy.srmise",
+        "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
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+# intersphinx_mapping = {'http://docs.python.org/': None}

doc/source/index.rst

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+#######
+|title|
+#######
+
+.. |title| replace:: diffpy.srmise documentation
+
+diffpy.srmise - Peak extraction and peak fitting tool for atomic pair distribution functions..
+
+| Software version |release|.
+| Last updated |today|.
+
+=======
+Authors
+=======
+
+diffpy.srmise is developed by Billinge Group
+and its community contributors.
+
+For a detailed list of contributors see
+https://github.com/diffpy/diffpy.srmise/graphs/contributors.
+
+============
+Installation
+============
+
+See the `README <https://github.com/diffpy/diffpy.srmise#installation>`_
+file included with the distribution.
+
+=================
+Table of contents
+=================
+.. toctree::
+   :titlesonly:
+
+   license
+   release
+   Package API <api/diffpy.srmise>
+
+=======
+Indices
+=======
+
+* :ref:`genindex`
+* :ref:`search`