Update template

.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# pyc files:
+*.pyc 
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# vim files
+*.sw*
+
+# folder
+tmp/
+.idea
+docs/source/
+
+### Git ###
+*.orig
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk

.gitlab-ci.yml

+image: python:latest
+
+# Change pip's cache directory to be inside the project directory since we can
+# only cache local items.
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
+# Pip's cache doesn't store the python packages
+# https://pip.pypa.io/en/stable/reference/pip_install/#caching
+#
+# If you want to also cache the installed packages, you have to install
+# them in a virtualenv and cache it as well.
+cache:
+  paths:
+    - .cache/pip
+    - venv/
+
+stages:
+  - build
+  - test
+  - deploy
+
+before_script:
+  - pip install virtualenv
+  - virtualenv venv
+  - source venv/bin/activate
+
+dist:
+  stage: build
+  script:
+    - python setup.py bdist_wheel
+    # an alternative approach is to install and run:
+    - pip install dist/*
+    # run the command here
+  artifacts:
+    paths:
+      - dist/*.whl
+    expire_in: 1h
+  only:
+    - tags
+
+pages:
+  stage: build
+  script:
+    - pip install sphinx sphinx_rtd_theme recommonmark
+    - cd docs
+    - make html
+    - cd ..
+    - mkdir -p public
+    - rm -rf public/*
+    - mv docs/_build/html/* public/  # add it to pages. Pages is exposing public/index.html
+  only:
+    - master
+  cache:
+    paths:
+      - public
+  artifacts:
+    paths:
+      - public
+      - docs
+
+lint:
+  stage: test
+  before_script:
+    - pip install -q flake8
+  script:
+    - flake8
+
+test:
+  stage: test
+  script:
+    - pip --version
+    - pip install tox  # you can also use tox
+    - tox
+  coverage: '/^TOTAL.+?(\d+\%)$/'
+  artifacts:
+    # paths:
+    # pa- report/unit
+    reports:
+      junit:
+        - report/junit.xml
+    
+gitlab-release:
+  image: inetprocess/gitlab-release
+  stage: deploy
+  before_script:
+    - echo "Starting release"
+  script:
+    - gitlab-release --message 'Automatic release' dist/*  # Note:
+  only:
+    - tags
+
+pypi:
+  image: docker.km3net.de/base/python:3
+  stage: deploy
+  cache: {}
+  before_script:
+    - echo "Starting upload to pypi"
+  script:
+    # Check if current_version is already uploaded
+    - VERSION=$((python -c "import configparser; config = configparser.ConfigParser(); config.read('setup.cfg'); print(config['bumpversion']['current_version'])") 2>&1)
+    - MODULE_NAME=$((python -c "import configparser; config = configparser.ConfigParser(); config.read('setup.cfg'); print(config['metadata']['name'])") 2>&1)
+    - PACKAGE_JSON_URL="https://pypi.org/pypi/$MODULE_NAME/json" 
+    - apt-get install -qq -y jq
+    - PYPI_VERSIONS=$(curl -s "$PACKAGE_JSON_URL" | jq  -r '.releases | keys | .[]' | sort -V)
+    - if [[ $PYPI_VERSIONS =~ $VERSION ]]; then echo "Version $VERSION is already uploaded!"; exit 1; fi
+    # Version not already uploaded so do it now.
+    - echo "Uploading version $VERSION"
+    - pip install -U twine
+    - python setup.py sdist
+    - twine upload dist/*
+  rules:
+    # for debuggin: git commit -am "deb" && git push && bumpversion patch && git tag -l --sort=-v:refname | head -n 1 | git push origin
+    - if: $CI_COMMIT_TAG =~ /^v[0-9]+\.[0-9]+\.[0-9]+$/

.readthedocs.yml

+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

AUTHORS.rst

+=======
+Credits
+=======
+This package was created with Cookiecutter_ and the `dboe/dough`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`dboe/dough`: https://gitlab.com/dboe/dough
+
+Development Lead
+----------------
+
+* Daniel Böckenhoff <dboe@ipp.mpg.de>
+
+Contributors
+------------
+
+None yet. Why not be the first?

CONTRIBUTING.rst

+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://gitlab.mpcdf.mpg.de/dboe/tfields/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+If you want quick feedback, it is helpful to mention speicific developers
+(@devloper_name) or @all. This will trigger a mail to the corresponding developer(s).
+
+Fix Bugs
+~~~~~~~~
+
+Look through the repository issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the remote issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+`tfields` could always use more :ref:`documentation<Documentation>`, whether as part of the
+official `tfields` docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Write Unittests or Doctests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+`tfields` profits a lot from better :ref:`testing<Testing>`. We encourage you to add unittests 
+(in the `tests` directory) or doctests (as part of docstrings or in the documentation).
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an `Issue <https://gitlab.mpcdf.mpg.de/dboe/tfields/issues>`_.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `tfields` for local development.
+
+1. Fork the `tfields` repo.
+2. Clone your fork locally::
+
+    $ git clone git@gitlab.mpcdf.mpg.de:dboe/tfields.git
+
+3. Set up your fork for local development::
+
+    $ cd tfields/
+    $ pip install .[dev]
+
+4. Step 3. already installed `pre-commit <https://pre-commit.com/>`_. Initialize it by running::
+
+    $ pre-commit install
+
+5. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+6. When you're done making changes, check that your changes pass flake8 and the
+   tests::
+
+    $ make test
+
+7. Commit your changes and push your branch to origin::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+8. Submit a pull request through the repository website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
+   https://gitlab.mpcdf.mpg.de/dboe/tfields/-/merge_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Testing
+-------
+
+To run tests, use::
+
+    $ make test
+
+To run a subset of tests, you have the following options::
+
+    $ pytest tests/test_package.py
+
+    $ pytest tests/test_package.py::Test_tfields::test_version_type
+
+    $ pytest --doctest-modules docs/usage.rst
+
+    $ pytest --doctest-modules tfields/core.py -k "MyClass.funciton_with_doctest"
+
+Use the '--trace' option to directly jump into a pdb debugger on fails. Check out the coverage of your api with::
+
+    $ make coverage
+
+Documentation
+-------------
+To compile the documentation (including automatically generated module api docs), run::
+
+    $ make doc
+
+Use doctests as much as possible in order to have tested examples in your documentation.
+
+Styleguide
+-----------
+Please follow the `google style guide <https://google.github.io/styleguide/pyguide.html>`_ illustrated
+by `this example <https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>`_.
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed.
+Then run::
+
+    $ bump2version patch # possible: major / minor / patch
+    $ git push
+    $ git push --tags
+
+or use the convenient alias for the above (patch increases only)::
+
+    $ make publish
+
+The CI will then deploy to PyPI if tests pass.

LICENSE.rst

+MIT License
+
+Copyright (c) 2020, Daniel Böckenhoff
+
+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.
+

Makefile

+SHELL := /bin/bash # Use bash syntax
+CURRENT_PATH := $(shell pwd)
+MODULE := $(shell basename "$(CURRENT_PATH)")
+VERSION := $(shell python -c "import sys; import $(MODULE); sys.stdout.write($(MODULE).__version__)")
+SOURCES := $(shell find $(MODULE) -name '*.py')
+DOCUMENTATION := $(shell find . -name '*.rst')
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SPHINXSOURCEDIR = ./docs
+SPHINXBUILDDIR  = docs/_build
+GITSTATUS = $(shell git status --porcelain)
+part ?= patch
+
+test: FORCE
+	flake8 rna tests
+	py.test
+
+coverage:
+	# coverage run $(MODULE) test
+	py.test --cov=$(MODULE) || true
+	# coverage report
+	coverage html
+	python -m webbrowser htmlcov/index.html
+
+clean:
+	coverage erase
+	rm -rf htmlcov
+	rm -rf docs/_build
+	rm -rf docs/source
+	rm -rf dist
+	rm -rf report
+	rm -rf .tox
+	rm -rf .pytest_cache
+	rm -rf *.egg-info
+	pre-commit clean
+
+publish:
+	# call optional with argument: make part=minor publish
+	bump2version $(part)  # possible: major / minor / patch
+	git push
+	git push --tags
+
+untag:
+	# remove last tag. mostly, because publishing failed
+	git tag -d v$(VERSION)
+	git push origin :refs/tags/v$(VERSION)
+
+requirements: setup.cfg
+	# We have all the information in the setup.cfg file. For some reasons (e.g. bug in setuptools or limitations to use setup.cfg in readthedocs) we still need a requirements file
+	python -c "import configparser; import os; config = configparser.ConfigParser(); config.read('setup.cfg'); deps = config['metadata']['install_requires'].split('\n'); deps = [x for x in deps if x]; head = '# Autogenerated by Makefile from setup.cfg install_requies section. Remove this line if you want to fix this file.'; path = 'requirements.txt'; f = open(path, 'r') if os.path.exists(path) else None; line = f.readline() if f else ''; quit('User defined requirements already existing.') if f and not line.startswith(head[:20]) else None; f = open('requirements.txt', 'w'); f.write('\n'.join([head] + deps))"
+
+doc: Makefile $(SOURCES) $(DOCUMENTATION) docs/conf.py docs/apidoc-template/*
+	# link apidoc to source and build html documentation with sphinx
+	python setup.py build_sphinx
+	# manual version would be
+	# # link apidoc to source
+	# sphinx-apidoc -o docs/source/ $(MODULE)
+	# # build html documentation with sphinx
+	# # @$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(0)
+	# sphinx-build -M html docs docs/_build
+	#
+	# open the html slides
+	python -m webbrowser docs/_build/html/index.html
+
+update:
+	# get up to date with the cookiecutter template 'dough'
+	# first check that no changes are existing
+	@echo $(GITSTATUS)
+	@if [ -z $(GITSTATUS) ]; then \
+	  	echo "Working directory clean."; \
+	else \
+		git status; \
+	  	echo "Your status is not clean! I can not update!"; \
+	    exit 1; \
+	fi
+	# Uninstall pre-commit
+	pre-commit uninstall
+	# Starting upgrade
+	cookiecutter_project_upgrader
+	# Install pre-commit again
+	pre-commit install
+
+FORCE: ;

README.rst

+=========================
+Introduction to `tfields`
+=========================
+
+
+.. pypi
+.. image:: https://img.shields.io/pypi/v/tfields.svg
+    :target: https://pypi.python.org/pypi/tfields
+
+.. ci
+    .. image:: https://img.shields.io/travis/dboe/tfields.svg
+        :target: https://travis-ci.com/dboe/tfields
+.. image:: https://gitlab.mpcdf.mpg.de/dboe/tfields/badges/master/pipeline.svg
+    :target: https://gitlab.mpcdf.mpg.de/dboe/tfields/commits/master
+
+.. coverage
+.. image:: https://gitlab.mpcdf.mpg.de/dboe/tfields/badges/master/coverage.svg
+    :target: https://gitlab.mpcdf.mpg.de/dboe/tfields/commits/master
+
+.. readthedocs
+.. image:: https://readthedocs.org/projects/tfields/badge/?version=latest
+    :target: https://tfields.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. pyup crosschecks your dependencies. Github is default, gitlab more complicated: https://pyup.readthedocs.io/en/latest/readme.html#run-your-first-update 
+    .. image:: https://pyup.io/repos/github/dboe/tfields/shield.svg
+        :target: https://pyup.io/repos/github/dboe/tfields/
+        :alt: Updates
+
+.. image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
+   :target: https://github.com/pre-commit/pre-commit
+   :alt: pre-commit
+
+
+Tensors, tensor fields, graphs, mesh manipulation, CAD and more on the basis of numpy.ndarrays. All objects keep track of their coordinate system. Symbolic math operations work for object manipulation.
+
+
+Licensed under the ``MIT License``
+
+Resources
+---------
+
+* Source code: https://gitlab.mpcdf.mpg.de/dboe/tfields
+* Documentation: https://tfields.readthedocs.io
+* Pypi: https://pypi.python.org/pypi/tfields
+
+
+Features
+--------
+
+The following features should be highlighted:
+
+* TODO

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+MODULE_PATH := $(shell cd ..; pwd)
+MODULE := $(shell basename "$(MODULE_PATH)")
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .