Package for PyPI

Package for PyPI using the cookiecutter template:

https://github.com/audreyr/cookiecutter-pypackage

The package is not yet deployed.

Factor the CLI into a separate file. Start minimal tests for octrees.

Many of the committed features are not yet functional or edited,
including:

- documentation
- manifests
- readthedocs
- tox
- travis

.editorconfig

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+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.gitignore

@@ -1,3 +1,62 @@
+# Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+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/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv python configuration file
+.python-version

.travis.yml

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+# Config file for automatic testing at travis-ci.org
+# This file will be regenerated if you run travis_pypi_setup.py
+
+language: python
+python: 3.5
+
+env:
+  - TOXENV=py27
+
+# command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
+install: pip install -U tox
+
+# command to run tests, e.g. python setup.py test
+script: tox -e ${TOXENV}
+
+# After you create the Github repo and add it to Travis, run the
+# travis_pypi_setup.py script to finish PyPI deployment setup
+deploy:
+  provider: pypi
+  distributions: sdist bdist_wheel
+  user: aschampion
+  password:
+    secure: PLEASE_REPLACE_ME
+  on:
+    tags: true
+    repo: aschampion/diluvian
+    condition: $TOXENV == py27

AUTHORS.rst

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+=======
+Credits
+=======
+
+* Andrew S. Champion <[email protected]>

CONTRIBUTING.rst

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+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+Development
+-----------
+
+Here's how to set up `diluvian` for local development.
+
+1. Fork the `diluvian` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/diluvian.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv diluvian
+    $ cd diluvian/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+
+    $ flake8 diluvian tests
+    $ python setup.py test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+

HISTORY.rst

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+=======
+History
+=======
+
+0.0.1 (2017-02-07)
+------------------
+
+* First release on PyPI.

LICENSE

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+
+MIT License
+
+Copyright (c) 2017, Andrew S. Champion
+
+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.
+

MANIFEST.in

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+
+include AUTHORS.rst
+
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

Makefile

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+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+try:
+	from urllib import pathname2url
+except:
+	from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+
+lint: ## check style with flake8
+	flake8 diluvian tests
+
+test: ## run tests quickly with the default Python
+	py.test
+
+
+test-all: ## run tests on every Python version with tox
+	tox
+
+coverage: ## check code coverage quickly with the default Python
+	coverage run --source diluvian -m pytest
+
+		coverage report -m
+		coverage html
+		$(BROWSER) htmlcov/index.html
+
+docs: ## generate Sphinx HTML documentation, including API docs
+	rm -f docs/diluvian.rst
+	rm -f docs/modules.rst
+	sphinx-apidoc -o docs/ diluvian
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html
+	$(BROWSER) docs/_build/html/index.html
+
+servedocs: docs ## compile the docs watching for changes
+	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+
+release: clean ## package and upload a release
+	python setup.py sdist upload
+	python setup.py bdist_wheel upload
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install

README.rst

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+===============================
+diluvian
+===============================
+
+
+.. image:: https://img.shields.io/pypi/v/diluvian.svg
+        :target: https://pypi.python.org/pypi/diluvian
+
+.. image:: https://img.shields.io/travis/aschampion/diluvian.svg
+        :target: https://travis-ci.org/aschampion/diluvian
+
+.. image:: https://readthedocs.org/projects/diluvian/badge/?version=latest
+        :target: https://diluvian.readthedocs.io/en/latest/?badge=latest
+        :alt: Documentation Status
+
+
+Flood filling networks for segmenting electron microscopy of neural tissue.
+
+
+* Free software: MIT license
+* Documentation: https://diluvian.readthedocs.io.

diluvian/__init__.py

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+# -*- coding: utf-8 -*-
+
+__author__ = """Andrew S. Champion"""
+__email__ = '[email protected]'
+__version__ = '0.0.1'