Initial commit.

.gitignore

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+# 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/

.gitlab-ci.yml

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+image: ubuntu:14.04
+# It might be a good idea to switch to a different base image and so avoid installing packages for each commit. 
+
+stages:
+    - test
+    - pages
+    - release
+
+before_script:
+    - apt-get update
+    - apt-get install -y software-properties-common
+    - apt-add-repository universe
+    - apt-get update
+    - apt-get install -y python-pip make
+    - pip install --upgrade sphinx sphinx-argparse sphinx_rtd_theme pytest pycmd 
+
+
+do_testing:
+  stage: test
+  script:
+    - make test
+  except:
+    - tags
+
+pages:
+  stage: pages
+  script: 
+    - pip install -e ./
+    - make docs
+    - mv docs/_build/html public
+  artifacts:
+    paths:
+    - public/
+  only:
+    - master
+  except:
+    - tags
+
+
+do_release:
+  stage: release
+  script:
+      #  Build project
+      - python setup.py sdist
+      #  Going to push project via ssh.
+      #  PYPI_KEY and PYPI_HOST should set up as project variables on Gitlab
+      #  PYPI_KEY is private key produced by ssh-keygen
+      - apt-get install -y openssh-client
+      - eval $(ssh-agent -s)
+      - ssh-add <(set +x; echo "$PYPI_KEY")
+      - scp -o StrictHostKeyChecking=no dist/* gitlab-ci-pypi@${PYPI_HOST}:/opt/ont-pypi/site-packages/
+  only:
+      #  Only do a release of tags marked explicit as release (match this regular expression)
+      - /^release_.*$/
+  except:
+      #  Do look for tags in branches
+      - branches

MANIFEST.in

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

Makefile

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+MODULE=wub
+
+.PHONY: clean clean-test clean-pyc clean-build docs com help 
+
+.DEFAULT_GOAL := help
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+help:
+	@python -c "$$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 $(MODULE)
+
+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 $(MODULE) setup.py test
+		coverage report -m
+		coverage html
+
+docs: ## generate Sphinx HTML documentation, including API docs
+	rm -f docs/$(MODULE).rst
+	rm -f docs/modules.rst
+	sphinx-apidoc -o docs/ $(MODULE)
+	(cd docs; ./cmd_tools.py > cmd_list.rst)
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html
+
+servedocs: docs ## compile the docs watching for changes
+	watchmedo shell-command -p '*.rst' -c '$(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
+
+com: ## commit all changes to git
+	git commit -a

README.md

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+Wub: tools and software library developed by the ONT Applications group
+=======================================================================
+
+
+Installation
+------------
+
+Install the package:
+
+```
+python setup.py install
+```
+
+Install the package in developer mode:
+
+```
+python setup.py develop
+```
+
+Run the tests:
+
+```
+make test
+```
+
+Build the documentation:
+
+```
+make docs
+```
+
+Issue `make help` to get a list of `make` targets.
+
+Documentation
+-------------
+
+Documentation can be found at: https://apps.git.oxfordnanolabs.local/wub
+
+Contributing
+------------
+
+- Please fork the repository and create a merge request to contribute.
+- Please respect the structure outlined in `scripts/_template_script.py` from command line tools so documentation can be generated automatically.
+- Use [bumpversion](http://bit.ly/2cSUryt) to manage package versioning.
+- The code should be [PEP8](https://www.python.org/dev/peps/pep-0008) compliant, which can be tested by `make lint`.
+- For more guidance regarding coding style please refer to the [Tao of Tang](https://git.oxfordnanolabs.local/research/tang/blob/master/tao.md).
+
+TODO
+----

docs/.gitignore

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+*.rst