Merge branch 'python3'

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "submodules/presentation"]
-	path = submodules/presentation
-	url = https://git.lumc.nl/j.f.j.laros/presentation.git

README.rst

@@ -0,0 +1,33 @@
+Barcode: Design and test NGS barcodes
+=====================================
+
+.. image:: https://img.shields.io/github/last-commit/jfjlaros/barcode.svg
+   :target: https://github.com/jfjlaros/barcode/graphs/commit-activity
+.. image:: https://travis-ci.org/jfjlaros/barcode.svg?branch=master
+   :target: https://travis-ci.org/jfjlaros/barcode
+.. image:: https://readthedocs.org/projects/barcode/badge/?version=latest
+   :target: https://barcode.readthedocs.io/en/latest
+.. image:: https://img.shields.io/github/release-date/jfjlaros/barcode.svg
+   :target: https://github.com/jfjlaros/barcode/releases
+.. image:: https://img.shields.io/github/release/jfjlaros/barcode.svg
+   :target: https://github.com/jfjlaros/barcode/releases
+.. image:: https://img.shields.io/pypi/v/barcode.svg
+   :target: https://pypi.org/project/barcode/
+.. image:: https://img.shields.io/github/languages/code-size/jfjlaros/barcode.svg
+   :target: https://github.com/jfjlaros/barcode
+.. image:: https://img.shields.io/github/languages/count/jfjlaros/barcode.svg
+   :target: https://github.com/jfjlaros/barcode
+.. image:: https://img.shields.io/github/languages/top/jfjlaros/barcode.svg
+   :target: https://github.com/jfjlaros/barcode
+.. image:: https://img.shields.io/github/license/jfjlaros/barcode.svg
+   :target: https://raw.githubusercontent.com/jfjlaros/barcode/master/LICENSE.md
+
+----
+
+Barcode is a program for the design and validation of sets of sequencing
+barcodes.
+
+Please see ReadTheDocs_ for the latest documentation.
+
+
+.. _ReadTheDocs: https://barcode.readthedocs.io/en/latest/index.html

barcode/__init__.py

@@ -1,29 +1,29 @@
-"""
-Barcode: Design NGS barcodes.
+from pkg_resources import get_distribution
 
+from .barcode import filter_distance, all_barcodes, filter_stretches
 
-Copyright (c) 2013-2016 Leiden University Medical Center <humgen@lumc.nl>
-Copyright (c) 2013-2016 Jeroen F.J. Laros <J.F.J.Laros@lumc.nl>
 
-Licensed under the MIT license, see the LICENSE file.
-"""
-from .barcode import filter_distance, all_barcodes, filter_stretches
+def _get_metadata(name):
+    pkg = get_distribution(__package__)
+
+    for line in pkg.get_metadata_lines(pkg.PKG_INFO):
+        if line.startswith('{}: '.format(name)):
+            return line.split(': ')[1]
 
+    return ''
 
-__version_info__ = ('0', '6', '0')
 
-__version__ = '.'.join(__version_info__)
-__author__ = 'LUMC, Jeroen F.J. Laros'
-__contact__ = 'J.F.J.Laros@lumc.nl'
-__homepage__ = 'https://git.lumc.nl/j.f.j.laros/barcode'
+_copyright_notice = 'Copyright (c) {} <{}>'.format(
+    _get_metadata('Author'), _get_metadata('Author-email'))
 
-usage = __doc__.split('\n\n\n')
+usage = [_get_metadata('Summary'), _copyright_notice]
 
 
 def doc_split(func):
     return func.__doc__.split('\n\n')[0]
 
 
 def version(name):
-    return '{} version {}\n\nAuthor   : {} <{}>\nHomepage : {}'.format(
-        name, __version__, __author__, __contact__, __homepage__)
+    return '{} version {}\n\n{}\nHomepage: {}'.format(
+        _get_metadata('Name'), _get_metadata('Version'), _copyright_notice,
+        _get_metadata('Home-page'))

barcode/cli.py

@@ -58,6 +58,7 @@ def main():
         description=usage[0], epilog=usage[1])
     parser.add_argument('-v', action='version', version=version(parser.prog))
     subparsers = parser.add_subparsers(dest='subcommand')
+    subparsers.required = True
 
     parser_make = subparsers.add_parser(
         'make', parents=[output_parser, distance_parser],

doc/presentation/Makefile

@@ -1 +1 @@
-../../submodules/presentation/Makefile
+../../.submodules/presentation/Makefile

doc/presentation/beamerthemelumc.sty

@@ -1 +1 @@
-../../submodules/presentation/beamerthemelumc.sty
+../../.submodules/presentation/beamerthemelumc.sty

doc/presentation/gen2phen_logo.eps

@@ -1 +1 @@
-../../submodules/presentation/gen2phen_logo.eps
+../../.submodules/presentation/gen2phen_logo.eps

doc/presentation/lgtc_logo.eps

@@ -1 +1 @@
-../../submodules/presentation/lgtc_logo.eps
+../../.submodules/presentation/lgtc_logo.eps

doc/presentation/lumc_logo.eps

@@ -1 +1 @@
-../../submodules/presentation/lumc_logo.eps
+../../.submodules/presentation/lumc_logo.eps

doc/presentation/lumc_logo_small.eps

@@ -1 +1 @@
-../../submodules/presentation/lumc_logo_small.eps
+../../.submodules/presentation/lumc_logo_small.eps

doc/presentation/nbic_logo.eps

@@ -1 +1 @@
-../../submodules/presentation/nbic_logo.eps
+../../.submodules/presentation/nbic_logo.eps

doc/presentation/ngi_logo.eps

@@ -1 +1 @@
-../../submodules/presentation/ngi_logo.eps
+../../.submodules/presentation/ngi_logo.eps

doc/presentation/nwo_logo_en.eps

@@ -1 +1 @@
-../../submodules/presentation/nwo_logo_en.eps
+../../.submodules/presentation/nwo_logo_en.eps

doc/presentation/nwo_logo_nl.eps

@@ -1 +1 @@
-../../submodules/presentation/nwo_logo_nl.eps
+../../.submodules/presentation/nwo_logo_nl.eps

doc/presentation/ul_logo.eps

@@ -1 +1 @@
-../../submodules/presentation/ul_logo.eps
+../../.submodules/presentation/ul_logo.eps

docs/CODE_OF_CONDUCT.md

@@ -0,0 +1,66 @@
+# Contributor Covenant Code of Conduct
+## Our Pledge
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone.
+
+## Our Standards
+Examples of behaviour that contributes to creating a positive environment
+include:
+
+- Using welcoming and inclusive language.
+- Being respectful of differing viewpoints and experiences.
+- Gracefully accepting constructive criticism.
+- Focusing on what is best for the community.
+- Showing empathy towards other community members.
+
+Examples of unacceptable behaviour by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual attention or
+  advances.
+- Trolling, insulting/derogatory comments, and personal or political attacks.
+- Public or private harassment.
+- Publishing others' private information, such as a physical or electronic
+  address, without explicit permission.
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting.
+
+## Our Responsibilities
+Project maintainers are responsible for clarifying the standards of acceptable
+behaviour and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behaviour.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviour that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be
+reported by contacting the project team at mailto:j.f.j.laros@lumc.nl. The
+project team will review and investigate all complaints, and will respond in a
+way that it deems appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an
+incident. Further details of specific enforcement policies may be posted
+separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at
+[http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

docs/CONTRIBUTING.md

@@ -0,0 +1,62 @@
+# Contributing
+Please follow these guidelines if you would like to contribute to the project.
+
+---
+
+## Table of Contents
+Please read through these guidelines before you get started:
+
+1. [Questions & Concerns](#questions--concerns)
+2. [Issues & Bugs](#issues--bugs)
+3. [Feature Requests](#feature-requests)
+4. [Submitting Pull Requests](#submitting-pull-requests)
+5. [Code Style](#code-style)
+
+## Questions & Concerns
+If you have any questions about using or developing for this project, reach out
+to @jfjlaros or send an [email][email].
+
+## Issues & Bugs
+Submit an [issue][issues] or [pull request][compare] with a fix if you find any
+bugs in the project. See [below](#submitting-pull-requests) for instructions on
+sending in pull requests, and be sure to reference the [code style
+guide](#code-style) first!
+
+When submitting an issue or pull request, make sure you are as detailed as
+possible and fill in all answers to questions asked in the templates. For
+example, an issue that simply states "X/Y/Z is not working!" will be closed.
+
+## Feature Requests
+Submit an [issue][issues] to request a new feature. Features fall into one of
+two categories:
+
+1. **Major**: Major changes should be discussed with me via [email][email]. I am
+   always open to suggestions and will get back to you as soon as I can!
+2. **Minor**: A minor feature can simply be added via a [pull request][compare].
+
+## Submitting Pull Requests
+Before you do anything, make sure you check the current list of [pull
+requests][pull] to ensure you are not duplicating anyone's work. Then, do the
+following:
+
+1. Fork the repository and make your changes in a git branch: `git checkout -b
+   my-branch base-branch`
+2. Read and follow the [code style guidelines](#code-style).
+3. Make sure your feature or fix does not break the project! Test thoroughly.
+4. Commit your changes, and be sure to leave a detailed commit message.
+5. Push your branch to your forked repo on GitHub: `git push origin my-branch`
+6. [Submit a pull request][compare] and hold tight!
+7. If any changes are requested by the project maintainers, make them and
+   follow this process again until the changes are merged in.
+
+## Code Style
+Please follow the coding style conventions detailed below:
+
+- For Python: [PEP 8 - Style Guide for Python Code][pep8].
+
+
+[email]: mailto:j.f.j.laros@lumc.nl
+[issues]: https://github.com/jfjlaros/barcode/issues/new
+[compare]: https://github.com/jfjlaros/barcode/compare
+[pull]: https://github.com/jfjlaros/barcode/pulls
+[pep8]: https://www.python.org/dev/peps/pep-0008/

docs/credits.rst

@@ -0,0 +1,10 @@
+Contributors
+============
+
+- Jeroen F.J. Laros <J.F.J.Laros@lumc.nl> (Original author, maintainer)
+
+Find out who contributed:
+
+::
+
+    git shortlog -s -e