Initial commit

.coveragerc

+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = pystencils_autodiff
+# omit = bad_file.py
+
+[paths]
+source =
+    src/
+    */site-packages/
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:

.gitignore

+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+tags
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.tox
+junit.xml
+coverage.xml
+.pytest_cache/
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/api/*
+docs/_rst/*
+docs/_build/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+.venv*/

AUTHORS.rst

+============
+Contributors
+============
+
+* Stephan Seitz <stephan.seitz@fau.de>

CHANGELOG.rst

+=========
+Changelog
+=========
+
+Version 0.1
+===========
+
+- Feature A added
+- FIX: nasty bug #1729 fixed
+- add your changes here!

LICENSE.txt

+The MIT License (MIT)
+
+Copyright (c) 2019 Stephan Seitz
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

+===================
+pystencils_autodiff
+===================
+
+
+Add a short description here!
+
+
+Description
+===========
+
+A longer description of your project goes here...
+
+
+Note
+====
+
+This project has been set up using PyScaffold 3.2. For details and usage
+information on PyScaffold see https://pyscaffold.org/.

docs/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+AUTODOCDIR    = api
+AUTODOCBUILD  = sphinx-apidoc
+PROJECT       = pystencils_autodiff
+MODULEDIR     = ../src/pystencils_autodiff
+
+# 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 clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext doc-requirements
+
+help:
+	@echo "Please use \`make <target>' where <target> 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 "  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)"
+
+clean:
+	rm -rf $(BUILDDIR)/* $(AUTODOCDIR)
+
+$(AUTODOCDIR): $(MODULEDIR)
+	mkdir -p $@
+	$(AUTODOCBUILD) -f -o $@ $^
+
+doc-requirements: $(AUTODOCDIR)
+
+html: doc-requirements
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml: doc-requirements
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml: doc-requirements
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle: doc-requirements
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json: doc-requirements
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp: doc-requirements
+	$(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."
+
+qthelp: doc-requirements
+	$(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 $(BUILDDIR)/qthelp/$(PROJECT).qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(PROJECT).qhc"
+
+devhelp: doc-requirements
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $HOME/.local/share/devhelp/$(PROJECT)"
+	@echo "# ln -s $(BUILDDIR)/devhelp $HOME/.local/share/devhelp/$(PROJEC)"
+	@echo "# devhelp"
+
+epub: doc-requirements
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+patch-latex:
+	find _build/latex -iname "*.tex" | xargs -- \
+		sed -i'' 's~includegraphics{~includegraphics\[keepaspectratio,max size={\\textwidth}{\\textheight}\]{~g'
+
+latex: doc-requirements
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	$(MAKE) patch-latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf: doc-requirements
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	$(MAKE) patch-latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja: doc-requirements
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text: doc-requirements
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man: doc-requirements
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo: doc-requirements
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info: doc-requirements
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext: doc-requirements
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes: doc-requirements
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck: doc-requirements
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest: doc-requirements
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml: doc-requirements
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml: doc-requirements
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/_static/.gitignore

+# Empty directory

docs/authors.rst

+.. _authors:
+.. include:: ../AUTHORS.rst

docs/changelog.rst

+.. _changes:
+.. include:: ../CHANGELOG.rst

docs/conf.py

+# -*- coding: utf-8 -*-
+#
+# 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 os
+import sys
+import inspect
+import shutil
+
+__location__ = os.path.join(os.getcwd(), os.path.dirname(
+    inspect.getfile(inspect.currentframe())))
+
+# 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.join(__location__, '../src'))
+
+# -- Run sphinx-apidoc ------------------------------------------------------
+# This hack is necessary since RTD does not issue `sphinx-apidoc` before running
+# `sphinx-build -b html . _build/html`. See Issue:
+# https://github.com/rtfd/readthedocs.org/issues/1139
+# DON'T FORGET: Check the box "Install your project inside a virtualenv using
+# setup.py install" in the RTD Advanced Settings.
+# Additionally it helps us to avoid running apidoc manually
+
+try:  # for Sphinx >= 1.7
+    from sphinx.ext import apidoc
+except ImportError:
+    from sphinx import apidoc
+
+output_dir = os.path.join(__location__, "api")
+module_dir = os.path.join(__location__, "../src/pystencils_autodiff")
+try:
+    shutil.rmtree(output_dir)
+except FileNotFoundError:
+    pass
+
+try:
+    import sphinx
+    from pkg_resources import parse_version
+
+    cmd_line_template = "sphinx-apidoc -f -o {outputdir} {moduledir}"
+    cmd_line = cmd_line_template.format(outputdir=output_dir, moduledir=module_dir)
+
+    args = cmd_line.split(" ")
+    if parse_version(sphinx.__version__) >= parse_version('1.7'):
+        args = args[1:]
+
+    apidoc.main(args)
+except Exception as e:
+    print("Running `sphinx-apidoc` failed!\n{}".format(e))
+
+# -- 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.intersphinx', 'sphinx.ext.todo',
+              'sphinx.ext.autosummary', 'sphinx.ext.viewcode', 'sphinx.ext.coverage',
+              'sphinx.ext.doctest', 'sphinx.ext.ifconfig', 'sphinx.ext.mathjax',
+              'sphinx.ext.napoleon']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+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 = u'pystencils_autodiff'
+copyright = u'2019, Stephan Seitz'
+
+# 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 = ''  # Is set by calling `setup.py docs`
+# The full version, including alpha/beta/rc tags.
+release = ''  # Is set by calling `setup.py docs`
+
+# 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 = ''
+# 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
+
+
+# -- 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 = 'alabaster'
+
+# 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 = {
+    'sidebar_width': '300px',
+    'page_width': '1200px'
+}
+
+# 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".
+try:
+    from pystencils_autodiff import __version__ as version
+except ImportError:
+    pass
+else:
+    release = version
+
+# 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 = ""
+
+# 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']
+
+# 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.
+htmlhelp_basename = 'pystencils_autodiff-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]).
+latex_documents = [
+  ('index', 'user_guide.tex', u'pystencils_autodiff Documentation',
+   u'Stephan Seitz', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+# latex_logo = ""
+
+# 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
+
+# -- External mapping ------------------------------------------------------------
+python_version = '.'.join(map(str, sys.version_info[0:2]))
+intersphinx_mapping = {
+    'sphinx': ('http://www.sphinx-doc.org/en/stable', None),
+    'python': ('https://docs.python.org/' + python_version, None),
+    'matplotlib': ('https://matplotlib.org', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy', None),
+    'sklearn': ('http://scikit-learn.org/stable', None),
+    'pandas': ('http://pandas.pydata.org/pandas-docs/stable', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+}

docs/index.rst

+===================
+pystencils_autodiff
+===================
+
+This is the documentation of **pystencils_autodiff**.
+
+.. note::
+
+    This is the main page of your project's `Sphinx`_ documentation.
+    It is formatted in `reStructuredText`_. Add additional pages
+    by creating rst-files in ``docs`` and adding them to the `toctree`_ below.
+    Use then `references`_ in order to link them from this page, e.g.
+    :ref:`authors` and :ref:`changes`.
+
+    It is also possible to refer to the documentation of other Python packages
+    with the `Python domain syntax`_. By default you can reference the
+    documentation of `Sphinx`_, `Python`_, `NumPy`_, `SciPy`_, `matplotlib`_,
+    `Pandas`_, `Scikit-Learn`_. You can add more by extending the
+    ``intersphinx_mapping`` in your Sphinx's ``conf.py``.
+
+    The pretty useful extension `autodoc`_ is activated by default and lets
+    you include documentation from docstrings. Docstrings can be written in
+    `Google style`_ (recommended!), `NumPy style`_ and `classical style`_.
+
+
+Contents
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   License <license>
+   Authors <authors>
+   Changelog <changelog>
+   Module Reference <api/modules>
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+.. _toctree: http://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html
+.. _reStructuredText: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
+.. _references: http://www.sphinx-doc.org/en/stable/markup/inline.html
+.. _Python domain syntax: http://sphinx-doc.org/domains.html#the-python-domain
+.. _Sphinx: http://www.sphinx-doc.org/
+.. _Python: http://docs.python.org/
+.. _Numpy: http://docs.scipy.org/doc/numpy
+.. _SciPy: http://docs.scipy.org/doc/scipy/reference/
+.. _matplotlib: https://matplotlib.org/contents.html#
+.. _Pandas: http://pandas.pydata.org/pandas-docs/stable
+.. _Scikit-Learn: http://scikit-learn.org/stable
+.. _autodoc: http://www.sphinx-doc.org/en/stable/ext/autodoc.html
+.. _Google style: https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings
+.. _NumPy style: https://numpydoc.readthedocs.io/en/latest/format.html
+.. _classical style: http://www.sphinx-doc.org/en/stable/domains.html#info-field-lists

docs/license.rst

+.. _license:
+
+=======
+License
+=======
+
+.. include:: ../LICENSE.txt

requirements.txt

+# =============================================================================
+# DEPRECATION WARNING:
+#
+# The file `requirements.txt` does not influence the package dependencies and
+# will not be automatically created in the next version of PyScaffold (v4.x).
+#
+# Please have look at the docs for better alternatives
+# (`Dependency Management` section).
+# =============================================================================
+#
+# Add your pinned requirements so that they can be easily installed with:
+# pip install -r requirements.txt
+# Remember to also add them in setup.cfg but unpinned.
+# Example:
+# numpy==1.13.3
+# scipy==1.0
+#

setup.cfg

+# This file is used to configure your project.
+# Read more about the various options under:
+# http://setuptools.readthedocs.io/en/latest/setuptools.html#configuring-setup-using-setup-cfg-files
+
+[metadata]
+name = pystencils_autodiff
+description = Add a short description here!
+author = Stephan Seitz
+author-email = stephan.seitz@fau.de
+license = mit
+long-description = file: README.rst
+long-description-content-type = text/x-rst; charset=UTF-8
+url = https://github.com/pyscaffold/pyscaffold/
+project-urls =
+    Documentation = https://pyscaffold.org/
+# Change if running only on Windows, Mac or Linux (comma-separated)
+platforms = any
+# Add here all kinds of additional classifiers as defined under
+# https://pypi.python.org/pypi?%3Aaction=list_classifiers
+classifiers =
+    Development Status :: 4 - Beta
+    Programming Language :: Python
+
+[options]
+zip_safe = False
+packages = find:
+include_package_data = True
+package_dir =
+    =src
+# DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD!
+setup_requires = pyscaffold>=3.2a0,<3.3a0
+# Add here dependencies of your project (semicolon/line-separated), e.g.
+# install_requires = numpy; scipy
+# The usage of test_requires is discouraged, see `Dependency Management` docs
+# tests_require = pytest; pytest-cov
+# Require a specific Python version, e.g. Python 2.7 or >= 3.4
+# python_requires = >=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*
+
+[options.packages.find]
+where = src
+exclude =
+    tests
+
+[options.extras_require]
+# Add here additional requirements for extra features, to install with:
+# `pip install pystencils_autodiff[PDF]` like:
+# PDF = ReportLab; RXP
+# Add here test requirements (semicolon/line-separated)
+testing =
+    pytest
+    pytest-cov
+
+[options.entry_points]
+# Add here console scripts like:
+# console_scripts =
+#     script_name = pystencils_autodiff.module:function
+# For example:
+# console_scripts =
+#     fibonacci = pystencils_autodiff.skeleton:run
+# And any other entry points, for example:
+# pyscaffold.cli =
+#     awesome = pyscaffoldext.awesome.extension:AwesomeExtension
+
+[test]
+# py.test options when running `python setup.py test`
+# addopts = --verbose
+extras = True
+
+[tool:pytest]
+# Options for py.test:
+# Specify command line options as you would do when invoking py.test directly.
+# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
+# in order to write a coverage file that can be read by Jenkins.
+addopts =
+    --cov pystencils_autodiff --cov-report term-missing
+    --verbose
+norecursedirs =
+    dist
+    build
+    .tox
+testpaths = tests
+
+[aliases]
+dists = bdist_wheel
+
+[bdist_wheel]
+# Use this option if your package is pure-python
+universal = 1
+
+[build_sphinx]
+source_dir = docs
+build_dir = docs/_build
+
+[devpi:upload]
+# Options for the devpi: PyPI server and packaging tool
+# VCS export must be deactivated since we are using setuptools-scm
+no-vcs = 1
+formats = bdist_wheel
+
+[flake8]
+# Some sane defaults for the code style checker flake8
+exclude =
+    .tox
+    build
+    dist
+    .eggs
+    docs/conf.py
+
+[pyscaffold]
+# PyScaffold's parameters when the project was created.
+# This will be used when updating. Do not change!
+version = 3.2
+package = pystencils_autodiff

setup.py

+# -*- coding: utf-8 -*-
+"""
+    Setup file for pystencils_autodiff.
+    Use setup.cfg to configure your project.
+
+    This file was generated with PyScaffold 3.2.
+    PyScaffold helps you to put up the scaffold of your new Python project.
+    Learn more under: https://pyscaffold.org/
+"""
+import sys
+
+from pkg_resources import require, VersionConflict
+from setuptools import setup
+
+try:
+    require('setuptools>=38.3')
+except VersionConflict:
+    print("Error: version of setuptools is too old (<38.3)!")
+    sys.exit(1)
+
+
+if __name__ == "__main__":
+    setup(use_pyscaffold=True)

src/pystencils_autodiff/__init__.py

+# -*- coding: utf-8 -*-
+from pkg_resources import get_distribution, DistributionNotFound
+
+try:
+    # Change here if project is renamed and does not equal the package name
+    dist_name = __name__
+    __version__ = get_distribution(dist_name).version
+except DistributionNotFound:
+    __version__ = 'unknown'
+finally:
+    del get_distribution, DistributionNotFound

src/pystencils_autodiff/skeleton.py

+# -*- coding: utf-8 -*-
+"""
+This is a skeleton file that can serve as a starting point for a Python
+console script. To run this script uncomment the following lines in the
+[options.entry_points] section in setup.cfg:
+
+    console_scripts =
+         fibonacci = pystencils_autodiff.skeleton:run
+
+Then run `python setup.py install` which will install the command `fibonacci`
+inside your current environment.
+Besides console scripts, the header (i.e. until _logger...) of this file can
+also be used as template for Python modules.
+
+Note: This skeleton file can be safely removed if not needed!
+"""
+
+import argparse
+import sys
+import logging
+
+from pystencils_autodiff import __version__
+
+__author__ = "Stephan Seitz"
+__copyright__ = "Stephan Seitz"
+__license__ = "mit"
+
+_logger = logging.getLogger(__name__)
+
+
+def fib(n):
+    """Fibonacci example function
+
+    Args:
+      n (int): integer
+
+    Returns:
+      int: n-th Fibonacci number
+    """
+    assert n > 0
+    a, b = 1, 1
+    for i in range(n-1):
+        a, b = b, a+b
+    return a
+
+
+def parse_args(args):
+    """Parse command line parameters
+
+    Args:
+      args ([str]): command line parameters as list of strings
+
+    Returns:
+      :obj:`argparse.Namespace`: command line parameters namespace
+    """
+    parser = argparse.ArgumentParser(
+        description="Just a Fibonacci demonstration")
+    parser.add_argument(
+        "--version",
+        action="version",
+        version="pystencils_autodiff {ver}".format(ver=__version__))
+    parser.add_argument(
+        dest="n",
+        help="n-th Fibonacci number",
+        type=int,
+        metavar="INT")
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        dest="loglevel",
+        help="set loglevel to INFO",
+        action="store_const",
+        const=logging.INFO)
+    parser.add_argument(
+        "-vv",
+        "--very-verbose",
+        dest="loglevel",
+        help="set loglevel to DEBUG",
+        action="store_const",
+        const=logging.DEBUG)
+    return parser.parse_args(args)
+
+
+def setup_logging(loglevel):
+    """Setup basic logging
+
+    Args:
+      loglevel (int): minimum loglevel for emitting messages
+    """
+    logformat = "[%(asctime)s] %(levelname)s:%(name)s:%(message)s"
+    logging.basicConfig(level=loglevel, stream=sys.stdout,
+                        format=logformat, datefmt="%Y-%m-%d %H:%M:%S")
+
+
+def main(args):
+    """Main entry point allowing external calls
+
+    Args:
+      args ([str]): command line parameter list
+    """
+    args = parse_args(args)
+    setup_logging(args.loglevel)
+    _logger.debug("Starting crazy calculations...")
+    print("The {}-th Fibonacci number is {}".format(args.n, fib(args.n)))
+    _logger.info("Script ends here")
+
+
+def run():
+    """Entry point for console_scripts
+    """
+    main(sys.argv[1:])
+
+
+if __name__ == "__main__":
+    run()

tests/conftest.py

+# -*- coding: utf-8 -*-
+"""
+    Dummy conftest.py for pystencils_autodiff.
+
+    If you don't know what this is for, just leave it empty.
+    Read more about conftest.py under:
+    https://pytest.org/latest/plugins.html
+"""
+
+# import pytest

tests/test_skeleton.py

+# -*- coding: utf-8 -*-
+
+import pytest
+from pystencils_autodiff.skeleton import fib
+
+__author__ = "Stephan Seitz"
+__copyright__ = "Stephan Seitz"
+__license__ = "mit"
+
+
+def test_fib():
+    assert fib(1) == 1
+    assert fib(2) == 1
+    assert fib(7) == 13
+    with pytest.raises(AssertionError):
+        fib(-10)